[maker-devel] Compilation Problems

[Felix Bemm]

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/Application/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/Application/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