Merge branch 'folder_rename' into 'master'

Folder rename

See merge request !81

docs.it4i/anselm/introduction.md

@@ -8,4 +8,4 @@ User data shared file-system (HOME, 320 TB) and job data shared file-system (SCR
 
 The PBS Professional workload manager provides [computing resources allocations and job execution](resources-allocation-policy/).
 
-Read more on how to [apply for resources](../general/applying-for-resources/), [obtain login credentials,](../general/obtaining-login-credentials/obtaining-login-credentials/) and [access the cluster](shell-and-data-access/).
+Read more on how to [apply for resources](../general/applying-for-resources/), [obtain login credentials](../general/obtaining-login-credentials/obtaining-login-credentials/) and [access the cluster](shell-and-data-access/).

docs.it4i/anselm/job-submission-and-execution.md

@@ -48,7 +48,7 @@ $ qsub -A OPEN-0-0 -q qfree -l select=10:ncpus=16 ./myjob
 
 In this example, we allocate 10 nodes, 16 cores per node, for 12 hours. We allocate these resources via the qfree queue. It is not required that the project OPEN-0-0 has any available resources left. Consumed resources are still accounted for. Jobscript myjob will be executed on the first node in the allocation.
 
-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.
+All qsub options may be [saved directly into the jobscript](#example-jobscript-for-mpi-calculation-with-preloaded-inputs). In such a case, no options to qsub are needed.
 
 ```bash
 $ qsub ./myjob
@@ -345,6 +345,8 @@ In some cases, it may be impractical to copy the inputs to scratch and outputs t
 !!! note
     Store the qsub options within the jobscript. Use **mpiprocs** and **ompthreads** qsub options to control the MPI job execution.
 
+### Example Jobscript for MPI Calculation With Preloaded Inputs
+
 Example jobscript for an MPI job with preloaded inputs and executables, options for qsub are stored within the script :
 
 ```bash
@@ -370,7 +372,7 @@ exit
 
 In this example, input and executable files are assumed preloaded manually in /scratch/$USER/myjob directory. Note the **mpiprocs** and **ompthreads** qsub options, controlling behavior of the MPI execution. The mympiprog.x is executed as one process per node, on all 100 allocated nodes. If mympiprog.x implements OpenMP threads, it will run 16 threads per node.
 
-More information is found in the [Running OpenMPI](../software/mpi/Running_OpenMPI/) and [Running MPICH2](../software/mpi/running-mpich2/)
+More information is found in the [Running OpenMPI](software/mpi/Running_OpenMPI/) and [Running MPICH2](software/mpi/running-mpich2/)
 sections.
 
 ### Example Jobscript for Single Node Calculation

docs.it4i/anselm/software/ansys/ansys-cfx.md

@@ -47,7 +47,7 @@ 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/). 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](../../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
 

docs.it4i/anselm/software/ansys/ansys-ls-dyna.md

@@ -50,6 +50,6 @@ 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/). [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](../../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=

docs.it4i/anselm/software/ansys/ls-dyna.md

@@ -30,6 +30,6 @@ module load lsdyna
 /apps/engineering/lsdyna/lsdyna700s i=input.k
 ```
 
-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.html). [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](../../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 LS-DYNA solver via parameter i=

docs.it4i/anselm/software/debuggers/allinea-performance-reports.md

@@ -29,7 +29,7 @@ Instead of [running your MPI program the usual way](../mpi/), use the the perf r
     $ 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/).
+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](../../job-submission-and-execution/).
 
 ## Example
 
@@ -56,4 +56,4 @@ Now lets profile the code:
     $ 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](../../../src/mympiprog_32p_2014-10-15_16-56.txt) and [mympiprog_32p\*.html](../../../src/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.

docs.it4i/anselm/software/debuggers/debuggers.md

@@ -57,4 +57,4 @@ Vampir is a GUI trace analyzer for traces in OTF format.
     $ vampir
 ```
 
-Read more at the [Vampir](../../salomon/software/debuggers/vampir/) page.
+Read more at the [Vampir](vampir/) page.

docs.it4i/anselm/software/debuggers/scalasca.md

@@ -11,7 +11,7 @@ Scalasca supports profiling of MPI, OpenMP and hybrid MPI+OpenMP applications.
 There are currently two versions of Scalasca 2.0 [modules](../../environment-and-modules/) installed on Anselm:
 
 * scalasca2/2.0-gcc-openmpi, for usage with [GNU Compiler](../compilers/) and [OpenMPI](../mpi/Running_OpenMPI/),
-* scalasca2/2.0-icc-impi, for usage with [Intel Compiler](../compilers.html) and [Intel MPI](../mpi/running-mpich2/).
+* scalasca2/2.0-icc-impi, for usage with [Intel Compiler](../compilers/) and [Intel MPI](../mpi/running-mpich2/).
 
 ## Usage
 

docs.it4i/anselm/software/debuggers/score-p.md

@@ -11,7 +11,7 @@ Score-P can be used as an instrumentation tool for [Scalasca](scalasca/).
 There are currently two versions of Score-P version 1.2.6 [modules](../../environment-and-modules/) installed on Anselm :
 
 * scorep/1.2.3-gcc-openmpi, for usage     with [GNU Compiler](../compilers/) and [OpenMPI](../mpi/Running_OpenMPI/)
-* scorep/1.2.3-icc-impi, for usage with [Intel Compiler](../compilers.html)> and [Intel MPI](../mpi/running-mpich2/)>.
+* scorep/1.2.3-icc-impi, for usage with [Intel Compiler](../compilers/)> and [Intel MPI](../mpi/running-mpich2/)>.
 
 ## Instrumentation
 

docs.it4i/anselm/software/debuggers/vampir.md

-# hVampir
+# Vampir
 
-Vampir is a commercial trace analysis and visualization 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](../../../salomon/software/debuggers/score-p/)) first to collect the traces.
+Vampir is a commercial trace analysis and visualization 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.
 
 ![](../../../img/Snmekobrazovky20160708v12.33.35.png)
 

docs.it4i/anselm/software/numerical-languages/octave.md

@@ -48,7 +48,7 @@ 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](http://support.it4i.cz/docs/anselm/resource-allocation-and-job-execution).
+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](../../job-submission-and-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.
 

docs.it4i/anselm/software/numerical-languages/r.md

@@ -66,7 +66,7 @@ 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/).
+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](../../job-submission-and-execution/).
 
 ## Parallel R
 
@@ -396,4 +396,4 @@ Example jobscript for [static Rmpi](r/#static-rmpi) parallel R execution, runnin
     exit
 ```
 
-For more information about jobscript and MPI execution refer to the [Job submission](../../resource-allocation-and-job-execution/job-submission-and-execution/) and general [MPI](../mpi/mpi/) sections.
+For more information about jobscript and MPI execution refer to the [Job submission](../../job-submission-and-execution/) and general [MPI](../mpi/mpi/) sections.

docs.it4i/anselm/software/numerical-libraries/hdf5.md

@@ -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/software/mpi/running-mpich2/).
+Run the example as [Intel MPI program](../mpi/running-mpich2/).
 
 For further information, please see the website: <http://www.hdfgroup.org/HDF5/>

docs.it4i/anselm/software/omics-master/overview.md

@@ -231,7 +231,7 @@ second one.
 
       --project>. Project ID of your supercomputer allocation.
 
-      --queue. [Queue](../../resource-allocation-and-job-execution/introduction.html) to run the jobs in.
+      --queue. [Queue](../../resources-allocation-policy/) to run the jobs in.
 ```
 
 Input, output and ped arguments are mandatory. If the output folder does not exist, the pipeline will create it.
@@ -278,7 +278,7 @@ Now, we can launch the pipeline (replace OPEN-0-0 with your Project ID):
     $ ngsPipeline -i /scratch/$USER/omics/sample_data/data -o /scratch/$USER/omics/results -p /scratch/$USER/omics/sample_data/data/file.ped --project OPEN-0-0 --queue qprod
 ```
 
-This command submits the processing [jobs to the queue](../../resource-allocation-and-job-execution/job-submission-and-execution.html).
+This command submits the processing [jobs to the queue](../../job-submission-and-execution/).
 
 If we want to re-launch the pipeline from stage 4 until stage 20 we should use the next command:
 
@@ -334,7 +334,7 @@ This listing show which tools are used in each step of the pipeline
 
 ## Interpretation
 
-The output folder contains all the subfolders with the intermediate data. This folder contains the final VCF with all the variants. This file can be uploaded into [TEAM](diagnostic-component-team.html) by using the VCF file button. It is important to note here that the entire management of the VCF file is local: no patient’s sequence data is sent over the Internet thus avoiding any problem of data privacy or confidentiality.
+The output folder contains all the subfolders with the intermediate data. This folder contains the final VCF with all the variants. This file can be uploaded into [TEAM](diagnostic-component-team/) by using the VCF file button. It is important to note here that the entire management of the VCF file is local: no patient’s sequence data is sent over the Internet thus avoiding any problem of data privacy or confidentiality.
 
 ![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.]\((../../../img/fig7.png)
 

docs.it4i/anselm/software/openfoam.md

@@ -45,7 +45,7 @@ In /opt/modules/modulefiles/engineering you can see installed engineering softwa
     lsdyna/7.x.x               openfoam/2.2.1-gcc481-openmpi1.6.5-SP
 ```
 
-For information how to use modules please [look here](../environment-and-modules/ "Environment and Modules ").
+For information how to use modules please [look here](../environment-and-modules/).
 
 ## Getting Started
 
@@ -112,7 +112,7 @@ Job submission
     $ qsub -A OPEN-0-0 -q qprod -l select=1:ncpus=16,walltime=03:00:00 test.sh
 ```
 
-For information about job submission please [look here](../resource-allocation-and-job-execution/job-submission-and-execution/ "Job submission").
+For information about job submission please [look here](../job-submission-and-execution/).
 
 ## Running Applications in Parallel
 

docs.it4i/anselm/software/paraview.md

@@ -26,7 +26,7 @@ To launch the server, you must first allocate compute nodes, for example
     $ qsub -I -q qprod -A OPEN-0-0 -l select=2
 ```
 
-to launch an interactive session on 2 nodes. Refer to [Resource Allocation and Job Execution](../resource-allocation-and-job-execution/introduction/) for details.
+to launch an interactive session on 2 nodes. Refer to [Resource Allocation and Job Execution](../job-submission-and-execution/) for details.
 
 After the interactive session is opened, load the ParaView module :
 

docs.it4i/anselm/software/kvirtualization.md → docs.it4i/anselm/software/virtualization.md

@@ -12,7 +12,7 @@ There are situations when Anselm's environment is not suitable for user needs.
 * Application requires privileged access to operating system
 * ... and combinations of above cases
 
-We offer solution for these cases - **virtualization**. Anselm's environment gives the possibility to run virtual machines on compute nodes. Users can create their own images of operating system with specific software stack and run instances of these images as virtual machines on compute nodes. Run of virtual machines is provided by standard mechanism of [Resource Allocation and Job Execution](../../resource-allocation-and-job-execution/introduction/).
+We offer solution for these cases - **virtualization**. Anselm's environment gives the possibility to run virtual machines on compute nodes. Users can create their own images of operating system with specific software stack and run instances of these images as virtual machines on compute nodes. Run of virtual machines is provided by standard mechanism of [Resource Allocation and Job Execution](../job-submission-and-execution/).
 
 Solution is based on QEMU-KVM software stack and provides hardware-assisted x86 virtualization.
 
@@ -202,7 +202,7 @@ Run script runs application from shared job directory (mapped as drive z:), proc
 
 ### Run Jobs
 
-Run jobs as usual, see  [Resource Allocation and Job Execution](../../resource-allocation-and-job-execution/introduction/). Use only full node allocation for virtualization jobs.
+Run jobs as usual, see  [Resource Allocation and Job Execution](../job-submission-and-execution/). Use only full node allocation for virtualization jobs.
 
 ### Running Virtual Machines
 

docs.it4i/general/accessing-the-clusters/graphical-user-interface/vnc.md

@@ -198,7 +198,7 @@ Allow incoming X11 graphics from the compute nodes at the login node:
 $ xhost +
 ```
 
-Get an interactive session on a compute node (for more detailed info [look here](../../../anselm/resource-allocation-and-job-execution/job-submission-and-execution/)). Use the **-v DISPLAY** option to propagate the DISPLAY on the compute node. In this example, we want a complete node (24 cores in this example) from the production queue:
+Get an interactive session on a compute node (for more detailed info [look here](../../../anselm/job-submission-and-execution/)). Use the **-v DISPLAY** option to propagate the DISPLAY on the compute node. In this example, we want a complete node (24 cores in this example) from the production queue:
 
 ```bash
 $ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A PROJECT_ID -q qprod -l select=1:ncpus=24

docs.it4i/salomon/software/ansys/ansys-cfx.md

@@ -47,7 +47,7 @@ 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/). 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](../../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
 

docs.it4i/salomon/software/ansys/ansys-ls-dyna.md

@@ -50,6 +50,6 @@ 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/). [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](../../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=