As I wrote, I compiled openmpi-1.2.3 by myself, using intel compilers and
libnuma, and of course following the official site indications.
--- Ye Mei <ymei.itcc.nju.edu.cn> wrote:
> you can download the source code of openmpi and compile it by yourself
> following the faq on the official site or following the way I pasted in my
> previous mails.
> then you can compile amber9 with openmpi support.
>
>
> 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
> 2007-07-25
>
>
> ======= 2007-07-24 23:05:02 Francesco Pietra wrote=======
>
> >Perhaps the openmpi version 1.2.3 has changed. There is no openmpi-1.2.3/bin
> >
> >The closest to what you suggest may be
> >
> >/usr/local/openmpi-1.2.3/ompi/mpi/f90 (which also contains c cxx f77)
> >
> >As to "include", what I only see is a file
> >
> >/usr/local/openmpi-1.2.3/acinclude.m4
> >
> >francesco
> >
> >--- Ye Mei <ymei.itcc.nju.edu.cn> wrote:
> >
> >> I guess the simplest way to do this is to replace ifort in config.h with
> >> /usr/local/openmpi-1.2.3/bin/mpif90
> >>
> >> 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 22:10:32 Francesco Pietra wrote=======
> >>
> >> >Hi Ye:
> >> >
> >> >As to icc, I found no problems in compiling on Debian (once I had
> prepared
> >> by
> >> >the aid of "alien" a deb package from the redhat package that intel
> >> provides).
> >> >
> >> >The ./configure of openmpi was different from your, actually it was
> >> according
> >> >to standards also approved on the Amber mailing list at that time. This
> >> means
> >> >that there is no /soft under /local, and there is no
> /openmpi/openmpi_intel.
> >> At
> >> >least, none where you indicated.
> >> >
> >> >Could you suggest another route to let Amber9 see what she wants to see
> from
> >> my
> >> >installation of openmpi? I prefer not to deviate too much from standards
> for
> >> >Linux, as Debian is rigorous to this concern, and I am no system expert
> to
> >> >remedy.
> >> >
> >> >Thanks
> >> >
> >> >francesco pietra
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >--- Ye Mei <ymei.itcc.nju.edu.cn> wrote:
> >> >
> >> >> I am sorry that I made a mistake in my previous mail.
> >> >> I added "-I/usr/local/soft/openmpi/openmpi_intel/include" to FFLAGS and
> >> >> FOPTFLAGS instead of FPPFLAGS and FFLAGS.
> >> >>
> >> >>
> >> >> 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 15:23:01 Francesco Pietra wrote=======
> >> >>
> >> >> >I forgot to mention that I made clear to Amber mailing list that
> openmpi
> >> was
> >> >> >compiled with intel, both fortran and C/C++. The answer was: the brand
> of
> >> C
> >> >> >compiler is irrelevant. I see from config.h that gcc is advicated
> >> >> >
> >> >> >
> >> >> >--- Francesco Pietra <chiendarret.yahoo.com> wrote:
> >> >> >
> >> >> >> Date: Tue, 24 Jul 2007 00:17:03 -0700 (PDT)
> >> >> >> From: Francesco Pietra <chiendarret.yahoo.com>
> >> >> >> Subject: Re: Re: AMBER: parallel compilation
> >> >> >> To: amber.scripps.edu
> >> >> >>
> >> >> >> 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
> >> >> >> > >>
> >> >> >> > >>
> >> >> -----------------------------------------------------------------------
> >> >> >> > >> The AMBER Mail Reflector
> >> >> >> > >> To post, send mail to amber.scripps.edu
> >> >> >> > >> To unsubscribe, send "unsubscribe amber" to
> majordomo.scripps.edu
> >> >> >> > >>
> >> >> >> > >
> >> >> >> > >
> >> >> >> > >
> >> >> >> > >
> >> >> >> > >
> >> >> >> >
> >> >> >>
> >> >>
> >>
>
>>>>____________________________________________________________________________________
> >> >> >> > >Get the Yahoo! toolbar and be alerted to new email wherever
> you're
> >> >> >> surfing.
> >> >> >> > >http://new.toolbar.yahoo.com/toolbar/features/mail/index.php
> >> >> >> >
> >> >> >> > = = = = = = = = = = = = = = = = = = = =
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> -----------------------------------------------------------------------
> >> >> >> > The AMBER Mail Reflector
> >> >> >> > To post, send mail to amber.scripps.edu
> >> >> >> > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >> >> >> >
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >>
> >> >>
> >>
>
>>>____________________________________________________________________________________
> >> >> >> Got a little couch potato?
> >> >> >> Check out fun summer activities for kids.
> >> >> >>
> >> >>
> >>
>
>>>http://search.yahoo.com/search?fr=oni_on_mail&p=summer+activities+for+kids&cs=bz
> >> >> >>
> >> >>
> >>
>
>>>#==============================================================================
> >> >> >> # AMBER Makefile configuration for compiler/architecture:
> ifort_x86_64
> >> >> >> # Generated via command: ./configure -openmpi ifort_x86_64
> >> >> >> #
> >> >> >> # Configuration script written mainly by Joe Krahn, Scott Brozell,
> and
> >> >> >> # Dave Case, with contributions from lots of people.
> >> >> >>
> >> >>
> >>
>
>>>#==============================================================================
> >> >> >>
> >> >> >>
> >> >>
> >>
>
>>>#------------------------------------------------------------------------------
> >> >> >> # Main AMBER source root directory
> >> >> >>
> >> >>
> >>
>
>>>#------------------------------------------------------------------------------
> >> >> >> AMBER_SRC=/usr/local/amber9/src
> >> >> >>
> >> >> >>
> >> >>
> >>
>
>>>#------------------------------------------------------------------------------
> >> >> >> # AMBERBUILDFLAGS provides a hook into the build process for
> >> installers;
> >> >> >> # for example, to build debug versions of the amber programs
> >> >> >> # make -e AMBERBUILDFLAGS="-DDEBUG -g"
> >> >> >>
> >> >>
> >>
>
>>>#------------------------------------------------------------------------------
> >> >> >> AMBERBUILDFLAGS=
> >> >> >>
> >> >> >>
> >> >>
> >>
>
>>>#------------------------------------------------------------------------------
> >> >> >> # LOCALFLAGS is intended for program specific modifications to the
> >> >> >> # Fortran build process and may be modified by the program's local
> >> >> makefile
> >> >> >>
> >> >>
> >>
>
>>>#------------------------------------------------------------------------------
> >> >> >> LOCALFLAGS=
> >> >> >>
> >> >> >>
> >> >>
> >>
>
>>>#------------------------------------------------------------------------------
> >> >> >> # Availability and method of delivery of math and optional libraries
> >> >> >>
> >> >>
> >>
>
>>>#------------------------------------------------------------------------------
> >> >> >> USE_BLASLIB=$(SOURCE_COMPILED)
> >> >> >> USE_LAPACKLIB=$(SOURCE_COMPILED)
> >> >> >> USE_LMODLIB=$(LMOD_UNAVAILABLE)
> >> >> >>
> >> >> >>
> >> >>
> >>
>
>>>#------------------------------------------------------------------------------
> >> >> >> # C compiler
> >> >> >>
> >> >>
> >>
>
>>>#------------------------------------------------------------------------------
> >> >> >> CC= gcc
> >> >> >> CPLUSPLUS=g++
> >> >> >> CFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2
> >> >> >> CPPFLAGS= $(AMBERBUILDFLAGS)
> >> >> >>
> >> >> >>
> >> >>
> >>
>
>>>#------------------------------------------------------------------------------
> >> >> >> # Fortran preprocessing and compiler.
> >> >> >> # FPPFLAGS holds the main Fortran options, such as whether MPI is
> used.
> >> >> >>
> >> >>
> >>
>
>>>#------------------------------------------------------------------------------
> >> >> >> FPPFLAGS= -I/usr/local/openmpi-1.2.3/include -P -DMPI
> >> $(AMBERBUILDFLAGS)
> >> >> >> FPP= cpp -traditional $(FPPFLAGS)
> >> >> >> FC= ifort
> >> >> >> FFLAGS= -w95 -mp1 -O0 $(LOCALFLAGS) $(AMBERBUILDFLAGS)
> >> >> >> FOPTFLAGS= -w95 -mp1 -ip -O3 -tpp7 -axWP $(LOCALFLAGS)
> >> >> $(AMBERBUILDFLAGS)
> >> >> >> FREEFORMAT_FLAG= -FR
> >> >> >>
> >> >> >>
> >> >>
> >>
>
>>>#------------------------------------------------------------------------------
> >> >> >> # Loader:
> >> >> >>
> >> >>
> >>
>
>>>#------------------------------------------------------------------------------
> >> >> >> LOAD= ifort $(LOCALFLAGS) $(AMBERBUILDFLAGS)
> >> >> >> LOADCC= gcc $(LOCALFLAGS) $(AMBERBUILDFLAGS)
> >> >> >> LOADLIB=
> >> >> >> LM= -lm
> >> >> >> LOADPTRAJ= ifort -nofor_main $(LOCALFLAGS) $(AMBERBUILDFLAGS)
> >> >> >> XHOME= /usr/X11R6
> >> >> >> XLIBS= -L/usr/X11R6/lib64 -L/usr/X11R6/lib
> >> >> >>
> >> >> >>
> >> >>
> >>
>
>>>#------------------------------------------------------------------------------
> >> >> >> # Other stuff:
> >> >> >>
> >> >>
> >>
>
>>>#------------------------------------------------------------------------------
> >> >> >> .SUFFIXES: .f90
> >> >> >> EMPTY=
> >> >> >> AR=ar rv $(EMPTY)
> >> >> >> M4=m4
> >> >> >> RANLIB=ranlib
> >> >> >> SFX=
> >> >> >> NETCDF=
> >> >> >> NETCDFLIB=
> >> >> >> MODULEDIR=-I
> >> >> >> MAKEDEPEND=$(AMBER_SRC)/../bin/amber_makedepend
> >> >> >> SLKO=skipDFTB
> >> >> >>
> >> >> >> # default rules for Fortran and C compilation:
> >> >> >>
> >> >> >> .f.o: $<
> >> >> >> $(FPP) $< > _$<
> >> >> >> $(FC) -c $(FFLAGS) -o $. _$<
> >> >> >>
> >> >> >> .c.o:
> >> >> >> $(CC) -c $(CFLAGS) $(CPPFLAGS) -o $. $<
> >> >> >>
> >> >> >>
> >> >> >
> >> >> >
> >> >> >
> >> >> >
> >> >>
> >>
>
>>>____________________________________________________________________________________
> >> >> >Choose the right car based on your needs. Check out Yahoo! Autos new
> Car
> >> >> Finder tool.
> >> >> >http://autos.yahoo.com/carfinder/
> >> >>
> >> >> = = = = = = = = = = = = = = = = = = = =
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >> -----------------------------------------------------------------------
> >> >> The AMBER Mail Reflector
> >> >> To post, send mail to amber.scripps.edu
> >> >> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >> >>
> >> >
> >> >
> >> >
> >> >
> >>
>
>____________________________________________________________________________________
> >> >Luggage? GPS? Comic books?
> >> >Check out fitting gifts for grads at Yahoo! Search
> >> >http://search.yahoo.com/search?fr=oni_on_mail&p=graduation+gifts&cs=bz
> >> >-----------------------------------------------------------------------
> >> >The AMBER Mail Reflector
> >> >To post, send mail to amber.scripps.edu
> >> >To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >> >
> >>
> >> = = = = = = = = = = = = = = = = = = = =
> >>
> >>
> >>
> >>
> >>
> >>
> >> -----------------------------------------------------------------------
> >> The AMBER Mail Reflector
> >> To post, send mail to amber.scripps.edu
> >> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >>
> >
> >
> >
> >
>
>____________________________________________________________________________________
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> >
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> = = = = = = = = = = = = = = = = = = = =
>
>
>
>
>
>
> -----------------------------------------------------------------------
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Received on Sun Jul 29 2007 - 06:07:04 PDT
