Re: [OMPI devel] Remove stale OPAL dss and opal_tree code

2021-02-18 Thread Jeff Squyres (jsquyres) via devel 
On Feb 18, 2021, at 10:55 AM, Ralph Castain via devel 
mailto:devel@lists.open-mpi.org>> wrote:

I'm planning on removing the OPAL dss (pack/unpack) code as part of my work to 
reduce the code base I historically supported. The pack/unpack functionality is 
now in PMIx (has been since v3.0 was released), and so we had duplicate 
capabilities spread across OPAL and PRRTE. I have already removed the PRRTE 
code in favor of unifying on PMIx as the lowest common denominator.

The following PR removes OPAL dss and an "opal_tree" class that called it but 
wasn't used anywhere in the code: https://github.com/open-mpi/ompi/pull/8492

I have updated the very few places in OMPI/OSHMEM that touched the dss to use 
the PMIx equivalents. Please take a look and note any concerns on the PR. Minus 
any objections, I'll plan on committing this after next Tuesday's telecon.

Duplicate / dead code removal: excellent!

--
Jeff Squyres
jsquy...@cisco.com

[OMPI devel] Remove stale OPAL dss and opal_tree code

2021-02-18 Thread Ralph Castain via devel 
Hi folks

I'm planning on removing the OPAL dss (pack/unpack) code as part of my work to 
reduce the code base I historically supported. The pack/unpack functionality is 
now in PMIx (has been since v3.0 was released), and so we had duplicate 
capabilities spread across OPAL and PRRTE. I have already removed the PRRTE 
code in favor of unifying on PMIx as the lowest common denominator.

The following PR removes OPAL dss and an "opal_tree" class that called it but 
wasn't used anywhere in the code: https://github.com/open-mpi/ompi/pull/8492

I have updated the very few places in OMPI/OSHMEM that touched the dss to use 
the PMIx equivalents. Please take a look and note any concerns on the PR. Minus 
any objections, I'll plan on committing this after next Tuesday's telecon.

Thanks
Ralph

Re: [OMPI devel] [EXT] Re: OpenMPI and maker - Multiple messages

2021-02-18 Thread Thomas Eylenbosch via devel 
All


Thank you all your help and for the example.

It seems openmpi is correctly installed like Gilles said

$ mpiexec --mca btl ^openib -N 5 ./hello_c
Hello, world, I am 0 of 5, (Open MPI v4.0.5, package: Open MPI 
easybu...@by0q5b.eu.seeds.basf.net 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 
easybu...@by0q5b.eu.seeds.basf.net 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 
easybu...@by0q5b.eu.seeds.basf.net 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 
easybu...@by0q5b.eu.seeds.basf.net 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 
easybu...@by0q5b.eu.seeds.basf.net Distribution, ident: 4.0.5, repo rev: 
v4.0.5, Aug 26, 2020, 129)

I will go back to the topic of maker where I will take a deeper look into the 
issue.

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
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




From: devel  On Behalf Of Gilles Gouaillardet 
via devel
Sent: Thursday, February 18, 2021 1:57 PM
To: Open MPI Developers 
Cc: Gilles Gouaillardet 
Subject: [EXT] Re: [OMPI devel] OpenMPI and maker - Multiple messages

Thomas,

in order to test Open MPI, you can download 
https://raw.githubusercontent.com/open-mpi/ompi/master/examples/hello_c.c

and build it

$ mpicc -o hello_c examples/hello_c.c

and then run
$ mpiexec --mca btl ^openib -N 5 ./hello_c

It should display 5 different lines (rank 0 to 4 of 5).
If you see the same line (I am 0 of 1) 5 times, this indicates an issue.

Cheers,

Gilles

On Thu, Feb 11, 2021 at 12:36 AM Thomas Eylenbosch via devel 
mailto:devel@lists.open-mpi.org>> 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
Postal Address: BASF Belgium Coordination Center CommV, Technologiepark 101, 
9052 Gent Zwijnaarde,

Re: [OMPI devel] OpenMPI and maker - Multiple messages

2021-02-18 Thread Gilles Gouaillardet via devel 
Thomas,

in order to test Open MPI, you can download
https://raw.githubusercontent.com/open-mpi/ompi/master/examples/hello_c.c

and build it

$ mpicc -o hello_c examples/hello_c.c

and then run
$ mpiexec --mca btl ^openib -N 5 ./hello_c

It should display 5 different lines (rank 0 to 4 of 5).
If you see the same line (I am 0 of 1) 5 times, this indicates an issue.

Cheers,

Gilles

On Thu, Feb 11, 2021 at 12:36 AM Thomas Eylenbosch via devel <
devel@lists.open-mpi.org> 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
> 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
>
>
>
>
>
>
>
>
>