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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