[gridengine users] mpirun segmentation fault

Subashini K subashinik2017 at gmail.com
Thu Sep 14 09:27:31 UTC 2017


Hi,

This is my script file.

#!/bin/bash -l
#$ -S /bin/bash
#$ -cwd
#$ -pe mpi 4
#$ -N smp2rdfeql2.sh

export PATH=/usr/local/gromacs/bin
export GMXLIB=/usr/local/gromacs/share/gromacs/top
export LD_LIBRARY_PATH=/usr/lib:/usr/li64
PATH=$PATH:"/opt/mpi/openmpi/1.3.3/intel/bin/"
export MPILIB=/opt/mpi/openmpi/1.3.3/intel/lib

gmx grompp -f mdp/eql2.mdp -o eql2 -pp eql2 -po eql2 -c eql -t eql
mpirun -np 4 gmx mdrun -ntmpi 1 -ntomp 8 -v -deffnm eql2

However, after execution, I get

[compute-0-4:09088] *** Process received signal ***
[compute-0-4:09088] Signal: Segmentation fault (11)
[compute-0-4:09088] Signal code: Address not mapped (1)
[compute-0-4:09088] Failing at address: (nil)
[compute-0-4:09088] [ 0] /lib64/libpthread.so.0 [0x3adea0de80]
[compute-0-4:09088] [ 1] /lib64/libc.so.6(vasprintf+0x150) [0x3ade2691a0]
[compute-0-4:09088] [ 2] /lib64/libc.so.6(asprintf+0x88) [0x3ade24d1c8]
[compute-0-4:09088] [ 3]
/opt/mpi/openmpi/1.3.3/intel/lib/openmpi/mca_plm_rsh.so [0x2b9eda681030]
[compute-0-4:09088] [ 4]
/opt/mpi/openmpi/1.3.3/intel/lib/libopen-pal.so.0(mca_base_select+0xba)
[0x2b9ed959e0ca]
[compute-0-4:09088] [ 5]
/opt/mpi/openmpi/1.3.3/intel/lib/libopen-rte.so.0(orte_plm_base_select+0x38)
[0x2b9ed934d308]
[compute-0-4:09088] [ 6]
/opt/mpi/openmpi/1.3.3/intel/lib/openmpi/mca_ess_hnp.so [0x2b9eda47c548]
[compute-0-4:09088] [ 7]
/opt/mpi/openmpi/1.3.3/intel/lib/libopen-rte.so.0(orte_init+0x12e)
[0x2b9ed93261ae]
[compute-0-4:09088] [ 8] mpirun [0x404718]
[compute-0-4:09088] [ 9] mpirun [0x403da7]
[compute-0-4:09088] [10] /lib64/libc.so.6(__libc_start_main+0xf4)
[0x3ade21d8b4]
[compute-0-4:09088] [11] mpirun [0x403cb9]
[compute-0-4:09088] *** End of error message ***


/opt/gridengine/default/spool/compute-0-4/job_scripts/5020911: line 12:
9088 Segmentation fault      (core dumped) mpirun -np 4 gmx mdrun -ntmpi 1
-ntomp 8 -v -deffnm eql2



What is the reason behind this?


Thanks,
Subashini.K
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