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Configuring fsl_sub

How to change fsl_sub's configuration for all jobs you run

Some of the operation of fsl_sub can be configured such that all runs will enable/disable features. To configure fsl_sub create a file ~/.fsl_sub.yml and add the configuration to this file - it is in YAML format. To see what the current configuration is use:

fsl_sub --show_config

Take care - the system configuration has been setup to be optimal for the cluster, changing these settings may cause your job to fail.

FSL_SUB.YML SECTIONS​

TOP LEVEL​​

These options control the basic operation of fsl_sub and are keys in a YAML dictionary. To change a setting add 'keyname: value' to your file with no indent.

​​Key name​​Default​Purpose​Examples/Allowed Options
​method ​'shell', 'sge' or 'slurm' ​Define whether to use the cluster ('sge') or run things without a cluster ('shell') ​'shell' or the name of an installed plugin, e.g. 'sge'
​ram_units ​'G' ​When -R is specified, what are the units ​'K', 'M', 'G', 'T', 'P'(!) - recommend this is not changed
​modulecmd ​False ​Where 'modulecmd' is not findable via PATH, where is the program ​Path to modulecmd
​export_vars ​Empty list = [] ​List of environment variables (with optional values) to always pass to jobs running on the cluster. List you provide will be added to the default list ​[SUBJECTSDIR, "MYVARIABLE=MYVALUE"]
The list can also be specified by starting a new line and adding items as '  - SUBJECTSDIR' (note the two spaces before the '-') on separate lines
​thread_control ​['OMP_NUM_THREADS', 'MKL_NUM_THREADS', 'MKL_DOMAIN_NUM_THREADS', 'OPENBLAS_NUM_THREADS', 'GOTO_NUM_THREADS'] ​Environment variables to set to ensure threads are limited to those requested by a parallel envrionment. Any values you configure will be added to the default list. ​Names of environment variables
​method_opts ​{} ​Control the method that runs your job ​See below
​coproc_opts ​{} ​Control the coprocessor options ​Should not be changed
​queues ​{} ​Control the queues ​Must not be changed

METHOD_O​PTS

These control how the shell and sge job runners operate, most of these should not be changed, but some useful ones include:
method_opts:
  shell:
    parallel_disable_matches:
      - "*_string"
parrallel_disable_matches enables you to specify portions of a command name that should never be attempted to be run in parallel when submitted as an array task but running with the shell backend. The default list contains '*_gpu' which ensures that the FSL GPU enabled tools do not attempt to start up in parallel as they are likely to be unable to access multiple GPUs. fsl_sub supports matching a full program name, a full path to a program and *<name> and <name>* to match the end or start of a program name respectively.
method_opts:
  sge:
    use_jobscript: True|False
    keep_jobscript: True|False
When the SGE backend submits your job it can either submit the job as a single command
qsub -q queue -qoption -qoption mycommand
or it can generate a BASH script with these configuration options in along with the command you specify, use_jobscript enables or disables the use of this job script submission method. If you would like to alway save these job scripts then set keep_jobscript to True (default on jalapeno) or to never save them set it to False. You can also control this on a job by job basis with the option --keep_jobscript, but where tasks don't allow this (e.g. FEAT) you can control this here.