From: Dong Luo (us917_at_yahoo.com)
Date: Thu Mar 03 2011 - 19:59:10 CST
Chris, the CVS version of namd/charm++ work. Only that I have to comment out MPI
checking in the configure file of charm++ because it fails on Bluegene/L. It is
not checked in charm++ 2.2.
Axel, namd/charm++ are cross-compiled on Bluegene/L because the login host uses
different OS compared to the cluster nodes. I did not figure out a way to test
From: Chris Harrison <charris5_at_gmail.com>
To: Dong Luo <us917_at_yahoo.com>
Sent: Thu, March 3, 2011 1:41:50 AM
Subject: Re: namd-l: NAMD2.7 on BluegeneL hang at "LDB: Central LB being
We've made recent improvements to startup and load-balancing. Can you
try the CVS version or one of the nightly builds of namd, with the most
recent git archive or nightly build of charm++?
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu Voice: 217-244-1733
http://www.ks.uiuc.edu/~char Fax: 217-244-6078
Dong Luo <us917_at_yahoo.com> writes:
> Date: Wed, 2 Mar 2011 19:42:57 -0800 (PST)
> From: Dong Luo <us917_at_yahoo.com>
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l: NAMD2.7 on BluegeneL hang at "LDB: Central LB being
> X-Mailer: YahooMailRC/555 YahooMailWebService/0.8.109.292656
> I'm trying to use colvars in NAMD2.7 for distance restraints. There is no
> precompiled version for BluegeneL in the download section. I downloaded the
> source code and compiled following the instructions on this link:
> However, the simulation (no matter with colvars or not) using this namd2 2.7
> version always hang after Startup phase 5 as shown in the log:
> Info: REMOVING COM VELOCITY 0.0209799 0.0192793 0.000362722
> Info: LARGEST PATCH (156) HAS 345 ATOMS
> Info: Startup phase 3 took 0.246489 s, 17.3047 MB of memory in use
> Info: PME using 40 and 32 processors for FFT and reciprocal sum.
> Info: PME GRID LOCATIONS: 7 15 23 27 31 39 47 55 59 63 ..
> Info: PME TRANS LOCATIONS: 3 11 19 29 35 43 51 61 67 75 ...
> Info: Startup phase 4 took 0.00254185 s, 17.3047 MB of memory in use
> Info: Startup phase 5 took 0.0261579 s, 17.3047 MB of memory in use
> LDB: Central LB being created...
> namd2 2.6 version can run normally, but lacks the colvars function I assume.
> Any directions?
> Thank you.
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