Thomas,
The post you are referencing suggests to run
mpiexec -mca btl ^openib -n 40 maker -help
but you are running
mpiexec -mca btl ^openib -N 5 gcc --version
which will run 5 instances of GCC. The out put you're seeing is totally
to be expected.
I don't think anyone here can help you with getting maker to work
correctly with MPI. I suggest you first check whether make is actually
configured to use MPI. The test using maker (as suggested in the post)
does not necessarily mean that Open MPI isn't working, it might also
happen if maker is not correctly configured.
One way to check whether Open MPI is working correctly on your system is
to use a simple MPI program that prints the world communicator size and
rank. Any MPI hello world program you find online should do.
Cheers
Joseph
On 2/18/21 1:39 PM, Thomas Eylenbosch via users wrote:
Hello
We are trying to run
maker(http://www.yandell-lab.org/software/maker.html) in combination
with OpenMPI
But when we are trying to submit a job with the maker and openmpi,
We see the following error in the log file:
--Next Contig--
#---------------------------------------------------------------------
Another instance of maker is processing *this*contig!!
SeqID: chrA10
Length: 17398227
#---------------------------------------------------------------------
According to
http://gmod.827538.n3.nabble.com/Does-maker-support-muti-processing-for-a-single-long-fasta-sequence-using-openMPI-td4061342.html
We have to run the following command mpiexec -mca btl ^openib -n 40
maker -help
“If you get a single help message then everything is fine. If you get
40 help messages, then MPI is not communicating correctly.”
We are using the following command to demonstrate what is going wrong:
mpiexec -mca btl ^openib -N 5 gcc --version
gcc (GCC) 10.2.0
Copyright (C) 2020 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
gcc (GCC) 10.2.0
Copyright (C) 2020 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
gcc (GCC) 10.2.0
Copyright (C) 2020 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
gcc (GCC) 10.2.0
Copyright (C) 2020 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
gcc (GCC) 10.2.0
Copyright (C) 2020 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
So we are getting the message 5 times, which means OpenMPI is not
correctly installed on our cluster?
We are using EasyBuild to build/install our OpenMPI module. ( with the
default OpenMPI easyblock module)
Best regards / met vriendelijke groeten*
Thomas Eylenbosch*
DevOps Engineer (OnSite), Gluo N.V.
*Currently available at BASF Belgium Coordination Center CommV*
Email: thomas.eylenbo...@partners.basf.com
<mailto:thomas.eylenbo...@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 <http://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
