diff --git a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/fftw.md b/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/fftw.md
index 97093adebedae07dc396ff3803068974c2f48f6f..e27676c6702ff264207f8a6a34d0bfc94619efdb 100644
--- a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/fftw.md
+++ b/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/fftw.md
@@ -71,6 +71,6 @@ Load modules and compile:
$ mpicc testfftw3mpi.c -o testfftw3mpi.x -Wl,-rpath=$LIBRARY_PATH -lfftw3_mpi
```
-Run the example as [Intel MPI program](../mpi-1/running-mpich2.html).
+Run the example as [Intel MPI program](../mpi/running-mpich2/).
-Read more on FFTW usage on the [FFTW website.](http://www.fftw.org/fftw3_doc/)
\ No newline at end of file
+Read more on FFTW usage on the [FFTW website.](http://www.fftw.org/fftw3_doc/)
\ No newline at end of file
diff --git a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/hdf5.md b/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/hdf5.md
index d41a4ed5ed7482692a136de9f9af18c54a31eec2..a92c3a689e9d19d6423067ea5a647db5fdd31a5a 100644
--- a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/hdf5.md
+++ b/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/hdf5.md
@@ -3,7 +3,7 @@ HDF5
Hierarchical Data Format library. Serial and MPI parallel version.
-[HDF5 (Hierarchical Data Format)](http://www.hdfgroup.org/HDF5/) is a general purpose library and file format for storing scientific data. HDF5 can store two primary objects: datasets and groups. A dataset is essentially a multidimensional array of data elements, and a group is a structure for organizing objects in an HDF5 file. Using these two basic objects, one can create and store almost any kind of scientific data structure, such as images, arrays of vectors, and structured and unstructured grids. You can also mix and match them in HDF5 files according to your needs.
+[HDF5 (Hierarchical Data Format)](http://www.hdfgroup.org/HDF5/) is a general purpose library and file format for storing scientific data. HDF5 can store two primary objects: datasets and groups. A dataset is essentially a multidimensional array of data elements, and a group is a structure for organizing objects in an HDF5 file. Using these two basic objects, one can create and store almost any kind of scientific data structure, such as images, arrays of vectors, and structured and unstructured grids. You can also mix and match them in HDF5 files according to your needs.
Versions **1.8.11** and **1.8.13** of HDF5 library are available on Anselm, compiled for **Intel MPI** and **OpenMPI** using **intel** and **gnu** compilers. These are available via modules:
@@ -23,7 +23,7 @@ Versions **1.8.11** and **1.8.13** of HDF5 library are available on Anselm, comp
The module sets up environment variables, required for linking and running HDF5 enabled applications. Make sure that the choice of HDF5 module is consistent with your choice of MPI library. Mixing MPI of different implementations may have unpredictable results.
->Be aware, that GCC version of **HDF5 1.8.11** has serious performance issues, since it's compiled with -O0 optimization flag. This version is provided only for testing of code compiled only by GCC and IS NOT recommended for production computations. For more informations, please see: <http://www.hdfgroup.org/ftp/HDF5/prev-releases/ReleaseFiles/release5-1811>
+>Be aware, that GCC version of **HDF5 1.8.11** has serious performance issues, since it's compiled with -O0 optimization flag. This version is provided only for testing of code compiled only by GCC and IS NOT recommended for production computations. For more informations, please see: <http://www.hdfgroup.org/ftp/HDF5/prev-releases/ReleaseFiles/release5-1811>
All GCC versions of **HDF5 1.8.13** are not affected by the bug, are compiled with -O3 optimizations and are recommended for production computations.
Example
@@ -84,6 +84,6 @@ Load modules and compile:
$ mpicc hdf5test.c -o hdf5test.x -Wl,-rpath=$LIBRARY_PATH $HDF5_INC $HDF5_SHLIB
```
-Run the example as [Intel MPI program](../anselm-cluster-documentation/software/mpi-1/running-mpich2.html).
+Run the example as [Intel MPI program](../anselm-cluster-documentation/software/mpi/running-mpich2/).
-For further informations, please see the website: <http://www.hdfgroup.org/HDF5/>
\ No newline at end of file
+For further informations, please see the website: <http://www.hdfgroup.org/HDF5/>
\ No newline at end of file
diff --git a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.md b/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.md
index 67c64a22321830163df2173d7dc44898dff2d6de..0a9c25c505a656ef26a1b08c1d8b1e04c98421f5 100644
--- a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.md
+++ b/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.md
@@ -11,7 +11,7 @@ Intel Math Kernel Library (Intel MKL) is a library of math kernel subroutines, e
$ module load mkl
```
-Read more at the [Intel MKL](../intel-suite/intel-mkl.html) page.
+Read more at the [Intel MKL](../intel-suite/intel-mkl/) page.
Intel Integrated Performance Primitives
---------------------------------------
@@ -21,7 +21,7 @@ Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX is avai
$ module load ipp
```
-Read more at the [Intel IPP](../intel-suite/intel-integrated-performance-primitives.html) page.
+Read more at the [Intel IPP](../intel-suite/intel-integrated-performance-primitives/) page.
Intel Threading Building Blocks
-------------------------------
@@ -31,4 +31,4 @@ Intel Threading Building Blocks (Intel TBB) is a library that supports scalable
$ module load tbb
```
-Read more at the [Intel TBB](../intel-suite/intel-tbb.html) page.
\ No newline at end of file
+Read more at the [Intel TBB](../intel-suite/intel-tbb/) page.
\ No newline at end of file
diff --git a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md b/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md
index 201fac4dc200667a1c3dad4dbda39d82a924d9fe..05aaf37a9a2598ca85d4539ea5d0468012467fd2 100644
--- a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md
+++ b/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md
@@ -69,8 +69,8 @@ To test if the MAGMA server runs properly we can run one of examples that are pa
**export OMP_NUM_THREADS=16**
-See more details at [MAGMA home page](http://icl.cs.utk.edu/magma/).
+See more details at [MAGMA home page](http://icl.cs.utk.edu/magma/).
References
----------
-[1] MAGMA MIC: Linear Algebra Library for Intel Xeon Phi Coprocessors, Jack Dongarra et. al, [http://icl.utk.edu/projectsfiles/magma/pubs/24-MAGMA_MIC_03.pdf](http://icl.utk.edu/projectsfiles/magma/pubs/24-MAGMA_MIC_03.pdf)
\ No newline at end of file
+[1] MAGMA MIC: Linear Algebra Library for Intel Xeon Phi Coprocessors, Jack Dongarra et. al, [http://icl.utk.edu/projectsfiles/magma/pubs/24-MAGMA_MIC_03.pdf](http://icl.utk.edu/projectsfiles/magma/pubs/24-MAGMA_MIC_03.pdf)
\ No newline at end of file
diff --git a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/petsc.md b/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/petsc.md
index 1afdbb886abd4e7a81abda016be2702b5058499e..f08618e77d3372504d6a83a89e3c2342d9febe3a 100644
--- a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/petsc.md
+++ b/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/petsc.md
@@ -9,13 +9,11 @@ PETSc (Portable, Extensible Toolkit for Scientific Computation) is a suite of bu
Resources
---------
-- [project webpage](http://www.mcs.anl.gov/petsc/)
-- [documentation](http://www.mcs.anl.gov/petsc/documentation/)
- - [PETSc Users
- Manual (PDF)](http://www.mcs.anl.gov/petsc/petsc-current/docs/manual.pdf)
- - [index of all manual
- pages](http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/singleindex.html)
-- PRACE Video Tutorial [part1](http://www.youtube.com/watch?v=asVaFg1NDqY), [part2](http://www.youtube.com/watch?v=ubp_cSibb9I), [part3](http://www.youtube.com/watch?v=vJAAAQv-aaw), [part4](http://www.youtube.com/watch?v=BKVlqWNh8jY), [part5](http://www.youtube.com/watch?v=iXkbLEBFjlM)
+- [project webpage](http://www.mcs.anl.gov/petsc/)
+- [documentation](http://www.mcs.anl.gov/petsc/documentation/)
+ - [PETSc Users Manual (PDF)](http://www.mcs.anl.gov/petsc/petsc-current/docs/manual.pdf)
+ - [index of all manual pages](http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/singleindex.html)
+- PRACE Video Tutorial [part1](http://www.youtube.com/watch?v=asVaFg1NDqY), [part2](http://www.youtube.com/watch?v=ubp_cSibb9I), [part3](http://www.youtube.com/watch?v=vJAAAQv-aaw), [part4](http://www.youtube.com/watch?v=BKVlqWNh8jY), [part5](http://www.youtube.com/watch?v=iXkbLEBFjlM)
Modules
-------
@@ -27,13 +25,13 @@ You can start using PETSc on Anselm by loading the PETSc module. Module names ob
module load petsc/3.4.4-icc-impi-mkl-opt
```
-where `variant` is replaced by one of `{dbg, opt, threads-dbg, threads-opt}`. The `opt` variant is compiled without debugging information (no `-g` option) and with aggressive compiler optimizations (`-O3 -xAVX`). This variant is suitable for performance measurements and production runs. In all other cases use the debug (`dbg`) variant, because it contains debugging information, performs validations and self-checks, and provides a clear stack trace and message in case of an error. The other two variants `threads-dbg` and `threads-opt` are `dbg` and `opt`, respectively, built with [OpenMP and pthreads threading support](http://www.mcs.anl.gov/petsc/features/threads.html).
+where `variant` is replaced by one of `{dbg, opt, threads-dbg, threads-opt}`. The `opt` variant is compiled without debugging information (no `-g` option) and with aggressive compiler optimizations (`-O3 -xAVX`). This variant is suitable for performance measurements and production runs. In all other cases use the debug (`dbg`) variant, because it contains debugging information, performs validations and self-checks, and provides a clear stack trace and message in case of an error. The other two variants `threads-dbg` and `threads-opt` are `dbg` and `opt`, respectively, built with [OpenMP and pthreads threading support](http://www.mcs.anl.gov/petsc/features/threads.html).
External libraries
------------------
PETSc needs at least MPI, BLAS and LAPACK. These dependencies are currently satisfied with Intel MPI and Intel MKL in Anselm `petsc` modules.
-PETSc can be linked with a plethora of [external numerical libraries](http://www.mcs.anl.gov/petsc/miscellaneous/external.html), extending PETSc functionality, e.g. direct linear system solvers, preconditioners or partitioners. See below a list of libraries currently included in Anselm `petsc` modules.
+PETSc can be linked with a plethora of [external numerical libraries](http://www.mcs.anl.gov/petsc/miscellaneous/external.html), extending PETSc functionality, e.g. direct linear system solvers, preconditioners or partitioners. See below a list of libraries currently included in Anselm `petsc` modules.
All these libraries can be used also alone, without PETSc. Their static or shared program libraries are available in
`$PETSC_DIR/$PETSC_ARCH/lib` and header files in `$PETSC_DIR/$PETSC_ARCH/include`. `PETSC_DIR` and `PETSC_ARCH` are environment variables pointing to a specific PETSc instance based on the petsc module loaded.
@@ -41,24 +39,24 @@ All these libraries can be used also alone, without PETSc. Their static or share
### Libraries linked to PETSc on Anselm (as of 11 April 2015)
- dense linear algebra
- - [Elemental](http://libelemental.org/)
+ - [Elemental](http://libelemental.org/)
- sparse linear system solvers
- - [Intel MKL Pardiso](https://software.intel.com/en-us/node/470282)
- - [MUMPS](http://mumps.enseeiht.fr/)
- - [PaStiX](http://pastix.gforge.inria.fr/)
- - [SuiteSparse](http://faculty.cse.tamu.edu/davis/suitesparse.html)
- - [SuperLU](http://crd.lbl.gov/~xiaoye/SuperLU/#superlu)
- - [SuperLU_Dist](http://crd.lbl.gov/~xiaoye/SuperLU/#superlu_dist)
+ - [Intel MKL Pardiso](https://software.intel.com/en-us/node/470282)
+ - [MUMPS](http://mumps.enseeiht.fr/)
+ - [PaStiX](http://pastix.gforge.inria.fr/)
+ - [SuiteSparse](http://faculty.cse.tamu.edu/davis/suitesparse.html)
+ - [SuperLU](http://crd.lbl.gov/~xiaoye/SuperLU/#superlu)
+ - [SuperLU_Dist](http://crd.lbl.gov/~xiaoye/SuperLU/#superlu_dist)
- input/output
- - [ExodusII](http://sourceforge.net/projects/exodusii/)
- - [HDF5](http://www.hdfgroup.org/HDF5/)
- - [NetCDF](http://www.unidata.ucar.edu/software/netcdf/)
+ - [ExodusII](http://sourceforge.net/projects/exodusii/)
+ - [HDF5](http://www.hdfgroup.org/HDF5/)
+ - [NetCDF](http://www.unidata.ucar.edu/software/netcdf/)
- partitioning
- - [Chaco](http://www.cs.sandia.gov/CRF/chac.html)
- - [METIS](http://glaros.dtc.umn.edu/gkhome/metis/metis/overview)
- - [ParMETIS](http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview)
- - [PT-Scotch](http://www.labri.fr/perso/pelegrin/scotch/)
+ - [Chaco](http://www.cs.sandia.gov/CRF/chac.html)
+ - [METIS](http://glaros.dtc.umn.edu/gkhome/metis/metis/overview)
+ - [ParMETIS](http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview)
+ - [PT-Scotch](http://www.labri.fr/perso/pelegrin/scotch/)
- preconditioners & multigrid
- - [Hypre](http://acts.nersc.gov/hypre/)
- - [Trilinos ML](http://trilinos.sandia.gov/packages/ml/)
- - [SPAI - Sparse Approximate Inverse](https://bitbucket.org/petsc/pkg-spai)
\ No newline at end of file
+ - [Hypre](http://acts.nersc.gov/hypre/)
+ - [Trilinos ML](http://trilinos.sandia.gov/packages/ml/)
+ - [SPAI - Sparse Approximate Inverse](https://bitbucket.org/petsc/pkg-spai)
\ No newline at end of file
diff --git a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/trilinos.md b/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/trilinos.md
index b19b95b2245d2a20838674139e87c4bd015b6ccd..c49c005f8835128d085b88df6b9846011c251013 100644
--- a/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/trilinos.md
+++ b/docs.it4i/anselm-cluster-documentation/software/numerical-libraries/trilinos.md
@@ -19,7 +19,7 @@ Current Trilinos installation on ANSELM contains (among others) the following ma
- **IFPACK** - distributed algebraic preconditioner (includes e.g. incomplete LU factorization)
- **Teuchos** - common tools packages. This package contains classes for memory management, output, performance monitoring, BLAS and LAPACK wrappers etc.
-For the full list of Trilinos packages, descriptions of their capabilities, and user manuals see [http://trilinos.sandia.gov.](http://trilinos.sandia.gov)
+For the full list of Trilinos packages, descriptions of their capabilities, and user manuals see [http://trilinos.sandia.gov.](http://trilinos.sandia.gov)
### Installed version
@@ -33,7 +33,7 @@ First, load the appropriate module:
$ module load trilinos
```
-For the compilation of CMake-aware project, Trilinos provides the FIND_PACKAGE( Trilinos ) capability, which makes it easy to build against Trilinos, including linking against the correct list of libraries. For details, see <http://trilinos.sandia.gov/Finding_Trilinos.txt>
+For the compilation of CMake-aware project, Trilinos provides the FIND_PACKAGE( Trilinos ) capability, which makes it easy to build against Trilinos, including linking against the correct list of libraries. For details, see <http://trilinos.sandia.gov/Finding_Trilinos.txt>
For compiling using simple makefiles, Trilinos provides Makefile.export system, which allows users to include important Trilinos variables directly into their makefiles. This can be done simply by inserting the following line into the makefile:
@@ -47,4 +47,4 @@ or
include Makefile.export.<package>
```
-if you are interested only in a specific Trilinos package. This will give you access to the variables such as Trilinos_CXX_COMPILER, Trilinos_INCLUDE_DIRS, Trilinos_LIBRARY_DIRS etc. For the detailed description and example makefile see <http://trilinos.sandia.gov/Export_Makefile.txt>.
\ No newline at end of file
+if you are interested only in a specific Trilinos package. This will give you access to the variables such as Trilinos_CXX_COMPILER, Trilinos_INCLUDE_DIRS, Trilinos_LIBRARY_DIRS etc. For the detailed description and example makefile see <http://trilinos.sandia.gov/Export_Makefile.txt>.
\ No newline at end of file
diff --git a/docs.it4i/anselm-cluster-documentation/software/omics-master/diagnostic-component-team.md b/docs.it4i/anselm-cluster-documentation/software/omics-master/diagnostic-component-team.md
index 0b1d54245bf02f31224a5e86ef320ebe3a62b183..b94fdf6f6dafbc9b68bf476c0834a0b1caf49cf3 100644
--- a/docs.it4i/anselm-cluster-documentation/software/omics-master/diagnostic-component-team.md
+++ b/docs.it4i/anselm-cluster-documentation/software/omics-master/diagnostic-component-team.md
@@ -3,9 +3,9 @@ Diagnostic component (TEAM)
### Access
-TEAM is available at the following address:Â <http://omics.it4i.cz/team/>
+TEAM is available at the following address:Â <http://omics.it4i.cz/team/>
->The address is accessible only via [VPN. ](../../accessing-the-cluster/vpn-access.html)
+>The address is accessible only via [VPN. ](../../accessing-the-cluster/vpn-access/)
### Diagnostic component (TEAM)
diff --git a/docs.it4i/anselm-cluster-documentation/software/omics-master/overview.md b/docs.it4i/anselm-cluster-documentation/software/omics-master/overview.md
index f9716d38d234b7be566aa6d4388050f42527766d..26bce4ba613cd4982c6e793f4b978b91213ed7d6 100644
--- a/docs.it4i/anselm-cluster-documentation/software/omics-master/overview.md
+++ b/docs.it4i/anselm-cluster-documentation/software/omics-master/overview.md
@@ -163,9 +163,9 @@ CellBase includes SNPs from dbSNP (16)^; SNP population frequencies from HapMap
We also import systems biology information like interactome information from IntAct (24). Reactome (25) stores pathway and interaction information in BioPAX (26) format. BioPAX data exchange format enables the integration of diverse pathway
resources. We successfully solved the problem of storing data released in BioPAX format into a SQL relational schema, which allowed us importing Reactome in CellBase.
-### [Diagnostic component (TEAM)](diagnostic-component-team.md)
+### [Diagnostic component (TEAM)](diagnostic-component-team/)
-### [Priorization component (BiERApp)](priorization-component-bierapp.md)
+### [Priorization component (BiERApp)](priorization-component-bierapp/)
Usage
-----
@@ -181,7 +181,7 @@ If we launch ngsPipeline with â€-h’, we will get the usage help:
```bash
$ ngsPipeline -h
- Usage: ngsPipeline.py [-h] -i INPUT -o OUTPUT -p PED --project PROJECT --queue
+ Usage: ngsPipeline.py [-h] -i INPUT -o OUTPUT -p PED --project PROJECT --queue
           QUEUE [--stages-path STAGES_PATH] [--email EMAIL]
[--prefix PREFIX] [-s START] [-e END] --log
@@ -235,7 +235,6 @@ Input, output and ped arguments are mandatory. If the output folder does not exi
Examples
---------------------
-
This is an example usage of NGSpipeline:
We have a folder with the following structure in
@@ -262,7 +261,7 @@ The ped file ( file.ped) contains the following info:
FAM sample_B 0 0 2 2
```
-Now, lets load the NGSPipeline module and copy the sample data to a [scratch directory](../../storage.html):
+Now, lets load the NGSPipeline module and copy the sample data to a [scratch directory](../../storage/storage/):
```bash
$ module load ngsPipeline
@@ -288,17 +287,16 @@ Details on the pipeline
------------------------------------
The pipeline calls the following tools:
-
-- [fastqc](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), quality control tool for high throughput
+- [fastqc](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), quality control tool for high throughput
sequence data.
-- [gatk](https://www.broadinstitute.org/gatk/), The Genome Analysis Toolkit or GATK is a software package developed at
+- [gatk](https://www.broadinstitute.org/gatk/), The Genome Analysis Toolkit or GATK is a software package developed at
the Broad Institute to analyze high-throughput sequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
-- [hpg-aligner](http://wiki.opencb.org/projects/hpg/doku.php?id=aligner:downloads), HPG Aligner has been designed to align short and long reads with high sensitivity, therefore any number of mismatches or indels are allowed. HPG Aligner implements and combines two well known algorithms: *Burrows-Wheeler Transform* (BWT) to speed-up mapping high-quality reads, and *Smith-Waterman*> (SW) to increase sensitivity when reads cannot be mapped using BWT.
-- [hpg-fastq](http://docs.bioinfo.cipf.es/projects/fastqhpc/wiki), a quality control tool for high throughput sequence data.
-- [hpg-variant](http://wiki.opencb.org/projects/hpg/doku.php?id=variant:downloads), The HPG Variant suite is an ambitious project aimed to provide a complete suite of tools to work with genomic variation data, from VCF tools to variant profiling or genomic statistics. It is being implemented using High Performance Computing technologies to provide the best performance possible.
-- [picard](http://picard.sourceforge.net/), Picard comprises Java-based command-line utilities that manipulate SAM files, and a Java API (HTSJDK) for creating new programs that read and write SAM files. Both SAM text format and SAM binary (BAM) format are supported.
-- [samtools](http://samtools.sourceforge.net/samtools-c.shtml), SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
-- [snpEff](http://snpeff.sourceforge.net/), Genetic variant annotation and effect prediction toolbox.
+- [hpg-aligner](http://wiki.opencb.org/projects/hpg/doku.php?id=aligner:downloads), HPG Aligner has been designed to align short and long reads with high sensitivity, therefore any number of mismatches or indels are allowed. HPG Aligner implements and combines two well known algorithms: *Burrows-Wheeler Transform* (BWT) to speed-up mapping high-quality reads, and *Smith-Waterman*> (SW) to increase sensitivity when reads cannot be mapped using BWT.
+- [hpg-fastq](http://docs.bioinfo.cipf.es/projects/fastqhpc/wiki), a quality control tool for high throughput sequence data.
+- [hpg-variant](http://wiki.opencb.org/projects/hpg/doku.php?id=variant:downloads), The HPG Variant suite is an ambitious project aimed to provide a complete suite of tools to work with genomic variation data, from VCF tools to variant profiling or genomic statistics. It is being implemented using High Performance Computing technologies to provide the best performance possible.
+- [picard](http://picard.sourceforge.net/), Picard comprises Java-based command-line utilities that manipulate SAM files, and a Java API (HTSJDK) for creating new programs that read and write SAM files. Both SAM text format and SAM binary (BAM) format are supported.
+- [samtools](http://samtools.sourceforge.net/samtools-c.shtml), SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
+- [snpEff](http://snpeff.sourceforge.net/), Genetic variant annotation and effect prediction toolbox.
This listing show which tools are used in each step of the pipeline :
@@ -341,7 +339,7 @@ The output folder contains all the subfolders with the intermediate data. This f
**Figure 7**. *TEAM upload panel.* *Once the file has been uploaded, a panel must be chosen from the Panel* list. Then, pressing the Run button the diagnostic process starts.
-Once the file has been uploaded, a panel must be chosen from the Panel list. Then, pressing the Run button the diagnostic process starts. TEAM searches first for known diagnostic mutation(s) taken from four databases: HGMD-public (20), [HUMSAVAR](http://www.uniprot.org/docs/humsavar), ClinVar (29)^ and COSMIC (23).
+Once the file has been uploaded, a panel must be chosen from the Panel list. Then, pressing the Run button the diagnostic process starts. TEAM searches first for known diagnostic mutation(s) taken from four databases: HGMD-public (20), [HUMSAVAR](http://www.uniprot.org/docs/humsavar), ClinVar (29)^ and COSMIC (23).
@@ -388,6 +386,6 @@ References
25. Croft,D., O’Kelly,G., Wu,G., Haw,R., Gillespie,M., Matthews,L., Caudy,M., Garapati,P., Gopinath,G., Jassal,B. et al. (2011) Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res., 39, D691–D697.
26. Demir,E., Cary,M.P., Paley,S., Fukuda,K., Lemer,C., Vastrik,I.,Wu,G., D’Eustachio,P., Schaefer,C., Luciano,J. et al. (2010) The BioPAX community standard for pathway data sharing. Nature Biotechnol., 28, 935–942.
27. Alemán Z, GarcĂa-GarcĂa F, Medina I, Dopazo J (2014): A web tool for the design and management of panels of genes for targeted enrichment and massive sequencing for clinical applications. Nucleic Acids Res 42: W83-7.
-28. [Alemán A](http://www.ncbi.nlm.nih.gov/pubmed?term=Alem%C3%A1n%20A%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)>, [Garcia-Garcia F](http://www.ncbi.nlm.nih.gov/pubmed?term=Garcia-Garcia%20F%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)>, [Salavert F](http://www.ncbi.nlm.nih.gov/pubmed?term=Salavert%20F%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)>, [Medina I](http://www.ncbi.nlm.nih.gov/pubmed?term=Medina%20I%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)>, [Dopazo J](http://www.ncbi.nlm.nih.gov/pubmed?term=Dopazo%20J%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)> (2014). A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies. [Nucleic Acids Res.](http://www.ncbi.nlm.nih.gov/pubmed/?term=BiERapp "Nucleic acids research.")>42 :W88-93.
+28. [Alemán A](http://www.ncbi.nlm.nih.gov/pubmed?term=Alem%C3%A1n%20A%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)>, [Garcia-Garcia F](http://www.ncbi.nlm.nih.gov/pubmed?term=Garcia-Garcia%20F%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)>, [Salavert F](http://www.ncbi.nlm.nih.gov/pubmed?term=Salavert%20F%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)>, [Medina I](http://www.ncbi.nlm.nih.gov/pubmed?term=Medina%20I%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)>, [Dopazo J](http://www.ncbi.nlm.nih.gov/pubmed?term=Dopazo%20J%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)> (2014). A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies. [Nucleic Acids Res.](http://www.ncbi.nlm.nih.gov/pubmed/?term=BiERapp "Nucleic acids research.")>42 :W88-93.
29. Landrum,M.J., Lee,J.M., Riley,G.R., Jang,W., Rubinstein,W.S., Church,D.M. and Maglott,D.R. (2014) ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res., 42, D980–D985.
30. Medina I, Salavert F, Sanchez R, de Maria A, Alonso R, Escobar P, Bleda M, Dopazo J: Genome Maps, a new generation genome browser. Nucleic Acids Res 2013, 41:W41-46.
\ No newline at end of file
diff --git a/docs.it4i/anselm-cluster-documentation/software/omics-master/priorization-component-bierapp.md b/docs.it4i/anselm-cluster-documentation/software/omics-master/priorization-component-bierapp.md
index 9d26f896434ded3483f4aa1b1f441220c5c968f5..0c6c893b5f8863fec6bd5a7d1dcadfffb167ab96 100644
--- a/docs.it4i/anselm-cluster-documentation/software/omics-master/priorization-component-bierapp.md
+++ b/docs.it4i/anselm-cluster-documentation/software/omics-master/priorization-component-bierapp.md
@@ -5,7 +5,7 @@ Priorization component (BiERApp)
BiERApp is available at the following address:Â <http://omics.it4i.cz/bierapp/>
->The address is accessible onlyvia [VPN. ](../../accessing-the-cluster/vpn-access.html)
+>The address is accessible onlyvia [VPN. ](../../accessing-the-cluster/vpn-access/)
###BiERApp
diff --git a/docs.it4i/anselm-cluster-documentation/software/operating-system.md b/docs.it4i/anselm-cluster-documentation/software/operating-system.md
index 9487d4fab704cb68677b605cb3f4427c91d3f9a1..9fbbe0e9caf7e454d39dcad4b6b4071889c2fff6 100644
--- a/docs.it4i/anselm-cluster-documentation/software/operating-system.md
+++ b/docs.it4i/anselm-cluster-documentation/software/operating-system.md
@@ -1,8 +1,7 @@
Operating System
===============
-##The operating system, deployed on ANSELM
-The operating system on Anselm is Linux - bullx Linux Server release 6.3.
+The operating system on Anselm is Linux - **bullx Linux Server release 6.X**
bullx Linux is based on Red Hat Enterprise Linux. bullx Linux is a Linux distribution provided by Bull and dedicated to HPC applications.
diff --git a/docs.it4i/salomon/accessing-the-cluster/accessing-the-cluster.md b/docs.it4i/salomon/accessing-the-cluster/accessing-the-cluster.md
index db5adec3341a28d362161615ad31cec85a955d77..822b7a0c1e784d1a8030c92ba6b69cd673f8c165 100644
--- a/docs.it4i/salomon/accessing-the-cluster/accessing-the-cluster.md
+++ b/docs.it4i/salomon/accessing-the-cluster/accessing-the-cluster.md
@@ -15,7 +15,7 @@ The Salomon cluster is accessed by SSH protocol via login nodes login1, login2,
|login1.salomon.it4i.cz|22|ssh|login1|
|login1.salomon.it4i.cz|22|ssh|login1|
-The authentication is by the [private key](../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
+The authentication is by the [private key](../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys/)
>Please verify SSH fingerprints during the first logon. They are identical on all login nodes:
f6:28:98:e4:f9:b2:a6:8f:f2:f4:2d:0a:09:67:69:80Â (DSA)
@@ -35,7 +35,7 @@ If you see warning message "UNPROTECTED PRIVATE KEY FILE!", use this command to
local $ chmod 600 /path/to/id_rsa
```
-On **Windows**, use [PuTTY ssh client](../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.html).
+On **Windows**, use [PuTTY ssh client](../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty/).
After logging in, you will see the command prompt:
@@ -55,11 +55,11 @@ Last login: Tue Jul 9 15:57:38 2013 from your-host.example.com
[username@login2.salomon ~]$
```
->The environment is **not** shared between login nodes, except for [shared filesystems](storage/storage.html).
+>The environment is **not** shared between login nodes, except for [shared filesystems](storage/storage/).
Data Transfer
-------------
-Data in and out of the system may be transferred by the [scp](http://en.wikipedia.org/wiki/Secure_copy) and sftp protocols.
+Data in and out of the system may be transferred by the [scp](http://en.wikipedia.org/wiki/Secure_copy) and sftp protocols.
In case large volumes of data are transferred, use dedicated data mover nodes cedge[1-3].salomon.it4i.cz for increased performance.
@@ -73,7 +73,7 @@ HTML commented section #1 (removed cedge servers from the table)
|login3.salomon.it4i.cz|22|scp, sftp|
|login4.salomon.it4i.cz|22|scp, sftp|
-The authentication is by the [private key](../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
+The authentication is by the [private key](../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys/)
HTML commented section #2 (ssh transfer performance data need to be verified)
@@ -93,7 +93,7 @@ or
local $ sftp -o IdentityFile=/path/to/id_rsa username@salomon.it4i.cz
```
-Very convenient way to transfer files in and out of the Salomon computer is via the fuse filesystem [sshfs](http://linux.die.net/man/1/sshfs)
+Very convenient way to transfer files in and out of the Salomon computer is via the fuse filesystem [sshfs](http://linux.die.net/man/1/sshfs)
```bash
local $ sshfs -o IdentityFile=/path/to/id_rsa username@salomon.it4i.cz:. mountpoint
@@ -109,6 +109,6 @@ $ man scp
$ man sshfs
```
-On Windows, use [WinSCP client](http://winscp.net/eng/download.php) to transfer the data. The [win-sshfs client](http://code.google.com/p/win-sshfs/) provides a way to mount the Salomon filesystems directly as an external disc.
+On Windows, use [WinSCP client](http://winscp.net/eng/download.php) to transfer the data. The [win-sshfs client](http://code.google.com/p/win-sshfs/) provides a way to mount the Salomon filesystems directly as an external disc.
-More information about the shared file systems is available [here](storage/storage.html).
\ No newline at end of file
+More information about the shared file systems is available [here](storage/storage/).
\ No newline at end of file
diff --git a/docs.it4i/salomon/accessing-the-cluster/outgoing-connections.md b/docs.it4i/salomon/accessing-the-cluster/outgoing-connections.md
index 43128e14b5b0ae5395b165754e6b8657c7dd154c..20914d048281c3ad1782a01920bb341f4db09bae 100644
--- a/docs.it4i/salomon/accessing-the-cluster/outgoing-connections.md
+++ b/docs.it4i/salomon/accessing-the-cluster/outgoing-connections.md
@@ -47,7 +47,7 @@ Note: Port number 6000 is chosen as an example only. Pick any free port.
Remote port forwarding from compute nodes allows applications running on the compute nodes to access hosts outside Salomon Cluster.
-First, establish the remote port forwarding form the login node, as [described above](outgoing-connections.html#port-forwarding-from-login-nodes).
+First, establish the remote port forwarding form the login node, as [described above](outgoing-connections/#port-forwarding-from-login-nodes).
Second, invoke port forwarding from the compute node to the login node. Insert following line into your jobscript or interactive shell
@@ -69,12 +69,12 @@ To establish local proxy server on your workstation, install and run SOCKS proxy
local $ ssh -D 1080 localhost
```
-On Windows, install and run the free, open source [Sock Puppet](http://sockspuppet.com/) server.
+On Windows, install and run the free, open source [Sock Puppet](http://sockspuppet.com/) server.
-Once the proxy server is running, establish ssh port forwarding from Salomon to the proxy server, port 1080, exactly as [described above](outgoing-connections.html#port-forwarding-from-login-nodes).
+Once the proxy server is running, establish ssh port forwarding from Salomon to the proxy server, port 1080, exactly as [described above](outgoing-connections/#port-forwarding-from-login-nodes).
```bash
local $ ssh -R 6000:localhost:1080 salomon.it4i.cz
```
-Now, configure the applications proxy settings to **localhost:6000**. Use port forwarding to access the [proxy server from compute nodes](outgoing-connections.html#port-forwarding-from-compute-nodes) as well .
\ No newline at end of file
+Now, configure the applications proxy settings to **localhost:6000**. Use port forwarding to access the [proxy server from compute nodes](outgoing-connections/#port-forwarding-from-compute-nodes) as well .
\ No newline at end of file
diff --git a/docs.it4i/salomon/accessing-the-cluster/vpn-access.md b/docs.it4i/salomon/accessing-the-cluster/vpn-access.md
index 0f8411cc9dc25a681030562e12c3d846e86015da..4155be83411e9c4869b180ffb94d4ac2044bacf5 100644
--- a/docs.it4i/salomon/accessing-the-cluster/vpn-access.md
+++ b/docs.it4i/salomon/accessing-the-cluster/vpn-access.md
@@ -18,7 +18,7 @@ It is impossible to connect to VPN from other operating systems.
VPN client installation
------------------------------------
-You can install VPN client from web interface after successful login with LDAP credentials on address <https://vpn.it4i.cz/user>
+You can install VPN client from web interface after successful login with LDAP credentials on address <https://vpn.it4i.cz/user>
@@ -47,7 +47,7 @@ Working with VPN client
You can use graphical user interface or command line interface to run VPN client on all supported operating systems. We suggest using GUI.
-Before the first login to VPN, you have to fill URLÂ **[https://vpn.it4i.cz/user](https://vpn.it4i.cz/user)** into the text field.
+Before the first login to VPN, you have to fill URLÂ **[https://vpn.it4i.cz/user](https://vpn.it4i.cz/user)** into the text field.
diff --git a/docs.it4i/salomon/environment-and-modules.md b/docs.it4i/salomon/environment-and-modules.md
index e47c9130c312613c490a1d7e845f04b28fbd2372..77b411f1ecb0778d98e7adbb9dadf02a953a6b0a 100644
--- a/docs.it4i/salomon/environment-and-modules.md
+++ b/docs.it4i/salomon/environment-and-modules.md
@@ -30,7 +30,7 @@ fi
In order to configure your shell for running particular application on Salomon we use Module package interface.
-Application modules on Salomon cluster are built using [EasyBuild](http://hpcugent.github.io/easybuild/ "EasyBuild"). The modules are divided into the following structure:
+Application modules on Salomon cluster are built using [EasyBuild](http://hpcugent.github.io/easybuild/ "EasyBuild"). The modules are divided into the following structure:
```bash
base: Default module class
@@ -120,5 +120,4 @@ On Salomon, we have currently following toolchains installed:
|gompi|GCC, OpenMPI|
|goolf|BLACS, FFTW, GCC, OpenBLAS, OpenMPI, ScaLAPACK|
|iompi|OpenMPI, icc, ifort|
- |iccifort|icc, ifort|
-
+ |iccifort|icc, ifort|
\ No newline at end of file
diff --git a/docs.it4i/salomon/hardware-overview.md b/docs.it4i/salomon/hardware-overview.md
index 555dbcf5f3ed7f2e1aa36ea4c9dd301f9e132e70..0fffddcc3fd6599716e6c85ed637984fa30df5c9 100644
--- a/docs.it4i/salomon/hardware-overview.md
+++ b/docs.it4i/salomon/hardware-overview.md
@@ -5,7 +5,7 @@ Introduction
------------
The Salomon cluster consists of 1008 computational nodes of which 576 are regular compute nodes and 432 accelerated nodes. Each node is a powerful x86-64 computer, equipped with 24 cores (two twelve-core Intel Xeon processors) and 128GB RAM. The nodes are interlinked by high speed InfiniBand and Ethernet networks. All nodes share 0.5PB /home NFS disk storage to store the user files. Users may use a DDN Lustre shared storage with capacity of 1.69 PB which is available for the scratch project data. The user access to the Salomon cluster is provided by four login nodes.
-[More about schematic representation of the Salomon cluster compute nodes IB topology](../network/ib-single-plane-topology.md).
+[More about schematic representation of the Salomon cluster compute nodes IB topology](../network/ib-single-plane-topology/).
@@ -19,7 +19,7 @@ General information
|Primary purpose|High Performance Computing|
|Architecture of compute nodes|x86-64|
|Operating system|CentOS 6.7 Linux|
-|[**Compute nodes**](../compute-nodes.md)||
+|[**Compute nodes**](../compute-nodes/)||
|Totally|1008|
|Processor|2x Intel Xeon E5-2680v3, 2.5GHz, 12cores|
|RAM|128GB, 5.3GB per core, DDR4@2133 MHz|
@@ -39,7 +39,7 @@ Compute nodes
|w/o accelerator|576|2x Intel Xeon E5-2680v3, 2.5GHz|24|128GB|-|
|MIC accelerated|432|2x Intel Xeon E5-2680v3, 2.5GHz|24|128GB|2x Intel Xeon Phi 7120P, 61cores, 16GB RAM|
-For more details please refer to the [Compute nodes](../compute-nodes.md).
+For more details please refer to the [Compute nodes](../compute-nodes/).
Remote visualization nodes
--------------------------
diff --git a/docs.it4i/salomon/introduction.md b/docs.it4i/salomon/introduction.md
index 9eb6ee3fa12616a662a18db4c7b64d0680080757..c18d771b2603ba5dc21dd61abe7e9e128cc2c884 100644
--- a/docs.it4i/salomon/introduction.md
+++ b/docs.it4i/salomon/introduction.md
@@ -1,9 +1,9 @@
Introduction
============
-Welcome to Salomon supercomputer cluster. The Salomon cluster consists of 1008 compute nodes, totaling 24192 compute cores with 129TB RAM and giving over 2 Pflop/s theoretical peak performance. Each node is a powerful x86-64 computer, equipped with 24 cores, at least 128GB RAM. Nodes are interconnected by 7D Enhanced hypercube Infiniband network and equipped with Intel Xeon E5-2680v3 processors. The Salomon cluster consists of 576 nodes without accelerators and 432 nodes equipped with Intel Xeon Phi MIC accelerators. Read more in [Hardware Overview](hardware-overview-1/hardware-overview.html).
+Welcome to Salomon supercomputer cluster. The Salomon cluster consists of 1008 compute nodes, totaling 24192 compute cores with 129TB RAM and giving over 2 Pflop/s theoretical peak performance. Each node is a powerful x86-64 computer, equipped with 24 cores, at least 128GB RAM. Nodes are interconnected by 7D Enhanced hypercube Infiniband network and equipped with Intel Xeon E5-2680v3 processors. The Salomon cluster consists of 576 nodes without accelerators and 432 nodes equipped with Intel Xeon Phi MIC accelerators. Read more in [Hardware Overview](hardware-overview/).
-The cluster runs [CentOS Linux](http://www.bull.com/bullx-logiciels/systeme-exploitation.html) operating system, which is compatible with the RedHat [ Linux family.](http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg)
+The cluster runs [CentOS Linux](http://www.bull.com/bullx-logiciels/systeme-exploitation.html) operating system, which is compatible with the RedHat [ Linux family.](http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg)
**Water-cooled Compute Nodes With MIC Accelerator**
diff --git a/docs.it4i/salomon/network/7d-enhanced-hypercube.md b/docs.it4i/salomon/network/7d-enhanced-hypercube.md
index 6d2a2eb5be5334ec3d02812951da1e2524a6c2c3..a8b8060d402091d6d70edd6c16a8bcb77956140a 100644
--- a/docs.it4i/salomon/network/7d-enhanced-hypercube.md
+++ b/docs.it4i/salomon/network/7d-enhanced-hypercube.md
@@ -1,7 +1,7 @@
7D Enhanced Hypercube
=====================
-[More about Job submission - Placement by IB switch / Hypercube dimension.](../resource-allocation-and-job-execution/job-submission-and-execution.md)
+[More about Job submission - Placement by IB switch / Hypercube dimension.](../resource-allocation-and-job-execution/job-submission-and-execution/)
Nodes may be selected via the PBS resource attribute ehc_[1-7]d .
@@ -15,7 +15,7 @@ Nodes may be selected via the PBS resource attribute ehc_[1-7]d .
|6D|ehc_6d|
|7D|ehc_7d|
-[Schematic representation of the Salomon cluster IB single-plain topology represents hypercube dimension 0](ib-single-plane-topology.md).
+[Schematic representation of the Salomon cluster IB single-plain topology represents hypercube dimension 0](ib-single-plane-topology/).
### 7D Enhanced Hypercube {#d-enhanced-hypercube}
diff --git a/docs.it4i/salomon/network/ib-single-plane-topology.md b/docs.it4i/salomon/network/ib-single-plane-topology.md
index c7d5a9ee882f089128205cba61234f8d53cc0897..9465638156997c3d17c400eb6a1e981836e1be12 100644
--- a/docs.it4i/salomon/network/ib-single-plane-topology.md
+++ b/docs.it4i/salomon/network/ib-single-plane-topology.md
@@ -17,7 +17,7 @@ Each colour in each physical IRU represents one dual-switch ASIC switch.
### IB single-plane topology - Accelerated nodes
-Each of the 3 inter-connected D racks are equivalent to one half of Mcell rack. 18x D rack with MIC accelerated nodes [r21-r38] are equivalent to 3 Mcell racks as shown in a diagram [7D Enhanced Hypercube](7d-enhanced-hypercube.md).
+Each of the 3 inter-connected D racks are equivalent to one half of Mcell rack. 18x D rack with MIC accelerated nodes [r21-r38] are equivalent to 3 Mcell racks as shown in a diagram [7D Enhanced Hypercube](7d-enhanced-hypercube/).
As shown in a diagram :
diff --git a/docs.it4i/salomon/network/network.md b/docs.it4i/salomon/network/network.md
index afe7789ef2b8e95806aac139b7f619fa775beb28..32f35b72dc99a670ada0483008ec4af912eccd5d 100644
--- a/docs.it4i/salomon/network/network.md
+++ b/docs.it4i/salomon/network/network.md
@@ -1,15 +1,15 @@
Network
=======
-All compute and login nodes of Salomon are interconnected by 7D Enhanced hypercube [Infiniband](http://en.wikipedia.org/wiki/InfiniBand) network and by Gigabit [Ethernet](http://en.wikipedia.org/wiki/Ethernet)
-network. Only [Infiniband](http://en.wikipedia.org/wiki/InfiniBand) network may be used to transfer user data.
+All compute and login nodes of Salomon are interconnected by 7D Enhanced hypercube [Infiniband](http://en.wikipedia.org/wiki/InfiniBand) network and by Gigabit [Ethernet](http://en.wikipedia.org/wiki/Ethernet)
+network. Only [Infiniband](http://en.wikipedia.org/wiki/InfiniBand) network may be used to transfer user data.
Infiniband Network
------------------
-All compute and login nodes of Salomon are interconnected by 7D Enhanced hypercube [Infiniband](http://en.wikipedia.org/wiki/InfiniBand) network (56 Gbps). The network topology is a [7D Enhanced hypercube](7d-enhanced-hypercube.md).
+All compute and login nodes of Salomon are interconnected by 7D Enhanced hypercube [Infiniband](http://en.wikipedia.org/wiki/InfiniBand) network (56 Gbps). The network topology is a [7D Enhanced hypercube](7d-enhanced-hypercube/).
-Read more about schematic representation of the Salomon cluster [IB single-plain topology](ib-single-plane-topology.md)
-([hypercube dimension](7d-enhanced-hypercube.md) 0).
+Read more about schematic representation of the Salomon cluster [IB single-plain topology](ib-single-plane-topology/)
+([hypercube dimension](7d-enhanced-hypercube/) 0).
The compute nodes may be accessed via the Infiniband network using ib0 network interface, in address range 10.17.0.0 (mask 255.255.224.0). The MPI may be used to establish native Infiniband connection among the nodes.
diff --git a/docs.it4i/salomon/prace.md b/docs.it4i/salomon/prace.md
index 8257589245f5eb768c551ffb58f8bb967a22df88..e7fe57a0502f1b7e5860a370934a38f432b36a97 100644
--- a/docs.it4i/salomon/prace.md
+++ b/docs.it4i/salomon/prace.md
@@ -3,22 +3,22 @@ PRACE User Support
Intro
-----
-PRACE users coming to Salomon as to TIER-1 system offered through the DECI calls are in general treated as standard users and so most of the general documentation applies to them as well. This section shows the main differences for quicker orientation, but often uses references to the original documentation. PRACE users who don't undergo the full procedure (including signing the IT4I AuP on top of the PRACE AuP) will not have a password and thus access to some services intended for regular users. This can lower their comfort, but otherwise they should be able to use the TIER-1 system as intended. Please see the [Obtaining Login Credentials section](../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html), if the same level of access is required.
+PRACE users coming to Salomon as to TIER-1 system offered through the DECI calls are in general treated as standard users and so most of the general documentation applies to them as well. This section shows the main differences for quicker orientation, but often uses references to the original documentation. PRACE users who don't undergo the full procedure (including signing the IT4I AuP on top of the PRACE AuP) will not have a password and thus access to some services intended for regular users. This can lower their comfort, but otherwise they should be able to use the TIER-1 system as intended. Please see the [Obtaining Login Credentials section](../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials/), if the same level of access is required.
-All general [PRACE User Documentation](http://www.prace-ri.eu/user-documentation/) should be read before continuing reading the local documentation here.
+All general [PRACE User Documentation](http://www.prace-ri.eu/user-documentation/) should be read before continuing reading the local documentation here.
Help and Support
------------------------
If you have any troubles, need information, request support or want to install additional software, please use [PRACE
Helpdesk](http://www.prace-ri.eu/helpdesk-guide264/).
-Information about the local services are provided in the [introduction of general user documentation](introduction.html). Please keep in mind, that standard PRACE accounts don't have a password to access the web interface of the local (IT4Innovations) request tracker and thus a new ticket should be created by sending an e-mail to support[at]it4i.cz.
+Information about the local services are provided in the [introduction of general user documentation](introduction/). Please keep in mind, that standard PRACE accounts don't have a password to access the web interface of the local (IT4Innovations) request tracker and thus a new ticket should be created by sending an e-mail to support[at]it4i.cz.
Obtaining Login Credentials
---------------------------
In general PRACE users already have a PRACE account setup through their HOMESITE (institution from their country) as a result of rewarded PRACE project proposal. This includes signed PRACE AuP, generated and registered certificates, etc.
-If there's a special need a PRACE user can get a standard (local) account at IT4Innovations. To get an account on the Salomon cluster, the user needs to obtain the login credentials. The procedure is the same as for general users of the cluster, so please see the corresponding [section of the general documentation here](../get-started-with-it4innovations/obtaining-login-credentials.html).
+If there's a special need a PRACE user can get a standard (local) account at IT4Innovations. To get an account on the Salomon cluster, the user needs to obtain the login credentials. The procedure is the same as for general users of the cluster, so please see the corresponding [section of the general documentation here](../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials/).
Accessing the cluster
---------------------
@@ -31,11 +31,11 @@ The user will need a valid certificate and to be present in the PRACE LDAP (plea
Most of the information needed by PRACE users accessing the Salomon TIER-1 system can be found here:
-- [General user's FAQ](http://www.prace-ri.eu/Users-General-FAQs)
-- [Certificates FAQ](http://www.prace-ri.eu/Certificates-FAQ)
-- [Interactive access using GSISSH](http://www.prace-ri.eu/Interactive-Access-Using-gsissh)
-- [Data transfer with GridFTP](http://www.prace-ri.eu/Data-Transfer-with-GridFTP-Details)
-- [Data transfer with gtransfer](http://www.prace-ri.eu/Data-Transfer-with-gtransfer)
+- [General user's FAQ](http://www.prace-ri.eu/Users-General-FAQs)
+- [Certificates FAQ](http://www.prace-ri.eu/Certificates-FAQ)
+- [Interactive access using GSISSH](http://www.prace-ri.eu/Interactive-Access-Using-gsissh)
+- [Data transfer with GridFTP](http://www.prace-ri.eu/Data-Transfer-with-GridFTP-Details)
+- [Data transfer with gtransfer](http://www.prace-ri.eu/Data-Transfer-with-gtransfer)
Before you start to use any of the services don't forget to create a proxy certificate from your certificate:
@@ -95,7 +95,7 @@ When logging from other PRACE system, the prace_service script can be used:
$ gsissh `prace_service -e -s salomon`
```
-Although the preferred and recommended file transfer mechanism is [using GridFTP](prace.html#file-transfers), the GSI SSH
+Although the preferred and recommended file transfer mechanism is [using GridFTP](prace/#file-transfers), the GSI SSH
implementation on Salomon supports also SCP, so for small files transfer gsiscp can be used:
```bash
@@ -110,9 +110,9 @@ implementation on Salomon supports also SCP, so for small files transfer gsiscp
### Access to X11 applications (VNC)
-If the user needs to run X11 based graphical application and does not have a X11 server, the applications can be run using VNC service. If the user is using regular SSH based access, please see the [section in general documentation](../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
+If the user needs to run X11 based graphical application and does not have a X11 server, the applications can be run using VNC service. If the user is using regular SSH based access, please see the [section in general documentation](../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/).
-If the user uses GSI SSH based access, then the procedure is similar to the SSH based access ([look here](../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)), only the port forwarding must be done using GSI SSH:
+If the user uses GSI SSH based access, then the procedure is similar to the SSH based access ([look here](../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/)), only the port forwarding must be done using GSI SSH:
```bash
$ gsissh -p 2222 salomon.it4i.cz -L 5961:localhost:5961
@@ -120,11 +120,11 @@ If the user uses GSI SSH based access, then the procedure is similar to the SSH
### Access with SSH
-After successful obtainment of login credentials for the local IT4Innovations account, the PRACE users can access the cluster as regular users using SSH. For more information please see the [section in general documentation](accessing-the-cluster/shell-and-data-access/shell-and-data-access.html).
+After successful obtainment of login credentials for the local IT4Innovations account, the PRACE users can access the cluster as regular users using SSH. For more information please see the [section in general documentation](accessing-the-cluster/shell-and-data-access/shell-and-data-access/).
File transfers
------------------
-PRACE users can use the same transfer mechanisms as regular users (if they've undergone the full registration procedure). For information about this, please see [the section in the general documentation](accessing-the-cluster/shell-and-data-access/shell-and-data-access.html).
+PRACE users can use the same transfer mechanisms as regular users (if they've undergone the full registration procedure). For information about this, please see [the section in the general documentation](accessing-the-cluster/shell-and-data-access/shell-and-data-access/).
Apart from the standard mechanisms, for PRACE users to transfer data to/from Salomon cluster, a GridFTP server running Globus Toolkit GridFTP service is available. The service is available from public Internet as well as from the internal PRACE network (accessible only from other PRACE partners).
@@ -203,7 +203,7 @@ Generally both shared file systems are available through GridFTP:
|/home|Lustre|Default HOME directories of users in format /home/prace/login/|
|/scratch|Lustre|Shared SCRATCH mounted on the whole cluster|
-More information about the shared file systems is available [here](storage.html).
+More information about the shared file systems is available [here](storage/storage/).
Please note, that for PRACE users a "prace" directory is used also on the SCRATCH file system.
@@ -216,13 +216,13 @@ Usage of the cluster
--------------------
There are some limitations for PRACE user when using the cluster. By default PRACE users aren't allowed to access special queues in the PBS Pro to have high priority or exclusive access to some special equipment like accelerated nodes and high memory (fat) nodes. There may be also restrictions obtaining a working license for the commercial software installed on the cluster, mostly because of the license agreement or because of insufficient amount of licenses.
-For production runs always use scratch file systems. The available file systems are described [here](storage/storage.html).
+For production runs always use scratch file systems. The available file systems are described [here](storage/storage/).
### Software, Modules and PRACE Common Production Environment
-All system wide installed software on the cluster is made available to the users via the modules. The information about the environment and modules usage is in this [section of general documentation](environment-and-modules.html).
+All system wide installed software on the cluster is made available to the users via the modules. The information about the environment and modules usage is in this [section of general documentation](environment-and-modules/).
-PRACE users can use the "prace" module to use the [PRACE Common Production Environment](http://www.prace-ri.eu/PRACE-common-production).
+PRACE users can use the "prace" module to use the [PRACE Common Production Environment](http://www.prace-ri.eu/PRACE-common-production).
```bash
$ module load prace
@@ -230,7 +230,7 @@ PRACE users can use the "prace" module to use the [PRACE Common Production Envir
### Resource Allocation and Job Execution
-General information about the resource allocation, job queuing and job execution is in this [section of general documentation](resource-allocation-and-job-execution/introduction.html).
+General information about the resource allocation, job queuing and job execution is in this [section of general documentation](resource-allocation-and-job-execution/introduction/).
For PRACE users, the default production run queue is "qprace". PRACE users can also use two other queues "qexp" and "qfree".
@@ -245,13 +245,13 @@ For PRACE users, the default production run queue is "qprace". PRACE users can a
### Accounting & Quota
-The resources that are currently subject to accounting are the core hours. The core hours are accounted on the wall clock basis. The accounting runs whenever the computational cores are allocated or blocked via the PBS Pro workload manager (the qsub command), regardless of whether the cores are actually used for any calculation. See [example in the general documentation](resource-allocation-and-job-execution/resources-allocation-policy.html).
+The resources that are currently subject to accounting are the core hours. The core hours are accounted on the wall clock basis. The accounting runs whenever the computational cores are allocated or blocked via the PBS Pro workload manager (the qsub command), regardless of whether the cores are actually used for any calculation. See [example in the general documentation](resource-allocation-and-job-execution/resources-allocation-policy/).
-PRACE users should check their project accounting using the [PRACE Accounting Tool (DART)](http://www.prace-ri.eu/accounting-report-tool/).
+PRACE users should check their project accounting using the [PRACE Accounting Tool (DART)](http://www.prace-ri.eu/accounting-report-tool/).
Users who have undergone the full local registration procedure (including signing the IT4Innovations Acceptable Use Policy) and who have received local password may check at any time, how many core-hours have been consumed by themselves and their projects using the command "it4ifree". Please note that you need to know your user password to use the command and that the displayed core hours are "system core hours" which differ from PRACE "standardized core hours".
->The **it4ifree** command is a part of it4i.portal.clients package, located here: <https://pypi.python.org/pypi/it4i.portal.clients>
+>The **it4ifree** command is a part of it4i.portal.clients package, located here: <https://pypi.python.org/pypi/it4i.portal.clients>
```bash
$ it4ifree
@@ -269,4 +269,4 @@ By default file system quota is applied. To check the current status of the quot
$ lfs quota -u USER_LOGIN /scratch
```
-If the quota is insufficient, please contact the [support](prace.html#help-and-support) and request an increase.
\ No newline at end of file
+If the quota is insufficient, please contact the [support](prace/#help-and-support) and request an increase.
\ No newline at end of file
diff --git a/docs.it4i/salomon/resource-allocation-and-job-execution/capacity-computing.md b/docs.it4i/salomon/resource-allocation-and-job-execution/capacity-computing.md
index 88a557d227ab8a5c96626e41ad8f52224f7d09d3..a387d5a9f67cebe4c0f42be9985ac7b9fe18da0c 100644
--- a/docs.it4i/salomon/resource-allocation-and-job-execution/capacity-computing.md
+++ b/docs.it4i/salomon/resource-allocation-and-job-execution/capacity-computing.md
@@ -9,13 +9,13 @@ However, executing huge number of jobs via the PBS queue may strain the system.
>Please follow one of the procedures below, in case you wish to schedule more than 100 jobs at a time.
-- Use [Job arrays](capacity-computing.md#job-arrays) when running huge number of [multithread](capacity-computing.md#shared-jobscript-on-one-node) (bound to one node only) or multinode (multithread across several nodes) jobs
-- Use [GNU parallel](capacity-computing.md#gnu-parallel) when running single core jobs
-- Combine[GNU parallel with Job arrays](capacity-computing.md#combining-job-arrays-and-gnu-parallel)Â when running huge number of single core jobs
+- Use [Job arrays](capacity-computing.md#job-arrays) when running huge number of [multithread](capacity-computing/#shared-jobscript-on-one-node) (bound to one node only) or multinode (multithread across several nodes) jobs
+- Use [GNU parallel](capacity-computing/#gnu-parallel) when running single core jobs
+- Combine[GNU parallel with Job arrays](capacity-computing/#combining-job-arrays-and-gnu-parallel)Â when running huge number of single core jobs
Policy
------
-1. A user is allowed to submit at most 100 jobs. Each job may be [a job array](capacity-computing.md#job-arrays).
+1. A user is allowed to submit at most 100 jobs. Each job may be [a job array](capacity-computing/#job-arrays).
2. The array size is at most 1000 subjobs.
Job arrays
@@ -75,7 +75,7 @@ If huge number of parallel multicore (in means of multinode multithread, e. g. M
### Submit the job array
-To submit the job array, use the qsub -J command. The 900 jobs of the [example above](capacity-computing.html#array_example) may be submitted like this:
+To submit the job array, use the qsub -J command. The 900 jobs of the [example above](capacity-computing/#array_example) may be submitted like this:
```bash
$ qsub -N JOBNAME -J 1-900 jobscript
@@ -146,7 +146,7 @@ Display status information for all user's subjobs.
$ qstat -u $USER -tJ
```
-Read more on job arrays in the [PBSPro Users guide](../../pbspro-documentation.html).
+Read more on job arrays in the [PBSPro Users guide](../../pbspro-documentation/).
GNU parallel
----------------
@@ -207,7 +207,7 @@ In this example, tasks from tasklist are executed via the GNU parallel. The job
### Submit the job
-To submit the job, use the qsub command. The 101 tasks' job of the [example above](capacity-computing.html#gp_example) may be submitted like this:
+To submit the job, use the qsub command. The 101 tasks' job of the [example above](capacity-computing/#gp_example) may be submitted like this:
```bash
$ qsub -N JOBNAME jobscript
@@ -288,7 +288,7 @@ When deciding this values, think about following guiding rules :
### Submit the job array
-To submit the job array, use the qsub -J command. The 992 tasks' job of the [example above](capacity-computing.html#combined_example) may be submitted like this:
+To submit the job array, use the qsub -J command. The 992 tasks' job of the [example above](capacity-computing/#combined_example) may be submitted like this:
```bash
$ qsub -N JOBNAME -J 1-992:32 jobscript
@@ -301,7 +301,7 @@ Please note the #PBS directives in the beginning of the jobscript file, dont' fo
Examples
--------
-Download the examples in [capacity.zip](capacity-computing-example), illustrating the above listed ways to run huge number of jobs. We recommend to try out the examples, before using this for running production jobs.
+Download the examples in [capacity.zip](capacity.zip), illustrating the above listed ways to run huge number of jobs. We recommend to try out the examples, before using this for running production jobs.
Unzip the archive in an empty directory on Anselm and follow the instructions in the README file
diff --git a/docs.it4i/salomon/resource-allocation-and-job-execution/capacity.zip b/docs.it4i/salomon/resource-allocation-and-job-execution/capacity.zip
new file mode 100644
index 0000000000000000000000000000000000000000..9ea4db6e7e6ec6c0b86bef89fbe69933957d9016
Binary files /dev/null and b/docs.it4i/salomon/resource-allocation-and-job-execution/capacity.zip differ
diff --git a/docs.it4i/salomon/resource-allocation-and-job-execution/introduction.md b/docs.it4i/salomon/resource-allocation-and-job-execution/introduction.md
index 7f07b0b6ca73a90319c9acc824b0212d4b951929..97e98a305c4eee06d371fcde8186a9b46cf6db4f 100644
--- a/docs.it4i/salomon/resource-allocation-and-job-execution/introduction.md
+++ b/docs.it4i/salomon/resource-allocation-and-job-execution/introduction.md
@@ -1,11 +1,11 @@
Resource Allocation and Job Execution
=====================================
-To run a [job](job-submission-and-execution.html), [computational resources](resources-allocation-policy.html) for this particular job must be allocated. This is done via the PBS Pro job workload manager software, which efficiently distributes workloads across the supercomputer. Extensive informations about PBS Pro can be found in the [official documentation here](../../pbspro-documentation.html), especially in the [PBS Pro User's Guide](https://docs.it4i.cz/pbspro-documentation/pbspro-users-guide).
+To run a [job](job-submission-and-execution/), [computational resources](resources-allocation-policy/) for this particular job must be allocated. This is done via the PBS Pro job workload manager software, which efficiently distributes workloads across the supercomputer. Extensive informations about PBS Pro can be found in the [official documentation here](../../pbspro-documentation/), especially in the [PBS Pro User's Guide](../../pbspro-documentation/).
Resources Allocation Policy
---------------------------
-The resources are allocated to the job in a fairshare fashion, subject to constraints set by the queue and resources available to the Project. [The Fairshare](job-priority.html) at Salomon ensures that individual users may consume approximately equal amount of resources per week. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following queues are available to Anselm users:
+The resources are allocated to the job in a fairshare fashion, subject to constraints set by the queue and resources available to the Project. [The Fairshare](job-priority/) at Salomon ensures that individual users may consume approximately equal amount of resources per week. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following queues are available to Anselm users:
- **qexp**, the Express queue
- **qprod**, the Production queue
@@ -16,7 +16,7 @@ The resources are allocated to the job in a fairshare fashion, subject to constr
>Check the queue status at <https://extranet.it4i.cz/rsweb/salomon/>
-Read more on the [Resource Allocation Policy](resources-allocation-policy.html) page.
+Read more on the [Resource Allocation Policy](resources-allocation-policy/) page.
Job submission and execution
----------------------------
@@ -24,4 +24,4 @@ Job submission and execution
The qsub submits the job into the queue. The qsub command creates a request to the PBS Job manager for allocation of specified resources. The **smallest allocation unit is entire node, 24 cores**, with exception of the qexp queue. The resources will be allocated when available, subject to allocation policies and constraints. **After the resources are allocated the jobscript or interactive shell is executed on first of the allocated nodes.**
-Read more on the [Job submission and execution](job-submission-and-execution.html) page.
\ No newline at end of file
+Read more on the [Job submission and execution](job-submission-and-execution/) page.
\ No newline at end of file
diff --git a/docs.it4i/salomon/resource-allocation-and-job-execution/job-priority.md b/docs.it4i/salomon/resource-allocation-and-job-execution/job-priority.md
index 43c44f123d18fb588fd7defbd1a2650b4886eb4b..87e40c4c918f9a467f3e6db68012d6f9ec9e2d0d 100644
--- a/docs.it4i/salomon/resource-allocation-and-job-execution/job-priority.md
+++ b/docs.it4i/salomon/resource-allocation-and-job-execution/job-priority.md
@@ -17,7 +17,7 @@ Queue priority is priority of queue where job is queued before execution.
Queue priority has the biggest impact on job execution priority. Execution priority of jobs in higher priority queues is always greater than execution priority of jobs in lower priority queues. Other properties of job used for determining job execution priority (fairshare priority, eligible time) cannot compete with queue priority.
-Queue priorities can be seen at <https://extranet.it4i.cz/rsweb/salomon/queues>
+Queue priorities can be seen at <https://extranet.it4i.cz/rsweb/salomon/queues>
### Fairshare priority
@@ -33,7 +33,7 @@ where MAX_FAIRSHARE has value 1E6, usage~Project~ is cumulated usage by all memb
Usage counts allocated corehours (ncpus*walltime). Usage is decayed, or cut in half periodically, at the interval 168 hours (one week). Jobs queued in queue qexp are not calculated to project's usage.
->Calculated usage and fairshare priority can be seen at <https://extranet.it4i.cz/rsweb/salomon/projects>.
+>Calculated usage and fairshare priority can be seen at <https://extranet.it4i.cz/rsweb/salomon/projects>.
Calculated fairshare priority can be also seen as Resource_List.fairshare attribute of a job.
@@ -67,4 +67,4 @@ Specifying more accurate walltime enables better schedulling, better execution t
### Job placement
-Job [placement can be controlled by flags during submission](job-submission-and-execution.html#job_placement).
\ No newline at end of file
+Job [placement can be controlled by flags during submission](job-submission-and-execution/#job_placement).
\ No newline at end of file
diff --git a/docs.it4i/salomon/resource-allocation-and-job-execution/job-submission-and-execution.md b/docs.it4i/salomon/resource-allocation-and-job-execution/job-submission-and-execution.md
index da291a92aebde8ffc528101a05bfbdab42c2723c..b0cf57a0670071b989407a5cd9a3ae77fc11caf4 100644
--- a/docs.it4i/salomon/resource-allocation-and-job-execution/job-submission-and-execution.md
+++ b/docs.it4i/salomon/resource-allocation-and-job-execution/job-submission-and-execution.md
@@ -74,7 +74,7 @@ In this example, we allocate 4 nodes, with 24 cores per node (totalling 96 cores
Per NUMA node allocation.
Jobs are isolated by cpusets.
-The UV2000 (node uv1) offers 3328GB of RAM and 112 cores, distributed in 14 NUMA nodes. A NUMA node packs 8 cores and approx. 236GB RAM. In the PBS the UV2000 provides 14 chunks, a chunk per NUMA node (see [Resource allocation policy](resources-allocation-policy.html)). The jobs on UV2000 are isolated from each other by cpusets, so that a job by one user may not utilize CPU or memory allocated to a job by other user. Always, full chunks are allocated, a job may only use resources of the NUMA nodes allocated to itself.
+The UV2000 (node uv1) offers 3328GB of RAM and 112 cores, distributed in 14 NUMA nodes. A NUMA node packs 8 cores and approx. 236GB RAM. In the PBS the UV2000 provides 14 chunks, a chunk per NUMA node (see [Resource allocation policy](resources-allocation-policy/)). The jobs on UV2000 are isolated from each other by cpusets, so that a job by one user may not utilize CPU or memory allocated to a job by other user. Always, full chunks are allocated, a job may only use resources of the NUMA nodes allocated to itself.
```bash
 $ qsub -A OPEN-0-0 -q qfat -l select=14 ./myjob
@@ -90,7 +90,7 @@ In this example, we allocate 2000GB of memory on the UV2000 for 72 hours. By req
### Useful tricks
-All qsub options may be [saved directly into the jobscript](job-submission-and-execution.html#PBSsaved). In such a case, no options to qsub are needed.
+All qsub options may be [saved directly into the jobscript](job-submission-and-execution/#PBSsaved). In such a case, no options to qsub are needed.
```bash
$ qsub ./myjob
@@ -139,11 +139,11 @@ Nodes may be selected via the PBS resource attribute ehc_[1-7]d .
$ qsub -A OPEN-0-0 -q qprod -l select=4:ncpus=24 -l place=group=ehc_1d -I
```
-In this example, we allocate 4 nodes, 24 cores, selecting only the nodes with [hypercube dimension](../network-1/7d-enhanced-hypercube.html) 1.
+In this example, we allocate 4 nodes, 24 cores, selecting only the nodes with [hypercube dimension](../network/7d-enhanced-hypercube/) 1.
### Placement by IB switch
-Groups of computational nodes are connected to chassis integrated Infiniband switches. These switches form the leaf switch layer of the [Infiniband network](../network-1.html) . Nodes sharing the leaf switch can communicate most efficiently. Sharing the same switch prevents hops in the network and provides for unbiased, most efficient network communication.
+Groups of computational nodes are connected to chassis integrated Infiniband switches. These switches form the leaf switch layer of the [Infiniband network](../network/) . Nodes sharing the leaf switch can communicate most efficiently. Sharing the same switch prevents hops in the network and provides for unbiased, most efficient network communication.
There are at most 9 nodes sharing the same Infiniband switch.
@@ -391,7 +391,7 @@ exit
In this example, some directory on the /home holds the input file input and executable mympiprog.x . We create a directory myjob on the /scratch filesystem, copy input and executable files from the /home directory where the qsub was invoked ($PBS_O_WORKDIR) to /scratch, execute the MPI programm mympiprog.x and copy the output file back to the /home directory. The mympiprog.x is executed as one process per node, on all allocated nodes.
->Consider preloading inputs and executables onto [shared scratch](../storage.html) before the calculation starts.
+>Consider preloading inputs and executables onto [shared scratch](../storage/storage/) before the calculation starts.
In some cases, it may be impractical to copy the inputs to scratch and outputs to home. This is especially true when very large input and output files are expected, or when the files should be reused by a subsequent calculation. In such a case, it is users responsibility to preload the input files on shared /scratch before the job submission and retrieve the outputs manually, after all calculations are finished.
@@ -428,7 +428,7 @@ HTML commented section #2 (examples need to be reworked)
>Local scratch directory is often useful for single node jobs. Local scratch will be deleted immediately after the job ends. Be very careful, use of RAM disk filesystem is at the expense of operational memory.
-Example jobscript for single node calculation, using [local scratch](../storage.html) on the node:
+Example jobscript for single node calculation, using [local scratch](../storage/storage/) on the node:
```bash
#!/bin/bash
diff --git a/docs.it4i/salomon/resource-allocation-and-job-execution/resources-allocation-policy.md b/docs.it4i/salomon/resource-allocation-and-job-execution/resources-allocation-policy.md
index 924af14835bf844523f1870095f517d0d387f52c..760a33fc57cdae6558536fd94f959d75cda212f4 100644
--- a/docs.it4i/salomon/resource-allocation-and-job-execution/resources-allocation-policy.md
+++ b/docs.it4i/salomon/resource-allocation-and-job-execution/resources-allocation-policy.md
@@ -3,7 +3,7 @@ Resources Allocation Policy
Resources Allocation Policy
---------------------------
-The resources are allocated to the job in a fairshare fashion, subject to constraints set by the queue and resources available to the Project. The Fairshare at Anselm ensures that individual users may consume approximately equal amount of resources per week. Detailed information in the [Job scheduling](job-priority.md) section. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following table provides the queue partitioning overview:
+The resources are allocated to the job in a fairshare fashion, subject to constraints set by the queue and resources available to the Project. The Fairshare at Anselm ensures that individual users may consume approximately equal amount of resources per week. Detailed information in the [Job scheduling](job-priority/) section. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following table provides the queue partitioning overview:
|queue |active project |project resources |nodes|min ncpus*|priority|authorization|walltime |
| --- | --- |
@@ -15,7 +15,7 @@ The resources are allocated to the job in a fairshare fashion, subject to constr
|**qfree** Free resource queue|yes |none required |752 nodes, max 86 per job |24 |-1024 |no |12 / 12h |
|**qviz** Visualization queue |yes |none required |2 (with NVIDIA Quadro K5000) |4 |150 |no |1 / 2h |
->**The qfree queue is not free of charge**. [Normal accounting](resources-allocation-policy.html#resources-accounting-policy) applies. However, it allows for utilization of free resources, once a Project exhausted all its allocated computational resources. This does not apply for Directors Discreation's projects (DD projects) by default. Usage of qfree after exhaustion of DD projects computational resources is allowed after request for this queue.
+>**The qfree queue is not free of charge**. [Normal accounting](resources-allocation-policy/#resources-accounting-policy) applies. However, it allows for utilization of free resources, once a Project exhausted all its allocated computational resources. This does not apply for Directors Discreation's projects (DD projects) by default. Usage of qfree after exhaustion of DD projects computational resources is allowed after request for this queue.
- **qexp**, the Express queue: This queue is dedicated for testing and running very small jobs. It is not required to specify a project to enter the qexp. There are 2 nodes always reserved for this queue (w/o accelerator), maximum 8 nodes are available via the qexp for a particular user. The nodes may be allocated on per core basis. No special authorization is required to use it. The maximum runtime in qexp is 1 hour.
- **qprod**, the Production queue: This queue is intended for normal production runs. It is required that active project with nonzero remaining resources is specified to enter the qprod. All nodes may be accessed via the qprod queue, however only 86 per job. Full nodes, 24 cores per node are allocated. The queue runs with medium priority and no special authorization is required to use it. The maximum runtime in qprod is 48 hours.
@@ -25,19 +25,19 @@ The resources are allocated to the job in a fairshare fashion, subject to constr
- **qfree**, the Free resource queue: The queue qfree is intended for utilization of free resources, after a Project exhausted all its allocated computational resources (Does not apply to DD projects by default. DD projects have to request for persmission on qfree after exhaustion of computational resources.). It is required that active project is specified to enter the queue, however no remaining resources are required. Consumed resources will be accounted to the Project. Only 178 nodes without accelerator may be accessed from this queue. Full nodes, 24 cores per node are allocated. The queue runs with very low priority and no special authorization is required to use it. The maximum runtime in qfree is 12 hours.
- **qviz**, the Visualization queue: Intended for pre-/post-processing using OpenGL accelerated graphics. Currently when accessing the node, each user gets 4 cores of a CPU allocated, thus approximately 73 GB of RAM and 1/7 of the GPU capacity (default "chunk"). If more GPU power or RAM is required, it is recommended to allocate more chunks (with 4 cores each) up to one whole node per user, so that all 28 cores, 512 GB RAM and whole GPU is exclusive. This is currently also the maximum allowed allocation per one user. One hour of work is allocated by default, the user may ask for 2 hours maximum.
->To access node with Xeon Phi co-processor user needs to specify that in [job submission select statement](job-submission-and-execution.md).
+>To access node with Xeon Phi co-processor user needs to specify that in [job submission select statement](job-submission-and-execution/).
### Notes
-The job wall clock time defaults to **half the maximum time**, see table above. Longer wall time limits can be [set manually, see examples](job-submission-and-execution.md).
+The job wall clock time defaults to **half the maximum time**, see table above. Longer wall time limits can be [set manually, see examples](job-submission-and-execution/).
Jobs that exceed the reserved wall clock time (Req'd Time) get killed automatically. Wall clock time limit can be changed for queuing jobs (state Q) using the qalter command, however can not be changed for a running job (state R).
-Salomon users may check current queue configuration at <https://extranet.it4i.cz/rsweb/salomon/queues>.
+Salomon users may check current queue configuration at <https://extranet.it4i.cz/rsweb/salomon/queues>.
### Queue status
->Check the status of jobs, queues and compute nodes at [https://extranet.it4i.cz/rsweb/salomon/](https://extranet.it4i.cz/rsweb/salomon)
+>Check the status of jobs, queues and compute nodes at [https://extranet.it4i.cz/rsweb/salomon/](https://extranet.it4i.cz/rsweb/salomon)
@@ -111,7 +111,7 @@ Resources Accounting Policy
### The Core-Hour
-The resources that are currently subject to accounting are the core-hours. The core-hours are accounted on the wall clock basis. The accounting runs whenever the computational cores are allocated or blocked via the PBS Pro workload manager (the qsub command), regardless of whether the cores are actually used for any calculation. 1 core-hour is defined as 1 processor core allocated for 1 hour of wall clock time. Allocating a full node (24 cores) for 1 hour accounts to 24 core-hours. See example in the [Job submission and execution](job-submission-and-execution.md) section.
+The resources that are currently subject to accounting are the core-hours. The core-hours are accounted on the wall clock basis. The accounting runs whenever the computational cores are allocated or blocked via the PBS Pro workload manager (the qsub command), regardless of whether the cores are actually used for any calculation. 1 core-hour is defined as 1 processor core allocated for 1 hour of wall clock time. Allocating a full node (24 cores) for 1 hour accounts to 24 core-hours. See example in the [Job submission and execution](job-submission-and-execution/) section.
### Check consumed resources
diff --git a/docs.it4i/salomon/software/ansys/ansys-cfx.md b/docs.it4i/salomon/software/ansys/ansys-cfx.md
index f5cf8a8bfa652bc1f2bc23b4c703894979c0f3a0..a450ed452af93df8aeffe089c0019775ab52b6e3 100644
--- a/docs.it4i/salomon/software/ansys/ansys-cfx.md
+++ b/docs.it4i/salomon/software/ansys/ansys-cfx.md
@@ -1,7 +1,7 @@
ANSYS CFX
=========
-[ANSYS CFX](http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+CFX)
+[ANSYS CFX](http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+CFX)
software is a high-performance, general purpose fluid dynamics program that has been applied to solve wide-ranging fluid flow problems for over 20 years. At the heart of ANSYS CFX is its advanced solver technology, the key to achieving reliable and accurate solutions quickly and robustly. The modern, highly parallelized solver is the foundation for an abundant choice of physical models to capture virtually any type of phenomena related to fluid flow. The solver and its many physical models are wrapped in a modern, intuitive, and flexible GUI and user environment, with extensive capabilities for customization and automation using session files, scripting and a powerful expression language.
To run ANSYS CFX in batch mode you can utilize/modify the default cfx.pbs script and execute it via the qsub command.
@@ -49,9 +49,9 @@ echo Machines: $hl
/ansys_inc/v145/CFX/bin/cfx5solve -def input.def -size 4 -size-ni 4x -part-large -start-method "Platform MPI Distributed Parallel" -par-dist $hl -P aa_r
```
-Header of the pbs file (above) is common and description can be find on [this site](../../resource-allocation-and-job-execution/job-submission-and-execution.md). SVS FEM recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
+Header of the pbs file (above) is common and description can be find on [this site](../../resource-allocation-and-job-execution/job-submission-and-execution/). SVS FEM recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
Working directory has to be created before sending pbs job into the queue. Input file should be in working directory or full path to input file has to be specified. >Input file has to be defined by common CFX def file which is attached to the cfx solver via parameter -def
**License**Â should be selected by parameter -P (Big letter **P**). Licensed products are the following: aa_r (ANSYSÂ **Academic**Â Research), ane3fl (ANSYS Multiphysics)-**Commercial**.
-[More about licensing here](licensing.md)
\ No newline at end of file
+[More about licensing here](licensing/)
\ No newline at end of file
diff --git a/docs.it4i/salomon/software/ansys/ansys-fluent.md b/docs.it4i/salomon/software/ansys/ansys-fluent.md
index 8fe15741c408e4a24edca228ad4bdda94d793a9a..e81ededc9e2c930ec870cd8befbc4270b6b45eb5 100644
--- a/docs.it4i/salomon/software/ansys/ansys-fluent.md
+++ b/docs.it4i/salomon/software/ansys/ansys-fluent.md
@@ -1,7 +1,7 @@
ANSYS Fluent
============
-[ANSYS Fluent](http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent)
+[ANSYS Fluent](http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent)
software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions for industrial applications ranging from air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants. Special models that give the software the ability to model in-cylinder combustion, aeroacoustics, turbomachinery, and multiphase systems have served to broaden its reach.
1. Common way to run Fluent over pbs file
@@ -39,7 +39,7 @@ NCORES=`wc -l $PBS_NODEFILE |awk '{print $1}'`
/ansys_inc/v145/fluent/bin/fluent 3d -t$NCORES -cnf=$PBS_NODEFILE -g -i fluent.jou
```
-Header of the pbs file (above) is common and description can be find on [this site](../../resource-allocation-and-job-execution/job-submission-and-execution.md). [SVS FEM](http://www.svsfem.cz) recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
+Header of the pbs file (above) is common and description can be find on [this site](../../resource-allocation-and-job-execution/job-submission-and-execution/). [SVS FEM](http://www.svsfem.cz) recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
Working directory has to be created before sending pbs job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common Fluent journal file which is attached to the Fluent solver via parameter -i fluent.jou
diff --git a/docs.it4i/salomon/software/ansys/ansys-ls-dyna.md b/docs.it4i/salomon/software/ansys/ansys-ls-dyna.md
index c2b18864670a33be6c60b2e6daf768f1731ad863..47c66dd254b0e00bc5964a382d5cfcf92c7a7ab8 100644
--- a/docs.it4i/salomon/software/ansys/ansys-ls-dyna.md
+++ b/docs.it4i/salomon/software/ansys/ansys-ls-dyna.md
@@ -1,7 +1,7 @@
ANSYS LS-DYNA
=============
-**[ANSYSLS-DYNA](http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/Explicit+Dynamics/ANSYS+LS-DYNA)** software provides convenient and easy-to-use access to the technology-rich, time-tested explicit solver without the need to contend with the complex input requirements of this sophisticated program. Introduced in 1996, ANSYS LS-DYNA capabilities have helped customers in numerous industries to resolve highly intricate design issues. ANSYS Mechanical users have been able take advantage of complex explicit solutions for a long time utilizing the traditional ANSYS Parametric Design Language (APDL) environment. These explicit capabilities are available to ANSYS Workbench users as well. The Workbench platform is a powerful, comprehensive, easy-to-use environment for engineering simulation. CAD import from all sources, geometry cleanup, automatic meshing, solution, parametric optimization, result visualization and comprehensive report generation are all available within a single fully interactive modern graphical user environment.
+**[ANSYSLS-DYNA](http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/Explicit+Dynamics/ANSYS+LS-DYNA)** software provides convenient and easy-to-use access to the technology-rich, time-tested explicit solver without the need to contend with the complex input requirements of this sophisticated program. Introduced in 1996, ANSYS LS-DYNA capabilities have helped customers in numerous industries to resolve highly intricate design issues. ANSYS Mechanical users have been able take advantage of complex explicit solutions for a long time utilizing the traditional ANSYS Parametric Design Language (APDL) environment. These explicit capabilities are available to ANSYS Workbench users as well. The Workbench platform is a powerful, comprehensive, easy-to-use environment for engineering simulation. CAD import from all sources, geometry cleanup, automatic meshing, solution, parametric optimization, result visualization and comprehensive report generation are all available within a single fully interactive modern graphical user environment.
To run ANSYS LS-DYNA in batch mode you can utilize/modify the default ansysdyna.pbs script and execute it via the qsub command.
@@ -51,6 +51,6 @@ echo Machines: $hl
/ansys_inc/v145/ansys/bin/ansys145 -dis -lsdynampp i=input.k -machines $hl
```
-Header of the pbs file (above) is common and description can be find on [this site](../../resource-allocation-and-job-execution/job-submission-and-execution.md). [SVS FEM](http://www.svsfem.cz) recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
+Header of the pbs file (above) is common and description can be find on [this site](../../resource-allocation-and-job-execution/job-submission-and-execution/). [SVS FEM](http://www.svsfem.cz) recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
Working directory has to be created before sending pbs job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common LS-DYNA .**k** file which is attached to the ansys solver via parameter i=
\ No newline at end of file
diff --git a/docs.it4i/salomon/software/ansys/ansys-mechanical-apdl.md b/docs.it4i/salomon/software/ansys/ansys-mechanical-apdl.md
index 56d5f78aa795a93e244e9209c2f6ff82ebc241a1..78da5be845044685ae194580cc439934940fc049 100644
--- a/docs.it4i/salomon/software/ansys/ansys-mechanical-apdl.md
+++ b/docs.it4i/salomon/software/ansys/ansys-mechanical-apdl.md
@@ -1,7 +1,7 @@
ANSYS MAPDL
===========
-**[ANSYS Multiphysics](http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/ANSYS+Multiphysics)**
+**[ANSYS Multiphysics](http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/ANSYS+Multiphysics)**
software offers a comprehensive product solution for both multiphysics and single-physics analysis. The product includes structural, thermal, fluid and both high- and low-frequency electromagnetic analysis. The product also contains solutions for both direct and sequentially coupled physics problems including direct coupled-field elements and the ANSYS multi-field solver.
To run ANSYS MAPDL in batch mode you can utilize/modify the default mapdl.pbs script and execute it via the qsub command.
@@ -50,9 +50,9 @@ echo Machines: $hl
/ansys_inc/v145/ansys/bin/ansys145 -b -dis -p aa_r -i input.dat -o file.out -machines $hl -dir $WORK_DIR
```
-Header of the pbs file (above) is common and description can be find on [this site](../../resource-allocation-and-job-execution/job-submission-and-execution.md). [SVS FEM](http://www.svsfem.cz) recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
+Header of the pbs file (above) is common and description can be find on [this site](../../resource-allocation-and-job-execution/job-submission-and-execution/). [SVS FEM](http://www.svsfem.cz) recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
Working directory has to be created before sending pbs job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common APDL file which is attached to the ansys solver via parameter -i
**License** should be selected by parameter -p. Licensed products are the following: aa_r (ANSYS **Academic** Research), ane3fl (ANSYS Multiphysics)-**Commercial**, aa_r_dy (ANSYS **Academic** AUTODYN)
-[More about licensing here](licensing.md)
\ No newline at end of file
+[More about licensing here](licensing/)
\ No newline at end of file
diff --git a/docs.it4i/salomon/software/ansys/ansys.md b/docs.it4i/salomon/software/ansys/ansys.md
index 53e175f0fe1ade524602d72648f550e5c35a6308..4f099ace1b79c98bdb38099f02076536c110a42a 100644
--- a/docs.it4i/salomon/software/ansys/ansys.md
+++ b/docs.it4i/salomon/software/ansys/ansys.md
@@ -1,9 +1,9 @@
Overview of ANSYS Products
==========================
-**[SVS FEM](http://www.svsfem.cz/)** as **[ANSYS Channel partner](http://www.ansys.com/)** for Czech Republic provided all ANSYS licenses for ANSELM cluster and supports of all ANSYS Products (Multiphysics, Mechanical, MAPDL, CFX, Fluent, Maxwell, LS-DYNA...) to IT staff and ANSYS users. If you are challenging to problem of ANSYS functionality contact please [hotline@svsfem.cz](mailto:hotline@svsfem.cz?subject=Ostrava%20-%20ANSELM)
+**[SVS FEM](http://www.svsfem.cz/)** as **[ANSYS Channel partner](http://www.ansys.com/)** for Czech Republic provided all ANSYS licenses for ANSELM cluster and supports of all ANSYS Products (Multiphysics, Mechanical, MAPDL, CFX, Fluent, Maxwell, LS-DYNA...) to IT staff and ANSYS users. If you are challenging to problem of ANSYS functionality contact please [hotline@svsfem.cz](mailto:hotline@svsfem.cz?subject=Ostrava%20-%20ANSELM)
-Anselm provides as commercial as academic variants. Academic variants are distinguished by "**Academic...**" word in the name of  license or by two letter preposition "**aa_**" in the license feature name. Change of license is realized on command line respectively directly in user's pbs file (see individual products). [ More about licensing here](ansys/licensing.html)
+Anselm provides as commercial as academic variants. Academic variants are distinguished by "**Academic...**" word in the name of  license or by two letter preposition "**aa_**" in the license feature name. Change of license is realized on command line respectively directly in user's pbs file (see individual products). [ More about licensing here](licensing/)
To load the latest version of any ANSYS product (Mechanical, Fluent, CFX, MAPDL,...) load the module:
diff --git a/docs.it4i/salomon/software/ansys/licensing.md b/docs.it4i/salomon/software/ansys/licensing.md
index eb87b15457fe2a9c1b67b495bb1f3ec15b461710..63842ea29dc85a0480bb5d34d8812d633f45844d 100644
--- a/docs.it4i/salomon/software/ansys/licensing.md
+++ b/docs.it4i/salomon/software/ansys/licensing.md
@@ -22,4 +22,4 @@ Available Versions
License Preferences
-------------------
-Please [see this page to set license preferences](setting-license-preferences.md).
+Please [see this page to set license preferences](setting-license-preferences/).
diff --git a/docs.it4i/salomon/software/ansys/workbench.md b/docs.it4i/salomon/software/ansys/workbench.md
index 298a03a900c7d54adbcbc639b28fd7cb0b363980..4877593a2b7bbcee39e0056847b145452bf274c3 100644
--- a/docs.it4i/salomon/software/ansys/workbench.md
+++ b/docs.it4i/salomon/software/ansys/workbench.md
@@ -3,7 +3,7 @@ Workbench
Workbench Batch Mode
--------------------
-It is possible to run Workbench scripts in batch mode. You need to configure solvers of individual components to run in parallel mode. Open your project in Workbench. Then, for example, in Mechanical, go to Tools - Solve Process Settings ..., click Advanced button as shown on the screenshot.
+It is possible to run Workbench scripts in batch mode. You need to configure solvers of individual components to run in parallel mode. Open your project in Workbench. Then, for example, in Mechanical, go to Tools - Solve Process Settings ...
diff --git a/docs.it4i/salomon/software/chemistry/INCAR b/docs.it4i/salomon/software/chemistry/INCAR
new file mode 100644
index 0000000000000000000000000000000000000000..4d2848958e6b7333abdb381bb664e1c389360741
--- /dev/null
+++ b/docs.it4i/salomon/software/chemistry/INCAR
@@ -0,0 +1,13 @@
+ PREC = Accurate
+ IBRION = -1
+ ENCUT = 500
+ EDIFF = 1.0e-08
+ ISMEAR = 0
+ SIGMA = 0.01
+ IALGO = 38
+ LREAL = .FALSE.
+ ADDGRID = .TRUE.
+ LWAVE = .FALSE.
+ LCHARG = .FALSE.
+ NCORE = 8
+ KPAR = 8
diff --git a/docs.it4i/salomon/software/chemistry/KPOINTS b/docs.it4i/salomon/software/chemistry/KPOINTS
new file mode 100644
index 0000000000000000000000000000000000000000..cae7400392404a4c9c4e3e7969722ed578825c51
--- /dev/null
+++ b/docs.it4i/salomon/software/chemistry/KPOINTS
@@ -0,0 +1,6 @@
+Automatic mesh
+0
+Monkhorst Pack
+ 3 3 3
+0.5 0.5 0.5
+
diff --git a/docs.it4i/salomon/software/chemistry/POSCAR b/docs.it4i/salomon/software/chemistry/POSCAR
new file mode 100644
index 0000000000000000000000000000000000000000..f72a61b992f3348c4260097c12b9bbb2bed40bc3
--- /dev/null
+++ b/docs.it4i/salomon/software/chemistry/POSCAR
@@ -0,0 +1,16 @@
+ Si
+ 1.0
+ 5.4335600309153529 0.0000000000000000 0.0000000000000000
+ 0.0000000000000000 5.4335600309153529 0.0000000000000000
+ 0.0000000000000000 0.0000000000000000 5.4335600309153529
+ Si
+ 8
+Direct
+ 0.8750000000000000 0.8750000000000000 0.8750000000000000
+ 0.8750000000000000 0.3750000000000000 0.3750000000000000
+ 0.3750000000000000 0.8750000000000000 0.3750000000000000
+ 0.3750000000000000 0.3750000000000000 0.8750000000000000
+ 0.1250000000000000 0.1250000000000000 0.1250000000000000
+ 0.1250000000000000 0.6250000000000000 0.6250000000000000
+ 0.6250000000000000 0.1250000000000000 0.6250000000000000
+ 0.6250000000000000 0.6250000000000000 0.1250000000000000
diff --git a/docs.it4i/salomon/software/chemistry/POTCAR b/docs.it4i/salomon/software/chemistry/POTCAR
new file mode 100644
index 0000000000000000000000000000000000000000..e69e8a3044c2885f5fc7d2b1e1c90ba7ffef914a
--- /dev/null
+++ b/docs.it4i/salomon/software/chemistry/POTCAR
@@ -0,0 +1,2208 @@
+ PAW_PBE Si 05Jan2001
+ 4.00000000000000
+ parameters from PSCTR are:
+ VRHFIN =Si: s2p2
+ LEXCH = PE
+ EATOM = 103.0669 eV, 7.5752 Ry
+
+ TITEL = PAW_PBE Si 05Jan2001
+ LULTRA = F use ultrasoft PP ?
+ IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no
+ RPACOR = 1.500 partial core radius
+ POMASS = 28.085; ZVAL = 4.000 mass and valenz
+ RCORE = 1.900 outmost cutoff radius
+ RWIGS = 2.480; RWIGS = 1.312 wigner-seitz radius (au A)
+ ENMAX = 245.345; ENMIN = 184.009 eV
+ ICORE = 2 local potential
+ LCOR = T correct aug charges
+ LPAW = T paw PP
+ EAUG = 322.069
+ DEXC = 0.000
+ RMAX = 1.950 core radius for proj-oper
+ RAUG = 1.300 factor for augmentation sphere
+ RDEP = 1.993 radius for radial grids
+ RDEPT = 1.837 core radius for aug-charge
+
+ Atomic configuration
+ 6 entries
+ n l j E occ.
+ 1 0 0.50 -1785.8828 2.0000
+ 2 0 0.50 -139.4969 2.0000
+ 2 1 1.50 -95.5546 6.0000
+ 3 0 0.50 -10.8127 2.0000
+ 3 1 0.50 -4.0811 2.0000
+ 3 2 1.50 -4.0817 0.0000
+ Description
+ l E TYP RCUT TYP RCUT
+ 0 -10.8127223 23 1.900
+ 0 -7.6451159 23 1.900
+ 1 -4.0811372 23 1.900
+ 1 2.4879257 23 1.900
+ 2 -4.0817478 7 1.900
+ Error from kinetic energy argument (eV)
+ NDATA = 100
+ STEP = 20.000 1.050
+ 10.1 9.04 8.56 7.65 7.23 6.44 5.73 5.40
+ 4.79 4.25 4.00 3.54 3.13 2.77 2.45 2.16
+ 1.91 1.69 1.50 1.24 1.10 0.975 0.812 0.718
+ 0.636 0.529 0.440 0.388 0.322 0.266 0.219 0.180
+ 0.148 0.121 0.986E-01 0.804E-01 0.614E-01 0.504E-01 0.392E-01 0.328E-01
+ 0.265E-01 0.220E-01 0.189E-01 0.166E-01 0.149E-01 0.135E-01 0.123E-01 0.109E-01
+ 0.977E-02 0.840E-02 0.707E-02 0.605E-02 0.488E-02 0.387E-02 0.290E-02 0.229E-02
+ 0.185E-02 0.152E-02 0.134E-02 0.125E-02 0.121E-02 0.117E-02 0.112E-02 0.102E-02
+ 0.915E-03 0.776E-03 0.640E-03 0.524E-03 0.425E-03 0.369E-03 0.331E-03 0.310E-03
+ 0.294E-03 0.273E-03 0.242E-03 0.210E-03 0.175E-03 0.146E-03 0.124E-03 0.113E-03
+ 0.105E-03 0.973E-04 0.879E-04 0.755E-04 0.633E-04 0.539E-04 0.478E-04 0.438E-04
+ 0.404E-04 0.362E-04 0.308E-04 0.264E-04 0.229E-04 0.209E-04 0.192E-04 0.170E-04
+ 0.145E-04 0.126E-04 0.112E-04 0.103E-04
+END of PSCTR-controll parameters
+ local part
+ 98.2657514061040
+ 0.84157827E+01 0.84210738E+01 0.84276982E+01 0.84387529E+01 0.84542581E+01
+ 0.84742396E+01 0.84987267E+01 0.85277503E+01 0.85613408E+01 0.85995259E+01
+ 0.86423293E+01 0.86897698E+01 0.87418601E+01 0.87986073E+01 0.88600119E+01
+ 0.89260684E+01 0.89967646E+01 0.90720817E+01 0.91519931E+01 0.92364635E+01
+ 0.93254478E+01 0.94188892E+01 0.95167180E+01 0.96188495E+01 0.97251831E+01
+ 0.98356006E+01 0.99499656E+01 0.10068122E+02 0.10189896E+02 0.10315092E+02
+ 0.10443494E+02 0.10574869E+02 0.10708960E+02 0.10845494E+02 0.10984175E+02
+ 0.11124688E+02 0.11266699E+02 0.11409854E+02 0.11553782E+02 0.11698093E+02
+ 0.11842379E+02 0.11986220E+02 0.12129179E+02 0.12270807E+02 0.12410647E+02
+ 0.12548229E+02 0.12683078E+02 0.12814715E+02 0.12942655E+02 0.13066413E+02
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+ -0.803952933881E-02 -0.854101053252E-02 -0.907302277019E-02 -0.963734470585E-02 -0.102358505368E-01
+ -0.108705143308E-01 -0.115434144674E-01 -0.122567381851E-01 -0.130127862287E-01 -0.138139775855E-01
+ -0.146628542996E-01 -0.155620863515E-01 -0.165144765871E-01 -0.175229656786E-01 -0.185906370974E-01
+ -0.197207220752E-01 -0.209166045292E-01 -0.221818259204E-01 -0.235200900133E-01 -0.249352675010E-01
+ -0.264314004551E-01 -0.280127065554E-01 -0.296835830510E-01 -0.314486103986E-01 -0.333125555181E-01
+ -0.352803746019E-01 -0.373572154063E-01 -0.395484189494E-01 -0.418595205316E-01 -0.442962499902E-01
+ -0.468645310902E-01 -0.495704799483E-01 -0.524204023797E-01 -0.554207900464E-01 -0.585783152843E-01
+ -0.618998244709E-01 -0.653923297941E-01 -0.690629992720E-01 -0.729191448635E-01 -0.769682085087E-01
+ -0.812177459231E-01 -0.856754079688E-01 -0.903489194169E-01 -0.952460549124E-01 -0.100374611944E+00
+ -0.105742380623E+00 -0.111357110073E+00 -0.117226471226E+00 -0.123358015834E+00 -0.129759131487E+00
+ -0.136436992474E+00 -0.143398506273E+00 -0.150650255536E+00 -0.158198435396E+00 -0.166048785958E+00
+ -0.174206519886E+00 -0.182676244971E+00 -0.191461881646E+00 -0.200566575426E+00 -0.209992604279E+00
+ -0.219741281025E+00 -0.229812850838E+00 -0.240206384069E+00 -0.250919664576E+00 -0.261949073908E+00
+ -0.273289471686E+00 -0.284934072667E+00 -0.296874321046E+00 -0.309099762684E+00 -0.321597916090E+00
+ -0.334354143130E+00 -0.347351520683E+00 -0.360570714663E+00 -0.373989858114E+00 -0.387584435372E+00
+ -0.401327174519E+00 -0.415187950525E+00 -0.429133701186E+00 -0.443128357849E+00 -0.457132790725E+00
+ -0.471104767691E+00 -0.484998921703E+00 -0.498766719483E+00 -0.512356422012E+00 -0.525713027989E+00
+ -0.538778196066E+00 -0.551490150480E+00 -0.563783586393E+00 -0.575589602443E+00 -0.586835694684E+00
+ -0.597445844316E+00 -0.607340718942E+00 -0.616437986018E+00 -0.624652715226E+00 -0.631897834510E+00
+ -0.638084607775E+00 -0.643123116697E+00 -0.646922744393E+00 -0.649392668142E+00 -0.650442370237E+00
+ -0.649982173269E+00 -0.647923800099E+00 -0.644180957099E+00 -0.638669934919E+00 -0.631310221677E+00
+ -0.622025123195E+00 -0.610742386067E+00 -0.597394819740E+00 -0.581920915553E+00 -0.564265460645E+00
+ -0.544380145344E+00 -0.522224163384E+00 -0.497764803837E+00 -0.470978034224E+00 -0.441849073512E+00
+ -0.410372953728E+00 -0.376555068042E+00 -0.340411701856E+00 -0.301970542890E+00 -0.261271164549E+00
+ -0.218365474934E+00 -0.173318123362E+00 -0.126206854463E+00 -0.771227997739E-01 -0.261706977118E-01
+ 0.265309653866E-01 0.808498960908E-01 0.136640013874E+00 0.193741540297E+00 0.251981141124E+00
+ 0.311172100787E+00 0.371114512072E+00 0.431595477829E+00 0.492389350851E+00 0.553258089799E+00
+ 0.613951880087E+00 0.674210269543E+00 0.733764172796E+00 0.792339126527E+00 0.849659904580E+00
+ 0.905455616556E+00 0.959462488428E+00 0.101141974424E+01 0.106105567211E+01 0.110806847980E+01
+ 0.115211437455E+01 0.119281223958E+01 0.122976095463E+01 0.126255737984E+01 0.129080748835E+01
+ 0.131413097418E+01 0.133216280306E+01 0.134455435589E+01 0.135097524786E+01 0.135111592592E+01
+ 0.134469077582E+01 0.133144140608E+01 0.131113985918E+01 0.128359157702E+01 0.124863807676E+01
+ 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
+ 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
+ 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
+ 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
+ 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
+ 0.000000000000E+00
+ End of Dataset
diff --git a/docs.it4i/salomon/software/chemistry/gofree-cond1.sh b/docs.it4i/salomon/software/chemistry/gofree-cond1.sh
new file mode 100644
index 0000000000000000000000000000000000000000..8dbf6d276685a7f2275a97e568bc18014c1a31c8
--- /dev/null
+++ b/docs.it4i/salomon/software/chemistry/gofree-cond1.sh
@@ -0,0 +1,23 @@
+#!/bin/bash
+#PBS -A OPEN-6-23
+#PBS -N Si-test1
+#PBS -q qfree
+#PBS -l select=1:ncpus=24:mpiprocs=24:ompthreads=1
+#PBS -l walltime=01:59:59
+##PBS-l mem=6gb
+#PBS -j oe
+#PBS -S /bin/bash
+module purge
+module load phono3py/0.9.14-ictce-7.3.5-Python-2.7.9
+export OMP_NUM_THREADS=1
+export I_MPI_COMPATIBILITY=4
+##export OMP_STACKSIZE=10gb
+##0 1 2 3 4 10 11 12 13 20 21 22 30 31 40 91 92 93 94 101 102 103 111 112 121 182 183 184 192 193 202 273 274 283 364
+cd $PBS_O_WORKDIR
+phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCAR --sigma 0.1 --br --write_gamma --gp="0 1 3 4 10"
+#phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCAR --sigma 0.1 --br --write_gamma --gp="11 12 13 20 21"
+#phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCAR --sigma 0.1 --br --write_gamma --gp="21 22 30 31 40"
+#phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCAR --sigma 0.1 --br --write_gamma --gp="91 92 93 94 101"
+#phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCAR --sigma 0.1 --br --write_gamma --gp="102 103 111 112 121"
+#phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCAR --sigma 0.1 --br --write_gamma --gp="182 183 184 192 193"
+#phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCAR --sigma 0.1 --br --write_gamma --gp="202 273 274 283 364"
diff --git a/docs.it4i/salomon/software/chemistry/molpro.md b/docs.it4i/salomon/software/chemistry/molpro.md
index f993cf58b57de39054e4f898531bfaf1d54ccede..5d0b5aec424f8025ffb29f3065325eba2f8cb94e 100644
--- a/docs.it4i/salomon/software/chemistry/molpro.md
+++ b/docs.it4i/salomon/software/chemistry/molpro.md
@@ -5,13 +5,13 @@ Molpro is a complete system of ab initio programs for molecular electronic struc
About Molpro
------------
-Molpro is a software package used for accurate ab-initio quantum chemistry calculations. More information can be found at the [official webpage](http://www.molpro.net/).
+Molpro is a software package used for accurate ab-initio quantum chemistry calculations. More information can be found at the [official webpage](http://www.molpro.net/).
License
-------
Molpro software package is available only to users that have a valid license. Please contact support to enable access to Molpro if you have a valid license appropriate for running on our cluster (eg. academic research group licence, parallel execution).
-To run Molpro, you need to have a valid license token present in " $HOME/.molpro/token". You can download the token from [Molpro website](https://www.molpro.net/licensee/?portal=licensee).
+To run Molpro, you need to have a valid license token present in " $HOME/.molpro/token". You can download the token from [Molpro website](https://www.molpro.net/licensee/?portal=licensee).
Installed version
-----------------
@@ -31,11 +31,11 @@ Compilation parameters are default:
Running
------
-Molpro is compiled for parallel execution using MPI and OpenMP. By default, Molpro reads the number of allocated nodes from PBS and launches a data server on one node. On the remaining allocated nodes, compute processes are launched, one process per node, each with 16 threads. You can modify this behavior by using -n, -t and helper-server options. Please refer to the [Molpro documentation](http://www.molpro.net/info/2010.1/doc/manual/node9.html) for more details.
+Molpro is compiled for parallel execution using MPI and OpenMP. By default, Molpro reads the number of allocated nodes from PBS and launches a data server on one node. On the remaining allocated nodes, compute processes are launched, one process per node, each with 16 threads. You can modify this behavior by using -n, -t and helper-server options. Please refer to the [Molpro documentation](http://www.molpro.net/info/2010.1/doc/manual/node9.html) for more details.
>The OpenMP parallelization in Molpro is limited and has been observed to produce limited scaling. We therefore recommend to use MPI parallelization only. This can be achieved by passing option mpiprocs=16:ompthreads=1 to PBS.
-You are advised to use the -d option to point to a directory in [SCRATCH filesystem](../../storage.md). Molpro can produce a large amount of temporary data during its run, and it is important that these are placed in the fast scratch filesystem.
+You are advised to use the -d option to point to a directory in [SCRATCH filesystem](../../storage/storage/). Molpro can produce a large amount of temporary data during its run, and it is important that these are placed in the fast scratch filesystem.
### Example jobscript
diff --git a/docs.it4i/salomon/software/chemistry/nwchem.md b/docs.it4i/salomon/software/chemistry/nwchem.md
index fd589860db9280bda7192dd86d5b7aa5f467dd18..dd257070c2b043549933cdb33db428b0a8ed5f78 100644
--- a/docs.it4i/salomon/software/chemistry/nwchem.md
+++ b/docs.it4i/salomon/software/chemistry/nwchem.md
@@ -7,7 +7,7 @@ Introduction
-------------------------
NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.
-[Homepage](http://www.nwchem-sw.org/index.php/Main_Page)
+[Homepage](http://www.nwchem-sw.org/index.php/Main_Page)
Installed versions
------------------
@@ -41,7 +41,7 @@ Running
Options
--------------------
-Please refer to [the documentation](http://www.nwchem-sw.org/index.php/Release62:Top-level)Â and in the input file set the following directives :
+Please refer to [the documentation](http://www.nwchem-sw.org/index.php/Release62:Top-level)Â and in the input file set the following directives :
- MEMORY : controls the amount of memory NWChem will use
-- SCRATCH_DIR : set this to a directory in [SCRATCH filesystem](../../storage.md) (or run the calculation completely in a scratch directory). For certain calculations, it might be advisable to reduce I/O by forcing "direct" mode, eg. "scf direct"
\ No newline at end of file
+- SCRATCH_DIR : set this to a directory in [SCRATCH filesystem](../../storage/storage/) (or run the calculation completely in a scratch directory). For certain calculations, it might be advisable to reduce I/O by forcing "direct" mode, eg. "scf direct"
\ No newline at end of file
diff --git a/docs.it4i/salomon/software/chemistry/phono3py.md b/docs.it4i/salomon/software/chemistry/phono3py.md
index 61cf61648fd08ba17539d19f9190989f7cae915b..c2d5326b8c83e0557cf5a2c95f019837ef3c845d 100644
--- a/docs.it4i/salomon/software/chemistry/phono3py.md
+++ b/docs.it4i/salomon/software/chemistry/phono3py.md
@@ -3,7 +3,7 @@ Phono3py
Introduction
-------------
-This GPL software calculates phonon-phonon interactions via the third order force constants. It allows to obtain lattice thermal conductivity, phonon lifetime/linewidth, imaginary part of self energy at the lowest order, joint density of states (JDOS) and weighted-JDOS. For details see Phys. Rev. B 91, 094306 (2015) and http://atztogo.github.io/phono3py/index.html
+This GPL software calculates phonon-phonon interactions via the third order force constants. It allows to obtain lattice thermal conductivity, phonon lifetime/linewidth, imaginary part of self energy at the lowest order, joint density of states (JDOS) and weighted-JDOS. For details see Phys. Rev. B 91, 094306 (2015) and [http://atztogo.github.io/phono3py/index.html](http://atztogo.github.io/phono3py/index.html)
>Load the phono3py/0.9.14-ictce-7.3.5-Python-2.7.9 module
@@ -16,7 +16,7 @@ Example of calculating thermal conductivity of Si using VASP code.
### Calculating force constants
-One needs to calculate second order and third order force constants using the diamond structure of silicon stored in [POSCAR](phono3py-input/poscar-si)Â (the same form as in VASP) using single displacement calculations within supercell.
+One needs to calculate second order and third order force constants using the diamond structure of silicon stored in [POSCAR](poscar-si)Â (the same form as in VASP) using single displacement calculations within supercell.
```bash
$ cat POSCAR
@@ -59,7 +59,7 @@ POSCAR-00006Â Â POSCAR-00015Â POSCAR-00024Â POSCAR-00033Â POSCAR-00042Â POS
POSCAR-00007Â Â POSCAR-00016Â POSCAR-00025Â POSCAR-00034Â POSCAR-00043Â POSCAR-00052Â POSCAR-00061Â POSCAR-00070Â POSCAR-00079Â POSCAR-00088Â POSCAR-00097Â POSCAR-00106
```
-For each displacement the forces needs to be calculated, i.e. in form of the output file of VASP (vasprun.xml). For a single VASP calculations one needs [KPOINTS](phono3py-input/KPOINTS), [POTCAR](phono3py-input/POTCAR), [INCAR](phono3py-input/INCAR) in your case directory (where you have POSCARS) and those 111 displacements calculations can be generated by [prepare.sh](phono3py-input/prepare.sh) script. Then each of the single 111 calculations is submitted [run.sh](phono3py-input/run.sh) by [submit.sh](phono3py-input/submit.sh).
+For each displacement the forces needs to be calculated, i.e. in form of the output file of VASP (vasprun.xml). For a single VASP calculations one needs [KPOINTS](KPOINTS), [POTCAR](POTCAR), [INCAR](INCAR) in your case directory (where you have POSCARS) and those 111 displacements calculations can be generated by [prepare.sh](prepare.sh) script. Then each of the single 111 calculations is submitted [run.sh](run.sh) by [submit.sh](submit.sh).
```bash
$./prepare.sh
@@ -153,7 +153,7 @@ one finds which grid points needed to be calculated, for instance using followin
$ phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCARÂ --sigma 0.1 --br --write-gamma --gp="0 1 2
```
-one calculates grid points 0, 1, 2. To automize one can use for instance scripts to submit 5 points in series, see [gofree-cond1.sh](phono3py-input/gofree-cond1.sh)
+one calculates grid points 0, 1, 2. To automize one can use for instance scripts to submit 5 points in series, see [gofree-cond1.sh](gofree-cond1.sh)
```bash
$ qsub gofree-cond1.sh
diff --git a/docs.it4i/salomon/software/chemistry/prepare.sh b/docs.it4i/salomon/software/chemistry/prepare.sh
new file mode 100644
index 0000000000000000000000000000000000000000..a057dbbadd94d0298e7a4ba19244cb753bea7a9f
--- /dev/null
+++ b/docs.it4i/salomon/software/chemistry/prepare.sh
@@ -0,0 +1,44 @@
+#!/bin/bash
+P=`pwd`
+
+# number of displacements
+poc=9
+
+ for i in `seq 1 $poc `;
+ do
+ cd $P
+ mkdir disp-0000"$i"
+ cd disp-0000"$i"
+ cp ../KPOINTS .
+ cp ../INCAR .
+ cp ../POTCAR .
+ cp ../POSCAR-0000"$i" POSCAR
+ echo $i
+ done
+
+poc=99
+
+ for i in `seq 10 $poc `;
+ do
+ cd $P
+ mkdir disp-000"$i"
+ cd disp-000"$i"
+ cp ../KPOINTS .
+ cp ../INCAR .
+ cp ../POTCAR .
+ cp ../POSCAR-000"$i" POSCAR
+ echo $i
+ done
+poc=111
+
+ for i in `seq 100 $poc `;
+ do
+ cd $P
+ mkdir disp-00"$i"
+ cd disp-00"$i"
+ cp ../KPOINTS .
+ cp ../INCAR .
+ cp ../POTCAR .
+ cp ../POSCAR-00"$i" POSCAR
+ echo $i
+ done
diff --git a/docs.it4i/salomon/software/chemistry/run.sh b/docs.it4i/salomon/software/chemistry/run.sh
new file mode 100644
index 0000000000000000000000000000000000000000..63faf63ba41f0f6846c8b59030a64ae9c1415a55
--- /dev/null
+++ b/docs.it4i/salomon/software/chemistry/run.sh
@@ -0,0 +1,31 @@
+#!/bin/bash
+#PBS -A IT4I-9-11
+#PBS -N Si-test
+#PBS -q qprod
+#PBS -l select=8:ncpus=16:mpiprocs=16:ompthreads=1
+#PBS -l walltime=23:59:59
+##PBS-l mem=6gb
+#PBS -j oe
+#PBS -S /bin/bash
+module load impi/4.1.1.036 intel/13.5.192 fftw3-mpi/3.3.3-icc
+export OMP_NUM_THREADS=1
+export I_MPI_COMPATIBILITY=4
+##export OMP_STACKSIZE=10gb
+b=`basename $PBS_O_WORKDIR`
+echo $b >log.vasp
+SCRDIR=/scratch/$USER/$b
+mkdir -p $SCRDIR
+cd $SCRDIR || exit
+
+# copy input file to scratch
+cp $PBS_O_WORKDIR/* .
+
+mpirun ~/bin/vasp5.4.1 > log.exc
+
+# copy output file to home
+cp * $PBS_O_WORKDIR/. && cd ..
+
+rm -rf "$SCRDIR"
+
+#exit
+exit
diff --git a/docs.it4i/salomon/software/chemistry/submit.sh b/docs.it4i/salomon/software/chemistry/submit.sh
new file mode 100644
index 0000000000000000000000000000000000000000..12fa02ecc489a10df486cfd2fc55065c02d4eea4
--- /dev/null
+++ b/docs.it4i/salomon/software/chemistry/submit.sh
@@ -0,0 +1,35 @@
+#!/bin/bash
+P=`pwd`
+
+# number of displacements
+poc=9
+
+ for i in `seq 1 $poc `;
+ do
+ cd $P
+ cd disp-0000"$i"
+ cp ../run.sh .
+ qsub run.sh
+ echo $i
+ done
+
+poc=99
+
+ for i in `seq 10 $poc `;
+ do
+ cd $P
+ cd disp-000"$i"
+ cp ../run.sh .
+ qsub run.sh
+ echo $i
+ done
+poc=111
+
+ for i in `seq 100 $poc `;
+ do
+ cd $P
+ cd disp-00"$i"
+ cp ../run.sh .
+ qsub run.sh
+ echo $i
+ done
diff --git a/docs.it4i/salomon/software/compilers.md b/docs.it4i/salomon/software/compilers.md
index 835c86e859324099c98bf921d71aa2cce623ad62..7b42984797a79e47274c3c833a51424a3d841fc3 100644
--- a/docs.it4i/salomon/software/compilers.md
+++ b/docs.it4i/salomon/software/compilers.md
@@ -53,7 +53,7 @@ PGDBG OpenMP/MPI debugger and PGPROF OpenMP/MPI profiler are available
$ pgprof &
```
-For more information, see the [PGI page](http://www.pgroup.com/products/pgicdk.htm).
+For more information, see the [PGI page](http://www.pgroup.com/products/pgicdk.htm).
GNU
---
@@ -187,8 +187,8 @@ For more informations see the man pages.
Java
----
-For information how to use Java (runtime and/or compiler), please read the [Java page](java.md).
+For information how to use Java (runtime and/or compiler), please read the [Java page](java/).
nVidia CUDA
-For information how to work with nVidia CUDA, please read the [nVidia CUDA page](../../anselm-cluster-documentation/software/nvidia-cuda.md).
\ No newline at end of file
+For information how to work with nVidia CUDA, please read the [nVidia CUDA page](../../anselm-cluster-documentation/software/nvidia-cuda/).
\ No newline at end of file
diff --git a/docs.it4i/salomon/software/comsol/comsol-multiphysics.md b/docs.it4i/salomon/software/comsol/comsol-multiphysics.md
index c4b69d9f1a49c520495b3d9de4eece4161d5a098..da096283fe339a2c21aed4c4335fa1e4c1285c84 100644
--- a/docs.it4i/salomon/software/comsol/comsol-multiphysics.md
+++ b/docs.it4i/salomon/software/comsol/comsol-multiphysics.md
@@ -3,13 +3,13 @@ COMSOL Multiphysics®
Introduction
-------------------------
-[COMSOL](http://www.comsol.com) is a powerful environment for modelling and solving various engineering and scientific problems based on partial differential equations. COMSOL is designed to solve coupled or multiphysics phenomena. For many standard engineering problems COMSOL provides add-on products such as electrical, mechanical, fluid flow, and chemical applications.
+[COMSOL](http://www.comsol.com) is a powerful environment for modelling and solving various engineering and scientific problems based on partial differential equations. COMSOL is designed to solve coupled or multiphysics phenomena. For many standard engineering problems COMSOL provides add-on products such as electrical, mechanical, fluid flow, and chemical applications.
-- [Structural Mechanics Module](http://www.comsol.com/structural-mechanics-module),
-- [Heat Transfer Module](http://www.comsol.com/heat-transfer-module),
-- [CFD Module](http://www.comsol.com/cfd-module),
-- [Acoustics Module](http://www.comsol.com/acoustics-module),
-- and [many others](http://www.comsol.com/products)
+- [Structural Mechanics Module](http://www.comsol.com/structural-mechanics-module),
+- [Heat Transfer Module](http://www.comsol.com/heat-transfer-module),
+- [CFD Module](http://www.comsol.com/cfd-module),
+- [Acoustics Module](http://www.comsol.com/acoustics-module),
+- and [many others](http://www.comsol.com/products)
COMSOL also allows an interface support for equation-based modelling of partial differential equations.
@@ -34,7 +34,7 @@ By default the **EDU variant** will be loaded. If user needs other version or va
$ module avail COMSOL
```
-If user needs to prepare COMSOL jobs in the interactive mode it is recommend to use COMSOL on the compute nodes via PBS Pro scheduler. In order run the COMSOL Desktop GUI on Windows is recommended to use the [Virtual Network Computing (VNC)](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-and-vnc.md).
+If user needs to prepare COMSOL jobs in the interactive mode it is recommend to use COMSOL on the compute nodes via PBS Pro scheduler. In order run the COMSOL Desktop GUI on Windows is recommended to use the [Virtual Network Computing (VNC)](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/).
```bash
$ xhost +
@@ -76,7 +76,7 @@ LiveLink™* *for MATLAB®
-------------------------
COMSOL is the software package for the numerical solution of the partial differential equations. LiveLink for MATLAB allows connection to the COMSOL®API (Application Programming Interface) with the benefits of the programming language and computing environment of the MATLAB.
-LiveLink for MATLAB is available in both **EDU** and **COM** **variant** of the COMSOL release. On the clusters 1 commercial (**COM**) license and the 5 educational (**EDU**) licenses of LiveLink for MATLAB (please see the [ISV Licenses](../isv_licenses.md)) are available. Following example shows how to start COMSOL model from MATLAB via LiveLink in the interactive mode.
+LiveLink for MATLAB is available in both **EDU** and **COM** **variant** of the COMSOL release. On the clusters 1 commercial (**COM**) license and the 5 educational (**EDU**) licenses of LiveLink for MATLAB (please see the [ISV Licenses](../isv_licenses/)) are available. Following example shows how to start COMSOL model from MATLAB via LiveLink in the interactive mode.
```bash
$ xhost +
diff --git a/docs.it4i/salomon/software/debuggers/Introduction.md b/docs.it4i/salomon/software/debuggers/Introduction.md
index c150402ae614f49e48bdeeb600d493cfc9d8b145..9b6beb85298ec94c66618dd7ee9007d58a81de37 100644
--- a/docs.it4i/salomon/software/debuggers/Introduction.md
+++ b/docs.it4i/salomon/software/debuggers/Introduction.md
@@ -11,15 +11,14 @@ Intel debugger
Intel debugger is no longer available since Parallel Studio version 2015
-The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use [X display](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-and-vnc.md)
-for running the GUI.
+The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment.
```bash
$ module load intel
$ idb
```
-Read more at the [Intel Debugger](../intel-suite/intel-debugger.md) page.
+Read more at the [Intel Debugger](../intel-suite/intel-debugger/) page.
Allinea Forge (DDT/MAP)
-----------------------
@@ -36,7 +35,7 @@ implementation.
$ forge
```
-Read more at the [Allinea DDT](allinea-ddt.md) page.
+Read more at the [Allinea DDT](allinea-ddt/) page.
Allinea Performance Reports
---------------------------
@@ -47,7 +46,7 @@ Allinea Performance Reports characterize the performance of HPC application runs
$ perf-report mpirun -n 64 ./my_application argument01 argument02
```
-Read more at the [Allinea Performance Reports](allinea-performance-reports.md) page.
+Read more at the [Allinea Performance Reports](allinea-performance-reports/) page.
RougeWave Totalview
-------------------
@@ -58,7 +57,7 @@ TotalView is a source- and machine-level debugger for multi-process, multi-threa
$ totalview
```
-Read more at the [Totalview](total-view.md) page.
+Read more at the [Totalview](total-view/) page.
Vampir trace analyzer
---------------------
@@ -69,4 +68,4 @@ Vampir is a GUI trace analyzer for traces in OTF format.
$ vampir
```
-Read more at the [Vampir](vampir.md) page.
\ No newline at end of file
+Read more at the [Vampir](vampir/) page.
\ No newline at end of file
diff --git a/docs.it4i/salomon/software/debuggers/aislinn.md b/docs.it4i/salomon/software/debuggers/aislinn.md
index d363c176fcdebc5583f87ef2253eb45ddcdc922d..f185923db3512c678432fa6d7d7fc72112947e6e 100644
--- a/docs.it4i/salomon/software/debuggers/aislinn.md
+++ b/docs.it4i/salomon/software/debuggers/aislinn.md
@@ -4,7 +4,7 @@ Aislinn
- Aislinn is a dynamic verifier for MPI programs. For a fixed input it covers all possible runs with respect to nondeterminism introduced by MPI. It allows to detect bugs (for sure) that occurs very rare in normal runs.
- Aislinn detects problems like invalid memory accesses, deadlocks, misuse of MPI, and resource leaks.
- Aislinn is open-source software; you can use it without any licensing limitations.
-- Web page of the project: <http://verif.cs.vsb.cz/aislinn/>
+- Web page of the project: <http://verif.cs.vsb.cz/aislinn/>
>Note
Aislinn is software developed at IT4Innovations and some parts are still considered experimental. If you have any questions or experienced any problems, please contact the author: <stanislav.bohm@vsb.cz>.
diff --git a/docs.it4i/salomon/software/debuggers/allinea-ddt.md b/docs.it4i/salomon/software/debuggers/allinea-ddt.md
index e929ddf3b08d4996f0a246b31b1ac16a750fd09c..53ebc20d48fae86208c5cf43af0125839ec98de3 100644
--- a/docs.it4i/salomon/software/debuggers/allinea-ddt.md
+++ b/docs.it4i/salomon/software/debuggers/allinea-ddt.md
@@ -94,4 +94,4 @@ Users can find original User Guide after loading the DDT module:
$DDTPATH/doc/userguide.pdf
```
-[1] Discipline, Magic, Inspiration and Science: Best Practice Debugging with Allinea DDT, Workshop conducted at LLNL by Allinea on May 10, 2013, [link](https://computing.llnl.gov/tutorials/allineaDDT/index.html)
\ No newline at end of file
+[1] Discipline, Magic, Inspiration and Science: Best Practice Debugging with Allinea DDT, Workshop conducted at LLNL by Allinea on May 10, 2013, [link](https://computing.llnl.gov/tutorials/allineaDDT/index.html)
\ No newline at end of file
diff --git a/docs.it4i/salomon/software/debuggers/allinea-performance-reports.md b/docs.it4i/salomon/software/debuggers/allinea-performance-reports.md
index f894c2ccc76f920294042c1ba86adaf4e4e39929..63b6b15a370150f655f804d17ad9f27cf342c6ad 100644
--- a/docs.it4i/salomon/software/debuggers/allinea-performance-reports.md
+++ b/docs.it4i/salomon/software/debuggers/allinea-performance-reports.md
@@ -1,76 +1,61 @@
-Allinea Performance Reports
+Allinea Performance Reports
===========================
-quick application profiling
-
-
Introduction
------------
+Allinea Performance Reports characterize the performance of HPC application runs. After executing your application through the tool, a synthetic HTML report is generated automatically, containing information about several metrics along with clear behavior statements and hints to help you improve the efficiency of your runs.
-Allinea Performance Reports characterize the performance of HPC
-application runs. After executing your application through the tool, a
-synthetic HTML report is generated automatically, containing information
-about several metrics along with clear behavior statements and hints to
-help you improve the efficiency of your runs.
-
-The Allinea Performance Reports is most useful in profiling MPI
-programs.
+The Allinea Performance Reports is most useful in profiling MPI rograms.
Our license is limited to 64 MPI processes.
Modules
-------
-
Allinea Performance Reports version 6.0 is available
+```bash
$ module load PerformanceReports/6.0
+```
-The module sets up environment variables, required for using the Allinea
-Performance Reports.Â
+The module sets up environment variables, required for using the Allinea Performance Reports.
Usage
-----
Use the the perf-report wrapper on your (MPI) program.
-Instead of [running your MPI program the usual
-way](../mpi-1.html), use the the perf report wrapper:
+Instead of [running your MPI program the usual way](../mpi/mpi/), use the the perf report wrapper:
+```bash
$ perf-report mpirun ./mympiprog.x
+```
-The mpi program will run as usual. The perf-report creates two
-additional files, in *.txt and *.html format, containing the
-performance report. Note that demanding MPI
-codes should be run within [ the queue
-system](../../resource-allocation-and-job-execution/job-submission-and-execution.html).
+The mpi program will run as usual. The perf-report creates two additional files, in *.txt and *.html format, containing the performance report. Note that demanding MPI codes should be run within [ the queue system](../../resource-allocation-and-job-execution/job-submission-and-execution/).
Example
-------
-
-In this example, we will be profiling the mympiprog.x MPI program, using
-Allinea performance reports. Assume that the code is compiled with intel
-compilers and linked against intel MPI library:
+In this example, we will be profiling the mympiprog.x MPI program, using Allinea performance reports. Assume that the code is compiled with intel compilers and linked against intel MPI library:
First, we allocate some nodes via the express queue:
+```bash
$ qsub -q qexp -l select=2:ppn=24:mpiprocs=24:ompthreads=1 -I
qsub: waiting for job 262197.dm2 to start
qsub: job 262197.dm2 ready
+```
Then we load the modules and run the program the usual way:
+```bash
$ module load intel impi PerfReports/6.0
$ mpirun ./mympiprog.x
+```
Now lets profile the code:
+```bash
$ perf-report mpirun ./mympiprog.x
+```
-Performance report files
-[mympiprog_32p*.txt](mympiprog_32p_2014-10-15_16-56.txt)
-and
-[mympiprog_32p*.html](mympiprog_32p_2014-10-15_16-56.html)
-were created. We can see that the code is very efficient on MPI and is
-CPU bounded.
-
+Performance report files [mympiprog_32p*.txt](mympiprog_32p_2014-10-15_16-56.txt) and [mympiprog_32p*.html](mympiprog_32p_2014-10-15_16-56.html) were created. We can see that the code is very efficient on MPI and is CPU bounded.
\ No newline at end of file
diff --git a/docs.it4i/salomon/software/debuggers/debuggers.md b/docs.it4i/salomon/software/debuggers/debuggers.md
deleted file mode 100644
index 208abd52dc1e5a0ec594296abaf37af370486af6..0000000000000000000000000000000000000000
--- a/docs.it4i/salomon/software/debuggers/debuggers.md
+++ /dev/null
@@ -1,61 +0,0 @@
-Debuggers and profilers summary
-===============================
-
-Introduction
-------------
-We provide state of the art programms and tools to develop, profile and debug HPC codes at IT4Innovations. On these pages, we provide an overview of the profiling and debugging tools available on Anslem at IT4I.
-
-Intel debugger
---------------
-The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use [X display](https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/resolveuid/11e53ad0d2fd4c5187537f4baeedff33) for running the GUI.
-
-```bash
- $ module load intel
- $ idb
-```
-
-Read more at the [Intel Debugger](intel-suite/intel-debugger.html) page.
-
-Allinea Forge (DDT/MAP)
------------------------
-Allinea DDT, is a commercial debugger primarily for debugging parallel MPI or OpenMP programs. It also has a support for GPU (CUDA) and Intel Xeon Phi accelerators. DDT provides all the standard debugging features (stack trace, breakpoints, watches, view variables, threads etc.) for every thread running as part of your program, or for every process even if these processes are distributed across a cluster using an MPI implementation.
-
-```bash
- $ module load Forge
- $ forge
-```
-
-Read more at the [Allinea DDT](debuggers/allinea-ddt.html) page.
-
-Allinea Performance Reports
----------------------------
-Allinea Performance Reports characterize the performance of HPC application runs. After executing your application through the tool, a synthetic HTML report is generated automatically, containing information about several metrics along with clear behavior statements and hints to help you improve the efficiency of your runs. Our license is limited to 64 MPI processes.
-
-```bash
- $ module load PerformanceReports/6.0
- $ perf-report mpirun -n 64 ./my_application argument01 argument02
-```
-
-Read more at the [Allinea Performance Reports](debuggers/allinea-performance-reports.html) page.
-
-RougeWave Totalview
--------------------
-TotalView is a source- and machine-level debugger for multi-process, multi-threaded programs. Its wide range of tools provides ways to analyze, organize, and test programs, making it easy to isolate and identify problems in individual threads and processes in programs of great complexity.
-
-```bash
- $ module load TotalView/8.15.4-6-linux-x86-64
- $ totalview
-```
-
-Read more at the [Totalview](debuggers/total-view.html) page.
-
-Vampir trace analyzer
----------------------
-Vampir is a GUI trace analyzer for traces in OTF format.
-
-```bash
- $ module load Vampir/8.5.0
- $ vampir
-```
-
-Read more at the [Vampir](../../salomon/software/debuggers/vampir.html) page.
\ No newline at end of file
diff --git a/docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.md b/docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.md
index d04d914497be20fb748e032ebadadd885e63fda6..6eea0816093d0d36afd8398648d7c60198367def 100644
--- a/docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.md
+++ b/docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.md
@@ -89,6 +89,6 @@ You can obtain this command line by pressing the "Command line..." button on Ana
References
----------
-1. <https://www.rcac.purdue.edu/tutorials/phi/PerformanceTuningXeonPhi-Tullos.pdf> Performance Tuning for Intel® Xeon Phi™ Coprocessors
-2. <https://software.intel.com/en-us/intel-vtune-amplifier-xe-support/documentation> >Intel® VTune™ Amplifier Support
-3. <https://software.intel.com/en-us/amplifier_help_linux>Â Linux user guide
\ No newline at end of file
+1. <https://www.rcac.purdue.edu/tutorials/phi/PerformanceTuningXeonPhi-Tullos.pdf> Performance Tuning for Intel® Xeon Phi™ Coprocessors
+2. <https://software.intel.com/en-us/intel-vtune-amplifier-xe-support/documentation> >Intel® VTune™ Amplifier Support
+3. <https://software.intel.com/en-us/amplifier_help_linux>
\ No newline at end of file
diff --git a/docs.it4i/salomon/software/debuggers/mympiprog_32p_2014-10-15_16-56.html b/docs.it4i/salomon/software/debuggers/mympiprog_32p_2014-10-15_16-56.html
new file mode 100644
index 0000000000000000000000000000000000000000..ce60070a9ee25a91973a577fd048d88f31d4680e
--- /dev/null
+++ b/docs.it4i/salomon/software/debuggers/mympiprog_32p_2014-10-15_16-56.html
@@ -0,0 +1,610 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<title>mympiprog.x - Performance Report</title>
+<style type="text/css">
+body {
+ font-family: "Lucida Grande", "Lucida Sans Unicode", "Bitstream Vera Sans",sans-serif;
+ font-size: 1em;
+ color: #2c1a0a;
+}
+div#content {
+ width: 900px;
+ margin-left: auto;
+ margin-right: auto;
+}
+.header {
+ padding-top: 16px;
+}
+.header_left {
+ float:left;
+ width: 532px;
+}
+.logo {
+ float: left;
+}
+.logo img { height: 150px; }
+#time_radar {
+ float: right;
+}
+#time_radar .legend_CPU { fill: #4fd32e; font-size: 1.5em; }
+#time_radar .legend_MPI { fill: #409ded; font-size: 1.5em; }
+#time_radar .legend_IO { fill: #ed8140; font-size: 1.5em; }
+.clear {
+ clear: both;
+}
+table {
+ border-spacing: 0;
+}
+td {
+ padding-left: 0;
+ padding-right: 16px;
+ padding-top: 1px;
+ padding-bottom: 1px;
+}
+#error {
+ border: 1px solid;
+ margin: 16px 0px;
+ padding: 16px 16px 16px 16px;
+ color: #C80000;
+ background-color: #FFC0C0;
+}
+#error p {
+ margin: 8px;
+}
+.application_details {
+ margin-top: 8px;
+ margin-left: 16px;
+ margin-right: 16px;
+}
+.application_details .details_key { width: 100px; color: #bdc4d5;}
+.application_details table {
+ table-layout: fixed;
+ width: 100%;
+ color: #37537b;
+}
+.application_details #cmdline {
+ word-wrap: break-word;
+}
+.application_details #exe_path {
+ word-wrap: break-word;
+}
+.summary {
+}
+hr {
+ margin-top: 32px;
+ margin-bottom: 32px;
+ visibility: hidden;
+}
+.summary .heading {
+ font-family: inherit;
+ font-size: 1.8em;
+ padding-bottom: 8px;
+}
+#summary_cpu_class {
+ font-weight: bold;
+}
+#summary_mpi_class {
+ font-weight: bold;
+}
+#summary_io_class {
+ font-weight: bold;
+}
+.overview_general_advice p {
+ margin-top: 8px;
+ margin-bottom: 8px;
+}
+.subsections {
+ margin-bottom: 32px;
+}
+.subsections .heading {
+ font-family: inherit;
+ font-size: 2em;
+ padding-bottom: 8px;
+}
+.subsections .heading_cpu {
+ padding-bottom: 8px;
+}
+.subsections .heading_mpi {
+ padding-bottom: 8px;
+}
+.subsections .heading_ram {
+ padding-bottom: 8px;
+}
+.subsections .heading_io {
+ padding-bottom: 8px;
+}
+.subsections .explanation {
+ font-size: 0.9em;
+ color: #404040;
+ padding-top: 8px;
+}
+
+.ltcol, .ctcol { float: left; width: 436px; padding-right: 16px; }
+.rtcol { float: right; width: 436px; }
+
+.heading_cpu { color: #4fd32e; font-size: 1.5em; }
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+.cpu_span { color: #4fd32e; }
+.mpi_span { color: #409ded; }
+.ram { color: #ed4040; }
+.io_span { color: #ed8140; }
+.bar_graph { width: 200px; }
+#cpu_bar { background-color: #4fd32e; width: 0; height: 2em; }
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+.balanced_span { color: #bb58d6; }
+.right_cell { text-align: right; }
+
+#cpu_chart { padding-top: 8px; }
+#cpu_chart td { font-size: 0.9em; padding-bottom: 8px; }
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+#cpu_num_bar { background-color: #4fd32e; width: 0; height: 1em; }
+#cpu_vec_bar { background-color: #3c9f23; width: 0; height: 1em; }
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+
+#mpi_chart { padding-top: 8px; }
+#mpi_chart td { font-size: 0.9em; padding-bottom: 8px; }
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+
+</style>
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+ return getHorizontalPosition(i, cfg.w/2, (Math.max(j.value, 0)/cfg.maxValue)*cfg.factor);
+ })
+ .attr("cy", function(j, i){
+ return getVerticalPosition(i, cfg.h/2, (Math.max(j.value, 0)/cfg.maxValue)*cfg.factor);
+ })
+ .attr("data-id", function(j){return j.axis})
+ .style("fill", cfg.color(series)).style("fill-opacity", .9)
+ .on('mouseover', function (d){
+ newX = parseFloat(d3.select(this).attr('cx')) - 10;
+ newY = parseFloat(d3.select(this).attr('cy')) - 5;
+ tooltip.attr('x', newX).attr('y', newY).text(d.value).transition(200).style('opacity', 1);
+ z = "polygon."+d3.select(this).attr("class");
+ g.selectAll("polygon").transition(200).style("fill-opacity", 0.1);
+ g.selectAll(z).transition(200).style("fill-opacity", .7);
+ })
+ .on('mouseout', function(){
+ tooltip.transition(200).style('opacity', 0);
+ g.selectAll("polygon").transition(200).style("fill-opacity", cfg.opacityArea);
+ })
+ .append("svg:title")
+ .text(function(j){return Math.max(j.value, 0)});
+
+ series++;
+ });
+ //Tooltip
+ tooltip = g.append('text').style('opacity', 0).style('font-family', 'sans-serif').style('font-size', '13px');
+ }
+}
+
+</script>
+<script type="text/javascript">window.onload = function() {
+ var cpu = 88.6;
+ var mpi = 11.4;
+ var io = 0.0;
+
+ // Draw radar chart, choose its color based on application classification
+ var radar_data = [[ { axis: "CPU", value: cpu },
+ { axis: "MPI", value: mpi },
+ { axis: "I/O", value: io } ]];
+ var radar_options = { w: 200, h: 200, factor: 0.7, fontSize: 16, radius: 0,
+ opacityArea: 0.64, maxValue: 100,
+ color: function() {
+ if ("cpu" == "io") return "#ed8140";
+ if ("cpu" == "cpu") return "#4fd32e";
+ if ("cpu" == "mpi") return "#409ded";
+ else return "#bb58d6";
+ }
+ };
+ RadarChart.draw("#time_radar", radar_data, radar_options);
+
+ // Wrap the exe path on slashes if necessary
+ var exe_path = document.getElementById("exe_path");
+ exe_path.innerHTML = exe_path.innerHTML.replace(/\//g, '/​'); // insert a zero width space after slashes as a word wrap hint
+
+ // Format our byte value numbers to show at most 2 decimal places, but only if required to attain 3 digits of precision
+ // 1234.56 -> "1234"
+ // 12.3456 -> "12.3"
+ // 1.23456 -> "1.23"
+ // 0.00000 -> "0.00"
+ var formatNumber = function(num) {
+ if (num > 100) return new Number(num).toFixed(0); // 1234.56 -> 1234
+ if (num > 10) return new Number(num).toFixed(1); // 12.3456 -> 12.3
+ else return new Number(num).toFixed(2); // 1.23456 -> 1.23 and 0 -> 0.00
+ }
+
+ // Parse a number, but return 0 for invalid numbers, not NaN
+ var toNumber = function(num_str) {
+ var num = Number(num_str)
+ return isNaN(num) ? 0 : num;
+ }
+
+ // Scale byte values to bytes, kB, MB or GB as appropriate
+ var fillBytes = function(base_name, bytes_str, per_second) {
+ var units = "bytes";
+ var scale = 1.0;
+ var bytes = Number(bytes_str)
+ if (isNaN(bytes) ) { units = "" ; }
+ else if (bytes > 1000000000) { units = "GB"; scale = 1*1000*1000*1000; }
+ else if (bytes > 1000000 ) { units = "MB"; scale = 1*1000*1000 }
+ else if (bytes > 1000 ) { units = "kB"; scale = 1*1000 }
+ var num = isNaN(bytes) ? bytes_str : formatNumber(bytes / scale);
+ var elementNum = document.getElementById(base_name + "_num");
+ elementNum.innerHTML = num;
+ var elementUnits = document.getElementById(base_name + "_units");
+ elementUnits.innerHTML = units + (per_second && !isNaN(bytes) ? "/s" : "");
+ };
+
+ // Fill all the byte numbers and their units with the scaled values
+ fillBytes("mpi_colrate", "1.65e+02", true);
+ fillBytes("mpi_p2prate", "0.00e+00", true);
+ fillBytes("io_readrate", "0.00e+00", true);
+ fillBytes("io_writerate", "0.00e+00", true);
+ fillBytes("ram_mean", "2.33e+07", false);
+ fillBytes("ram_peak", "2.35e+07", false);
+
+ // Set widths for all graphs
+ var bar = function(name, width) {
+ var rounded = Math.round(width);
+ if (!isFinite(rounded) || rounded < 1)
+ document.getElementById(name).style.width = "1px"
+ else
+ document.getElementById(name).style.width = rounded + "px";
+ };
+ bar("cpu_bar", cpu * 2);
+ bar("mpi_bar", mpi * 2);
+ bar("io_bar", io * 2);
+
+ bar("cpu_num_bar", toNumber("50.0") / 2);
+ bar("cpu_vec_bar", toNumber("50.0") / 2);
+ bar("cpu_mem_bar", toNumber("0.0") / 2);
+ bar("cpu_other_bar", toNumber("0.0") / 2);
+
+ bar("mpi_col_bar", toNumber("100.0") / 2);
+ bar("mpi_p2p_bar", toNumber("0.0") / 2);
+ var mpi_scale = Math.max(toNumber("1.65e+02"), toNumber("0.00e+00"));
+ bar("mpi_colrate_bar", 50 * toNumber("1.65e+02") / mpi_scale);
+ bar("mpi_p2prate_bar", 50 * toNumber("0.00e+00") / mpi_scale);
+
+ bar("io_read_bar", toNumber("0.0") / 2);
+ bar("io_write_bar", toNumber("0.0") / 2);
+ var io_scale = Math.max(toNumber("0.00e+00"), toNumber("0.00e+00"));
+ bar("io_readrate_bar", 50 * toNumber("0.00e+00") / io_scale);
+ bar("io_writerate_bar", 50 * toNumber("0.00e+00") / io_scale);
+
+ bar("ram_mean_bar", 50 * toNumber("2.33e+07") / toNumber("2.35e+07"));
+ bar("ram_peak_bar", 50);
+ bar("ram_node_bar", toNumber("2.8") / 2);
+
+ // Formatting replacement helper function
+ var replaceIn = function(elementId, re, new_text) {
+ element = document.getElementById(elementId);
+ element.innerHTML = element.innerHTML.replace(re, new_text);
+ };
+
+ // Add formatting for the overview advice section
+ replaceIn('overview_advice', /CPU/g, '<span class="cpu_span">CPU</span>');
+ replaceIn('overview_advice', /MPI/g, '<span class="mpi_span">MPI</span>');
+ replaceIn('overview_advice', /I\/O/g, '<span class="io_span">I\/O</span>');
+
+ // Add formatting for the CPU advice section
+ if ( 88.6 < 0.05 )
+ replaceIn('cpu_explanation', /application code/g, '<span class="cpu_span">application code</span>');
+ replaceIn('cpu_explanation', /vectorized instructions/g, '<span class="cpu_vec_span">vectorized instructions</span>');
+ replaceIn('cpu_explanation', /memory accesses/g, '<span class="cpu_mem_span">memory accesses</span>');
+ replaceIn('cpu_explanation', /memory-bound/g, '<span class="cpu_mem_span">memory-bound</span>');
+ replaceIn('cpu_explanation', /arithmetic-bound/g, '<span class="cpu_num_span">arithmetic-bound</span>');
+ replaceIn('cpu_explanation', /numerical computation/g, '<span class="cpu_num_span">numerical computation</span>');
+
+ // Add formatting for the MPI advice section
+ if ( 11.4 < 0.05 )
+ replaceIn('mpi_explanation', /MPI/g, '<span class="mpi_span">MPI</span>');
+ replaceIn('mpi_explanation', /collective calls/g, '<span class="mpi_col_span">collective calls</span>');
+ replaceIn('mpi_explanation', /point-to-point calls/g, '<span class="mpi_p2p_span">point-to-point calls</span>');
+ replaceIn('mpi_explanation', / very low/g, ' <span class="mpi_colrate_span">very low</span>');
+ replaceIn('mpi_explanation', / low/g, ' <span class="mpi_colrate_span">low</span>');
+ replaceIn('mpi_explanation', / average/g, ' <span class="mpi_colrate_span">average</span>');
+ replaceIn('mpi_explanation', / very high/g, ' <span class="mpi_colrate_span">very high</span>');
+ replaceIn('mpi_explanation', / high/g, ' <span class="mpi_colrate_span">high</span>');
+
+ // Add formatting for the I/O advice section
+ if ( 0.0 < 0.05 )
+ replaceIn('io_explanation', /I\/O/g, '<span class="io_span">I/O</span>');
+ replaceIn('io_explanation', /read operations/g, '<span class="io_read_span">read operations</span>');
+ replaceIn('io_explanation', /write operations/g, '<span class="io_write_span">write operations</span>');
+ replaceIn('io_explanation', / very low/g, ' <span class="io_readrate_span">very low</span>');
+ replaceIn('io_explanation', / low/g, ' <span class="io_readrate_span">low</span>');
+ replaceIn('io_explanation', / average/g, ' <span class="io_readrate_span">average</span>');
+ replaceIn('io_explanation', / very high/g, ' <span class="io_readrate_span">very high</span>');
+ replaceIn('io_explanation', / high/g, ' <span class="io_readrate_span">high</span>');
+
+ // Add formatting for the RAM advice section
+ replaceIn('ram_explanation', /high/g, ' <span class="ram_node_span">high</span>');
+ replaceIn('ram_explanation', /well-balanced/g, '<span class="ram_peak_span">well-balanced</span>');
+ replaceIn('ram_explanation', /significant variation/g, '<span class="ram_peak_span">significant variation</span>');
+ replaceIn('ram_explanation', /peak node memory usage/g, '<span class="ram_node_span">peak node memory usage</span>');
+
+ // Hide the error warning if the script got this far
+ document.getElementById('error').style.display = 'none';
+};
+</script>
+</head>
+
+<body>
+<div id="content">
+
+<div class="header">
+ <div class="logo"><img src="http://content.allinea.com/downloads/performance-report-logo.png" alt="Allinea Performance Reports" /></div>
+ <div class="header_left">
+ <div class="application_details">
+ <table>
+ <tr><td class="details_key">Executable:</td><td id="exe_name">mympiprog.x</td></tr>
+ <tr><td class="details_key">Resources:</td><td id="num_procs">32 processes, 2 nodes</td></tr>
+ <tr><td class="details_key">Machine:</td><td id="machine_name">cn182</td></tr>
+ <tr><td class="details_key">Start time:</td><td id="start_date">Wed Oct 15 16:56:23 2014</td></tr>
+ <tr><td class="details_key">Total time:</td><td id="time_string">7 seconds (0 minutes)</td></tr>
+ <tr><td class="details_key">Full path:</td><td id="exe_path">/home/user</td></tr>
+ <tr><td class="details_key">Notes:</td><td id="notes"></td></tr>
+ </table>
+ </div>
+ </div>
+ <div id="time_radar"></div>
+ <div class="clear"></div>
+</div>
+<hr />
+<div id="error">
+<p><strong>Error: javascript is not running</strong></p>
+<p>The graphs in this Performance Report require <strong>javascript</strong>, which is disabled or not working.</p>
+<p>Check whether your javascript support is enabled or try another browser.<p>
+<p>Remember, you can always contact <a href="mailto:support@allinea.com">support@allinea.com</a>, we're very nice!</p>
+</div>
+<div class="summary">
+ <div class="heading">Summary: mympiprog.x is <span class="cpu_span">CPU-bound</span> in this configuration</div>
+ <div>The total wallclock time was spent as follows:</div>
+ <table class="summary_table">
+ <tr><td class="heading_cpu">CPU</td><td class="percent">88.6%</td><td class="bar_graph"><div id="cpu_bar" /></td>
+ <td class="details"><p>Time spent running application code. High values are usually good.</p><p>This is <span id="summary_cpu_class">high</span>; check the CPU performance section for optimization advice.</p></td></tr>
+ <tr><td class="heading_mpi">MPI</td><td class="percent">11.4%</td><td class="bar_graph"><div id="mpi_bar" /></td>
+ <td class="details"><p>Time spent in MPI calls. High values are usually bad.</p><p>This is <span id="summary_mpi_class">very low</span>; this code may benefit from increasing the process count.</p></td></tr>
+ <tr><td class="heading_io">I/O</td><td class="percent">0.0%</td><td class="bar_graph"><div id="io_bar" /></td>
+ <td class="details"><p>Time spent in filesystem I/O. High values are usually bad.</p><p>This is <span id="summary_io_class">negligible</span>; there's no need to investigate I/O performance.</p></td></tr>
+ </table>
+ <div class="overview_general_advice"><p>This application run was <span class="cpu_span">CPU-bound</span>. A breakdown of this time and advice for investigating further is in the <span class="cpu_span">CPU</span> section below.</p><p id="overview_advice">As very little time is spent in MPI calls, this code may also benefit from running at larger scales.</p></div>
+</div>
+<hr />
+<div class="subsections">
+ <div class="ltcol">
+ <div class="heading_cpu">CPU</div>
+ <div>A breakdown of how the <span class="cpu_span">88.6</span>% total CPU time was spent:</div>
+ <table id="cpu_chart">
+ <tr><td>Scalar numeric ops</td><td class="right_cell"><span class="cpu_num_span">50.0</span>%</td><td class="mini_bar_graph"><div id="cpu_num_bar" /></td></tr>
+ <tr><td>Vector numeric ops</td><td class="right_cell"><span class="cpu_vec_span">50.0</span>%</td><td class="mini_bar_graph"><div id="cpu_vec_bar" /></td></tr>
+ <tr><td>Memory accesses</td><td class="right_cell"><span class="cpu_mem_span">0.0</span>%</td><td class="mini_bar_graph"><div id="cpu_mem_bar" /></td></tr>
+ <tr><td>Other</td><td class="right_cell"><span class="cpu_other_span">0.0</span>%</td><td class="mini_bar_graph"><div id="cpu_other_bar" /></td></tr>
+ </table>
+ <div id="cpu_explanation">
+ <div class="explanation">The per-core performance is arithmetic-bound. Try to increase the amount of time spent in vectorized instructions by analyzing the compiler's vectorization reports.</div>
+ <div class="explanation"></div>
+ </div>
+ </div>
+ <div class="rtcol">
+ <div class="heading_mpi">MPI</div>
+ <div>Of the <span class="mpi_span">11.4</span>% total time spent in MPI calls:</div>
+ <table id="mpi_chart">
+ <tr><td>Time in collective calls</td><td class="right_cell"><span class="mpi_col_span">100.0</span>%</td><td class="mini_bar_graph"><div id="mpi_col_bar" /></td></tr>
+ <tr><td>Time in point-to-point calls</td><td class="right_cell"><span class="mpi_p2p_span">0.0</span>%</td><td class="mini_bar_graph"><div id="mpi_p2p_bar" /></td></tr>
+ <tr><td>Effective process collective rate</td><td class="right_cell"><span class="mpi_colrate_span"><span id="mpi_colrate_num">1.65e+02</span></span> <span id="mpi_colrate_units"></span></td><td class="mini_bar_graph"><div id="mpi_colrate_bar" /></td></tr>
+ <tr><td>Effective process point-to-point rate</td><td class="right_cell"><span class="mpi_p2prate_span"><span id="mpi_p2prate_num">0.00e+00</span></span> <span id="mpi_p2prate_units"></span></td><td class="mini_bar_graph"><div id="mpi_p2prate_bar" /></td></tr>
+ </table>
+ <div id="mpi_explanation">
+ <div class="explanation">Most of the time is spent in collective calls with a very low transfer rate. This suggests load imbalance is causing synchonization overhead; use an MPI profiler to investigate further.</div>
+ <div class="explanation"></div>
+ </div>
+ </div>
+ <div class="clear"></div>
+</div>
+<div class="subsections">
+ <div class="ltcol">
+ <div class="heading_io">I/O</div>
+ <div>A breakdown of how the <span class="io_span">0.0</span>% total I/O time was spent:</div>
+ <table id="io_chart">
+ <tr><td>Time in reads</td><td class="right_cell"><span class="io_read_span">0.0</span>%</td><td class="mini_bar_graph"><div id="io_read_bar" /></td></tr>
+ <tr><td>Time in writes</td><td class="right_cell"><span class="io_write_span">0.0</span>%</td><td class="mini_bar_graph"><div id="io_write_bar" /></td></tr>
+ <tr><td>Effective process read rate</td><td class="right_cell"><span class="io_readrate_span"><span id="io_readrate_num">0.00e+00</span></span> <span id="io_readrate_units"></span></td><td class="mini_bar_graph"><div id="io_readrate_bar" /></td></tr>
+ <tr><td>Effective process write rate</td><td class="right_cell"><span class="io_writerate_span"><span id="io_writerate_num">0.00e+00</span></span> <span id="io_writerate_units"></span></td><td class="mini_bar_graph"><div id="io_writerate_bar" /></td></tr>
+ </table>
+ <div id="io_explanation">
+ <div class="explanation">No time is spent in I/O operations. There's nothing to optimize here!</div>
+ <div class="explanation"></div>
+ </div>
+ </div>
+ <div class="rtcol">
+ <div class="heading_ram">Memory</div>
+ <div>Per-process memory usage may also affect scaling:</div>
+ <table id="ram_chart">
+ <tr><td>Mean process memory usage</td><td class="right_cell"><span class="ram_mean_span"><span id="ram_mean_num">2.33e+07</span></span> <span id="ram_mean_units"></span></td><td class="mini_bar_graph"><div id="ram_mean_bar" /></td></tr>
+ <tr><td>Peak process memory usage</td><td class="right_cell"><span class="ram_peak_span"><span id="ram_peak_num">2.35e+07</span></span> <span id="ram_peak_units"></span></td><td class="mini_bar_graph"><div id="ram_peak_bar" /></td></tr>
+ <tr><td>Peak node memory usage</td><td class="right_cell"><span class="ram_node_span">2.8</span>%</td><td class="mini_bar_graph"><div id="ram_node_bar" /></td></tr>
+ </table>
+ <div id="ram_explanation">
+ <div class="explanation">The peak node memory usage is very low. You may be able to reduce the amount of allocation time used by running with fewer MPI processes and more data on each process.</div>
+ <div class="explanation"></div>
+ </div>
+ </div>
+ <div class="clear"></div>
+</div>
+</div> <!-- content -->
+</body>
+</html>
diff --git a/docs.it4i/salomon/software/debuggers/mympiprog_32p_2014-10-15_16-56.txt b/docs.it4i/salomon/software/debuggers/mympiprog_32p_2014-10-15_16-56.txt
new file mode 100644
index 0000000000000000000000000000000000000000..de8449179640fd943a9f007f9eda084b11f2a455
--- /dev/null
+++ b/docs.it4i/salomon/software/debuggers/mympiprog_32p_2014-10-15_16-56.txt
@@ -0,0 +1,50 @@
+Executable: mympiprog.x
+Resources: 32 processes, 2 nodes
+Machine: cn182
+Started on: Wed Oct 15 16:56:23 2014
+Total time: 7 seconds (0 minutes)
+Full path: /home/user
+Notes:
+
+Summary: mympiprog.x is CPU-bound in this configuration
+CPU: 88.6% |========|
+MPI: 11.4% ||
+I/O: 0.0% |
+This application run was CPU-bound. A breakdown of this time and advice for investigating further is found in the CPU section below.
+As very little time is spent in MPI calls, this code may also benefit from running at larger scales.
+
+CPU:
+A breakdown of how the 88.6% total CPU time was spent:
+Scalar numeric ops: 50.0% |====|
+Vector numeric ops: 50.0% |====|
+Memory accesses: 0.0% |
+Other: 0.0% |
+The per-core performance is arithmetic-bound. Try to increase the amount of time spent in vectorized instructions by analyzing the compiler's vectorization reports.
+
+
+MPI:
+A breakdown of how the 11.4% total MPI time was spent:
+Time in collective calls: 100.0% |=========|
+Time in point-to-point calls: 0.0% |
+Effective collective rate: 1.65e+02 bytes/s
+Effective point-to-point rate: 0.00e+00 bytes/s
+Most of the time is spent in collective calls with a very low transfer rate. This suggests load imbalance is causing synchonization overhead; use an MPI profiler to investigate further.
+
+
+I/O:
+A breakdown of how the 0.0% total I/O time was spent:
+Time in reads: 0.0% |
+Time in writes: 0.0% |
+Effective read rate: 0.00e+00 bytes/s
+Effective write rate: 0.00e+00 bytes/s
+No time is spent in I/O operations. There's nothing to optimize here!
+
+
+Memory:
+Per-process memory usage may also affect scaling:
+Mean process memory usage: 2.33e+07 bytes
+Peak process memory usage: 2.35e+07 bytes
+Peak node memory usage: 2.8% |
+The peak node memory usage is very low. You may be able to reduce the amount of allocation time used by running with fewer MPI processes and more data on each process.
+
+
diff --git a/docs.it4i/salomon/software/debuggers/total-view.md b/docs.it4i/salomon/software/debuggers/total-view.md
index 0568ccc42e90a23a199da92962c720f6cc6d7d94..82e526bfb6168a2b28153b3980cefaf37e71e33d 100644
--- a/docs.it4i/salomon/software/debuggers/total-view.md
+++ b/docs.it4i/salomon/software/debuggers/total-view.md
@@ -14,7 +14,7 @@ On the cluster users can debug OpenMP or MPI code that runs up to 64 parallel pr
Debugging of GPU accelerated codes is also supported.
-You can check the status of the licenses [here](https://extranet.it4i.cz/rsweb/anselm/license/totalview).
+You can check the status of the licenses [here](https://extranet.it4i.cz/rsweb/anselm/license/totalview).
Compiling Code to run with TotalView
------------------------------------
@@ -47,16 +47,13 @@ Compile the code:
Before debugging, you need to compile your code with theses flags:
->**-g** : Generates extra debugging information usable by GDB. -g3
-includes even more debugging information. This option is available for
-GNU and INTEL C/C++ and Fortran compilers.
+>**-g** : Generates extra debugging information usable by GDB. -g3 includes even more debugging information. This option is available for GNU and INTEL C/C++ and Fortran compilers.
>**-O0** : Suppress all optimizations.
Starting a Job with TotalView
-----------------------------
-Be sure to log in with an X window forwarding enabled. This could mean
-using the -X in the ssh:
+Be sure to log in with an X window forwarding enabled. This could mean using the -X in the ssh:
```bash
ssh -X username@salomon.it4i.cz
@@ -117,7 +114,7 @@ the entire function:
**source /apps/all/OpenMPI/1.10.1-GNU-4.9.3-2.25/etc/openmpi-totalview.tcl**
-You need to do this step only once. See also [OpenMPI FAQ entry](https://www.open-mpi.org/faq/?category=running#run-with-tv)
+You need to do this step only once. See also [OpenMPI FAQ entry](https://www.open-mpi.org/faq/?category=running#run-with-tv)
Now you can run the parallel debugger using:
@@ -152,4 +149,4 @@ More information regarding the command line parameters of the TotalView can be f
Documentation
-------------
-[1] The [TotalView documentation](http://www.roguewave.com/support/product-documentation/totalview-family.aspx#totalview) web page is a good resource for learning more about some of the advanced TotalView features.
\ No newline at end of file
+[1] The [TotalView documentation](http://www.roguewave.com/support/product-documentation/totalview-family.aspx#totalview) web page is a good resource for learning more about some of the advanced TotalView features.
\ No newline at end of file
diff --git a/docs.it4i/salomon/software/debuggers/valgrind.md b/docs.it4i/salomon/software/debuggers/valgrind.md
index ddbfd78954f6f0485d2cbf6482b0850c406843da..ddd82fcb1a3ff3be961180b72542f0b19be9b00a 100644
--- a/docs.it4i/salomon/software/debuggers/valgrind.md
+++ b/docs.it4i/salomon/software/debuggers/valgrind.md
@@ -7,7 +7,7 @@ About Valgrind
--------------
Valgrind is an open-source tool, used mainly for debuggig memory-related problems, such as memory leaks, use of uninitalized memory etc. in C/C++ applications. The toolchain was however extended over time with more functionality, such as debugging of threaded applications, cache profiling, not limited only to C/C++.
-Valgind is an extremely useful tool for debugging memory errors such as [off-by-one](http://en.wikipedia.org/wiki/Off-by-one_error). Valgrind uses a virtual machine and dynamic recompilation of binary code, because of that, you can expect that programs being debugged by Valgrind run 5-100 times slower.
+Valgind is an extremely useful tool for debugging memory errors such as [off-by-one](http://en.wikipedia.org/wiki/Off-by-one_error). Valgrind uses a virtual machine and dynamic recompilation of binary code, because of that, you can expect that programs being debugged by Valgrind run 5-100 times slower.
The main tools available in Valgrind are :
@@ -16,7 +16,7 @@ The main tools available in Valgrind are :
- **Hellgrind** and **DRD** can detect race conditions in multi-threaded applications.
- **Cachegrind**, a cache profiler.
- **Callgrind**, a callgraph analyzer.
-- For a full list and detailed documentation, please refer to the [official Valgrind documentation](http://valgrind.org/docs/).
+- For a full list and detailed documentation, please refer to the [official Valgrind documentation](http://valgrind.org/docs/).
Installed versions
------------------
diff --git a/docs.it4i/salomon/software/debuggers/vampir.md b/docs.it4i/salomon/software/debuggers/vampir.md
index 254aac993af10649e4584e3a11114897939e98ac..1ca43b4b5df6f16ae06fc6e4c90d541dd1b02ce6 100644
--- a/docs.it4i/salomon/software/debuggers/vampir.md
+++ b/docs.it4i/salomon/software/debuggers/vampir.md
@@ -1,7 +1,7 @@
Vampir
======
-Vampir is a commercial trace analysis and visualisation tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as [Score-P](score-p.md)) first to collect the traces.
+Vampir is a commercial trace analysis and visualisation tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as [Score-P](score-p/)) first to collect the traces.
@@ -20,5 +20,5 @@ You can find the detailed user manual in PDF format in $EBROOTVAMPIR/doc/vampir-
References
----------
-1. <https://www.vampir.eu>
+1. <https://www.vampir.eu>
diff --git a/docs.it4i/salomon/software/intel-suite/intel-advisor.md b/docs.it4i/salomon/software/intel-suite/intel-advisor.md
index 7088e53c57a72075114b3c6aea2c5b519eea77b2..f8e86de141b212aaeec40e96671a3dc84072d60c 100644
--- a/docs.it4i/salomon/software/intel-suite/intel-advisor.md
+++ b/docs.it4i/salomon/software/intel-suite/intel-advisor.md
@@ -27,6 +27,6 @@ In the left pane, you can switch between Vectorization and Threading workflows.
References
----------
-1. [Intel® Advisor 2015 Tutorial: Find Where to Add Parallelism - C++ Sample](https://software.intel.com/en-us/advisorxe_2015_tut_lin_c)
-2. [Product page](https://software.intel.com/en-us/intel-advisor-xe)
-3. [Documentation](https://software.intel.com/en-us/intel-advisor-2016-user-guide-linux)
\ No newline at end of file
+1. [Intel® Advisor 2015 Tutorial: Find Where to Add Parallelism - C++ Sample](https://software.intel.com/en-us/advisorxe_2015_tut_lin_c)
+2. [Product page](https://software.intel.com/en-us/intel-advisor-xe)
+3. [Documentation](https://software.intel.com/en-us/intel-advisor-2016-user-guide-linux)
\ No newline at end of file
diff --git a/docs.it4i/salomon/software/intel-suite/intel-compilers.md b/docs.it4i/salomon/software/intel-suite/intel-compilers.md
index b496c4feb14d36c9582326b531c1dc6c05d0102b..2ad30c5fae0af41c4b22849cef724f3dd53f2a10 100644
--- a/docs.it4i/salomon/software/intel-suite/intel-compilers.md
+++ b/docs.it4i/salomon/software/intel-suite/intel-compilers.md
@@ -27,7 +27,7 @@ The compiler recognizes the omp, simd, vector and ivdep pragmas for OpenMP paral
$ ifort -ipo -O3 -xCORE-AVX2 -qopt-report1 -qopt-report-phase=vec -openmp myprog.f mysubroutines.f -o myprog.x
```
-Read more at <https://software.intel.com/en-us/intel-cplusplus-compiler-16.0-user-and-reference-guide>
+Read more at <https://software.intel.com/en-us/intel-cplusplus-compiler-16.0-user-and-reference-guide>
Sandy Bridge/Ivy Bridge/Haswell binary compatibility
----------------------------------------------------
diff --git a/docs.it4i/salomon/software/intel-suite/intel-debugger.md b/docs.it4i/salomon/software/intel-suite/intel-debugger.md
index 8622cc3fc6e2875a3b83652f81c1dc66751e9b80..bf3005ddd24cdd597b931be77e5c00e412b2f366 100644
--- a/docs.it4i/salomon/software/intel-suite/intel-debugger.md
+++ b/docs.it4i/salomon/software/intel-suite/intel-debugger.md
@@ -5,7 +5,7 @@ IDB is no longer available since Intel Parallel Studio 2015
Debugging serial applications
-----------------------------
-The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use [X display](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.md) for running the GUI.
+The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use [X display](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/) for running the GUI.
```bash
$ module load intel/2014.06
@@ -19,7 +19,7 @@ The debugger may run in text mode. To debug in text mode, use
$ idbc
```
-To debug on the compute nodes, module intel must be loaded. The GUI on compute nodes may be accessed using the same way as in [the GUI section](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-and-vnc.md)
+To debug on the compute nodes, module intel must be loaded. The GUI on compute nodes may be accessed using the same way as in [the GUI section](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/)
Example:
@@ -42,7 +42,7 @@ Debugging parallel applications
### Small number of MPI ranks
-For debugging small number of MPI ranks, you may execute and debug each rank in separate xterm terminal (do not forget the [X display](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-and-vnc.md)). Using Intel MPI, this may be done in following way:
+For debugging small number of MPI ranks, you may execute and debug each rank in separate xterm terminal (do not forget the [X display](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/)). Using Intel MPI, this may be done in following way:
```bash
$ qsub -q qexp -l select=2:ncpus=24 -X -I
@@ -74,4 +74,4 @@ Run the idb debugger in GUI mode. The menu Parallel contains number of tools for
Further information
-------------------
-Exhaustive manual on idb features and usage is published at Intel website, <https://software.intel.com/sites/products/documentation/doclib/iss/2013/compiler/cpp-lin/>
\ No newline at end of file
+Exhaustive manual on idb features and usage is published at Intel website, <https://software.intel.com/sites/products/documentation/doclib/iss/2013/compiler/cpp-lin/>
\ No newline at end of file
diff --git a/docs.it4i/salomon/software/intel-suite/intel-inspector.md b/docs.it4i/salomon/software/intel-suite/intel-inspector.md
index d3a3dcd80c63c36472844a6afb441107a565e2af..81c6abb2b2b9ff785c0424c6865ff3fd216eb2e2 100644
--- a/docs.it4i/salomon/software/intel-suite/intel-inspector.md
+++ b/docs.it4i/salomon/software/intel-suite/intel-inspector.md
@@ -35,6 +35,6 @@ Results obtained from batch mode can be then viewed in the GUI by selecting File
References
----------
-1. [Product page](https://software.intel.com/en-us/intel-inspector-xe)
-2. [Documentation and Release Notes](https://software.intel.com/en-us/intel-inspector-xe-support/documentation)
-3. [Tutorials](https://software.intel.com/en-us/articles/inspectorxe-tutorials)
\ No newline at end of file
+1. [Product page](https://software.intel.com/en-us/intel-inspector-xe)
+2. [Documentation and Release Notes](https://software.intel.com/en-us/intel-inspector-xe-support/documentation)
+3. [Tutorials](https://software.intel.com/en-us/articles/inspectorxe-tutorials)
\ No newline at end of file
diff --git a/docs.it4i/salomon/software/intel-suite/intel-integrated-performance-primitives.md b/docs.it4i/salomon/software/intel-suite/intel-integrated-performance-primitives.md
index 87d28155a2001fc39e94086ea4c4f0c68d925e93..8f57de9bbd9886304c8bfa67183d198c764727d7 100644
--- a/docs.it4i/salomon/software/intel-suite/intel-integrated-performance-primitives.md
+++ b/docs.it4i/salomon/software/intel-suite/intel-integrated-performance-primitives.md
@@ -77,6 +77,6 @@ You will need the ipp module loaded to run the ipp enabled executable. This may
Code samples and documentation
------------------------------
-Intel provides number of [Code Samples for IPP](https://software.intel.com/en-us/articles/code-samples-for-intel-integrated-performance-primitives-library), illustrating use of IPP.
+Intel provides number of [Code Samples for IPP](https://software.intel.com/en-us/articles/code-samples-for-intel-integrated-performance-primitives-library), illustrating use of IPP.
-Read full documentation on IPP [on Intel website,](http://software.intel.com/sites/products/search/search.php?q=&x=15&y=6&product=ipp&version=7.1&docos=lin) in particular the [IPP Reference manual.](http://software.intel.com/sites/products/documentation/doclib/ipp_sa/71/ipp_manual/index.htm)
\ No newline at end of file
+Read full documentation on IPP [on Intel website,](http://software.intel.com/sites/products/search/search.php?q=&x=15&y=6&product=ipp&version=7.1&docos=lin) in particular the [IPP Reference manual.](http://software.intel.com/sites/products/documentation/doclib/ipp_sa/71/ipp_manual/index.htm)
\ No newline at end of file
diff --git a/docs.it4i/salomon/software/intel-suite/intel-mkl.md b/docs.it4i/salomon/software/intel-suite/intel-mkl.md
index 4eb6c6bf0ee1b57b535953e7a3e426ee3c910c64..b84ad87d8b00346e2fc5ff6d68a93b5368dd4c11 100644
--- a/docs.it4i/salomon/software/intel-suite/intel-mkl.md
+++ b/docs.it4i/salomon/software/intel-suite/intel-mkl.md
@@ -15,7 +15,7 @@ Intel Math Kernel Library (Intel MKL) is a library of math kernel subroutines, e
- Data Fitting Library, which provides capabilities for spline-based approximation of functions, derivatives and integrals of functions, and search.
- Extended Eigensolver, a shared memory version of an eigensolver based on the Feast Eigenvalue Solver.
-For details see the [Intel MKL Reference Manual](http://software.intel.com/sites/products/documentation/doclib/mkl_sa/11/mklman/index.htm).
+For details see the [Intel MKL Reference Manual](http://software.intel.com/sites/products/documentation/doclib/mkl_sa/11/mklman/index.htm).
Intel MKL version 11.2.3.187 is available on the cluster
@@ -38,7 +38,7 @@ Intel MKL library provides number of interfaces. The fundamental once are the LP
### Linking
-Linking Intel MKL libraries may be complex. Intel [mkl link line advisor](http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor) helps. See also [examples](intel-mkl.md#examples) below.
+Linking Intel MKL libraries may be complex. Intel [mkl link line advisor](http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor) helps. See also [examples](intel-mkl/#examples) below.
You will need the mkl module loaded to run the mkl enabled executable. This may be avoided, by compiling library search paths into the executable. Include rpath on the compile line:
@@ -115,7 +115,7 @@ In this example, we compile, link and run the cblas_dgemm example, using LP64
MKL and MIC accelerators
------------------------
-The Intel MKL is capable to automatically offload the computations o the MIC accelerator. See section [Intel Xeon Phi](../intel-xeon-phi.md) for details.
+The Intel MKL is capable to automatically offload the computations o the MIC accelerator. See section [Intel Xeon Phi](../intel-xeon-phi/) for details.
LAPACKE C Interface
-------------------
@@ -123,4 +123,4 @@ MKL includes LAPACKE C Interface to LAPACK. For some reason, although Intel is t
Further reading
---------------
-Read more on [Intel website](http://software.intel.com/en-us/intel-mkl), in particular the [MKL users guide](https://software.intel.com/en-us/intel-mkl/documentation/linux).
\ No newline at end of file
+Read more on [Intel website](http://software.intel.com/en-us/intel-mkl), in particular the [MKL users guide](https://software.intel.com/en-us/intel-mkl/documentation/linux).
\ No newline at end of file
diff --git a/docs.it4i/salomon/software/intel-suite/intel-parallel-studio-introduction.md b/docs.it4i/salomon/software/intel-suite/intel-parallel-studio-introduction.md
index 429c1d2525f6e46ab68cbba62a7ec9d42e223344..88787b2443787145d2ac4bc0f21e1d26a2cc8de8 100644
--- a/docs.it4i/salomon/software/intel-suite/intel-parallel-studio-introduction.md
+++ b/docs.it4i/salomon/software/intel-suite/intel-parallel-studio-introduction.md
@@ -25,30 +25,29 @@ The Intel compilers version 131.3 are available, via module iccifort/2013.5.192-
$ ifort -v
```
-Read more at the [Intel Compilers](intel-compilers.md) page.
+Read more at the [Intel Compilers](intel-compilers/) page.
Intel debugger
--------------
IDB is no longer available since Parallel Studio 2015.
-The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use [X display](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-and-vnc.md) for running the GUI.
-
+The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment.
```bash
$ module load intel
$ idb
```
-Read more at the [Intel Debugger](intel-debugger.md) page.
+Read more at the [Intel Debugger](intel-debugger/) page.
Intel Math Kernel Library
-------------------------
- Intel Math Kernel Library (Intel MKL) is a library of math kernel subroutines, extensively threaded and optimized for maximum performance. Intel MKL unites and provides these basic components: BLAS, LAPACK, ScaLapack, PARDISO, FFT, VML, VSL, Data fitting, Feast Eigensolver and many more.
+Intel Math Kernel Library (Intel MKL) is a library of math kernel subroutines, extensively threaded and optimized for maximum performance. Intel MKL unites and provides these basic components: BLAS, LAPACK, ScaLapack, PARDISO, FFT, VML, VSL, Data fitting, Feast Eigensolver and many more.
```bash
$ module load imkl
```
-Read more at the [Intel MKL](intel-mkl.md) page.
+Read more at the [Intel MKL](intel-mkl/) page.
Intel Integrated Performance Primitives
---------------------------------------
@@ -58,7 +57,7 @@ Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX is avai
$ module load ipp
```
-Read more at the [Intel IPP](intel-integrated-performance-primitives.md) page.
+Read more at the [Intel IPP](intel-integrated-performance-primitives/) page.
Intel Threading Building Blocks
-------------------------------
@@ -68,4 +67,4 @@ Intel Threading Building Blocks (Intel TBB) is a library that supports scalable
$ module load tbb
```
-Read more at the [Intel TBB](intel-tbb.md) page.
\ No newline at end of file
+Read more at the [Intel TBB](intel-tbb/) page.
\ No newline at end of file
diff --git a/docs.it4i/salomon/software/intel-suite/intel-tbb.md b/docs.it4i/salomon/software/intel-suite/intel-tbb.md
index 820a4fcddf848cfbb21f0cb360e7f43f578bc0e0..80e0541c8893e6959d3c9e89d3ac328b70a98ace 100644
--- a/docs.it4i/salomon/software/intel-suite/intel-tbb.md
+++ b/docs.it4i/salomon/software/intel-suite/intel-tbb.md
@@ -3,7 +3,7 @@ Intel TBB
Intel Threading Building Blocks
------------------------------
-Intel Threading Building Blocks (Intel TBB) is a library that supports scalable parallel programming using standard ISO C++ code. It does not require special languages or compilers. To use the library, you specify tasks, not threads, and let the library map tasks onto threads in an efficient manner. The tasks are executed by a runtime scheduler and may be offloaded to [MIC accelerator](../intel-xeon-phi.md).
+Intel Threading Building Blocks (Intel TBB) is a library that supports scalable parallel programming using standard ISO C++ code. It does not require special languages or compilers. To use the library, you specify tasks, not threads, and let the library map tasks onto threads in an efficient manner. The tasks are executed by a runtime scheduler and may be offloaded to [MIC accelerator](../intel-xeon-phi/).
Intel TBB version 4.3.5.187 is available on the cluster.
@@ -38,4 +38,4 @@ You will need the tbb module loaded to run the tbb enabled executable. This may
Further reading
---------------
-Read more on Intel website, <http://software.intel.com/sites/products/documentation/doclib/tbb_sa/help/index.htm>
\ No newline at end of file
+Read more on Intel website, <http://software.intel.com/sites/products/documentation/doclib/tbb_sa/help/index.htm>
\ No newline at end of file
diff --git a/docs.it4i/salomon/software/intel-suite/intel-trace-analyzer-and-collector.md b/docs.it4i/salomon/software/intel-suite/intel-trace-analyzer-and-collector.md
index c9123d6cd87123dba42dc4dbd4ab2df4a0c8b8ab..c8ae0919a6440ce106fa25edb97ba3c9a10f2ee9 100644
--- a/docs.it4i/salomon/software/intel-suite/intel-trace-analyzer-and-collector.md
+++ b/docs.it4i/salomon/software/intel-suite/intel-trace-analyzer-and-collector.md
@@ -22,7 +22,7 @@ The trace will be saved in file myapp.stf in the current directory.
Viewing traces
--------------
-To view and analyze the trace, open ITAC GUI in a [graphical environment](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-and-vnc.md):
+To view and analyze the trace, open ITAC GUI in a [graphical environment](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/):
```bash
$ module load itac/9.1.2.024
@@ -37,6 +37,6 @@ Please refer to Intel documenation about usage of the GUI tool.
References
----------
-1. [Getting Started with Intel® Trace Analyzer and Collector](https://software.intel.com/en-us/get-started-with-itac-for-linux)
-2. [Intel® Trace Analyzer and Collector - Documentation](http://Intel®%20Trace%20Analyzer%20and%20Collector%20-%20Documentation)
+1. [Getting Started with Intel® Trace Analyzer and Collector](https://software.intel.com/en-us/get-started-with-itac-for-linux)
+2. [Intel® Trace Analyzer and Collector - Documentation](http://Intel®%20Trace%20Analyzer%20and%20Collector%20-%20Documentation)
diff --git a/docs.it4i/salomon/software/intel-xeon-phi.md b/docs.it4i/salomon/software/intel-xeon-phi.md
index d9017bf810a6e2039737ae4a2cb36b2550fc85c5..c93595ba0c57ac249cb9962a3d11f0bf36397e69 100644
--- a/docs.it4i/salomon/software/intel-xeon-phi.md
+++ b/docs.it4i/salomon/software/intel-xeon-phi.md
@@ -241,7 +241,7 @@ Automatic Offload using Intel MKL Library
-----------------------------------------
Intel MKL includes an Automatic Offload (AO) feature that enables computationally intensive MKL functions called in user code to benefit from attached Intel Xeon Phi coprocessors automatically and transparently.
-Behavioral of automatic offload mode is controlled by functions called within the program or by environmental variables. Complete list of controls is listed [ here](http://software.intel.com/sites/products/documentation/doclib/mkl_sa/11/mkl_userguide_lnx/GUID-3DC4FC7D-A1E4-423D-9C0C-06AB265FFA86.htm).
+Behavioral of automatic offload mode is controlled by functions called within the program or by environmental variables. Complete list of controls is listed [ here](http://software.intel.com/sites/products/documentation/doclib/mkl_sa/11/mkl_userguide_lnx/GUID-3DC4FC7D-A1E4-423D-9C0C-06AB265FFA86.htm).
The Automatic Offload may be enabled by either an MKL function call within the code:
@@ -255,7 +255,7 @@ or by setting environment variable
$ export MKL_MIC_ENABLE=1
```
-To get more information about automatic offload please refer to "[Using Intel® MKL Automatic Offload on Intel ® Xeon Phi™ Coprocessors](http://software.intel.com/sites/default/files/11MIC42_How_to_Use_MKL_Automatic_Offload_0.pdf)" white paper or [ Intel MKL documentation](https://software.intel.com/en-us/articles/intel-math-kernel-library-documentation).
+To get more information about automatic offload please refer to "[Using Intel® MKL Automatic Offload on Intel ® Xeon Phi™ Coprocessors](http://software.intel.com/sites/default/files/11MIC42_How_to_Use_MKL_Automatic_Offload_0.pdf)" white paper or [ Intel MKL documentation](https://software.intel.com/en-us/articles/intel-math-kernel-library-documentation).
### Automatic offload example
@@ -494,7 +494,7 @@ After executing the complied binary file, following output should be displayed.
...
```
->More information about this example can be found on Intel website: <http://software.intel.com/en-us/vcsource/samples/caps-basic/>
+>More information about this example can be found on Intel website: <http://software.intel.com/en-us/vcsource/samples/caps-basic/>
The second example that can be found in "/apps/intel/opencl-examples" directory is General Matrix Multiply. You can follow the the same procedure to download the example to your directory and compile it.
@@ -884,4 +884,4 @@ Please note each host or accelerator is listed only per files. User has to speci
Optimization
------------
-For more details about optimization techniques please read Intel document [Optimization and Performance Tuning for Intel® Xeon Phi™ Coprocessors](http://software.intel.com/en-us/articles/optimization-and-performance-tuning-for-intel-xeon-phi-coprocessors-part-1-optimization "http://software.intel.com/en-us/articles/optimization-and-performance-tuning-for-intel-xeon-phi-coprocessors-part-1-optimization")
\ No newline at end of file
+For more details about optimization techniques please read Intel document [Optimization and Performance Tuning for Intel® Xeon Phi™ Coprocessors](http://software.intel.com/en-us/articles/optimization-and-performance-tuning-for-intel-xeon-phi-coprocessors-part-1-optimization "http://software.intel.com/en-us/articles/optimization-and-performance-tuning-for-intel-xeon-phi-coprocessors-part-1-optimization")
\ No newline at end of file
diff --git a/docs.it4i/salomon/software/java.md b/docs.it4i/salomon/software/java.md
index aa3bbd30df23f13587382a260f3731f766dd3ebd..66df04d052fbfb76072c71b5eeb574ebc23b3eb3 100644
--- a/docs.it4i/salomon/software/java.md
+++ b/docs.it4i/salomon/software/java.md
@@ -20,7 +20,9 @@ Check for java version and path
With the module loaded, not only the runtime environment (JRE), but also the development environment (JDK) with the compiler is available.
+```bash
$ javac -version
$ which javac
+```
-Java applications may use MPI for interprocess communication, in conjunction with OpenMPI. Read more on <http://www.open-mpi.org/faq/?category=java>. This functionality is currently not supported on Anselm cluster. In case you require the java interface to MPI, please contact [cluster support](https://support.it4i.cz/rt/).
\ No newline at end of file
+Java applications may use MPI for interprocess communication, in conjunction with OpenMPI. Read more on <http://www.open-mpi.org/faq/?category=java>. This functionality is currently not supported on Anselm cluster. In case you require the java interface to MPI, please contact [cluster support](https://support.it4i.cz/rt/).
\ No newline at end of file
diff --git a/docs.it4i/salomon/software/mpi/Running_OpenMPI.md b/docs.it4i/salomon/software/mpi/Running_OpenMPI.md
index 37867fc398e5a62e586bea27af93caa9ef878931..1211cb35fae519eb936496bb44e9fc2dbc7b6db8 100644
--- a/docs.it4i/salomon/software/mpi/Running_OpenMPI.md
+++ b/docs.it4i/salomon/software/mpi/Running_OpenMPI.md
@@ -53,7 +53,7 @@ The mpiprocs and ompthreads parameters allow for selection of number of running
### One MPI process per node
-Follow this example to run one MPI process per node, 24 threads per process.Â
+Follow this example to run one MPI process per node, 24 threads per process.
```bash
$ qsub -q qexp -l select=4:ncpus=24:mpiprocs=1:ompthreads=24 -I
diff --git a/docs.it4i/salomon/software/mpi/mpi.md b/docs.it4i/salomon/software/mpi/mpi.md
index 61ee8307166eee55ed26e58d11a870be3486d21f..b06e4e5e6eb6b20d11157998caf648c28e7bbaf1 100644
--- a/docs.it4i/salomon/software/mpi/mpi.md
+++ b/docs.it4i/salomon/software/mpi/mpi.md
@@ -42,7 +42,7 @@ Examples:
$ module load gompi/2015b
```
-In this example, we activate the latest OpenMPI with latest GNU compilers (OpenMPI 1.8.6 and GCC 5.1). Please see more information about toolchains in section [Environment and Modules](../../environment-and-modules.md) .
+In this example, we activate the latest OpenMPI with latest GNU compilers (OpenMPI 1.8.6 and GCC 5.1). Please see more information about toolchains in section [Environment and Modules](../../environment-and-modules/) .
To use OpenMPI with the intel compiler suite, use
@@ -137,6 +137,6 @@ In the previous two cases with one or two MPI processes per node, the operating
### Running OpenMPI
-The [**OpenMPI 1.8.6**](http://www.open-mpi.org/) is based on OpenMPI. Read more on [how to run OpenMPI](Running_OpenMPI.md) based MPI.
+The [**OpenMPI 1.8.6**](http://www.open-mpi.org/) is based on OpenMPI. Read more on [how to run OpenMPI](Running_OpenMPI/) based MPI.
-The Intel MPI may run on the[Intel Xeon Ph](../intel-xeon-phi.md)i accelerators as well. Read more on [how to run Intel MPI on accelerators](../intel-xeon-phi.md).
\ No newline at end of file
+The Intel MPI may run on the[Intel Xeon Ph](../intel-xeon-phi/)i accelerators as well. Read more on [how to run Intel MPI on accelerators](../intel-xeon-phi/).
\ No newline at end of file
diff --git a/docs.it4i/salomon/software/mpi/mpi4py-mpi-for-python.md b/docs.it4i/salomon/software/mpi/mpi4py-mpi-for-python.md
index ab593f3d6c348f85b12cef9d015a5cb162a7a76e..74ce3b56fade2949fff0464439ccc3e98e370509 100644
--- a/docs.it4i/salomon/software/mpi/mpi4py-mpi-for-python.md
+++ b/docs.it4i/salomon/software/mpi/mpi4py-mpi-for-python.md
@@ -27,7 +27,7 @@ You need to import MPI to your python program. Include the following line to the
from mpi4py import MPI
```
-The MPI4Py enabled python programs [execute as any other OpenMPI](Running_OpenMPI.md) code.The simpliest way is to run
+The MPI4Py enabled python programs [execute as any other OpenMPI](Running_OpenMPI/) code.The simpliest way is to run
```bash
$ mpiexec python <script>.py
@@ -93,4 +93,4 @@ Execute the above code as:
$ mpiexec --map-by core --bind-to core python hello_world.py
```
-In this example, we run MPI4Py enabled code on 4 nodes, 24 cores per node (total of 96 processes), each python process is bound to a different core. More examples and documentation can be found on [MPI for Python webpage](https://pythonhosted.org/mpi4py/usrman/index.md).
\ No newline at end of file
+In this example, we run MPI4Py enabled code on 4 nodes, 24 cores per node (total of 96 processes), each python process is bound to a different core. More examples and documentation can be found on [MPI for Python webpage](https://pythonhosted.org/mpi4py/usrman/index.md).
\ No newline at end of file
diff --git a/docs.it4i/salomon/software/numerical-languages/introduction.md b/docs.it4i/salomon/software/numerical-languages/introduction.md
index 1bc6e2628d008c49a549fce90c71c7a19df68cf1..e3a66c3111db0d1dfe20a8f3e8699c73646c3dc8 100644
--- a/docs.it4i/salomon/software/numerical-languages/introduction.md
+++ b/docs.it4i/salomon/software/numerical-languages/introduction.md
@@ -16,7 +16,7 @@ MATLAB®^ is a high-level language and interactive environment for numerical com
$ matlab
```
-Read more at the [Matlab page](matlab.md).
+Read more at the [Matlab page](matlab/).
Octave
------
@@ -27,7 +27,7 @@ GNU Octave is a high-level interpreted language, primarily intended for numerica
$ octave
```
-Read more at the [Octave page](octave.md).
+Read more at the [Octave page](octave/).
R
---
@@ -39,4 +39,4 @@ The R is an interpreted language and environment for statistical computing and g
$ R
```
-Read more at the [R page](r.md).
\ No newline at end of file
+Read more at the [R page](r/).
\ No newline at end of file
diff --git a/docs.it4i/salomon/software/numerical-languages/matlab.md b/docs.it4i/salomon/software/numerical-languages/matlab.md
index d78bdce8ca780e11fb3ff5e36b786cda4714277a..c3feda0ccba6b841cdb5fc031514cee76cb69d61 100644
--- a/docs.it4i/salomon/software/numerical-languages/matlab.md
+++ b/docs.it4i/salomon/software/numerical-languages/matlab.md
@@ -22,9 +22,9 @@ By default the EDU variant is marked as default. If you need other version or va
If you need to use the Matlab GUI to prepare your Matlab programs, you can use Matlab directly on the login nodes. But for all computations use Matlab on the compute nodes via PBS Pro scheduler.
-If you require the Matlab GUI, please follow the general informations about [running graphical applications](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-and-vnc.md).
+If you require the Matlab GUI, please follow the general informations about [running graphical applications](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/).
-Matlab GUI is quite slow using the X forwarding built in the PBS (qsub -X), so using X11 display redirection either via SSH or directly by xauth (please see the "GUI Applications on Compute Nodes over VNC" part [here](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-and-vnc.md)) is recommended.
+Matlab GUI is quite slow using the X forwarding built in the PBS (qsub -X), so using X11 display redirection either via SSH or directly by xauth (please see the "GUI Applications on Compute Nodes over VNC" part [here](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/)) is recommended.
To run Matlab with GUI, use
@@ -44,7 +44,7 @@ Running parallel Matlab using Distributed Computing Toolbox / Engine
------------------------------------------------------------------------
Distributed toolbox is available only for the EDU variant
-The MPIEXEC mode available in previous versions is no longer available in MATLAB 2015. Also, the programming interface has changed. Refer to [Release Notes](http://www.mathworks.com/help/distcomp/release-notes.html#buanp9e-1).
+The MPIEXEC mode available in previous versions is no longer available in MATLAB 2015. Also, the programming interface has changed. Refer to [Release Notes](http://www.mathworks.com/help/distcomp/release-notes.html#buanp9e-1).
Delete previously used file mpiLibConf.m, we have observed crashes when using Intel MPI.
@@ -66,7 +66,7 @@ With the new mode, MATLAB itself launches the workers via PBS, so you can either
### Parallel Matlab interactive session
-Following example shows how to start interactive session with support for Matlab GUI. For more information about GUI based applications on Anselm see [this page](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-and-vnc.md).
+Following example shows how to start interactive session with support for Matlab GUI. For more information about GUI based applications on Anselm see [this page](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/).
```bash
$ xhost +
@@ -215,7 +215,7 @@ This method is a "hack" invented by us to emulate the mpiexec functionality foun
Please note that this method is experimental.
-For this method, you need to use SalomonDirect profile, import it using [the same way as SalomonPBSPro](matlab.md#running-parallel-matlab-using-distributed-computing-toolbox---engine)
+For this method, you need to use SalomonDirect profile, import it using [the same way as SalomonPBSPro](matlab.md#running-parallel-matlab-using-distributed-computing-toolbox---engine)
This is an example of m-script using direct mode:
@@ -246,11 +246,11 @@ This is an example of m-script using direct mode:
### Non-interactive Session and Licenses
-If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the " -l __feature__matlab__MATLAB=1" for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please [look here](../../../anselm-cluster-documentation/software/isv_licenses.md).
+If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the " -l __feature__matlab__MATLAB=1" for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please [look here](../../../anselm-cluster-documentation/software/isv_licenses/).
The licensing feature of PBS is currently disabled.
-In case of non-interactive session please read the [following information](../../../anselm-cluster-documentation/software/isv_licenses.md) on how to modify the qsub command to test for available licenses prior getting the resource allocation.
+In case of non-interactive session please read the [following information](../../../anselm-cluster-documentation/software/isv_licenses/) on how to modify the qsub command to test for available licenses prior getting the resource allocation.
### Matlab Distributed Computing Engines start up time
@@ -275,4 +275,4 @@ Since this is a SMP machine, you can completely avoid using Parallel Toolbox and
### Local cluster mode
-You can also use Parallel Toolbox on UV2000. Use l[ocal cluster mode](matlab.md#parallel-matlab-batch-job-in-local-mode), "SalomonPBSPro" profile will not work.
\ No newline at end of file
+You can also use Parallel Toolbox on UV2000. Use l[ocal cluster mode](matlab/#parallel-matlab-batch-job-in-local-mode), "SalomonPBSPro" profile will not work.
\ No newline at end of file
diff --git a/docs.it4i/salomon/software/numerical-languages/octave.md b/docs.it4i/salomon/software/numerical-languages/octave.md
index 3c598b37c57ff896984b112ca0fb1062e7a68ae3..21587e3f4b186afa25c5778d870d6f7aad90663d 100644
--- a/docs.it4i/salomon/software/numerical-languages/octave.md
+++ b/docs.it4i/salomon/software/numerical-languages/octave.md
@@ -1,7 +1,7 @@
Octave
======
-GNU Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems, and for performing other numerical experiments. It also provides extensive graphics capabilities for data visualization and manipulation. Octave is normally used through its interactive command line interface, but it can also be used to write non-interactive programs. The Octave language is quite similar to Matlab so that most programs are easily portable. Read more on <http://www.gnu.org/software/octave/>
+GNU Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems, and for performing other numerical experiments. It also provides extensive graphics capabilities for data visualization and manipulation. Octave is normally used through its interactive command line interface, but it can also be used to write non-interactive programs. The Octave language is quite similar to Matlab so that most programs are easily portable. Read more on <http://www.gnu.org/software/octave/>
Two versions of octave are available on the cluster, via module
@@ -46,7 +46,7 @@ To run octave in batch mode, write an octave script, then write a bash jobscript
exit
```
-This script may be submitted directly to the PBS workload manager via the qsub command. The inputs are in octcode.m file, outputs in output.out file. See the single node jobscript example in the [Job execution section](../../resource-allocation-and-job-execution.md).
+This script may be submitted directly to the PBS workload manager via the qsub command. The inputs are in octcode.m file, outputs in output.out file. See the single node jobscript example in the [Job execution section](../../resource-allocation-and-job-execution/).
The octave c compiler mkoctfile calls the GNU gcc 4.8.1 for compiling native c code. This is very useful for running native c subroutines in octave environment.
@@ -54,4 +54,4 @@ The octave c compiler mkoctfile calls the GNU gcc 4.8.1 for compiling native c c
$ mkoctfile -v
```
-Octave may use MPI for interprocess communication This functionality is currently not supported on the cluster cluster. In case you require the octave interface to MPI, please contact our [cluster support](https://support.it4i.cz/rt/).
\ No newline at end of file
+Octave may use MPI for interprocess communication This functionality is currently not supported on the cluster cluster. In case you require the octave interface to MPI, please contact our [cluster support](https://support.it4i.cz/rt/).
\ No newline at end of file
diff --git a/docs.it4i/salomon/software/numerical-languages/parallel.pdf b/docs.it4i/salomon/software/numerical-languages/parallel.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..d33d5a99c6e37258bec707a3d2f0aa4e20f5f4a5
Binary files /dev/null and b/docs.it4i/salomon/software/numerical-languages/parallel.pdf differ
diff --git a/docs.it4i/salomon/software/numerical-languages/r.md b/docs.it4i/salomon/software/numerical-languages/r.md
index 5617640dd7ef96988f023334fd04fd0c193a3a4c..38e71b4ff253ee32f114fa464f962f1dddb0dccf 100644
--- a/docs.it4i/salomon/software/numerical-languages/r.md
+++ b/docs.it4i/salomon/software/numerical-languages/r.md
@@ -11,7 +11,7 @@ Another convenience is the ease with which the C code or third party libraries m
Extensive support for parallel computing is available within R.
-Read more on <http://www.r-project.org/>, <http://cran.r-project.org/doc/manuals/r-release/R-lang.html>
+Read more on <http://www.r-project.org/>, <http://cran.r-project.org/doc/manuals/r-release/R-lang.html>
Modules
-------
@@ -68,11 +68,11 @@ Example jobscript:
exit
```
-This script may be submitted directly to the PBS workload manager via the qsub command. The inputs are in rscript.R file, outputs in routput.out file. See the single node jobscript example in the [Job execution section](../../resource-allocation-and-job-execution/job-submission-and-execution.md).
+This script may be submitted directly to the PBS workload manager via the qsub command. The inputs are in rscript.R file, outputs in routput.out file. See the single node jobscript example in the [Job execution section](../../resource-allocation-and-job-execution/job-submission-and-execution/).
Parallel R
----------
-Parallel execution of R may be achieved in many ways. One approach is the implied parallelization due to linked libraries or specially enabled functions, as [described above](r.md#interactive-execution). In the following sections, we focus on explicit parallelization, where parallel constructs are directly stated within the R script.
+Parallel execution of R may be achieved in many ways. One approach is the implied parallelization due to linked libraries or specially enabled functions, as [described above](r/#interactive-execution). In the following sections, we focus on explicit parallelization, where parallel constructs are directly stated within the R script.
Package parallel
--------------------
@@ -93,7 +93,7 @@ More information and examples may be obtained directly by reading the documentat
> vignette("parallel")
```
-Download the package [parallell](package-parallel-vignette) vignette.
+Download the package [parallell](package-parallel-vignette.pdf) vignette.
The forking is the most simple to use. Forking family of functions provide parallelized, drop in replacement for the serial apply() family of functions.
@@ -148,9 +148,9 @@ Package Rmpi
------------
package Rmpi provides an interface (wrapper) to MPI APIs.
-It also provides interactive R slave environment. On the cluster, Rmpi provides interface to the [OpenMPI](../mpi/Running_OpenMPI.md).
+It also provides interactive R slave environment. On the cluster, Rmpi provides interface to the [OpenMPI](../mpi/Running_OpenMPI/).
-Read more on Rmpi at <http://cran.r-project.org/web/packages/Rmpi/>, reference manual is available at <http://cran.r-project.org/web/packages/Rmpi/Rmpi.pdf>
+Read more on Rmpi at <http://cran.r-project.org/web/packages/Rmpi/>, reference manual is available at <http://cran.r-project.org/web/packages/Rmpi/Rmpi.pdf>
When using package Rmpi, both openmpi and R modules must be loaded
@@ -349,7 +349,7 @@ mpi.apply Rmpi example:
mpi.quit()
```
-The above is the mpi.apply MPI example for calculating the number π. Only the slave processes carry out the calculation. Note the **mpi.parSapply(), ** function call. The package parallel [example](r.md#package-parallel)[above](r.md#package-parallel) may be trivially adapted (for much better performance) to this structure using the mclapply() in place of mpi.parSapply().
+The above is the mpi.apply MPI example for calculating the number π. Only the slave processes carry out the calculation. Note the **mpi.parSapply(), ** function call. The package parallel [example](r/#package-parallel)[above](r/#package-parallel) may be trivially adapted (for much better performance) to this structure using the mclapply() in place of mpi.parSapply().
Execute the example as:
@@ -365,7 +365,7 @@ Parallel execution
------------------
The R parallel jobs are executed via the PBS queue system exactly as any other parallel jobs. User must create an appropriate jobscript and submit via the **qsub**
-Example jobscript for [static Rmpi](r.md#static-rmpi) parallel R execution, running 1 process per core:
+Example jobscript for [static Rmpi](r/#static-rmpi) parallel R execution, running 1 process per core:
```bash
#!/bin/bash
@@ -394,7 +394,7 @@ Example jobscript for [static Rmpi](r.md#static-rmpi) parallel R execution, runn
exit
```
-For more information about jobscripts and MPI execution refer to the [Job submission](../../resource-allocation-and-job-execution/job-submission-and-execution.md) and general [MPI](../mpi.md) sections.
+For more information about jobscripts and MPI execution refer to the [Job submission](../../resource-allocation-and-job-execution/job-submission-and-execution/) and general [MPI](../mpi/mpi/) sections.
Xeon Phi Offload
----------------
@@ -404,4 +404,4 @@ By leveraging MKL, R can accelerate certain computations, most notably linear al
$ export MKL_MIC_ENABLE=1
```
-[Read more about automatic offload](../intel-xeon-phi.md)
\ No newline at end of file
+[Read more about automatic offload](../intel-xeon-phi/)
\ No newline at end of file
diff --git a/docs.it4i/salomon/software/operating-system.md b/docs.it4i/salomon/software/operating-system.md
index b692a3f7368be44a5c3ee40114b0e5e00df21693..3112b6359ab7eeea4434a99caebd21e570eedbd7 100644
--- a/docs.it4i/salomon/software/operating-system.md
+++ b/docs.it4i/salomon/software/operating-system.md
@@ -1,8 +1,6 @@
Operating System
================
-**The operating system, deployed on Salomon cluster**
-
-The operating system on Salomon is Linux - CentOS 6.6.
+The operating system on Salomon is Linux - **CentOS 6.X**
The CentOS Linux distribution is a stable, predictable, manageable and reproducible platform derived from the sources of Red Hat Enterprise Linux (RHEL).
\ No newline at end of file
diff --git a/docs.it4i/salomon/storage/cesnet-data-storage.md b/docs.it4i/salomon/storage/cesnet-data-storage.md
index 8185c1bdd05c63070d3cf2c5686804af5222828a..e7e2c02930982e719cc701d4858e2b88c62518c3 100644
--- a/docs.it4i/salomon/storage/cesnet-data-storage.md
+++ b/docs.it4i/salomon/storage/cesnet-data-storage.md
@@ -5,7 +5,7 @@ Introduction
------------
Do not use shared filesystems at IT4Innovations as a backup for large amount of data or long-term archiving purposes.
->The IT4Innovations does not provide storage capacity for data archiving. Academic staff and students of research institutions in the Czech Republic can use [CESNET Storage service](https://du.cesnet.cz/).
+>The IT4Innovations does not provide storage capacity for data archiving. Academic staff and students of research institutions in the Czech Republic can use [CESNET Storage service](https://du.cesnet.cz/).
The CESNET Storage service can be used for research purposes, mainly by academic staff and students of research institutions in the Czech Republic.
@@ -13,20 +13,20 @@ User of data storage CESNET (DU) association can become organizations or an indi
User may only use data storage CESNET for data transfer and storage which are associated with activities in science, research, development, the spread of education, culture and prosperity. In detail see “Acceptable Use Policy CESNET Large Infrastructure (Acceptable Use Policy, AUP)”.
-The service is documented at <https://du.cesnet.cz/wiki/doku.php/en/start>. For special requirements please contact directly CESNET Storage Department via e-mail [du-support(at)cesnet.cz](mailto:du-support@cesnet.cz).
+The service is documented at <https://du.cesnet.cz/wiki/doku.php/en/start>. For special requirements please contact directly CESNET Storage Department via e-mail [du-support(at)cesnet.cz](mailto:du-support@cesnet.cz).
The procedure to obtain the CESNET access is quick and trouble-free.
-(source [https://du.cesnet.cz/](https://du.cesnet.cz/wiki/doku.php/en/start "CESNET Data Storage"))
+(source [https://du.cesnet.cz/](https://du.cesnet.cz/wiki/doku.php/en/start "CESNET Data Storage"))
CESNET storage access
---------------------
### Understanding Cesnet storage
->It is very important to understand the Cesnet storage before uploading data. Please read <https://du.cesnet.cz/en/navody/home-migrace-plzen/start> first.
+>It is very important to understand the Cesnet storage before uploading data. Please read <https://du.cesnet.cz/en/navody/home-migrace-plzen/start> first.
-Once registered for CESNET Storage, you may [access the storage](https://du.cesnet.cz/en/navody/faq/start) in number of ways. We recommend the SSHFS and RSYNC methods.
+Once registered for CESNET Storage, you may [access the storage](https://du.cesnet.cz/en/navody/faq/start) in number of ways. We recommend the SSHFS and RSYNC methods.
### SSHFS Access
@@ -80,7 +80,7 @@ Rsync is a fast and extraordinarily versatile file copying tool. It is famous fo
Rsync finds files that need to be transferred using a "quick check" algorithm (by default) that looks for files that have changed in size or in last-modified time. Any changes in the other preserved attributes (as requested by options) are made on the destination file directly when the quick check indicates that the file's data does not need to be updated.
-More about Rsync at <https://du.cesnet.cz/en/navody/rsync/start#pro_bezne_uzivatele>
+More about Rsync at <https://du.cesnet.cz/en/navody/rsync/start#pro_bezne_uzivatele>
Transfer large files to/from Cesnet storage, assuming membership in the Storage VO
diff --git a/docs.it4i/salomon/storage/storage.md b/docs.it4i/salomon/storage/storage.md
index 3352868da0a2b82f84e5566766c4605687ee771b..2e352602e64843963a2dcda7c0cbfc19820f7bc8 100644
--- a/docs.it4i/salomon/storage/storage.md
+++ b/docs.it4i/salomon/storage/storage.md
@@ -3,33 +3,33 @@ Storage
Introduction
------------
-There are two main shared file systems on Salomon cluster, the [HOME](storage.md#home)and [SCRATCH](storage.md#shared-filesystems).
+There are two main shared file systems on Salomon cluster, the [HOME](storage/#home)and [SCRATCH](storage/#shared-filesystems).
All login and compute nodes may access same data on shared filesystems. Compute nodes are also equipped with local (non-shared) scratch, ramdisk and tmp filesystems.
Policy (in a nutshell)
----------------------
>Use [ for your most valuable data and programs.
-Use [WORK](storage.md#work) for your large project files.
-Use [TEMP](storage.md#temp) for large scratch data.
+Use [WORK](storage/#work) for your large project files.
+Use [TEMP](storage/#temp) for large scratch data.
->Do not use for [archiving](storage.md#archiving)!
+>Do not use for [archiving](storage/#archiving)!
Archiving
-------------
-Please don't use shared filesystems as a backup for large amount of data or long-term archiving mean. The academic staff and students of research institutions in the Czech Republic can use [CESNET storage service](../../anselm-cluster-documentation/storage/cesnet-data-storage.md), which is available via SSHFS.
+Please don't use shared filesystems as a backup for large amount of data or long-term archiving mean. The academic staff and students of research institutions in the Czech Republic can use [CESNET storage service](../../anselm-cluster-documentation/storage/cesnet-data-storage/), which is available via SSHFS.
Shared Filesystems
----------------------
-Salomon computer provides two main shared filesystems, the [ HOME filesystem](storage.md#home-filesystem) and the [SCRATCH filesystem](storage.md#scratch-filesystem). The SCRATCH filesystem is partitioned to [WORK and TEMP workspaces](storage.md#shared-workspaces). The HOME filesystem is realized as a tiered NFSÂ disk storage. The SCRATCH filesystem is realized as a parallel Lustre filesystem. Both shared file systems are accessible via the Infiniband network. Extended ACLs are provided on both HOME/SCRATCH filesystems for the purpose of sharing data with other users using fine-grained control.
+Salomon computer provides two main shared filesystems, the [ HOME filesystem](storage/#home-filesystem) and the [SCRATCH filesystem](storage/#scratch-filesystem). The SCRATCH filesystem is partitioned to [WORK and TEMP workspaces](storage/#shared-workspaces). The HOME filesystem is realized as a tiered NFSÂ disk storage. The SCRATCH filesystem is realized as a parallel Lustre filesystem. Both shared file systems are accessible via the Infiniband network. Extended ACLs are provided on both HOME/SCRATCH filesystems for the purpose of sharing data with other users using fine-grained control.
###HOME filesystem
-The HOME filesystem is realized as a Tiered filesystem, exported via NFS. The first tier has capacity 100TB, second tier has capacity 400TB. The filesystem is available on all login and computational nodes. The Home filesystem hosts the [HOME workspace](storage.md#home).
+The HOME filesystem is realized as a Tiered filesystem, exported via NFS. The first tier has capacity 100TB, second tier has capacity 400TB. The filesystem is available on all login and computational nodes. The Home filesystem hosts the [HOME workspace](storage/#home).
###SCRATCH filesystem
-The architecture of Lustre on Salomon is composed of two metadata servers (MDS) and six data/object storage servers (OSS). Accessible capacity is 1.69 PB, shared among all users. The SCRATCH filesystem hosts the [WORK and TEMP workspaces](storage.md#shared-workspaces).
+The architecture of Lustre on Salomon is composed of two metadata servers (MDS) and six data/object storage servers (OSS). Accessible capacity is 1.69 PB, shared among all users. The SCRATCH filesystem hosts the [WORK and TEMP workspaces](storage/#shared-workspaces).
Configuration of the SCRATCH Lustre storage
@@ -45,11 +45,11 @@ Configuration of the SCRATCH Lustre storage
### Understanding the Lustre Filesystems
-(source <http://www.nas.nasa.gov>)
+(source <http://www.nas.nasa.gov>)
A user file on the Lustre filesystem can be divided into multiple chunks (stripes) and stored across a subset of the object storage targets (OSTs) (disks). The stripes are distributed among the OSTs in a round-robin fashion to ensure load balancing.
-When a client (a compute node from your job) needs to create or access a file, the client queries the metadata server ( MDS) and the metadata target ( MDT) for the layout and location of the [file's stripes](http://www.nas.nasa.gov/hecc/support/kb/Lustre_Basics_224.html#striping). Once the file is opened and the client obtains the striping information, the MDS is no longer involved in the file I/O process. The client interacts directly with the object storage servers (OSSes) and OSTs to perform I/O operations such as locking, disk allocation, storage, and retrieval.
+When a client (a compute node from your job) needs to create or access a file, the client queries the metadata server ( MDS) and the metadata target ( MDT) for the layout and location of the [file's stripes](http://www.nas.nasa.gov/hecc/support/kb/Lustre_Basics_224.html#striping). Once the file is opened and the client obtains the striping information, the MDS is no longer involved in the file I/O process. The client interacts directly with the object storage servers (OSSes) and OSTs to perform I/O operations such as locking, disk allocation, storage, and retrieval.
If multiple clients try to read and write the same part of a file at the same time, the Lustre distributed lock manager enforces coherency so that all clients see consistent results.
@@ -102,7 +102,7 @@ Another good practice is to make the stripe count be an integral factor of the n
Large stripe size allows each client to have exclusive access to its own part of a file. However, it can be counterproductive in some cases if it does not match your I/O pattern. The choice of stripe size has no effect on a single-stripe file.
-Read more on <http://wiki.lustre.org/manual/LustreManual20_HTML/ManagingStripingFreeSpace.html>
+Read more on <http://wiki.lustre.org/manual/LustreManual20_HTML/ManagingStripingFreeSpace.html>
Disk usage and quota commands
------------------------------------------
@@ -207,20 +207,20 @@ other::---
Default ACL mechanism can be used to replace setuid/setgid permissions on directories. Setting a default ACL on a directory (-d flag to setfacl) will cause the ACL permissions to be inherited by any newly created file or subdirectory within the directory. Refer to this page for more information on Linux ACL:
-[http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html ](http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html)
+[http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html ](http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html)
Shared Workspaces
---------------------
###HOME
-Users home directories /home/username reside on HOME filesystem. Accessible capacity is 0.5PB, shared among all users. Individual users are restricted by filesystem usage quotas, set to 250GB per user. If 250GB should prove as insufficient for particular user, please contact [support](https://support.it4i.cz/rt), the quota may be lifted upon request.
+Users home directories /home/username reside on HOME filesystem. Accessible capacity is 0.5PB, shared among all users. Individual users are restricted by filesystem usage quotas, set to 250GB per user. If 250GB should prove as insufficient for particular user, please contact [support](https://support.it4i.cz/rt), the quota may be lifted upon request.
>The HOME filesystem is intended for preparation, evaluation, processing and storage of data generated by active Projects.
The HOMEÂ should not be used to archive data of past Projects or other unrelated data.
-The files on HOME will not be deleted until end of the [users lifecycle](../../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md).
+The files on HOME will not be deleted until end of the [users lifecycle](../../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials/).
The workspace is backed up, such that it can be restored in case of catasthropic failure resulting in significant data loss. This backup however is not intended to restore old versions of user data or to restore (accidentaly) deleted files.
@@ -257,7 +257,7 @@ The WORK workspace is hosted on SCRATCH filesystem. The SCRATCH is realized as L
### TEMP
-The TEMP workspace resides on SCRATCH filesystem. The TEMP workspace accesspoint is /scratch/temp. Users may freely create subdirectories and files on the workspace. Accessible capacity is 1.6P, shared among all users on TEMP and WORK. Individual users are restricted by filesystem usage quotas, set to 100TB per user. The purpose of this quota is to prevent runaway programs from filling the entire filesystem and deny service to other users. >If 100TB should prove as insufficient for particular user, please contact [support](https://support.it4i.cz/rt), the quota may be lifted upon request.
+The TEMP workspace resides on SCRATCH filesystem. The TEMP workspace accesspoint is /scratch/temp. Users may freely create subdirectories and files on the workspace. Accessible capacity is 1.6P, shared among all users on TEMP and WORK. Individual users are restricted by filesystem usage quotas, set to 100TB per user. The purpose of this quota is to prevent runaway programs from filling the entire filesystem and deny service to other users. >If 100TB should prove as insufficient for particular user, please contact [support](https://support.it4i.cz/rt), the quota may be lifted upon request.
>The TEMP workspace is intended for temporary scratch data generated during the calculation as well as for high performance access to input and output files. All I/O intensive jobs must use the TEMP workspace as their working directory.