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
>> >> >
>> >>
>> >>
>> >>
>> >>
>> >>
>>
>>____________________________________________________________________________________
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>> >>
>>
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>>
>>#==============================================================================
>> >> # 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/
>>
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>>
>>
>>
>>
>>
>>
>> -----------------------------------------------------------------------
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>> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>>
>
>
>
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Received on Wed Jul 25 2007 - 06:07:34 PDT
