VMD-L Mailing List
From: Corenflos, Steven Charles (scorenfl_at_indiana.edu)
Date: Tue Feb 05 2008 - 12:15:47 CST
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Is this an appropriate forum to ask for help with namd? I've tried contacting the e-mail address listed for namd but haven't gotten any response after a week or so.
Basically we have a dual-processor, quad-core Xeon system running Ubuntu 64-bit linux. While we can get namd to run on a single processor we're running into difficulties getting it to run on all 8 cores. Perhaps it is the package I'm using--I downloaded the Linux-AMD64-TCP package in case we later tried to make it run jobs not only on the local server but also spread the workload onto other machines.
I've tried various combinations of commands I've found suggested in different places:
> charmrun +p8 namd2 sim.conf
> namd2 +p8 sim.conf
> charmrun namd2 ++local +p8 sim.conf
None of these have worked.
Any help on how to get this working would be greatly appreciated.
Here is some sample output when trying to run the program:
user_at_server:~/namd/namd-1cwp/1cwp-NT0-vmd-H$ namd2 +p8 1cwp-NT0-vmd-H.conf | tee -a 1cwp-NT0-vmd-H.log
To use multiple processors, you must run this program as:
> charmrun +p8 namd2 <args>
or build the net-linux-amd64-tcp-iccstatic-smp version of Charm++.
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: unexpected call to exit by user program. Must use CkExit, not exit!
Charm++ fatal error:
unexpected call to exit by user program. Must use CkExit, not exit!
Charm++: standalone mode (not using charmrun)
Stack Traceback:
[0] CmiAbort+0x33 [0x7f17f5]
[1] namd2 [0x7f1862]
[2] exit+0xe0 [0x2aeb123d5500]
[3] namd2 [0x7efc68]
[4] ConverseInit+0x1c6 [0x7f08e4]
[5] _ZN7BackEnd4initEiPPc+0x2b [0x4ba9a5]
[6] main+0x47 [0x4b656f]
[7] __libc_start_main+0xf4 [0x2aeb123beb44]
[8] _ZNSt8ios_base4InitD1Ev+0x3a [0x4b28da]
user_at_server:~/namd/namd-1cwp/1cwp-NT0-vmd-H$ charmrun +p8 namd2 1cwp-NT0-vmd-H.conf | tee -a 1cwp-NT0-vmd-H.log
user_at_localhost's password: user_at_localhost's password: user_at_localhost's password: user_at_localhost's password: user_at_localhost's password: user_at_localhost's password: user_at_localhost's password: user_at_localhost's password:
Charmrun rsh(localhost.1)> Cannot locate this node-program: /home/user/namd/namd-1cwp/1cwp-NT0-vmd-H/namd2
Charmrun rsh(localhost.1)> Exiting with error code 1
user_at_server:~/namd/namd-1cwp/1cwp-NT0-vmd-H$
user_at_server:~/namd/namd-1cwp/1cwp-NT0-vmd-H$ charmrun namd2 ++local +p8 1cwp-NT0-vmd-H.conf | tee -a 1cwp-NT0-vmd-H.log
execve failed to start process "namd2" with status: -1
- Next message: Irene Newhouse: "RE: VMD, NAMDenergy & AMBER parameters"
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- Reply: Axel Kohlmeyer: "Re: namd help?"
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