Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..."

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 charm++. Dong   ________________________________ From: Chris Harrison <charris5_at_gmail.com> To: Dong Luo <us917_at_yahoo.com> Cc: namd-l_at_ks.uiuc.edu Sent: Thu, March 3, 2011 1:41:50 AM Subject: Re: namd-l: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." 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++? Best, Chris -- 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 >  created..." > X-Mailer: YahooMailRC/555 YahooMailWebService/0.8.109.292656 > > Hi, > > 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: > http://bluegene.bnl.gov/comp/buildnamd.html > > 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. > > Dong > > > >     

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:23:38 CST