Analysis of config.h and errors.log by comepetents in openmpi, who do not know
Amber, may help. It is clear at this point that the issue can only be solved
with help from Amber compilation experts. Notice please that openmpi is in use
for other apploications and I am not allowed to change from intel to other
compiler for it.
The analysis follows in the next two paragraphs:
I see that "ifort" is being used to build Amber (instead of using mpif77 or
mpif90), and I don't see any reference to the MPI libraries in the final link
line to create the "sander.MPI" executable, which is probably why it says it
can't find all those symbols.
Because Open MPI wrapper compilers to build themselves are not used (which
would automatically get all the proper header files and libraries) you can only
hope to come out with help from people familiar with Amber, which unfortunately
is not my case.
Thanks
francesco pietra
--- Francesco Pietra <chiendarret.yahoo.com> wrote:
> Date: Tue, 24 Jul 2007 23:24:22 -0700 (PDT)
> From: Francesco Pietra <chiendarret.yahoo.com>
> Subject: Amber9 parallel compilation openmpi issues
> To: Amber <amber.scripps.edu>
>
> Because the intervening interventions may have blurred the original message
> concerning unsuccessful attempts at compiling Amber9 parallel, this is posted
> here again. Serial compilation was OK.
>
> openmpi-1.2.3 was compiled on Debian Linux amd64 etch with
>
> ./configure CC=/opt/intel/cce/9.1.042/bin/icc
> CXX=/opt/intel/cce/9.1.042/bin/icpc F77=/opt/intel/fce/9.1.036/bin/ifort
> FC=/opt/intel/fce/9.1.036/bin/ifort --with-libnuma=/usr/lib
>
> Both
>
> ompi_info |grep libnuma
>
> and
>
> ompi_info |grep maffinity
>
> reported positively.
>
> If useful to know:
>
> /usr/local/openmpi-1.2.3/ompi/mpi/f90 (which also contains c cxx f77).
>
>
>
> Amber9 parallel compilation was attempted on the same machine by first
> setting:
>
> export MPI_HOME=/usr/local/openmpi-1.2.3
>
> Then:
>
> make clean
>
> ./configure -openmpi ifort_x86_64
>
> (must say that I did not find on the configure help a flag for the intel C
> compiler used for openmpi, though probably this is not the issue; the
> application is set to use gcc)
>
> make parallel >& errors.log
>
>
> In attachment: errors.logREN and config.hREN (renamed in order to have true
> attachments with gnome of this i386 desktop)
>
> Thanks
>
> francesco pietra
>
>
>
>
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Received on Sun Jul 29 2007 - 06:07:10 PDT
