Job is not running showing error

Users/Site Administrators
1

Dear All,

I have compiled the VASP software in the following folder:

/home/phd/20/cheankit/new_vasp/vasp.5.4.4.pl2

and I was running a test job in the

/home/phd/20/cheankit/test

folder, but I was getting the following errors.

Abort(805913861) on node 8 (rank 8 in comm 0): Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(107): MPI_Comm_rank(comm=0x0, rank=0x2d34834) failed
PMPI_Comm_rank(64).: Invalid communicator
Abort(805913861) on node 9 (rank 9 in comm 0): Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(107): MPI_Comm_rank(comm=0x0, rank=0x2d34834) failed
PMPI_Comm_rank(64).: Invalid communicator
Abort(805913861) on node 10 (rank 10 in comm 0): Fatal error in PMPI_Comm_rank: Invalid communicator, error stack:
PMPI_Comm_rank(107): MPI_Comm_rank(comm=0x0, rank=0x2d34834) failed
PMPI_Comm_rank(64).: Invalid communicator

Job Script:

#!/bin/bash
#PBS -N test
#PBS -l nodes=1:ppn=16
#PBS -q qreg_1day_small
#PBS -l mem=6gb
#PBS -o outtest.log
#PBS -e Error.log

cd $PBS_O_WORKDIR

#module load compilers/openmpi/3.0.0
module load compilers/intel/2019.5.075
module load compilers/gcc/9.3.0

mpirun -np 16 /home/phd/20/cheankit/new_vasp/vasp.5.4.4.pl2/bin/vasp_std

Could you kindly rectify this problem?

2

@AJITH . The above issue is not related to the work load manager. Could you please let us know which version of PBS Pro you are using on your cluster. Please go through the forum discussion and update your resources requests from nodes to select and ppn to ncpus and mem is a host level resource and not job wide resource.

Could you please check whether you can execute the mpirun without using PBS Pro and whether this runs sucessefully.

#module load compilers/openmpi/3.0.0
module load compilers/intel/2019.5.075
module load compilers/gcc/9.3.0
mpirun -np 16 /home/phd/20/cheankit/new_vasp/vasp.5.4.4.pl2/bin/vasp_std

3

Dear Adarsh,
The installed open PBS version is :

pbs_version = 14.0.1

4

Thank you @AJITH . Did you get a chance to the bare commandline only for vasp and does it work?