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

[Thomas Eylenbosch]

Hello

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
Postal Address: BASF Belgium Coordination Center CommV, Technologiepark 101, 9052 Gent Zwijnaarde, Belgium

BASF Belgium Coordination Center CommV
Scheldelaan 600, 2040 Antwerpen, België
RPR Antwerpen (afd. Antwerpen)
BTW BE0862.390.376

www.basf.be

Deutsche Bank AG
IBAN: BE43 8262 8044 4801
BIC: DEUTBEBE


Information on data protection can be found here: https://www.basf.com/global/en/legal/data-protection-at-basf.html




-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20210223/320fc01a/attachment-0002.html>