Re: Problem running REMD simulation

From: Nicholus Bhattacharjee (nicholusbhattacharjee_at_gmail.com)
Date: Tue Aug 25 2015 - 04:59:07 CDT

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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