<> ------ = Submitting jobs = ---- Whatever you read here may need to be adjusted to fit your specific case. Do not hesitate to ask for some help wen needed. == Filesystems == Some but not all partitions are available to the compute nodes. Compute nodes will not be able to access any data from filesystems that are not listed here. /work /scratch /home/ == Slurm partitions == There are currently 2 partitions, '''normal''' and '''bigmem'''. The '''normal''' partition is the default partition if you submit a job without precising witch partition should be used you job will be placed in one of the normal partition. The normal partition has limited RAM of 250GB, in case you need more than that please use the '''bigmem''' partition. Use ''-p'' option can be used to specify the needed partition. == Load necessary software == By default only some software will be available when login. To be able use other software scripts you should first load then. The command '''module''' will help you to manage the modules dependencies. to check which software are available, ready to be used without importing anything, {{{ module avail }}} Expected output is, {{{ --------------------------------------------------- /opt/ohpc/pub/moduledeps/gnu8-openmpi3 ---------------------------------------------------- adios/1.13.1 hypre/2.18.1 netcdf-cxx/4.3.1 petsc/3.12.0 py2-scipy/1.2.1 scorep/6.0 trilinos/12.14.1 boost/1.71.0 imb/2018.1 netcdf-fortran/4.5.2 phdf5/1.10.5 py3-mpi4py/3.0.1 sionlib/1.7.4 dimemas/5.4.1 mfem/4.0 netcdf/4.7.1 pnetcdf/1.12.0 py3-scipy/1.2.1 slepc/3.12.0 extrae/3.7.0 mpiP/3.4.1 omb/5.6.2 ptscotch/6.0.6 scalapack/2.0.2 superlu_dist/6.1.1 fftw/3.3.8 mumps/5.2.1 opencoarrays/2.8.0 py2-mpi4py/3.0.2 scalasca/2.5 tau/2.28 -------------------------------------------------------- /opt/ohpc/pub/moduledeps/gnu8 -------------------------------------------------------- hdf5/1.10.5 metis/5.1.0 mvapich2/2.3.2 openblas/0.3.7 pdtoolkit/3.25 py3-numpy/1.15.3 likwid/4.3.4 mpich/3.3.1 ocr/1.0.1 openmpi3/3.1.4 (L) py2-numpy/1.15.3 superlu/5.2.1 ------------------------------------------------------------- /tools/modulefiles -------------------------------------------------------------- MEGAHIT/1.2.9 ---------------------------------------------------------- /opt/ohpc/pub/modulefiles ---------------------------------------------------------- EasyBuild/3.9.4 clustershell/1.8.2 gnu7/7.3.0 llvm5/5.0.1 pmix/2.2.2 valgrind/3.15.0 autotools (L) cmake/3.15.4 gnu8/8.3.0 (L) ohpc (L) prun/1.3 (L) charliecloud/0.11 gnu/5.4.0 hwloc/2.1.0 papi/5.7.0 singularity/3.4.1 Where: L: Module is loaded Use "module spider" to find all possible modules. Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys". }}} To to check which software are installed, can be used after importing, {{{ module list }}} Expected output is, {{{ Currently Loaded Modules: 1) autotools 2) prun/1.3 3) gnu8/8.3.0 4) openmpi3/3.1.4 5) ohpc }}} == Example of batch script == {{{#!highlight bash #!/bin/bash #SBATCH -J test # Job name #SBATCH -o /work/<>/job.%j.out # Name of stdout output file (%j expands to jobId) #SBATCH -p normal # Partition to use, another possible value is bigmem #SBATCH -N 1 # Total number of nodes requested #SBATCH -n 16 # Total number of mpi tasks requested #SBATCH -t 01:30:00 # Run time ([d-]hh:mm:ss) - 1.5 hours # Load your software/command module load CMD/version # Run your command CMD [OPTIONS] ARGUMENTS }}}