[maker-devel] Maker 2.31 fails with MPI.pm

[Carson Holt]

Hi Ann,

Build.PL just configures (the status message only shows me your configuration choices).  You still have to run './Build install’.  Your error shows that you configured maker for MPI but never ran the install step successfully.

You should get something like this —>

$ ./Build install
Installing MAKER...
Configuring MAKER with MPI support
Installing maker/2.31.8/src/../perl/lib/Parallel/Application/MPI.pm
Installing maker/2.31.8/src/../perl/lib/auto/Parallel/Application/MPI/MPI.so
Installing maker/2.31.8/src/../perl/lib/auto/Parallel/Application/MPI/MPI.inl
cp blib/config-x86_64-linux-thread-multi-5.010001 maker/2.31.8/src/../perl/config-x86_64-linux-thread-multi-5.010001


Thanks,
Carson



> On Jun 11, 2015, at 3:44 PM, Ann Danowitz <adanowitz8 at gmail.com> wrote:
> 
> Hello Yandell maker gurus,
> 
> Installed Maker 2.31 with MPICH2 .
> No errors with Build.PL and Build install 
> ==============================================================================
> STATUS MAKER v2.31.8
> ==============================================================================
> PERL Dependencies:	VERIFIED
> External Programs:	VERIFIED
> External C Libraries:	VERIFIED
> MPI SUPPORT:		ENABLED
> MWAS Web Interface:	DISABLED
> MAKER PACKAGE:		CONFIGURATION OK
> 
> but with the following command, maker fails:
> 
> dcopetti at bam:/opt/bam_processing/Dario/MAKER_mpi[4:21pm]> mpiexec -n 20 /opt/maker/bin/maker maker_opts_wg_bam_mpi.ctl maker_bopts_wg_bam_mpi.ctl maker_exe_wg_bam_mpi.ctl
> 
>  at /opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 236.
> --> rank=NA, hostname=bam.genome.arizona.edu <http://bam.genome.arizona.edu/>
>     ...propagated at /usr/local/share/perl5/Inline/C.pm line 772.
> --> rank=NA, hostname=bam.genome.arizona.edu <http://bam.genome.arizona.edu/>
>  at /opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 256.
>     Parallel::Application::MPI::_bind("/usr/lib64/openmpi/bin/mpicc", "/usr/include", "/opt/maker/bin/../perl", "") called at /opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 213
>     Parallel::Application::MPI::_load() called at /opt/maker/bin/../perl/lib/Parallel/Application/MPI.pm line 74
>     Parallel::Application::MPI::MPI_Init() called at /opt/maker/bin/maker line 279
> 
> {line 279     stat = MPI_Init(&PL_origargc, &PL_origargv);}
> 
> make: *** No targets specified and no makefile found.  Stop.
> 
> A problem was encountered while attempting to compile and install your Inline
> C code. The command that failed was:
>   make > out.make 2>&1
> 
> [root at bam ~]# more /opt/maker/perl/build/Parallel/Application/MPI/out.make_install
> Makefile:123: warning: NUL character seen; rest of line ignored
> Makefile:123: *** missing separator.  Stop.
> 
> also from out.make in the same directory:
> make: *** [MPI.c] mv: cannot stat `MPI.xsc': No such file or directory
> make: *** [MPI.c] Error 1
>  or directory
> make: *** [MPI.c] Error 1
> 
> What values are not getting passed to MPI.pm?
> 
> Many thanks for any help!
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