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

From: Ye Mei <ymei.itcc.nju.edu.cn>
Date: Tue, 24 Jul 2007 18:07:31 +0800

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.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.yahoo.com> wrote:
>
>> Date: Tue, 24 Jul 2007 00:17:03 -0700 (PDT)
>> From: Francesco Pietra <chiendarret.yahoo.com>
>> Subject: Re: Re: AMBER: parallel compilation
>> To: amber.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.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.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.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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Received on Wed Jul 25 2007 - 06:07:30 PDT
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