NAMD at Data Star SDSC

From: Shahid Qamar (qamar13_at_hotmail.com)
Date: Mon Nov 22 2004 - 15:19:11 CST

Hi,
I am attempting to setup NAMD jobs on the DataStar computing facility.
I am using the following command on the interactive p655 nodes,
dspoe.sdsc.edu.
poe /usr/local/apps/NAMD_2.5_Source/IBM-SP-xlC/namd2 cv.txt -nodes 1
-tasks_per_node 8 > run_job1.log
>
The program runs but then crashes after several cycles with the
following error message: (files are in /gpfs/sqamar/job1)

        register.h> CkRegisteredInfo<32,> called with invalid index 34 (should
be less than 0)

I contacted people at data star and they gave me a modiefied command

poe /usr/local/apps/NAMD_2.5_Source/IBM-SP-xlC/namd2 cv.txt -nodes 1
-tasks_per_node 8 -rmpool 1 -euilib us -euidevice sn_all > run_job1.log

When I use this command then my job runs for 33000-44000 steps and then it
just does not wrok. It looks it is stucked and i have to kill the
application.

Any body knows whats going on and any body is running SMD on SDSC data star.

Your help will be appreciated.

Best regards,
Shahid

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:38:01 CST