From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Wed May 20 2015 - 11:58:13 CDT
Those directions are for Win64-multicore binaries. What you have is a
Win64-MPI binary, which must be launched with mpiexec. You almost
certainly want the Win64-multicore version instead. The MPI version is
only needed for multi-node paralellism or replica exchange.
On Fri, 15 May 2015, Kukol, Andreas wrote:
> I obtained the precompiled namd binary for Windows and I am trying to run it using 4 CPU cores:
>> c:\NAMD_2.9_Win64-MPI\namd2.exe +p4 ionized.namd > ionized.log
> However, I get the following error message:
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: Unknown command-line option +p4
> Also including a space '+p 4' does not work. Namd2 without +p works fine, but a bit slow.
> This is the info from 'notes.txt' that was included in the download:
> Windows, Mac OX X (Intel), and Linux-x86_64-multicore released binaries
> are based on "multicore" builds of Charm++ that can run multiple threads.
> These multicore builds lack a network layer, so they can only be used on
> a single machine. For best performance use one thread per processor
> with the +p option:
> namd2 +p<procs> <configfile>
> If I run namd2 without any input, I get the following info:
> Charm++> Running on MPI version: 2.0
> Charm++> level of thread support used: MPI_THREAD_SINGLE (desired: MPI_THREAD_SI
> 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 0.000 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 1 processors, 1 nodes, 1 physical nodes.
> Info: CPU topology information available.
> Info: Charm++/Converse parallel runtime startup completed at 0.016 s
> Any help would be appreciated.
> Many thanks
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