Submitting jobs
Contents
Whatever you read here may need to be adjusted to fit your specific case.
Do not hesitate to ask for some help when 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 which partition should be used. Your job will be placed in the normal partition (250GB).
The normal partition has limited RAM of 250GB, in case you need more than that please use the bigmem partition.
Use -p to specify needed partition.
Load necessary software
By default only some software will be available at login. To be able to use other software scripts you should first load them.
The command module will help you to manage modules and their dependencies.
To check which programs are loaded (ready to be used), use the command below.
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 programs are available (can be loaded). 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 these 3 steps,
Locate the module, module avail
Check how to load it, module spider <<MODULENAME/VERSION>>
Load your module using the instructions module load <<MODULENAME/VERSION>>
Check that the module is loaded, module list
Enjoy!!!
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 -e /work/<<UID>>/job.%j.err # Name of stderr output file (%j expands to jobId)
6 #SBATCH -p normal # Partition to use, another possible value is bigmem
7 #SBATCH -N 1 # Total number of nodes requested
8 #SBATCH -n 16 # Total number of cpu requested or total number of mpi tasks
9 #SBATCH -t 01:30:00 # Run time ([d-]hh:mm:ss) - 1.5 hours
10 #SBATCH --mail-type=ALL
11 #SBATCH --mail-user=your.email@wur.nl
12
13 # Load your software/command
14 module load CMD/version
15
16 # Run your command
17 CMD [OPTIONS] ARGUMENTS
To run a sbatch script use
sbatch <<script name>>
Here are some explanation for obscure elements,
- Line starting with #SBATCH
- Those lines are option given to sbatch. They are different from the command you are running.
- We use %j in the -o option
- This is a place holder, it will be replaced by the job id of your run. The use of that makes it easier to find out which standard output correspond to which task. It could be removed but make sure that all the tasks have a specific output file.
- -N 1
- Given the limited number of nodes, all users are invited to only use 1 node. Most bioinfo software can not be run on more than 1 node so don't waste resources.
- -t option
This sets a limit of time for your task to run. If 00:05:00, your job will run for 5 minutes. What if it is not finished? You will have to rerun it again giving a higher time. If the command you are running has the ability to continue from a checkpoint, you can use that ability to reduce the running time. This parameter is difficult to estimate in most cases, do not hesitate to over estimate at the beginning.
Example of sbtach script
Let's assume a few things here,
- You need to be logged in
- Your data is available
- The needed software is available
- 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 -e /work/test/job.%j.err # Name of stderr output file (%j expands to jobId)
6 #SBATCH -p normal # Partition to use, another possible value is bigmem
7 #SBATCH -N 1 # Total number of nodes requested
8 #SBATCH -n 16 # Total number of cpu or total number of mpi tasks
9 #SBATCH -t 01:30:00 # Run time ([d-]hh:mm:ss) - 1.5 hours
10 #SBATCH --mail-type=ALL
11 #SBATCH --mail-user=felix.homa@wur.nl
12
13 # Load your available meghit
14 module load MEGAHIT/1.2.9
15
16 # Defining variable for work directory
17 based=/work/test
18 # Defining variable for temporary directory
19 # We do this because our command uses tmp folder
20 tmp_dir=$based/tmp
21 # Defining variable for output directory
22 output_dir=$based/output
23 # Defining variable for forward and reverse read file
24 f_read=/tools/test_data/assembly/r3_1.fa.gz
25 r_read=/tools/test_data/assembly/r3_2.fa.gz
26
27 # Creating temporary folder
28 # Megahit will complain if "output" folder already exists
29 mkdir $tmp_dir
30
31 # Command to run
32 # We use previously defined varibales to set the values of megahit options
33 megahit -1 $f_read -2 $r_read --tmp-dir $tmp_dir --out-dir $output_dir --out-prefix r3