From: zhilei chen (zchen4_at_uiuc.edu)
Date: Mon Jan 19 2004 - 11:51:11 CST
Hi,
I have some problems with namd 2.5 running on Linux cluster. I am not
sure whether it is the software problem or the computer problem. I ran
the job on "titan.ncsa.uiuc.edu". It worked before, with 8 nodes (16
prcessors), but failed with 16 nodes (32 processors). The job was
running for 24 hours ( the time limit) and I didn't get any output file,
except the error report log file.
Here is part of the error log file I obtained. It seems that namd
started properly, but somehow get stucked after it started.
I don't know what to do now. Any suggestions?
Thanks
Zhilei
-----------------------------
log file:
...................
Info: 666 IMPROPERS
Info: 0 EXCLUSIONS
Info: 40113 RIGID BONDS
Info: 86157 DEGREES OF FREEDOM
Info: 14670 HYDROGEN GROUPS
Info: TOTAL MASS = 256975 amu
Info: TOTAL CHARGE = 2.89269e-06 e
Info: *****************************
Info: Entering startup phase 0 with 98896 kB of memory in use.
Info: Entering startup phase 1 with 98896 kB of memory in use.
Info: Entering startup phase 2 with 101144 kB of memory in use.
Info: Entering startup phase 3 with 101480 kB of memory in use.
Info: PATCH GRID IS 4 (PERIODIC) BY 5 (PERIODIC) BY 3 (PERIODIC)
Info: REMOVING COM VELOCITY -0.0626917 -0.0199185 -0.0476978
Info: LARGEST PATCH (25) HAS 745 ATOMS
VMI/GM: (22) send completed with send error 0x00000012
VMI/GM: (23) send completed with send error 0x00000012
VMI/GM: (31) send completed with send error 0x00000012
VMI/GM: (30) send completed with send error 0x00000012
VMI/GM: (21) send completed with send error 0x00000012
VMI/GM: (20) send completed with send error 0x00000012
VMI/GM: (25) send completed with send error 0x00000012
VMI/GM: (24) send completed with send error 0x00000012
VMI/GM: (28) send completed with send error 0x00000012
VMI/GM: (29) send completed with send error 0x00000012
VMI/GM: (26) send completed with send error 0x00000012
VMI/GM: (27) send completed with send error 0x00000012
VMI/GM: (15) send completed with send error 0x00000012
VMI/GM: (14) send completed with send error 0x00000012
VMI/GM: (15) send completed with send error 0x00000012
VMI/GM: (14) send completed with send error 0x00000012
VMI/GM: (15) send completed with send error 0x00000012
VMI/GM: (14) send completed with send error 0x00000012
VMI/GM: (15) send completed with send error 0x00000012
VMI/GM: (14) send completed with send error 0x00000012
VMI/GM: (15) send completed with send error 0x00000012
VMI/GM: (14) send completed with send error 0x00000012
VMI/GM: (15) send completed with send error 0x00000012
VMI/GM: (14) send completed with send error 0x00000012
VMI: Termination request on node 28. Requesting clean shutdown.
VMI: Termination request from node 28. Node 31 cleanly shutting down.
VMI: Sending shutdown msg ...Done.
VMI: Termination handler executed. Node 28 going down with sigcode 5
VMI: Sending shutdown msg to our lower peer.
VMI: Termination request on node 28. Requesting clean shutdown.
VMI: Sending shutdown msg to our lower peer.
VMI: Termination request from node 28. Node 25 cleanly shutting down.
VMI: Sending shutdown msg ...Done.
VMI: Termination handler executed. Node 28 going down with sigcode 5
VMI: Termination request from node 28. Node 15 cleanly shutting down.
VMI: Sending shutdown msg ...Done.
VMI: Termination request from node 28. Node 18 cleanly shutting down.
VMI: Sending shutdown msg ...Done.
VMI: Termination handler executed. Node 28 going down with sigcode 5
VMI: Termination handler executed. Node 28 going down with sigcode 5
VMI: Termination request from node 28. Node 26 cleanly shutting down.
.........
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