AMBER Archive (2007)

Subject: Re: Re: Fwd: Re: Re: AMBER: parallel compilation

From: Ye Mei (ymei_at_itcc.nju.edu.cn)
Date: Tue Jul 24 2007 - 09:26:26 CDT

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_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 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_at_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_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 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_at_yahoo.com> wrote:
>> >
>> >> Date: Tue, 24 Jul 2007 00:17:03 -0700 (PDT)
>> >> From: Francesco Pietra <chiendarret_at_yahoo.com>
>> >> Subject: Re: Re: AMBER: parallel compilation
>> >> To: amber_at_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_at_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_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
>> >> > >>
>> >> > >>
>> -----------------------------------------------------------------------
>> >> > >> The AMBER Mail Reflector
>> >> > >> To post, send mail to amber_at_scripps.edu
>> >> > >> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>> >> > >>
>> >> > >
>> >> > >
>> >> > >
>> >> > >
>> >> > >
>> >> >
>> >>
>>
>>>____________________________________________________________________________________
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>> >> >
>> >> > = = = = = = = = = = = = = = = = = = = =
>> >> >
>> >> >
>> >> > 　　　　　　　
>> >> >
>> >> >
>> >> >
>> >> > -----------------------------------------------------------------------
>> >> > The AMBER Mail Reflector
>> >> > To post, send mail to amber_at_scripps.edu
>> >> > To unsubscribe, send "unsubscribe amber" to majordomo_at_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 $@ $<
>> >>
>> >>
>> >
>> >
>> >
>> >
>>
>>____________________________________________________________________________________
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>> Finder tool.
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>>
>> = = = = = = = = = = = = = = = = = = = =
>>
>>
>> 　　　　　　　
>>
>>
>>
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
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>>
>
>
>
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