AMBER Archive (2007)

Subject: Re: Re: AMBER: parallel compilation

From: Ye Mei (ymei_at_itcc.nju.edu.cn)
Date: Tue Jul 24 2007 - 01:44:43 CDT

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_at_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_at_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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