Re: NAMD compile error

From: itvasile_at_nipne.ro
Date: Tue Dec 16 2008 - 14:20:48 CST

Hello Axel,

I have the namd2 binary but it doesn't work. When I'm running a pbs job
with 'charmrun namd2 inputfile > outputfile' it ends suddently and in
the error_file of the pbs job it says "warning:regcache incompatible with
malloc" multiple times. Then
"/opt/NAMD_2.6_Source/Linux-x86_64/namd2:signal 9" a couple of times, and
at the end "Killed by signal 15." several times.

That's why I returned to the recompilation of NAMD, because I think that
here is the problem.

Regards,
_____________________________________________________________________
   Dipl. Eng. Drd. Ionut VASILE
   Junior Researcher
   Horia Hulubei National Institute of Physics and Nuclear Engineering
   ROMANIA
   http://www.nipne.ro

Axel Kohlmeyer said:
> On Tue, 16 Dec 2008, itvasile_at_nipne.ro wrote:
>
> IV> Hello,
>
> hello ionut,
>
> [...]
> IV> src/flipbinpdb.c:51: warning: incompatible implicit declaration of
> IV> built-in function 'exit'
> IV> src/flipbinpdb.c:62: warning: incompatible implicit declaration of
> IV> built-in function 'exit'
> IV> ~~~~~~~~~~~~~~~
> IV>
> IV> I must mention that I tried compiling with the compilers from mpich-mx
> IV> 1.2.7..7, based on GNU gcc 4.1.2.
> IV> Any help is highly appreciated.
>
> these are just warnings and related to additional external binaries
> called flipbinpdb and flibdcd that are not required to run namd.
> do you have a namd2 binary? does it work? that is what matters.
>
> cheers,
> axel.
>
>
> IV> Thank you
> IV>
> IV> _____________________________________________________________________
> IV> Dipl. Eng. Drd. Ionut VASILE
> IV> Junior Researcher
> IV> Horia Hulubei National Institute of Physics and Nuclear Engineering
> IV> ROMANIA
> IV> http://www.nipne.ro
> IV>
> IV>
>
> --
> =======================================================================
> 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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