[maker-devel] maker MPI

[Kathryn E. Bushley]

Greetings,

We are reinstalling maker after a system upgrade and having some  
issues with getting MPI version running.  One question, will maker  
only run in MPI-CH2 or will it also run in LAM-MPI?  When trying to  
run in MPI-CH2, we get this error:

/local/cluster/mpich2-1.2.1p1/bin/mpdboot -f  
/home/bpp/bushleyk/MPI2/fungi0_machinefile.txt
cd /pseudospace2/bushleyk/MAKER/Testrun;  
/local/cluster/mpich2-1.2.1p1/bin/mpiexec -machinefile  
/home/bpp/bushleyk/MPI2/fungi0_machinefile.txt -n 4  
'/local/cluster/MAKER_2.10/bin/mpi_maker'
/usr/bin/perl: symbol lookup error:  
/local/cluster/MAKER_2.10/bin/../perl/lib/auto/Parallel/MPIcar/MPIcar.so:  
undefined symbol: Perl_Tstack_sp_ptr
/usr/bin/perl: symbol lookup error:  
/local/cluster/MAKER_2.10/bin/../perl/lib/auto/Parallel/MPIcar/MPIcar.so:  
undefined symbol: Perl_Tstack_sp_ptr
/usr/bin/perl: symbol lookup error:  
/local/cluster/MAKER_2.10/bin/../perl/lib/auto/Parallel/MPIcar/MPIcar.so:  
undefined symbol: Perl_Tstack_sp_ptr
/usr/bin/perl: symbol lookup error:  
/local/cluster/MAKER_2.10/bin/../perl/lib/auto/Parallel/MPIcar/MPIcar.so:  
undefined symbol: Perl_Tstack_sp_ptr
make: *** [maker] Error 127

which maybe means it's not finding the right perl?


When trying to run in LAM-MPI we get this error, was wondering what  
the MAKER/EVALUATOR is?

ERROR: Cannot start process. MAKER/EVALUATOR already running
with different settings in this same directory.


FATAL ERROR
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
/local/cluster/spatafora/RepeatMasker/RepeatMasker  
/pseudospace2/bushleyk/MAKER/Testrun/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.all.rb -species all -dir /pseudospace2/bushleyk/MAKER/Testrun/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500 -pa  
1
#-------------------------------#
-----------------------------------------------------------------------------
It seems that [at least] one of the processes that was started with
mpirun did not invoke MPI_INIT before quitting (it is possible that
more than one process did not invoke MPI_INIT -- mpirun was only
notified of the first one, which was on node n0).

mpirun can *only* be used with MPI programs (i.e., programs that
invoke MPI_INIT and MPI_FINALIZE).  You can use the "lamexec" program
to run non-MPI programs over the lambooted nodes.
-----------------------------------------------------------------------------
Received SIGTERM
make: *** [maker_new] Error 252








Best,

Kathryn


"To err is human...to really foul up requires the root password."


Kathryn E. Bushley
Postdoctoral Researcher
2082 Cordley Hall
Department of Botany and Plant Pathology
Oregon State University
Corvallis, OR 97331
office: (541) 737-5284
cell: (541) 908-0116