From: Alex Smith (cupkec_at_hotmail.com)
Date: Thu Nov 22 2012 - 05:44:28 CST
Hello, I'm using latest version of NAMD 2.9 Win64-MPI and Windows Server 2008 R2 HPC with about 40 physical computing nodes. No matter how i try to run execute namd (mpiexec, job submit, trough HPC cluster manager, see below) , namd does not migrate and execute on computing nodes, but is allways executed on local machine. c:\>mpiexec -np 10 \\HPC-server\install\NAMD\namd2.exe \\HPC-server\install\NAMD\1-2-sphere\ubq_ws_eq.conf > \\HPC-server\install\NAMD\_ubq_ws_eq.log
andc:\>job submit /numnodes:10 mpiexec -cores 4 \\HPC-server\install\NAMD\namd2.exe \\HPC-server\install\NAMD\ubq_ws_eq.conf > \\HPC-server\install\NAMD\_ubq_ws_eq.log
I don't get any errors, results seem OK. Manual states, that namd should be executed as any other MPI job. I can execute other MPI jobs without any problem, so cluster seems to be working OK. I noticed "Info: Running on 4 processors, 4 nodes, 1 physical nodes.". Why is physical nodes always 1? What is proper way of running namd on Win2008 HPC cluster? Output: Charm++> Running on MPI version: 2.0
Charm++> level of thread support used: MPI_THREAD_SINGLE (desired: MPI_THREAD_SINGLE)
Charm++> Running on non-SMP mode
Converse/Charm++ Commit ID: v6.4.0-beta1-0-g5776d21
 isomalloc.c> Disabling isomalloc because mmap() does not work
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 unique compute nodes (4-way SMP).
Charm++> cpu topology info is gathered in 0.015 seconds.
Info: NAMD 2.9 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 60400 for mpi-win64
Info: Built Mon Apr 30 14:30:56 CDT 2012 by jcphill on cs-dexterity
Info: Running on 4 processors, 4 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.062 s
Info: 5.01953 MB of memory in use based on GetProcessMemoryInfo
Info: Configuration file is \\HPC-server\install\NAMD\1-2-sphere\ubq_ws_eq.conf
Info: Changed directory to \\HPC-server\install\NAMD\1-2-sphere Cheers, Alex
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