Re: NAMD crashed with TclForce turned on

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sat Aug 09 2008 - 17:14:26 CDT

On Thu, Aug 7, 2008 at 3:48 PM, Cojocaru,Vlad
<vlad.cojocaru_at_eml-r.villa-bosch.de> wrote:
>
> Sorry,
>
> in fact it does compile with tcl8.5 but it crashes with tclforces scripts

..and it works, too. i just compiled the current NAMD cvs code together
with tcl8.5.3 on my desktop and i can run, e.g., the tcl-forces tutorial inputs
without a problem.

-DUSE_NON_CONST is no longer required (in fact you have to undefine it
to be able to compile).

in conclusion the crashes are most likely due to miscompiled code due
to overoptimization
and/or compiler bugs or inconsistent use of header files (an
older/installed header file was used
instead of the one matching the library.

thought you might want to know...

cheers,
   axel.

> ...
>
> Mea culpa
>
> vlad
>
> -----Original Message-----
> From: Cojocaru,Vlad
> Sent: Thu 8/7/2008 9:43 PM
> To: Chi-Cheng Chiu; Axel Kohlmeyer
> Cc: namd-l_at_ks.uiuc.edu
> Subject: RE: namd-l: NAMD crashed with TclForce turned on
>
> Yes,
>
> 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
> vlad
>
>
> -----Original Message-----
> From: Chi-Cheng Chiu [mailto:ccchiu_at_student.utdallas.edu]
> Sent: Thu 8/7/2008 6:17 PM
> To: Axel Kohlmeyer; Cojocaru,Vlad
> Cc: namd-l_at_ks.uiuc.edu
> 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:
> 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.
>>
>
>
>

-- 
=======================================================================
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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