Fwd: vmd-l: Re: wrapping option in namd

From: Christian Jorgensen (chrisjorg_at_gmail.com)
Date: Mon Jun 23 2014 - 04:59:50 CDT

Dear NAMD users,

I'm trying to call Tclforces using NAMD 2.9 Linux-x86_64-MPI

Charm++> Running on MPI version: 2.2
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
Charm++> MPI timer is synchronized
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 unique compute nodes (512-way SMP).
Charm++> cpu topology info is gathered in 0.384 seconds.

However when I do, I get the error:

TCL: Starting Tcl forces
MPT ERROR: STDOUT or STDERR buffer exhausted.
MPI: Set MPI_UNBUFFERED_STDIO or output no more than about 8192 characters
MPI: between newlines.

/usr/local/bin/logusage: Abnormal termination of process 173056
/usr/local/bin/logusage: Failing command: /opt/sgi/mpt/mpt-2.09/bin/mpirun
-np 64
/usr/local/Chem-Apps/NAMD/NAMD_2.9_23062014/Linux-x86_64-MPT-iccstatic/namd2
mineq-02.conf
/usr/local/bin/logusage: Killed
NAMD version 2.9 - All files generated by NAMD are in
/home/columbus/cj10/Equilibration directory
"mineq-02.log" 874L, 37205C

I have run the same calculation successfully with NAMD 2.9
Linux-x86_64-multicore
Does anyone know what the problem is with the MPI architecture? I've looked
around on the
list there have been some reports of issues calling the Tcl library, or a
possible MPI library disconnect
with the Tcl library?

Thanks

Christian

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