From: Santosh Kumar Chaudhary (skc_at_physics.iisc.ernet.in)
Date: Thu Dec 18 2014 - 00:09:48 CST
Hi,
Sorry, earlier i have not defined my problem clearly. Hope this will. I
have an octacore system, for running namd we just need to source namd2 and
the command: namd2 +p8 +idlepoll namd.conf> namd.out. In bluegene i am
submitting job as -
#!/bin/sh
# @ job_type = bluegene
# @ executable = /usr/bin/mpirun
# @ arguments = -exe /bgl/loadl/jobs/hello.rts -cwd /bgl/loadl/jobs -shell
ssh
# @ error = inp.err
# @ output = inp.out
# @ environment = COPY_ALL
# @ notification = always
# @ bg_size = 32
# @ class = pnode32-24h
# @ queue
/usr/bin/mpirun -cwd /gpfs/bglscratch/phyabsws/tk_run/ -mode SMP -np 32
/home/phd/09/phyabsws/namd-sunlnx/NAMD_2.8_Linux-x86_64/namd2
/gpfs/bglscratch/phyabsws/tk_run/tk_nergy_min.conf
and getting error as
<Dec 18 11:48:35.071149> FE_MPI (ERROR): waitForBackendConnections() -
Timed out waiting for the backend to connect
<Dec 18 11:48:35.071472> FE_MPI (ERROR): Failed to get control and data
connections from service node
<Dec 18 11:48:50.066201> FE_MPI (ERROR): Failure list:
<Dec 18 11:48:50.066264> FE_MPI (ERROR): - 1. Failed to execute Back-End
mpirun on service node (failure #13)
This is the first time using supercomputer for namd simulation. Please
help me in solving this issue.
thanks and regards
santosh
> It's unclear what you are asking. The setup (and the choice of a
> particular for force field) should be all the same across different
> platforms. Are you asking how to run NAMD in parallel on that machine?
>
> One problem which NAMD on the BlueGenes (L and P at least) is larger
> system can't be run because of the small memory size (if memory serves
> well it was a problem with load balancing needed ample memory or so).
>
> Cheers,
> Hannes.
>
> ________________________________________
> From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of
> Santosh Kumar Chaudhary [skc_at_physics.iisc.ernet.in]
> Sent: 17 December 2014 12:21
> To: NAMD list
> Subject: namd-l: setting up namd simulation in IBM Blue Gene/L
>
> Dear All,
>
> I want to set-up NAMD simulation with amber forcefield in BlueGene. There
> are very less information on web to set up NAMD in bluegene. Please guide
> me in this.
>
>
> --
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-- Santosh Kumar Chaudhary Graduate Student Prof.K.Sekar's Lab Supercomputer Education and Research Center Rm.no-352, old CES Building Indian Institute of Science Bangalore - 560012 Ph No - 9739044199 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
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