AMBER Archive (2007)

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

From: Ye Mei (ymei_at_itcc.nju.edu.cn)
Date: Tue Jul 24 2007 - 21:27:04 CDT

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_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
2007-07-25

======= 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_at_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_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
>> >> >> > >>
>> >> >> > >
>> >> >> > >
>> >> >> > >
>> >> >> > >
>> >> >> > >
>> >> >> >
>> >> >>
>> >>
>>
>>>>____________________________________________________________________________________
>> >> >> > >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_at_scripps.edu
>> >> >> > To unsubscribe, send "unsubscribe amber" to majordomo_at_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_at_scripps.edu
>> >> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>> >>
>> >
>> >
>> >
>> >
>>
>____________________________________________________________________________________
>> >Luggage? GPS? Comic books?
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>> >-----------------------------------------------------------------------
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>> >To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>> >
>>
>> = = = = = = = = = = = = = = = = = = = =
>>
>>
>> 　　　　　　　
>>
>>
>>
>> -----------------------------------------------------------------------
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