Thanks. config.h attached
If relevant, I should also mention that I first attempted to ./config Amber9
without having set MPI_HOME. In that occasion, besides a warning that that env
variable should be set, the message also indicated to set MPI_HOME to where are
located subdirectories include/ and lib/ containing:
mpi.f
libmpi.a
liblam.a
liblamf77mpi.a
I posed the question to the openmpi mailing list. They answered that all that
is out of their standards, and can't help.
So that I simply set MPI_HOME as indicated in my previous mail
Thanks
francesco pietra
--- Ye Mei <ymei.itcc.nju.edu.cn> wrote:
> Paste config.h here please.
> MPI library is missing during the linking. Maybe you should modify config.h
> and add mpi library to the link option.
>
>
> Best regards,
>
> Ye Mei
> Ph. D.
> ymei.itcc.nju.edu.cn
> Institute of Theoretical and Computational Chemistry
> Key Laboratory of Mesoscopic Chemistry of MOE
> School of Chemistry and Chemical Engineering
> Nanjing University
> Nanjing 210093
> P.R.China
> 2007-07-24
>
>
> ======= 2007-07-24 14:25:21 Francesco Pietra wrote=======
>
> >Thanks.
> >
> >Unfortunately parallel compilation failed, while serial had been successful.
> >What I did (Amber9 Debian Linux amd64 etch):
> >
> >openmpi-1.2.3 compiled 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
> >
> >ompi_info |grep libnuma
> >
> >ompi_info |grep maffinity
> >
> >reported OK
> >
> >Then I set:
> >
> >export MPI_HOME=/usr/local/openmpi-1.2.3
> >
> >Then:
> >
> >make clean
> >
> >./configure -openmpi ifort_x86_64
> >
> >make parallel
> >
> >returned
> >
> >make[1]: [Sander_MPI] Error 1
> >make: *** [parallel] Error 2.
> >
> >
> >Then I did:
> >
> >make clean
> >
> >./configure -openmpi ifort_x86_64
> >
> >make parallel >& errors.log
> >
> >
> >That log file is attached. Unfortunately, the very many errors of type
> >"undefined references to 'mpi_bcast'" are unclear to me.
> >
> >Thanks for help.
> >
> >francesco pietra
> >
> >
> >
> >./configure -openmpi ifort_x86_64
> >
> >reported:
> >
> >Error, MPI_HOME must be set.
> >
> >OK, for my installation and bash it should be
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >--- "David A. Case" <case.scripps.edu> wrote:
> >
> >> On Mon, Jul 23, 2007, Francesco Pietra wrote:
> >>
> >> > I compiled OpenMPI with "ifort" and "icc".
> >> >
> >> > For the successful serial compilation of Amber9 I only set
> "ifort_x86_64"
> >> for
> >> > my platform in ./configure. Then, I noticed that also "gcc" was used for
> >> the
> >> > compilation.
> >> >
> >> > Should the equivalent (if any) for "icc" be set in ./configure for the
> >> parallel
> >> > compilation that I am ready to carry out? Or Sander and pmend and what
> else
> >> is
> >> > compiled parallel use only the fortran compiler?
> >>
> >> It's not clear if you tried what you have, and it failed, or if you have
> not
> >> yet tried anything. Don't be afraid to experiment!
> >>
> >> I don't *think* it makes any difference which C compiler is used.
> >>
> >> ...dac
> >>
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> >
> >
> >
> >
> >
>
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Received on Wed Jul 25 2007 - 06:07:28 PDT
