[maker-devel] Compilation Problems

[Carson Holt]

I'm Glad it worked.

Thanks,
Carson


On 13-01-09 10:53 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:

>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/Applic
>>>at
>>> 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/Appli
>>>ca
>>> 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
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org