Re: NAMD crashed with TclForce turned on

From: Chi-Cheng Chiu (ccchiu_at_student.utdallas.edu)
Date: Thu Aug 07 2008 - 11:17:16 CDT

Thanks for the idea!
We compiled NAMD linking to Tcl8.5 by setting up the
"arch/Linux-amd64.tcl" file:
TCLINCL=-I/usr/include
TCLLIB=-L/usr/lib64 -ltcl8.5 -ldl
TCLFLAGS=-DNAMD_TCL -DUSE_NON_CONST
TCL=$(TCLINCL) $(TCLFLAGS)

We also tried setup env
LD_LIBRARY_PATH=/usr/lib64

but we still get "signal 11" error when running NAMD through mpirun
with tclforce turn on.
In NAMD archive, there's an article saying that NAMD hasn't been tested
with Tcl8.5. Could the problem be the compatibility of Tcl 8.5 wiht
NAMD?

Thanks in advance

Cheers,

Chi-cheng

Axel Kohlmeyer wrote:

>On Wed, 6 Aug 2008, Chi-Cheng Chiu wrote:
>
>CCC> Hi All,
>CCC> We compile charm++(version 6.0) and namd on a cluster with AMD
Opteron
>CCC> 280 and Myrinet MX connection using MPI and PGI compiler. We can
launch
>
>why PGI? g++/gcc is usually significantly faster _and_ much more
reliable.
>
>CCC> NAMD with mpirun normally. Yet if we turn on TclForce, NAMD
crashed
>CCC> with the following error info while loading the atom's coordinate:
>CCC>
>CCC> /net/ss/cm/u1/son051000/N/Linux-amd64-MPI/namd2:signal 11
>CCC> MX:s47.utdallas.edu:Remote endpoint is closed,
peer=00:60:dd:47:ec:a9
>CCC> (s75.utdal
>CCC> las.edu:0)
>
>CCC> We are not sure which part of NAMD went wrong. Does anyone have an
idea
>CCC> about this?
>
>most likely the tcl interpreter? without seeing what was leading up
>to the segfault (=signal 11) it is difficult to tell.
>
>please also see the discussion on the very same subject of compiling
>and running with tcl from the last few days in the list archives.
>
>cheers,
> axel.
>
>CCC>
>CCC> Thanks
>CCC>
>CCC> Chi-cheng
>CCC>
>
>--
>=======================================================================
>Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
>Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
>tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
>=======================================================================
>If you make something idiot-proof, the universe creates a better idiot.
>

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