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-======README====== +( moved to quick:start )
- +
-File name: USING CHPC SUN FUSION +
- +
-File realease date: 29 January 2013 +
- +
-File version: 6.00 +
- +
-Author: Technical Team +
- +
-Email: helpdesk@chpc.ac.za +
- +
-Website: www.chpc.ac.za +
- +
-Contact: 021 658 2740/58/60 +
- +
- +
-=====Compilers, libraries and modules===== +
- +
- +
-Compilers and libraries that CHPC support are available from the following folders: +
- +
-  * compilers: ''/opt/gridware/compilers'' +
-  * libraries: ''/opt/gridware/libraries'' +
- +
-To use our libraries , compiliers and some applications you will have to load them as modules. +
- +
-Here is an example on how to use an amber at CHPC : +
- +
-  module list           ### this will show you modules that are currently loaded in your environment +
-  module avail          ### this will show you modules that are available for the cluster +
-  module add intel      ### loading an intel 2011 module +
-  module add amber      ### loading amber2012 with ambertools module +
- +
-You can also use Intel compilers by adding the following modules: +
- +
-|''module add intel''            |Intel 11.1| +
-|''module add inteltools''      |Intel 12.0| +
-|''module add intel2012''        |Intel 12.1| +
- +
-or sunstudio and gnu +
- +
-|''module add sunstudio''| XXX comment? | +
-|''module add gcc/version''      |''version''=4.6.3 or 4.7.2| +
-|''module add clustertools''| XXX comment? | +
-|''module add openmpi/openmpi-1.6.1-gnu''    |compiled with GNU compiler version 4.XXX| +
-|''module add openmpi/openmpi-1.6.1-intel''  |compiled with Intel compiler version 12.1| +
- +
- +
-^ Code Name ^ Version ^ Directory ^ Notes | +
-|gcc |4.5.1 |/opt/gridware/compilers |with-gmp| +
-|zlib |1.2.7 |/opt/gridware/compilers |with gcc| +
-|ImageMagick |6.7.9 |/opt/gridware/compilers |with intel 2012| +
-|NCO |4.2.1 |/opt/gridware/compilers |with gcc-4.5.1 , intel 11 and openmpi-1.4.2-intel| +
-|netcdf-gnu |4.1.2 |/opt/gridware/libraries |with gcc | +
-|netcdf-intel |4.1.2 |/opt/gridware/libraries |with intel 2012| +
-|Mvapich2 (r5668) |1.8 |/opt/gridware/libraries |with intel 2012| +
-|mvapich |2.1.8 |/opt/gridware/libraries |with gcc| +
-|HDF5 |1.8.9 |/opt/gridware/compilers |with intel 11.1| +
-|OpenMPI |1.6.1 |/opt/gridware/compilers/OpenMPI |with intel 2012| +
-|OpenMPI |1.6.1 |/opt/gridware/compilers/OpenMPI |with gcc| +
-|FFTW |3.3.2 |/opt/gridware/libraries |with intel 2012 , using mvapich2(r5668) mpi lib| +
-|FFTW |2.1.5 |/opt/gridware/libraries |with intel 2012 , using mvapich2(r5668) mpi lib| +
- +
-Applications like gaussian and amber have their own modules. +
- +
-Note that CHPC only support applications that are installed in ''/opt/gridware/applications'' +
- +
-We discourage users from installing any applications on their home directories. Users can install their own applications in /opt/gridware/users/ which will also not be supported by CHPC. +
- +
- +
- +
- +
-=====Logging in===== +
- +
-To connect to the Sun systems (eg. M9000, Nehalem cluster) ''ssh'' to ''sun.chpc.ac.za'' and log in using the username and password sent to you by the CHPC. +
- +
-If you wish to use the IBM system (eg. the Blue Gene/P) use ''ssh'' to go to ''ssh.chpc.ac.za'' instead. +
- +
-[[guide:connect|more...]] +
- +
- +
- +
-=====SUN FUSION INFRASTRUSTURE===== +
- +
- +
-^Cluster ^ Nodes ^ CPU ^ Speed ^ ppn ^ RAM ^ OS | +
-| HARPERTOWN |  48|2x Xeon | 3.0 Ghz|  8|  16GB|  Redhat 5.8| +
-| NEHALEM |  288|2x Xeon| 2.93Ghz|  8|  12GB|  Centos 5.8| +
-| WESTMERE |  96|2x Xeon| 2.93Ghz|  12|  24GB|  Centos 5.8| +
-| DELL WESTMERE |  240|2x Xeon|2.93Ghz|  12|  36GB|  Centos 5.8| +
-| SUN SPARC M9000 |  1|Sparc| x |  512|  128GB| Solaris 10| +
-| VISUALISATION SERVER |  1| 4x AMD Opteron| 2.3Ghz|  16|  64GB|  Redhat 5.1| +
- +
-*ppn Refers to number of cores per node +
- +
- +
-====XXX Interconnect???==== +
- +
-====XXX Other Info???==== +
- +
- +
-=====SUBMITTING A JOB USING MOAB===== +
- +
- +
-Note that more information on how to use Moab and Moab flags you can visit [[http://www.clusterresources.com/]] +
- +
- +
-''test.job'' example: +
- +
-XXX explain that user needs to create a plain text file for the job script XXX +
- +
-<code> +
-#!bin/bash +
-#MSUB -l nodes=1:ppn=12 +
-#MSUB -l walltime=2:00:00 +
-#MSUB -l feature=dell|westmere +
-#MSUB -m be +
-#MSUB -V +
-#MSUB -o /lustre/SCRATCH2/users/username/file.out +
-#MSUB -e /lustre/SCRATCH2/users/username/file.err +
-#MSUB -d /lustre/SCRATCH2/users/username/ +
-#MSUB -mb +
-  +
- +
-##### Running commands +
- +
-nproc=`cat $PBS_NODEFILE | wc -l` +
-mpirun -np $ncproc -machinefile $PBS_NODEFILE <executable> <innput> +
-</code> +
- +
- +
-submit test: +
- +
-  msub test.job +
- +
-You can view your job using the following : +
- +
-  checkjob -v -v jobid +
- +
- +
-=====STORAGE===== +
- +
- +
-CHPC offer 450TB shared temporary lustre storage for users to store their output files. This is a temporary storage, users are advised to remove their data after each successful run. Data will be purged when the storage approaches 80%. Read CHPC Storage Policy: [[http://www.chpc.ac.za/use-policy]] +
- +
-The home directory ''/export/home/'' is backed up daily. Only files that need to be backed up should be stored here. Only max 5GB data per user should be stored in this directory. Applications installed on this directories will not be supported. +
- +
-If there are any request for storage please send it to ''helpdesk@chpc.ac.za'' +
- +
-^Code Name ^Version ^Module ^Directory ^Notes    ^ +
-|gcc |4.5.1 |''gcc'' |''/opt/gridware/compilers'' |with-gmp    | +
-|zlib |1.2.7 |''???'' |''/opt/gridware/compilers'' |with gcc    | +
-|ImageMagick |6.7.9 |''???'' |''/opt/gridware/compilers'' |with Intel 2012| +
-|NCO |4.2.1 |''???'' |''/opt/gridware/compilers'' |with gcc-4.5.1, intel 11 and openmpi-1.4.2-intel| +
-|netcdf-gnu |4.1.2 |''???'' |''/opt/gridware/libraries'' |with gcc| +
-|netcdf-intel |4.1.2 |''???'' |''/opt/gridware/libraries'' |with intel 2012| +
-|mvapich2 |1.8 |''???'' |''/opt/gridware/libraries'' |with intel 2012| +
-|mvapich |2.1.8 |''???'' |''/opt/gridware/libraries'' |with gcc| +
-|HDF5 |1.8.9 |''???'' |''/opt/gridware/compilers'' |with intel 11.1| +
-|OpenMPI |1.6.1 |''???'' |''/opt/gridware/compilers/OpenMPI'' |with intel 2012| +
-|OpenMPI |1.6.1 |''???'' |''/opt/gridware/compilers/OpenMPI'' |with gcc| +
-|FFTW |3.3.2 |''???'' |''/opt/gridware/libraries'' |with intel 2012, using mvapich2 (r5668) mpi lib| +
-|FFTW |2.1.5 |''???'' |''/opt/gridware/libraries'' |with intel 2012, using mvapich2 (r5668) mpi lib| +
- +
- +
-XXX WHAT ARE THE MODULE NAMES FOR THESE??? +
- +
-XXX WHERE IS BLAS, ATLAS, LAPACK ??? +
- +
- +
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