Molcas Forum

Kalpa

Member

Registered: 2022-04-09

Posts: 13

slurmstepd: error: *** JOB 733512 ON cn011 CANCELLED AT 2022-04-05T23:

Respected sir,
I am a beginner of molcas software. I am trying to run simple jobs where I am getting some error given in the subject.
In the error file, "job733512.err" the following lines showed up

The following have been reloaded with a version change:
  1) gcc/9.2.0 => gcc/10.2.0
  2) intel/2019.5.281 => intel/2020.2.254
  3) molcas/19.11 => molcas/19.11_Intel_2020

slurmstepd: error: *** JOB 733512 ON cn011 CANCELLED AT 2022-04-05T23:11:02 DUE TO TIME LIMIT ***

My input files were:
water.xyz

  3
Angstrom
  O 0.000000  0.000000  0.000000
  H  0.758602  0.000000  0.504284
  H  0.758602  0.000000  -0.504284

water.input

&GATEWAY
 coord=water.xyz
 basis=STO-3G
&SEWARD
&SCF

script file is:
molcasjob.sh
----------------------------------------------------------------------

#!/bin/bash
#SBATCH -N 2
#SBATCH --ntasks=40
#SBATCH --job-name=molcas-test-job
#SBATCH --output=job.%j.out
#SBATCH --error=job.%j.err
#SBATCH --time=06:00:00  ##Walltime upto 4-00:00:00
#SBATCH --partition=cpu

ulimit -l unlimited
ulimit -s unlimited
ulimit -c unlimited

module load molcas/19.11_Intel_2020

export GAROOT=/home/apps/openmolcas/depd/ga
export TMPDIR=`pwd`
export MOLCAS=/home/apps/openmolcas
source /opt/ohpc/pub/intel2020_u2/compilers_and_libraries_2020.2.254/linux/mpi/intel64/bin/mpivars.sh release
source /opt/ohpc/pub/intel2020_u2/compilers_and_libraries_2020.2.254/linux/mkl/bin/mklvars.sh intel64
mpirun  -np 40 pymolcas water.input

-----------------------------------------------------------------------------------------------------------------------

By looking at the error file, I guess there is a problem in the time limit. But how can I resolve that... How can I know how much time should be fixed here.

Thank you

Ignacio

Administrator

From: Uppsala

Registered: 2015-11-03

Posts: 1,204

Re: slurmstepd: error: *** JOB 733512 ON cn011 CANCELLED AT 2022-04-05T23:

6 hours should be more than enough for a SCF of water with minimal basis. There could be a problem with compilation, but:

1) 40 parallel processes is definitely overkill. Besides, each process will be using the amount of memory specified by MOLCAS_MEM (2GB by default). If you have 20 process per physical node, does each node have at least 40GB of RAM?

2) Do not run mpirun. Instead, just pass -np to pymolcas, or define the variable MOLCAS_NPROCS.

3) If you used a multithreaded BLAS/LAPACK library, you may want to define MOLCAS_THREADS too, otherwise each process may end up using all available cores...