AMBER Archive (2007)

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

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Tue Jul 24 2007 - 09:07:10 CDT

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
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> >> > >>
> >> > >
> >> > >
> >> > >
> >> > >
> >> > >
> >> >
> >>
>
>>____________________________________________________________________________________
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> >> >
> >> > -----------------------------------------------------------------------
> >> > The AMBER Mail Reflector
> >> > To post, send mail to amber_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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