Slurm Migration Issues

This page documents the known issues for migrating jobs from Torque to Slurm.

$PBS_NODEFILE and $SLURM_JOB_NODELIST

Please be aware that $PBS_NODEFILE is a file while $SLURM_JOB_NODELIST is a string variable. 

The analog on Slurm to cat $PBS_NODEFILE is srun hostname | sort -n 

Environment variables are not evaluated in job script directives

Environement variables do not work in a slurm directive inside a job script.

The job script job.txt including  #SBATCH --output=$HOME/jobtest.out won't work in Slurm. Please use the following instead:

sbatch --output=$HOME/jobtest.out job.txt 

Using mpiexec with Intel MPI

Intel MPI (all versions through 2019.x) is configured to support PMI and Hydra process managers. It is recommended to use srun as the MPI program launcher. This is a possible symptom of using  mpiexec/mpirun:

srun: error: PMK_KVS_Barrier duplicate request from task 0

as well as:

MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found

If you prefer using mpiexec/mpirun with SLURM, please add the following code to the batch script before running any MPI executable:

unset I_MPI_PMI_LIBRARY 
export I_MPI_JOB_RESPECT_PROCESS_PLACEMENT=0   # the option -ppn only works if you set this before

Executables with a certain MPI library using SLURM PMI2 interface

e.g.

Stopping mpi4py python processes during an interactive job session only from a login node:

$ salloc -t 15:00 --ntasks-per-node=4
salloc: Pending job allocation 20822
salloc: job 20822 queued and waiting for resources
salloc: job 20822 has been allocated resources
salloc: Granted job allocation 20822
salloc: Waiting for resource configuration
salloc: Nodes p0511 are ready for job
# don't login to one of the allocated nodes, stay on the login node
$ module load python/3.7-2019.10
$ source activate testing
(testing) $ srun --quit-on-interrupt python mpi4py-test.py
# enter <ctrl-c>
^Csrun: sending Ctrl-C to job 20822.5
Hello World (from process 0)
process 0 is sleeping...
Hello World (from process 2)
process 2 is sleeping...
Hello World (from process 3)
process 3 is sleeping...
Hello World (from process 1)
process 1 is sleeping...
Traceback (most recent call last):
File "mpi4py-test.py", line 16, in <module>
time.sleep(15)
KeyboardInterrupt
Traceback (most recent call last):
File "mpi4py-test.py", line 16, in <module>
time.sleep(15)
KeyboardInterrupt
Traceback (most recent call last):
File "mpi4py-test.py", line 16, in <module>
time.sleep(15)
KeyboardInterrupt
Traceback (most recent call last):
File "mpi4py-test.py", line 16, in <module>
time.sleep(15)
KeyboardInterrupt
srun: Job step aborted: Waiting up to 32 seconds for job step to finish.
slurmstepd: error: *** STEP 20822.5 ON p0511 CANCELLED AT 2020-09-04T10:13:44 ***
# still in the job and able to restart the processes
(testing)

pbsdcp with Slurm

pbsdcp with gather option sometimes does not work correctly. It is suggested to use sbcast for scatter option and sgather  for gather option instead of pbsdcp. Please be aware that there is no wildcard (*) option for sbcast / sgather . And there is no recursive option for sbcast.In addition, the destination file/directory must exist. 

Here are some simple examples:

sbcast <src_file> <nodelocaldir>/<dest_file>
sgather <src_file> <shareddir>/<dest_file>
sgather -r --keep <src_dir> <sharedir>/dest_dir>

Signal handling in slurm

The below script needs to use a wait command for the user-defined signal USR1 to be received by the process.

The sleep process is backgrounded using & wait so that the bash shell can receive signals and execute the trap commands instead of ignoring the signals while the sleep process is running.

#!/bin/bash
#SBATCH --job-name=minimal_trap
#SBATCH --time=2:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --output=%x.%A.log
#SBATCH --signal=B:USR1@60

function my_handler() {
  echo "Catching signal"
  touch $SLURM_SUBMIT_DIR/job_${SLURM_JOB_ID}_caught_signal
  exit
}

trap my_handler USR1
trap my_handler TERM

sleep 3600 &
wait

reference: https://bugs.schedmd.com/show_bug.cgi?id=9715

'mail' does not work; use 'sendmail'

The 'mail' does not work in a batch job; use 'sendmail' instead as:

sendmail user@example.com <<EOF
subject: Output path from $SLURM_JOB_ID
from: user@example.com
...
EOF

'srun' with no arguments is to allocate a single task when using 'sinteractive'

srun with no arguments is to allocate a single task when using sinteractive to request an interactive job, even you request more than one task. Please pass the needed arguments to srun:

[xwang@owens-login04 ~]$ sinteractive -n 2 -A PZS0712
...
[xwang@o0019 ~]$ srun hostname
o0019.ten.osc.edu
[xwang@o0019 ~]$ srun -n 2 hostname
o0019.ten.osc.edu
o0019.ten.osc.edu

Please submit any issue using the webform below: