From: Guoxiong Su (gsu3_at_mail.uh.edu)
Date: Thu May 12 2011 - 14:13:59 CDT
Dear all,
I am trying to run REMD on Ranger, a Linux cluster of TACC. My spawning
command is "mpirun -np $procs_per_host -hostfile $nfile $namd $conf". At
first, I used 4 replicas, 16 processors per replica, and it worked. However,
when I switched to production run, using 16 replicas instead, 16 processors
per replica, 256 processors in total, NAMD stopped after "TCL: SERVER
CONNECTED". My log file is as following:
Charm++> Running on MPI version: 1.2 multi-thread support: 0 (max supported:
-1)
Warning> Randomization of stack pointer is turned on in kernel, thread
migration may not work! Run 'echo 0 > /proc/sys/kernel/randomize_va_space'
as root to disable it, or try run with '+isomalloc_sync'.
Charm++> Running on 1 unique compute nodes (16-way SMP).
Charm++> Cpu topology info:
PE to node map: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Node to PE map:
Chip #0: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
Charm++> cpu topology info is gathered in 0.002 seconds.
Info: NAMD 2.7 for Linux-x86_64
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
Info:
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 60202 for mpi-linux-x86_64
Info: Built Fri Jan 28 10:21:27 CST 2011 by root on
build.ranger.tacc.utexas.edu
Info: 1 NAMD 2.7 Linux-x86_64 16 i115-105.ranger.tacc.utexas.edu
guoxiong
Info: Running on 16 processors.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.065798 s
Info: 86.4844 MB of memory in use based on /proc/self/stat
Info: Changed directory to output
Info: Configuration file is output.job0.0.log.nrc
TCL: SERVER CONNECTED
Can anyone help me with it please? Thank you.
Yours sincerely,
-- Guoxiong Su Cheung group Department of Physics University of Houston
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:57:07 CST