2010/9/25 case <case.biomaps.rutgers.edu>
> On Sat, Sep 25, 2010, Su Qiu wrote:
>
> > Following your suggestions, we have included /opt/intel/fce/9.0/lib in
> your
> > LD_LIBRARY_PATH
> > environment variable, but still encountered the same error.
>
> Sorry, I have lost track of the previous emails here, and can't seem to
> find
> them in the archives. Did you also check that the missing library file is
> in /opt/intel/fce/9.0/lib?
> Yes, the missing file libimf.so is in opt/intel/fce/9.0/lib, which can be
> found
>
by using the locate command.
> >
> > Given the warning in the first line of our config.h file, quote "#
> WARNING -
> > There are unresolved problems (compiler internal errors) ", there might
> be
> > some internal problems with the compiler, do you think so?
>
> I don't remember this part, and would need details; I don't understand how
> Amber's config.h could have such a first line.
>
> If I'm not mistaken, the config.h should be a file generated during
configuration,
based on the corresponding information in the config_data folder.
Our system is a linux_opteron ifort(intel fortran 90) mpich configuration,
and we found
the corresponding file linux_opteron.ifort.mpich in the config_data folder.
The linux_opteron.ifort.mpich file and the generated config.h have the same
content, beginning
with "# WARNING - There are unresolved problems (compiler internal errors)
"
Here is the full content of the two files:
# WARNING - There are unresolved problems (compiler internal errors)
# when using ifort to compile pmemd. This file is a placeholder.
setenv MPICH_INCLUDE $MPICH_HOME/include
setenv MPICH_LIBDIR $MPICH_HOME/lib
setenv MPILIB "-L$MPICH_LIBDIR -lmpich"
setenv PREPROCFLAGS "-DMPI -DSLOW_NONBLOCKING_MPI -DDIRFRC_VECT_OPT"
setenv CPP "/lib/cpp -traditional -I$MPICH_INCLUDE"
setenv OPT_LO "ifort -c -auto -tpp7 -O0"
setenv OPT_MED "ifort -c -auto -tpp7 -O2"
setenv OPT_HI "ifort -c -auto -tpp7 -xW -ip -O3"
setenv LOAD "ifort "
setenv LOADLIB " -limf -lsvml $MPILIB"
I have checked all the other files with different configuration information
(eg. linux_opteron.ifc7.lam,
linux_p3.ifc7.mpich) in the config_data folder, but none of them has the
same "warning".
Is that a systematic problem, or a compiler problem? Or did I pick the wrong
compiler?
> Amber8 is over six years old, and the compilers you are using probably
> weren't
> available back then. I recommend you consider upgrading; as an
> alternative,
> try the gnu compiler suite.
>
> Yes, the compiler may not be compatible with Amber8, so if I try using
> another compiler, it might
work, right?
>
Thanks a lot!
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Sep 25 2010 - 19:00:04 PDT
