RE: NAMD crashed with TclForce turned on

From: Cojocaru,Vlad (
Date: Thu Aug 07 2008 - 14:43:02 CDT


Namd does not compile with tcl8.5. As I wrote in the last email of that discussion, you should either use the precompiled libraries provided on the namd page or compile yourself tcl 8.4.19 with the -DUSE_NON_CONST defined in the CFLAGS. tcl8.3.x does not configure in a newer version of bash ..

Hope this helps

-----Original Message-----
From: Chi-Cheng Chiu []
Sent: Thu 8/7/2008 6:17 PM
To: Axel Kohlmeyer; Cojocaru,Vlad
Subject: Re: namd-l: NAMD crashed with TclForce turned on
Thanks for the idea!
We compiled NAMD linking to Tcl8.5 by setting up the
"arch/Linux-amd64.tcl" file:
TCLLIB=-L/usr/lib64 -ltcl8.5 -ldl

We also tried setup env

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

Thanks in advance



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
>CCC> 280 and Myrinet MX connection using MPI and PGI compiler. We can
>why PGI? g++/gcc is usually significantly faster _and_ much more
>CCC> NAMD with mpirun normally. Yet if we turn on TclForce, NAMD
>CCC> with the following error info while loading the atom's coordinate:
>CCC> /net/ss/cm/u1/son051000/N/Linux-amd64-MPI/namd2:signal 11
>CCC> endpoint is closed,
>CCC> (s75.utdal
>CCC> We are not sure which part of NAMD went wrong. Does anyone have an
>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.
> axel.
>CCC> Thanks
>CCC> Chi-cheng
>Axel Kohlmeyer
> 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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