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 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

to check which software are available, ready to be used without importing anything. The same command can be used to search a specific package.

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 search for a module,

module avail <<keyword>>
#OR
module spider <<keyword>>

To load a module do,

module load <<MODULENAME/VERSION>>

Loading a module can be done following those 3 steps,

1. Locate the module, module avail

2. Check how to load it, module spider <<MODULENAME/VERSION>>

3. Load you module using the instructions from step 2

Read more about module usage https://lmod.readthedocs.io/en/latest/010_user.html

Prototype of batch script

This prototype should be in a script file, for example, my_first_script.sbatch

   1 #!/bin/bash
   2 
   3 #SBATCH -J test               # Job name
   4 #SBATCH -o /work/<<UID>>/job.%j.out   # Name of stdout output file (%j expands to jobId)
   5 #SBATCH -p normal             # Partition to use, another possible value is bigmem
   6 #SBATCH -N 1                  # Total number of nodes requested
   7 #SBATCH -n 16                 # Total number of cpu or total number of mpi tasks
   8 #SBATCH -t 01:30:00           # Run time ([d-]hh:mm:ss) - 1.5 hours
   9 
  10 # Load your software/command
  11 module load CMD/version
  12 
  13 # Run your command
  14 CMD [OPTIONS] ARGUMENTS

To run a sbatch script use

sbatch <<script name>>

Example of sbtach script

Let's assume a few things here,

1. You need to be logged in
2. Your data is available
3. The needed software is available
4. The test will be run in folder /work/test/

Preparing for the run,

   1 mkdir /work/test/

Let's try to run an assembly using megahit,

   1 #!/bin/bash
   2 
   3 #SBATCH -J test               # Job name
   4 #SBATCH -o /work/test/job.%j.out   # Name of stdout output file (%j expands to jobId)
   5 #SBATCH -p normal             # Partition to use, another possible value is bigmem
   6 #SBATCH -N 1                  # Total number of nodes requested
   7 #SBATCH -n 16                 # Total number of cpu or total number of mpi tasks
   8 #SBATCH -t 01:30:00           # Run time ([d-]hh:mm:ss) - 1.5 hours
   9 
  10 # Load your available meghit
  11 module load MEGAHIT/1.2.9
  12 
  13 #Work directory
  14 based=/work/test
  15 tmp_dir=$based/tmp
  16 output_dir=$based/output
  17 f_read=/tools/test_data/assembly/r3_1.fa.gz
  18 r_read=/tools/test_data/assembly/r3_2.fa.gz
  19 
  20 #Creating necessary folder
  21 mkdir $output_dir $tmp_dir
  22 
  23 # Running my command
  24 megahit -1 $f_read -2 $r_read --tmp-dir $tmp_dir --out-prefix $output_dir/r3