Commit 8b98c2ab authored by Lukáš Krupčík's avatar Lukáš Krupčík

* -> *

parent 2b9f45a7
Pipeline #2022 passed with stages
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......@@ -69,8 +69,8 @@ Anselm is equipped with Intel Sandy Bridge processors Intel Xeon E5-2665 (nodes
* speed: 2.4 GHz, up to 3.1 GHz using Turbo Boost Technology
* peak performance: 19.2 GFLOP/s per core
* caches:
* L2: 256 KB per core
* L3: 20 MB per processor
* L2: 256 KB per core
* L3: 20 MB per processor
* memory bandwidth at the level of the processor: 51.2 GB/s
### Intel Sandy Bridge E5-2470 Processor
......@@ -79,8 +79,8 @@ Anselm is equipped with Intel Sandy Bridge processors Intel Xeon E5-2665 (nodes
* speed: 2.3 GHz, up to 3.1 GHz using Turbo Boost Technology
* peak performance: 18.4 GFLOP/s per core
* caches:
* L2: 256 KB per core
* L3: 20 MB per processor
* L2: 256 KB per core
* L3: 20 MB per processor
* memory bandwidth at the level of the processor: 38.4 GB/s
Nodes equipped with Intel Xeon E5-2665 CPU have set PBS resource attribute cpu_freq = 24, nodes equipped with Intel Xeon E5-2470 CPU have set PBS resource attribute cpu_freq = 23.
......@@ -103,28 +103,28 @@ Intel Turbo Boost Technology is used by default, you can disable it for all nod
* 2 sockets
* Memory Controllers are integrated into processors.
* 8 DDR3 DIMMs per node
* 4 DDR3 DIMMs per CPU
* 1 DDR3 DIMMs per channel
* Data rate support: up to 1600MT/s
* 8 DDR3 DIMMs per node
* 4 DDR3 DIMMs per CPU
* 1 DDR3 DIMMs per channel
* Data rate support: up to 1600MT/s
* Populated memory: 8 x 8 GB DDR3 DIMM 1600 MHz
### Compute Node With GPU or MIC Accelerator
* 2 sockets
* Memory Controllers are integrated into processors.
* 6 DDR3 DIMMs per node
* 3 DDR3 DIMMs per CPU
* 1 DDR3 DIMMs per channel
* Data rate support: up to 1600MT/s
* 6 DDR3 DIMMs per node
* 3 DDR3 DIMMs per CPU
* 1 DDR3 DIMMs per channel
* Data rate support: up to 1600MT/s
* Populated memory: 6 x 16 GB DDR3 DIMM 1600 MHz
### Fat Compute Node
* 2 sockets
* Memory Controllers are integrated into processors.
* 16 DDR3 DIMMs per node
* 8 DDR3 DIMMs per CPU
* 2 DDR3 DIMMs per channel
* Data rate support: up to 1600MT/s
* 16 DDR3 DIMMs per node
* 8 DDR3 DIMMs per CPU
* 2 DDR3 DIMMs per channel
* Data rate support: up to 1600MT/s
* Populated memory: 16 x 32 GB DDR3 DIMM 1600 MHz
......@@ -99,7 +99,7 @@ We recommend, that startup script
* maps Job Directory from host (from compute node)
* runs script (we call it "run script") from Job Directory and waits for application's exit
* for management purposes if run script does not exist wait for some time period (few minutes)
* for management purposes if run script does not exist wait for some time period (few minutes)
* shutdowns/quits OS
For Windows operating systems we suggest using Local Group Policy Startup script, for Linux operating systems rc.local, runlevel init script or similar service.
......
......@@ -10,8 +10,8 @@ PETSc (Portable, Extensible Toolkit for Scientific Computation) is a suite of bu
* [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)
* [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
......@@ -37,24 +37,24 @@ 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://www.nersc.gov/users/software/programming-libraries/math-libraries/petsc/)
* [Trilinos ML](http://trilinos.sandia.gov/packages/ml/)
* [SPAI - Sparse Approximate Inverse](https://bitbucket.org/petsc/pkg-spai)
* [Hypre](http://www.nersc.gov/users/software/programming-libraries/math-libraries/petsc/)
* [Trilinos ML](http://trilinos.sandia.gov/packages/ml/)
* [SPAI - Sparse Approximate Inverse](https://bitbucket.org/petsc/pkg-spai)
......@@ -96,12 +96,12 @@ BAM is the binary representation of SAM and keeps exactly the same information a
Some features
* Quality control
* reads with N errors
* reads with multiple mappings
* strand bias
* paired-end insert
* reads with N errors
* reads with multiple mappings
* strand bias
* paired-end insert
* Filtering: by number of errors, number of hits
* Comparator: stats, intersection, ...
* Comparator: stats, intersection, ...
** Input: ** BAM file.
......
......@@ -81,22 +81,22 @@ The architecture of Lustre on Anselm is composed of two metadata servers (MDS) a
Configuration of the storages
* HOME Lustre object storage
* One disk array NetApp E5400
* 22 OSTs
* 227 2TB NL-SAS 7.2krpm disks
* 22 groups of 10 disks in RAID6 (8+2)
* 7 hot-spare disks
* One disk array NetApp E5400
* 22 OSTs
* 227 2TB NL-SAS 7.2krpm disks
* 22 groups of 10 disks in RAID6 (8+2)
* 7 hot-spare disks
* SCRATCH Lustre object storage
* Two disk arrays NetApp E5400
* 10 OSTs
* 106 2TB NL-SAS 7.2krpm disks
* 10 groups of 10 disks in RAID6 (8+2)
* 6 hot-spare disks
* Two disk arrays NetApp E5400
* 10 OSTs
* 106 2TB NL-SAS 7.2krpm disks
* 10 groups of 10 disks in RAID6 (8+2)
* 6 hot-spare disks
* Lustre metadata storage
* One disk array NetApp E2600
* 12 300GB SAS 15krpm disks
* 2 groups of 5 disks in RAID5
* 2 hot-spare disks
* One disk array NetApp E2600
* 12 300GB SAS 15krpm disks
* 2 groups of 5 disks in RAID5
* 2 hot-spare disks
\###HOME
......
......@@ -129,18 +129,18 @@ A FAQ about certificates can be found here: [Certificates FAQ](certificates-faq/
Follow these steps **only** if you can not obtain your certificate in a standard way. In case you choose this procedure, please attach a **scan of photo ID** (personal ID or passport or drivers license) when applying for [login credentials](obtaining-login-credentials/#the-login-credentials).
* Go to [CAcert](www.cacert.org).
* If there's a security warning, just acknowledge it.
* If there's a security warning, just acknowledge it.
* Click _Join_.
* Fill in the form and submit it by the _Next_ button.
* Type in the e-mail address which you use for communication with us.
* Don't forget your chosen _Pass Phrase_.
* Type in the e-mail address which you use for communication with us.
* Don't forget your chosen _Pass Phrase_.
* You will receive an e-mail verification link. Follow it.
* After verifying, go to the CAcert's homepage and login using _Password Login_.
* Go to _Client Certificates_ _New_.
* Tick _Add_ for your e-mail address and click the _Next_ button.
* Click the _Create Certificate Request_ button.
* You'll be redirected to a page from where you can download/install your certificate.
* Simultaneously you'll get an e-mail with a link to the certificate.
* Simultaneously you'll get an e-mail with a link to the certificate.
## Installation of the Certificate Into Your Mail Client
......
......@@ -61,7 +61,7 @@ Salomon is equipped with Intel Xeon processors Intel Xeon E5-2680v3. Processors
* speed: 2.5 GHz, up to 3.3 GHz using Turbo Boost Technology
* peak performance: 19.2 GFLOP/s per core
* caches:
* Intel® Smart Cache: 30 MB
* Intel® Smart Cache: 30 MB
* memory bandwidth at the level of the processor: 68 GB/s
### MIC Accelerator Intel Xeon Phi 7120P Processor
......@@ -71,7 +71,7 @@ Salomon is equipped with Intel Xeon processors Intel Xeon E5-2680v3. Processors
GHz, up to 1.333 GHz using Turbo Boost Technology
* peak performance: 18.4 GFLOP/s per core
* caches:
* L2: 30.5 MB
* L2: 30.5 MB
* memory bandwidth at the level of the processor: 352 GB/s
## Memory Architecture
......@@ -82,9 +82,9 @@ Memory is equally distributed across all CPUs and cores for optimal performance.
* 2 sockets
* Memory Controllers are integrated into processors.
* 8 DDR4 DIMMs per node
* 4 DDR4 DIMMs per CPU
* 1 DDR4 DIMMs per channel
* 8 DDR4 DIMMs per node
* 4 DDR4 DIMMs per CPU
* 1 DDR4 DIMMs per channel
* Populated memory: 8 x 16 GB DDR4 DIMM >2133 MHz
### Compute Node With MIC Accelerator
......@@ -102,6 +102,6 @@ MIC Accelerator Intel Xeon Phi 7120P Processor
* 2 sockets
* Memory Controllers are are connected via an
Interprocessor Network (IPN) ring.
* 16 GDDR5 DIMMs per node
* 8 GDDR5 DIMMs per CPU
* 2 GDDR5 DIMMs per channel
* 16 GDDR5 DIMMs per node
* 8 GDDR5 DIMMs per CPU
* 2 GDDR5 DIMMs per channel
......@@ -35,14 +35,14 @@ The architecture of Lustre on Salomon is composed of two metadata servers (MDS)
Configuration of the SCRATCH Lustre storage
* SCRATCH Lustre object storage
* Disk array SFA12KX
* 540 x 4 TB SAS 7.2krpm disk
* 54 x OST of 10 disks in RAID6 (8+2)
* 15 x hot-spare disk
* 4 x 400 GB SSD cache
* Disk array SFA12KX
* 540 x 4 TB SAS 7.2krpm disk
* 54 x OST of 10 disks in RAID6 (8+2)
* 15 x hot-spare disk
* 4 x 400 GB SSD cache
* SCRATCH Lustre metadata storage
* Disk array EF3015
* 12 x 600 GB SAS 15 krpm disk
* Disk array EF3015
* 12 x 600 GB SAS 15 krpm disk
### Understanding the Lustre File Systems
......
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