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Hello, I am trying to run a REMD simulation. I have 24 temperatures available in 24 different directories named as {temp-1, temp-2…temp-24}. The equilibration with its respective temperatures worked out fine. I have the respective .tpr files in each directory that are ready to be executed. Now to start the REMD simulation i am using the following commands.
#PBS -N Ala6-REMD-equilibration
#PBS -q iiser
#PBS -o output.o
#PBS -e error.err
#PBS -l walltime=48:00:00
#PBS -l select=3:ncpus=24
#PBS -V
export OMP_NUM_THREADS=24
cd $PBS_O_WORKDIR
mpirun -np 72 gmx_mpi_d mdrun -deffnm remd -multidir temp-{1…24} -replex 1000
Here I am trying to use 3 cores for every simulation of the 24 and thus I have set the number of threads as 24 to match the number of simulations. Hence I have asked a total of 3 nodes with 24 cores each summing up to be 72 cores in total. Each .tpr file in the different directories are named as remd.tpr.
On a side note, each node that is available for me has 40 cores at my disposal.
So here comes my main question. Upon submitting the job, the job seems to be running on the allotted computer resources but no files are being generated. Upon force terminating the job, I get the following error file.
[mpiexec@node05] HYDU_sock_write (…/…/utils/sock/sock.c:418): write error (Bad file descriptor)
[mpiexec@node05] HYD_pmcd_pmiserv_send_signal (…/…/pm/pmiserv/pmiserv_cb.c:253): unable to write data to proxy
[mpiexec@node05] ui_cmd_cb (…/…/pm/pmiserv/pmiserv_pmci.c:176): unable to send signal downstream
[mpiexec@node05] HYDT_dmxu_poll_wait_for_event (…/…/tools/demux/demux_poll.c:76): callback returned error status
[mpiexec@node05] HYD_pmci_wait_for_completion (…/…/pm/pmiserv/pmiserv_pmci.c:520): error waiting for event
[mpiexec@node05] main (…/…/ui/mpich/mpiexec.c:1157): process manager error waiting for completion
Could someone help me out what is causing this issue? I am new to scripting and the usage of GROMACS, kindly please excuse me if I am asking any silly questions.
Thank you, Regards.
Karan