NAMD at Data Star SDSC

From: Shahid Qamar (
Date: Mon Nov 22 2004 - 15:19:11 CST

I am attempting to setup NAMD jobs on the DataStar computing facility.
I am using the following command on the interactive p655 nodes,
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

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

Your help will be appreciated.

Best regards,

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