[maker-devel] Compilation Problems

[Carson Holt]

It is a problem with compilation of the shared libraries in MPICH2.  You
can try recompiling MPICH2 and adding '-fPIC' to your CFLAGS, CCFLAGS and
CXXFLAGS environmental variables.  Alternatively I would recommend not
using MPICH2 3.0.1 for production purposes as it is not really MPICH2 it
is the new MPICH3.  It is their first attempt to provide full support of
the new MPI-3 standard, so compared to other MPICH2 releases which all use
the MPI-2 standard it will be very buggy.  So avoid it unless your inner
geek loves the pain that comes from working with bleeding edge advances.
I would recommend using the last release of MPICH2 which was version 1.5.

Thanks,
Carson


On 13-01-09 10:09 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:

>Hi,
>
>I am trying to compile maker (2.27-beta) with MPI support on Ubuntu
>12.04 LTS. I have a MPI version from the repository (openMPI 1.5.4) and
>a self compiled version (MPICH2 3.0.1) at hand. The latter one was
>compiled with the -enable-shared flag. I got the following error during
>the maker install command with both versions:
>
>Configuring MAKER with MPI support
>/usr/bin/perl /usr/share/perl/5.14/ExtUtils/xsubpp  -typemap
>"/usr/share/perl/5.14/ExtUtils/typemap"   MPI.xs > MPI.xsc && mv MPI.xsc
>MPI.c
>/software/mpich/bin/mpicc -c
>-I"/storage/software/intel64/maker-2.27-beta/src"
>-I/software/mpich/include -D_REENTRANT -D_GNU_SOURCE -DDEBIAN
>-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include
>-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g   -DVERSION=\"0.00\"
>-DXS_VERSION=\"0.00\" -fPIC "-I/usr/lib/perl/5.14/CORE"   MPI.c
>MPI.xs: In Funktion »_MPI_Send«:
>MPI.xs:42:5: Warnung: Übergabe des Arguments 3 von »Perl_sv_2pv_flags«
>von inkompatiblem Zeigertyp [standardmäßig aktiviert]
>/usr/lib/perl/5.14/CORE/proto.h:3565:21: Anmerkung: »STRLEN * const«
>erwartet, aber Argument hat Typ »int *«
>Running Mkbootstrap for Parallel::Application::MPI ()
>chmod 644 MPI.bs
>rm -f blib/arch/auto/Parallel/Application/MPI/MPI.so
>/software/mpich/bin/mpicc  -shared -O2 -g -L/usr/local/lib
>-fstack-protector MPI.o  -o
>blib/arch/auto/Parallel/Application/MPI/MPI.so 	\
>	     	\
>	
>/usr/bin/ld:
>/storage/software/intel64/mpich-3.01/lib/libmpich.a(comm_rank.o):
>relocation R_X86_64_32 against `MPIR_ThreadInfo' can not be used when
>making a shared object; recompile with -fPIC
>/storage/software/intel64/mpich-3.01/lib/libmpich.a: could not read
>symbols: Bad value
>collect2: ld gab 1 als Ende-Status zurück
>make: *** [blib/arch/auto/Parallel/Application/MPI/MPI.so] Fehler 1
>
>A problem was encountered while attempting to compile and install your
>Inline
>C code. The command that failed was:
>  make > out.make 2>&1
>
>The build directory was:
>/storage/software/intel64/maker-2.27-beta/src/blib/build/Parallel/Applicat
>ion/MPI
>
>To debug the problem, cd to the build directory, and inspect the output
>files.
>
> at
>/storage/software/intel64/maker-2.27-beta/src/../perl/lib/Parallel/Applica
>tion/MPI.pm
>line 223
>
>Does anybody have an idea, what is happening here?
>
>Best regards
>Felix
>
>-- 
>Felix Bemm
>Department of Bioinformatics
>University of Würzburg, Germany
>Tel: +49 931 - 31 83696
>Fax: +49 931 - 31 84552
>felix.bemm at uni-wuerzburg.de
>
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