From: Chewning, Joseph (Joseph.Chewning_at_targacept.com)
Date: Tue Oct 04 2011 - 07:04:31 CDT
I have a question about isomalloc. Don't I need this to be able to run a job on more than one node? What does the MPI_THREAD_SINGLE mean? Could this be the problem with slowness on multi-node run? Below is a cope of my output header:
Charm++> Running on MPI version: 2.0 multi-thread support: MPI_THREAD_SINGLE (max supported: MPI_THREAD_SINGLE)
 isomalloc.c> Disabling isomalloc because mmap() does not work
Charm++> Running on 2 unique compute nodes (32-way SMP).
Charm++> cpu topology info is gathered in 0.016 seconds.
Info: NAMD 2.8 for Win64-MPI
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: for updates, documentation, and support information.
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info: Based on Charm++/Converse 60303 for mpi-win64
Info: Built Sat May 28 11:53:54 CDT 2011 by jcphill on cs-dexterity
Info: Running on 64 processors, 64 nodes, 2 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.0929999 s
Info: 12.9219 MB of memory in use based on GetProcessMemoryInfo
Info: Configuration file is \\HPC-Prod\Jobs\Test_Job\ch25.conf
Info: Changed directory to \\HPC-Prod\Jobs\Test_Job
TCL: Suspending until startup complete.
Warning: The following variables were set in the
Warning: configuration file but will be ignored:
Warning: consexp (constraints)
Warning: conskcol (constraints)
Warning: constraintScaling (constraints)
Info: EXTENDED SYSTEM FILE npt38.xsc
Joseph Chewning, MCSE
Informatics Team Lead
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