AMBER Archive (2007)

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

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Tue Jul 24 2007 - 02:19:58 CDT

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
> > >>
> > >> -----------------------------------------------------------------------
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> > >> To post, send mail to amber_at_scripps.edu
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> > >>
> > >
> > >
> > >
> > >
> > >
> >
>
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> >
> > 　　　　　　　
> >
> >
> >
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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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