Is this line export LD_LIBRARY_PATH=/usr/lib:/usr/li64
a typo in the post, or is this how it really is in your script? On Thu, Sep 14, 2017 at 2:27 AM, Subashini K <[email protected]> wrote: > 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 > > _______________________________________________ > users mailing list > [email protected] > https://gridengine.org/mailman/listinfo/users > > -- Ian Kaufman Research Systems Administrator UC San Diego, Jacobs School of Engineering ikaufman AT ucsd DOT edu
_______________________________________________ users mailing list [email protected] https://gridengine.org/mailman/listinfo/users
