[gmx-users] help to solve this problem

[valiente]

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 at 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=200000000
>> #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`"
>>
>> #########################################################
>>
>> 5000000 steps,  50000.0 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:valiente at fbio.uh.cu
Fax:+5378321321 Tel: +5378324830
**********************************************************