From: Peter Freddolino (petefred_at_umich.edu)
Date: Tue Aug 25 2015 - 23:25:00 CDT
Hi Nicholus,
You ought to be running it through charmrun with this build of namd. For a local run on my laptop I can do the following:
mpirun ~/src/NAMD_2.10_MacOSX-x86_64-netlrts/charmrun ~/src/NAMD_2.10_MacOSX-x86_64-netlrts/namd2 ++local ++p 6 +replicas 6 aslov2_ja_metaRE_run01.namd +stdout output/rep_%d/rep%d_run01.log
(you can change the paths accordingly)
Omitting the charmrun portion yields the same error that you saw.
Best,
Peter
> On Aug 25, 2015, at 5:59 AM, Nicholus Bhattacharjee <nicholusbhattacharjee_at_gmail.com> wrote:
>
> Hello Douglas and Norman,
>
> Thanks for the reply. Douglas I have downloaded "NAMD_2.10_Linux-x86_64-netlrts" and tried running the same job with the following command
>
> $ mpirun /home/nicholus/softwares/NAMD_2.10_Linux-x86_64-netlrts/namd2 +replicas 8 job0.conf +stdout output/%d/job0.%d.log
>
> The resultant error is
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Charm++: standalone mode (not using charmrun)
> Charm++> Running in non-SMP mode: numPes 1
> namd2: machine-common-core.c:863: create_partition_map: Assertion `(_Cmi_numnodes_global % _partitionInfo.numPartitions) == 0' failed.
> --------------------------------------------------------------------------
> mpirun noticed that process rank 0 with PID 3679 on node crim1 exited on signal 6 (Aborted).
> --------------------------------------------------------------------------
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> Could you please tell me what wrong I am doing. Thanks onece again.
>
>
> On Tue, Aug 25, 2015 at 11:16 AM, Douglas Houston <DouglasR.Houston_at_ed.ac.uk> wrote:
> Hi Nicholus,
>
> Are you using a NAMD build based on a patched MPI build of Charm++? I had to compile NAMD from source (by following the instructions in the notes.txt file).
>
> Alternatively there is a version on the NAMD download page called "Linux-x86_64-netlrts (Multi-copy algorithms)" which might be what you want (although it's hard to tell).
>
> cheers,
> Doug
>
>
>
> Quoting Nicholus Bhattacharjee <nicholusbhattacharjee_at_gmail.com> on Tue, 25 Aug 2015 10:01:36 +0200:
>
> Hello,
>
> I am reposting the query as I have not got any reply.
>
> I am trying to run REMD simulation using NAMD. I am following the
> suggestions given in
>
> http://www.ks.uiuc.edu/Research/namd/2.9/ug/node66.html
>
> I did the following
>
> example$ mkdir output
> example$ cd output
> output$ mkdir 0 1 2 3 4 5 6 7
> output$ cd ..
> example$ mpirun /usr/local/NAMD_2.9_Linux-x86_64-multicore/namd2 +replicas
> 8 job0.conf +stdout output/%d/job0.%d.log
>
> I got the error message
> %%%%%%%%%%%%%%%%%%%%%%%%%%%
> FATAL ERROR: Unknown command-line option +replicas
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: Unknown command-line option +replicas
>
> Charm++ fatal error:
> FATAL ERROR: Unknown command-line option +replicas
> %%%%%%%%%%%%%%%%%%%%%%%%%%
>
> The second part of the question is about running REMD using AMBER topology
> file.
> For running normal simulation we change in the configuration file
> "structure XXX.psf" by
> amber yes
> parmfile XXX.top"
>
> Now in REMD configuration file what we change for the following line
>
> set psf_file "XXX.psf"
>
>
>
>
>
> _____________________________________________________
> Dr. Douglas R. Houston
> Lecturer
> Institute of Structural and Molecular Biology
> Room 3.23, Michael Swann Building
> King's Buildings
> University of Edinburgh
> Edinburgh, EH9 3JR, UK
> Tel. 0131 650 7358
> http://tinyurl.com/douglasrhouston
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
>
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