Re: [gmx-users] help to solve this problem
Dear Justin: when I try in my computer the simulation runs well, the problem is when I try to run in the cluster. Follow in attach my log files generated in the cluster (PlmII+Inhibitor_free.log) and locally (PlmII+Inhibitor-local.log). With kind regards, Pedro On 19/11/14 13:15, Justin Lemkul wrote: On 11/19/14 12:37 PM, valiente wrote: Dear gromacs users: I'm trying to run a MD simulation using gromacs 4.6.5 in a cluster but when I submit my job using the following script: /bin/bash #Name of your job #PBS -N PlmII+Inhibitor_free #number of nodes you are using #PBS -l nodes=8 #time #PBS -l walltime=48:00:00 #which queue you are submitting to #PBS -q qwork@mp2 # go to our working directory cd $PBS_O_WORKDIR # add module module rm mvapich2_intel64/1.6_ofed module add openmpi_intel64/1.4.3_ofed module rm gromacs64/4.5.4_ompi module add gromacs64/4.6.5_ompi # choose mpi-tasks per node *** there are 24 cores/node export ppn=24 # set your executable file myExe=`which mdrun_mpi` # start the application export RUN_NAME=PlmII+Inhibitor_free export P4_GLOBMEMSIZE=2 #export OPTIONS=" -cpi PlmII+Inhibitor_free.cpt -dlb yes" #export OPTIONS=" -cpi prot_md.cpt -dlb yes" #actual command line mpiexec -n $[PBS_NUM_NODES*ppn] -npernode $ppn $myExe -deffnm $RUN_NAME $OPTIONS echo "Job finished at: `date`" # 500 steps, 5.0 ps. [cp1854:24892] *** Process received signal *** [cp1854:24892] Signal: Segmentation fault (11) [cp1854:24892] Signal code: (128) [cp1854:24892] Failing at address: (nil) [cp1854:24892] [ 0] /lib64/libpthread.so.0() [0x3e6480f710] [cp1854:24892] [ 1] /opt/gromacs64/4.6.5/bin/../lib/libmd_mpi.so.8(nbnxn_kernel_simd_4xn_tab_comb_lb_energrp+0x4183) [0x2b4214b3b7c3] [cp1854:24892] [ 2] /opt/gromacs64/4.6.5/bin/../lib/libmd_mpi.so.8(nbnxn_kernel_simd_4xn+0x4b1) [0x2b4214bb9951] [cp1854:24892] [ 3] /opt/intel/composerxe-2011.5.220/compiler/lib/intel64/libiomp5.so(__kmp_invoke_microtask+0x93) [0x2b4217dfbb83] [cp1854:24892] *** End of error message *** -- mpiexec noticed that process rank 0 with PID 24892 on node cp1854 exited on signal 11 (Segmentation fault). Your simulation is crashing. Check the .log file for any hints, but otherwise run locally or interactively to diagnose. -Justin -- ** Dr. Pedro Alberto Valiente Flores Profesor e Investigador Auxiliar Jefe Laboratorio de Bioinformática y Dinámica Biomolecular Centro de Estudios de Proteínas Facultad de Biología Universidad de La Habana Email:valie...@fbio.uh.cu Fax:+5378321321 Tel: +5378324830 ** -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] help to solve this problem
Dear gromacs users: I'm trying to run a MD simulation using gromacs 4.6.5 in a cluster but when I submit my job using the following script: /bin/bash #Name of your job #PBS -N PlmII+Inhibitor_free #number of nodes you are using #PBS -l nodes=8 #time #PBS -l walltime=48:00:00 #which queue you are submitting to #PBS -q qwork@mp2 # go to our working directory cd $PBS_O_WORKDIR # add module module rm mvapich2_intel64/1.6_ofed module add openmpi_intel64/1.4.3_ofed module rm gromacs64/4.5.4_ompi module add gromacs64/4.6.5_ompi # choose mpi-tasks per node *** there are 24 cores/node export ppn=24 # set your executable file myExe=`which mdrun_mpi` # start the application export RUN_NAME=PlmII+Inhibitor_free export P4_GLOBMEMSIZE=2 #export OPTIONS=" -cpi PlmII+Inhibitor_free.cpt -dlb yes" #export OPTIONS=" -cpi prot_md.cpt -dlb yes" #actual command line mpiexec -n $[PBS_NUM_NODES*ppn] -npernode $ppn $myExe -deffnm $RUN_NAME $OPTIONS echo "Job finished at: `date`" # 500 steps, 5.0 ps. [cp1854:24892] *** Process received signal *** [cp1854:24892] Signal: Segmentation fault (11) [cp1854:24892] Signal code: (128) [cp1854:24892] Failing at address: (nil) [cp1854:24892] [ 0] /lib64/libpthread.so.0() [0x3e6480f710] [cp1854:24892] [ 1] /opt/gromacs64/4.6.5/bin/../lib/libmd_mpi.so.8(nbnxn_kernel_simd_4xn_tab_comb_lb_energrp+0x4183) [0x2b4214b3b7c3] [cp1854:24892] [ 2] /opt/gromacs64/4.6.5/bin/../lib/libmd_mpi.so.8(nbnxn_kernel_simd_4xn+0x4b1) [0x2b4214bb9951] [cp1854:24892] [ 3] /opt/intel/composerxe-2011.5.220/compiler/lib/intel64/libiomp5.so(__kmp_invoke_microtask+0x93) [0x2b4217dfbb83] [cp1854:24892] *** End of error message *** -- mpiexec noticed that process rank 0 with PID 24892 on node cp1854 exited on signal 11 (Segmentation fault). -- ** Dr. Pedro Alberto Valiente Flores Profesor e Investigador Auxiliar Jefe Laboratorio de Bioinformática y Dinámica Biomolecular Centro de Estudios de Proteínas Facultad de Biología Universidad de La Habana Email:valie...@fbio.uh.cu Fax:+5378321321 Tel: +5378324830 ** -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] help to solve this problem
Dear gromacs users: I'm trying to run a MD simulation using gromacs 4.6.5 in a cluster but when I submit my job using the following script: /bin/bash #Name of your job #PBS -N PlmII+Inhibitor_free #number of nodes you are using #PBS -l nodes=8 #time #PBS -l walltime=48:00:00 #which queue you are submitting to #PBS -q qwork@mp2 # go to our working directory cd $PBS_O_WORKDIR # add module module rm mvapich2_intel64/1.6_ofed module add openmpi_intel64/1.4.3_ofed module rm gromacs64/4.5.4_ompi module add gromacs64/4.6.5_ompi # choose mpi-tasks per node *** there are 24 cores/node export ppn=24 # set your executable file myExe=`which mdrun_mpi` # start the application export RUN_NAME=PlmII+Inhibitor_free export P4_GLOBMEMSIZE=2 #export OPTIONS=" -cpi PlmII+Inhibitor_free.cpt -dlb yes" #export OPTIONS=" -cpi prot_md.cpt -dlb yes" #actual command line mpiexec -n $[PBS_NUM_NODES*ppn] -npernode $ppn $myExe -deffnm $RUN_NAME $OPTIONS echo "Job finished at: `date`" # I have the following error: cp2456:22501] *** Process received signal *** [cp2456:22501] Signal: Segmentation fault (11) [cp2456:22501] Signal code: (128) [cp2456:22501] Failing at address: (nil) [cp2456:22501] [ 0] /lib64/libpthread.so.0() [0x3638c0f710] [cp2456:22501] [ 1] /opt/gromacs64/4.6.5/bin/../lib/libmd_mpi.so.8(nbnxn_kernel_simd_4xn_tab_comb_lb_energrp+0x4183) [0x2b88117267c3] [cp2456:22501] [ 2] /opt/gromacs64/4.6.5/bin/../lib/libmd_mpi.so.8(nbnxn_kernel_simd_4xn+0x4b1) [0x2b88117a4951] [cp2456:22501] [ 3] /opt/intel/composerxe-2011.5.220/compiler/lib/intel64/libiomp5.so(__kmp_invoke_microtask+0x93) [0x2b88149e6b83] [cp2456:22501] *** End of error message *** -- mpiexec noticed that process rank 0 with PID 22501 on node cp2456 exited on signal 11 (Segmentation fault). with kind regards, Pedro -- ** Dr. Pedro Alberto Valiente Flores Profesor e Investigador Auxiliar Jefe Laboratorio de Bioinformática y Dinámica Biomolecular Centro de Estudios de Proteínas Facultad de Biología Universidad de La Habana Email:valie...@fbio.uh.cu Fax:+5378321321 Tel: +5378324830 ** -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
