HI,
Try to run smaller jobs. For example, split your jobs in to 10 * 10ns. So that you will never cross the wall time.
Best Regards
Elvis Martis
Mumbai, INDIA.
________________________________________
From: Garima Singh <garimabioinfo.gmail.com>
Sent: 06 September 2017 16:19
To: amber.ambermd.org
Subject: [AMBER] MD terminate in HPC
Dear Amber user ,
100 ns of MD simulation run on HPC . There is limitation in wall
time 48 hr. Md has terminate after wall time completion i restart the job
3rd time with command
mpirun -np 32 sander.MPI -O -i Prod.in -o Prod3.out -p cd5_50n.prmtop -c
Prod2.rst \-r Prod3.rst -x Prod3.mdcrd -inf Prod3.info
there is error msg.
application called MPI_Abort(MPI_COMM_WORLD, 2) - process 0
[16:cn0782.cmmacs.ernet.in] unexpected disconnect completion event from [11:
cn0781.cmmacs.ernet.in]
Assertion failed in file ../../dapl_conn_rc.c at line 1128: 0
internal ABORT - process 16
I could not understand why ? kindly help me?
*Thank You and Best Wishes*
--
*Regards*
Garima Singh
AcSIR-PhD Fellow
Biotechnology Division
C/o Dr. Ashok Sharma (Chief Scientist and Head Biotechnology Division)
Central Institute Of Medicinal And Aromatic Plant
CSIR-CIMAP
Lucknow
garimabioinfo.gmail.com
*INDIA* Please don't print this e-mail unless you really need to. Be Green !
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Received on Wed Sep 06 2017 - 06:00:03 PDT
