10.15.2. Run FS on a cluster (NIH’s Biowulf) with AFNI

Introduction

Download script: fs_biowulf.tcsh

Overview

We assume you have read the general notes on running FreeSurfer (FS; specifically recon-all) and AFNI together.

For those of us using NIH’s Biowulf cluster to run FS, there are some extra considerations, conveniences and caveats. We cover some of those here and provide some recommendations. At the bottom of this page, we provide a script for running FS’s recon-all and the AFNI converter @SUMA_Make_Spec_FS completely, just specifying the input dset, the subject ID and a couple relevant path names.

We focus on tcsh scripting here, because those are what we mostly use (for syntax convenience and relative readability).

For reference:

Note

You can check the jobs you have submitted on Biowulf with:

sjobs -u USERNAME

... for example to see if your job is running or just queueing, and to get your job ID number.

Module loading FS (and other things) in a script

When using Biowulf, there a couple things to know about loading modules in a script, esp. if you are using FreeSurfer.

  1. If all three of the following are true for your use usage case:

    • your terminal shell is bash (i.e., if echo $0 shows something with “bash” in it)

    • your script is tcsh or csh (i.e., the shebang at the top is #!/bin/tcsh or #!/usr/bin/env tcsh or similar)

    • your script loads one or more modules (i.e., it contains module load ...)

    ... then you need to include the following line before loading the module(s):

    source /etc/profile.d/modules.csh
    

    This is described more in the Using modules in scripts section here, if you don’t believe me.

  2. When using FreeSurfer, you also need to source the magical setup file for the particular shell. For a tcsh script, you need to include the following line after loading the module(s):

    source $FREESURFER_HOME/SetUpFreeSurfer.csh
    

    ... where $FREESURFER_HOME should be a known variable within the shell once you have loaded the FreeSurfer module, so you don’t need to worry about defining it yourself.

Thus, when I have a tcsh script to run FreeSurfer and AFNI (and yes, I do use bash as my login shell), I include the following lines at the very top (just after the shebang):

source /etc/profile.d/modules.csh
module load afni freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh

And you can, too!

Using scratch disks as temporary directories

The read/write I/O in the main Biowulf directories where you likely work and save things can be pretty slow. It is actually better to work on temporarily-allocated “scratch” disks and then copy everything back to where you actually want it in your own file tree.

These scratch space allocations are made when you submit your script to run using sbatch, by including an option like --gres=lscratch:10. This would give me a 10GB directory on the scratch disk, in the toplevel directory called /lscratch/$SLURM_JOBID, where $SLURM_JOBID is provided by the job allocation system. Reading/writing in this upper level directory would also be slow, so we would allocate a subdirectory based on this, say /lscratch/$SLURM_JOBID/SUBJ_ID, where SUBJ_ID would be our subject ID or something.

The way we typically include this in a script is to do the following:

  • Define a directory we want to output to within our real directory structure.

  • Then check if we have asked for+been allocated space on the scratch disk for temporary I/O, by asking if a directory /lscratch/$SLURM_JOBID exists. This will be true if we have submitted our job to the slurm system with sbatch or slurm with a particular --gres=lscratch:VALUE option, where VALUE should be replaced with amount of desired disk space, in units of GB.

    • If the directory does exist, we can write our outputs there first, and then later copy everything back (more efficient when we have large jobs that read/write a lot of data)

    • If it does not exist, we will just output to our desired location directly (the less efficient way, likely, for larger work)

The chunk of code to do this could look like:

set subj   = sub-001
set dir_fs = ./group_analysis_dir

# Set temporary output directory; then requires using something like
# this on the swarm command line: --sbatch '--gres=lscratch:10'.
# These variables used again *after* the main commands, if running
# on Biowulf.
if ( -d /lscratch/$SLURM_JOBID ) then
  set tempdir = /lscratch/$SLURM_JOBID
  set usetemp = 1
else
  set tempdir = ${dir_fs}
  set usetemp = 0
endif

Note

Just checking if $SLURM_JOBID is defined is not a good enough condition here. Starting a sinteractive or spersist node is actually a slurm job itself, so the $SLURM_JOBID variable will be defined even then, and that doesn’t mean we have space allocated on the scratch disk. Though, we could start the session with a --gres=lscratch:VALUE option, and in that case make use of temporary scratch disk space then.

Then, after we have done our work, we can see if we need to copy everything back. If we don’t, all our data should be in the right spot already (${dir_fs}, above). If we do, it is just a matter of doing the copy. The following if condition covers all we should need:

# Again, Biowulf-running considerations: if processing went fine and
# we were using a temporary directory, copy data back.
if( $usetemp && -d ${tempdir} ) then
    echo "++ Copy from: ${tempdir}"
    echo "          to: ${dir_fs}"
    \mkdir -p ${dir_fs}
    \cp -pr ${tempdir}/${subj} ${dir_fs}/.
endif

A general biowulf script

Let’s take what we have learned above and create a full script to run FS’s recon-all and AFNI’s @SUMA_Make_Spec_FS. The script will be broad enough to be submitted using sbatch or slurm (for using the scratch disk as a temporary dir), or just with tcsh .. (which might be a good deal slower, due to disk I/O).

We control the allocated memory, number of CPUs, and scratch disk space when we submit the job with sbatch. Here, I intend to use the -parallel option in recon-all (see timing results here), so I will allocate 4 CPUs to use (though note that the program can sometimes crash using this option; see the end of this section of the notes for more on the error/crash). In the script, the if ( $?SLURM_CPUS_PER_TASK ) ... conditional can then set our OMP_NUM_THREADS value to match this; if we weren’t using sbatch to submit the job, this variable simply wouldn’t exist, and no harm is done.

We put a comment in the top of the script for one way to run this script with sbatch. At present, the “norm” partition nodes seem like a good ones to use. I am not certain if the “quick” partition (which maxes out at 4 hours of usage) gives us enough time to reliably finish a recon-all run, even with the -parallel option. If you find it does, then you can add that as a partition option via --partition=norm,quick.

You should also set the amount of time for allocated running. The default is 2 hrs. I am setting it here for 12 hrs: with -parallel, I really hope it doesn’t take this long. Requesting too long of a run time allocation might mean you have to wait longer for resources to come your way to actually run (the same is true of overestimating the amount of scratch disk space you need; 10 GB could likely be reduced for FS with 1 mm isotropic voxels, but the data only gets gzipped at the end of its run).

Note

If you forget to set the walltime properly or decide later you need more, then you are in luck! Biowulf has a nice feature whereby you can expand (or reduce) the walltime on the fly, using the newwall command. To change a job with job ID 12345 to run for 12 hours, run the following in the terminal:

newwall --jobid 12345 --time 12:00:00

Terminal text will tell you if you are successful. After a few seconds or so, you can also verify the update by checking your resources with:

sjobs -u USERNAME

To run this script, you just need to provide 4 pieces of information at the top:

input

variable meaning/description

dset

input anatomical dset (likely a raw, T1w volume)

subj

subject ID; will be used for both FS output directory name and later volume/surface file names

dir_fs

top level directory for FS output: can be relative or absolute path, and does not need to exist already (will be created on the fly); the actual output directory for this subject will be ${dir_fs}/{subj}

dir_echo

directory where text output monitoring/recording the terminal output will go

Here is the script:

#!/bin/tcsh

###  Run this command with something like
#
#   sbatch                                                            \
#      --partition=norm                                               \
#      --cpus-per-task=4                                              \
#      --mem=4g                                                       \
#      --time=12:00:00                                                \
#      --gres=lscratch:10                                             \
#      do_*.tcsh
#
# ===================================================================

source /etc/profile.d/modules.csh
module load afni freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh

set dset     = anat_02_anon.reface.nii.gz
set subj     = sub_02
set dir_fs   = group_fs
set dir_echo = .

# ---------------- Biowulf slurm check and initializing ----------------

# Set thread count if we are running SLURM
if ( $?SLURM_CPUS_PER_TASK ) then
  setenv OMP_NUM_THREADS $SLURM_CPUS_PER_TASK
endif

# Set temporary output directory; then requires using something like
# this on the swarm command line: --sbatch '--gres=lscratch:50'.
# These variables used again *after* the main commands, if running
# on Biowulf.
if ( -d /lscratch/$SLURM_JOBID ) then
  set tempdir = /lscratch/$SLURM_JOBID
  set usetemp = 1
else
  set tempdir = ${dir_fs}
  set usetemp = 0
endif

\mkdir -p ${tempdir}

# record any failures; def: no errors
set EXIT_CODE = 0

# ---------------------- Run programs of interest ----------------------

set nomp   = `afni_check_omp`
echo "++ Should be using this many threads: ${nomp}"                  \
     > ${dir_echo}/o.00_fs_${subj}.txt


time recon-all                                                        \
    -all                                                              \
    -3T                                                               \
    -sd      ${tempdir}                                               \
    -subjid  ${subj}                                                  \
    -i       ${dset}                                                  \
    -parallel                                                         \
    |& tee -a ${dir_echo}/o.00_fs_${subj}.txt

if ( $status ) then
    echo "** ERROR running FS recon-all"                              \
        |& tee -a ${dir_echo}/o.00_fs_${subj}.txt
    set EXIT_CODE = 1
    goto JUMP_EXIT
else
    echo "++ GOOD run of FS recon-all"                                \
        |& tee -a ${dir_echo}/o.00_fs_${subj}.txt
endif


@SUMA_Make_Spec_FS                                                    \
    -fs_setup                                                         \
    -NIFTI                                                            \
    -sid    ${subj}                                                   \
    -fspath ${tempdir}/${subj}                                        \
    |& tee  ${dir_echo}/o.01_suma_makespec_${subj}.txt

if ( $status ) then
    echo "** ERROR running @SUMA_Make_Spec_FS"                        \
        |& tee -a ${dir_echo}/o.01_suma_makespec_${subj}.txt
    set EXIT_CODE = 2
    goto JUMP_EXIT
else
    echo "++ GOOD run of @SUMA_Make_Spec_FS"                          \
        |& tee -a ${dir_echo}/o.01_suma_makespec_${subj}.txt
endif

# ===================================================================

JUMP_EXIT:

# ---------------- Biowulf slurm finish and copying ----------------

# Again, Biowulf-running considerations: if processing went fine and
# we were using a temporary directory, copy data back.
if( $usetemp && -d ${tempdir} ) then
    echo "++ Copy from: ${tempdir}"
    echo "          to: ${dir_fs}"
    \mkdir -p ${dir_fs}
    \cp -pr ${tempdir}/${subj} ${dir_fs}/.
endif

# ----------------------------------------------------------------------

if ( $EXIT_CODE ) then
    echo "** Something failed in Step ${EXIT_CODE} for subj: ${subj}"
else
    echo "++ Copy complete for subj: ${subj}"
endif

# ===================================================================

Et voila!

Here is an example of the job info while running recon-all using a script similar to the above (based on the job info, I moderated the memory allocation above, to be more efficient).

Biowulf usage for memory (top) and CPUs (bottom) about 2 hours into a recon-all run. I had allocated 4 CPUs (useful!) and 10 GB (wasteful!).

Example Biowulf Dashboard job info

../../_images/fs_biowulf_usage.png

Looping over a group of subjects

The above could be made into a script used to loop over subjects by having another script have a list of subject IDs and paths. That script could loop over those subjects, submitting an sbatch job every time, with this script taking 4 arguments (to fill the top variables).