From: Avisek Das (avisek_at_uchicago.edu)
Date: Mon Jun 01 2015 - 12:22:46 CDT
Thank you for your reply. I have figured out the right command line options and it worked. The command I used, which ran successfully, was
$CHARMRUM ++local ++p 32 $NAMD_EXE +replicas 16 initial.conf +stdout output/%02d/job00.%04d.log
If, I understand it correctly, this command runs NAMD with 32 processing elements on my entire machine taking all the 8 cores.
Is there a way to specify the number of processors to be used by charmrun/namd? I mean, what do I do if I want to do the same thing on 4 cores instead of 8.
Thanks a lot,
From: Norman Geist [norman.geist_at_uni-greifswald.de]
Sent: Monday, June 01, 2015 2:43 AM
To: namd-l_at_ks.uiuc.edu; Avisek Das
Subject: RE: namd-l: Using the multi-copy version of NAMD on a linux workstation
You need at least 2*#replicas processes. Please also tell us what “would not start” actually means?
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of Avisek Das
Sent: Friday, May 29, 2015 9:43 PM
Subject: namd-l: Using the multi-copy version of NAMD on a linux workstation
I am interested in using the multi-copy algorithms in NAMD on my Linux workstation. It is a standard Dell Precision workstation with 8 cores. I want to do this for debugging some codes.
I downloaded the installation listed under "Linux-x86_64-netlrts<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=&AccessCode=&ArchiveID=1320> (Multi-copy algorithms)" and tried to run it with the following command.
charmrun +p4 ++local ./namd2 +replicas 16 initial.conf +stdout output/%02d/job00.%04d.log
The program would not start. My questions are:
1. Is this the right version of NAMD for using the multiple copy algorithms?
2. If yes, what is the correct way to launch the executable.
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