[maker-devel] maker/openmpi multiple jobs dont "see" each other

[Thomas Eylenbosch]

Hello

My apologies if this email has been received twice, but it seems I was not accepted yet for the mailing list.

We are trying to run a maker job with the combination of openmpi.
And we are using the following qsub script

#!/bin/bash


## SGE settings
#$ -N j_maker_20210204_112200_53455
#$ -pe openmpi 8
#$ -o log.out
#$ -e log.err
#$ -M campaga2
#$ -hard
#$ -q main.largemem,main.regular
#$ -l vf=6.250G,h_rss=55G
##
...
# Run the command
mpiexec -n 8     \
$installpath/maker "maker_opts.ctl" "maker_bopts.ctl" "maker_exe.ctl"


But we receive the following error:
it seems that the multiple jobs dont "see" each other which cause the following message


--Next Contig--



#---------------------------------------------------------------------

Another instance of maker is processing this contig!!

SeqID: chrA10

Length: 17398227

#---------------------------------------------------------------------

Which is probably related with the following topic:
http://gmod.827538.n3.nabble.com/Does-maker-support-muti-processing-for-a-single-long-fasta-sequence-using-openMPI-td4061342.html

maker is installed with the openmpi options, and our openmpi software is correctly installed
I have downloaded this example: https://raw.githubusercontent.com/open-mpi/ompi/master/examples/hello_c.c
And I build it and run it, and it seems openmpi is correctly installed.

piexec --mca btl ^openib -N 5 ./hello_c

Hello, world, I am 0 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129)

Hello, world, I am 1 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129)

Hello, world, I am 3 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129)

Hello, world, I am 4 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129)

Hello, world, I am 2 of 5, (Open MPI v4.0.5, package: Open MPI easybuild@$servername Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129)
It is displaying 5 different lines (rank 0 to 4 of 5).

Could you help us with the "Another instance of maker is processing this contig" error message ?


Best regards / met vriendelijke groeten
Thomas Eylenbosch
DevOps Engineer (OnSite), Gluo N.V.

Currently available at BASF Belgium Coordination Center CommV
Email: thomas.eylenbosch at partners.basf.com<mailto:thomas.eylenbosch at partners.basf.com>
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