AMBER Archive (2007)

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

From: Ye Mei (ymei_at_itcc.nju.edu.cn)
Date: Tue Jul 24 2007 - 05:07:31 CDT

It seems that you donot point to the right directory containing openmpi libs.
Here is what I did:
1. to compile openmpi. Compilation failed with CC=icc, so I use gcc/g++ to compile C/C++ code. But this has nothing to do with Amber.
   export FC=ifort
   export F77=ifort
   ./configure --prefix=/usr/local/soft/openmpi/openmpi_intel
   make clean
   make
   make install
2. to configure Amber9
   export MKL_HOME=/usr/local/soft/intel/mkl/9.0
   export AMBERHOME=/home/ymei/amber9
   ./configure -openmpi ifort_x86_64
   then I modified config.h and add "-I/usr/local/soft/openmpi/openmpi_intel/include" to FPPFLAGS and FFLAGS.
   make clean; make parallel

I also include my config.h in the attachment.

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
>> > >>
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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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  • application/octet-stream attachment: config.h

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