[maker-devel] Compilation Problems

[Felix Bemm]

Thanks Carson,

version change (to mpich2 1.5) fixed the problem. I did not realize that
I was downloading some mpich3 after all. Thanks again for the fast help!

Best regards
Felix

On 09.01.2013 16:18, Carson Holt wrote:
> 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
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-- 
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