From: Ana Celia Araujo Vila Verde (avilaverde_at_engr.psu.edu)
Date: Sun Feb 04 2007 - 14:33:41 CST
Dear NAMD developers,
I tried running RE simulations using 10 or more replicas and they never go past the initial stages, although no error message every appears. The simulation just doesn't go anywhere. If I try the same simulation and use 9 replicas or less, all seems to be good. This seems to happen irrespective of whether I try to run the job interactively (all replicas running in a single node) or through PBS in the local cluster. I had a look at the replica exchange scripts but I didn't find any obvious limitations to the number of replicas.
Could the NAMD developers clarify whether such a limitation exists or not? Knowing for sure that it doesn't exist would help my Sys Admin sort out the origin of the problem.
Thanks,
Ana
Main *log file
"
TEMPERATURE 0: 298
TEMPERATURE 1: 341
TEMPERATURE 2: 390
TEMPERATURE 3: 446
TEMPERATURE 4: 510
TEMPERATURE 5: 584
TEMPERATURE 6: 668
TEMPERATURE 7: 764
TEMPERATURE 8: 874
TEMPERATURE 9: 1000
starting replica 8 sock4 128.118.2.177 39842
starting replica 1 sock24 128.118.2.177 39845
starting replica 4 sock26 128.118.2.177 39846
starting replica 9 sock27 128.118.2.177 39849
starting replica 5 sock28 128.118.2.177 39850
starting replica 2 sock29 128.118.2.177 39853
starting replica 0 sock30 128.118.2.177 39854
starting replica 7 sock31 128.118.2.177 39857
starting replica 6 sock32 128.118.2.177 39858
starting replica 3 sock33 128.118.2.177 39860
SERVER: cd /home6/acv12/sim262; pwd"
*log for one of the replicas
"Charm++: standalone mode (not using charmrun)
Charm++: scheduler running in netpoll mode.
Info: NAMD 2.6 for Linux-amd64-TCP
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 50900 for net-linux-amd64-tcp-iccstatic
Info: Built Wed Aug 30 12:54:53 CDT 2006 by jim on belfast.ks.uiuc.edu
Info: 1 NAMD 2.6 Linux-amd64-TCP 1 lionxb.aset.psu.edu acv12
Info: Running on 1 processors.
Info: 7476 kB of memory in use.
Info: Memory usage based on mallinfo
Info: Changed directory to /home6/acv12/sim262/output
Info: Configuration file is sim262RE.job0.0.log.nrc"
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:21 CST