[OMPI users] Is the mpi.3 manpage out of date?

2020-08-25 Thread Riebs, Andy via users 
In searching to confirm my belief that recent versions of Open MPI support the 
MPI-3.1 standard, I was a bit surprised to find this in the mpi.3 man page from 
the 4.0.2 release:

"The  outcome,  known  as  the MPI Standard, was first published in 1993; its 
most recent version (MPI-2) was published in July 1997. Open MPI 1.2 includes 
all MPI 1.2-compliant and MPI 2-compliant routines."

(For those who are manpage-averse, see < 
https://www.open-mpi.org/doc/v4.0/man3/MPI.3.php>.)

I'm willing to bet that y'all haven't been sitting on your hands since Open MPI 
1.2 was released!

Andy

--
Andy Riebs
andy.ri...@hpe.com
Hewlett Packard Enterprise
High Performance Computing Software Engineering
+1 404 648 9024

Re: [OMPI users] Can't start jobs with srun.

2020-04-27 Thread Riebs, Andy via users 
Lost a line…

Also helpful to check

$ srun -N3 which ompi_info

From: users [mailto:users-boun...@lists.open-mpi.org] On Behalf Of Riebs, Andy 
via users
Sent: Monday, April 27, 2020 10:59 AM
To: Open MPI Users 
Cc: Riebs, Andy 
Subject: Re: [OMPI users] Can't start jobs with srun.

Y’know, a quick check on versions and PATHs might be a good idea here. I 
suggest something like

$ srun  -N3  ompi_info  |&  grep  "MPI repo"

to confirm that all nodes are running the same version of OMPI.

From: users [mailto:users-boun...@lists.open-mpi.org] On Behalf Of Prentice 
Bisbal via users
Sent: Monday, April 27, 2020 10:25 AM
To: users@lists.open-mpi.org<mailto:users@lists.open-mpi.org>
Cc: Prentice Bisbal mailto:pbis...@pppl.gov>>
Subject: Re: [OMPI users] [External] Re: Can't start jobs with srun.


Ralph,

PMI2 support works just fine. It's just PMIx that seems to be the problem.

We rebuilt Slurm with PMIx 3.1.5, but the problem persists. I've opened a 
ticket with Slurm support to see if it's a problem on Slurm's end.

Prentice
On 4/26/20 2:12 PM, Ralph Castain via users wrote:
It is entirely possible that the PMI2 support in OMPI v4 is broken - I doubt it 
is used or tested very much as pretty much everyone has moved to PMIx. In fact, 
we completely dropped PMI-1 and PMI-2 from OMPI v5 for that reason.

I would suggest building Slurm with PMIx v3.1.5 
(https://github.com/openpmix/openpmix/releases/tag/v3.1.5) as that is what OMPI 
v4 is using, and launching with "srun --mpi=pmix_v3"


On Apr 26, 2020, at 10:07 AM, Patrick Bégou via users 
mailto:users@lists.open-mpi.org>> wrote:

I have also this problem on servers I'm benching at DELL's lab with
OpenMPI-4.0.3. I've tried  a new build of OpenMPI with "--with-pmi2". No
change.
Finally my work around in the slurm script was to launch my code with
mpirun. As mpirun was only finding one slot per nodes I have used
"--oversubscribe --bind-to core" and checked that every process was
binded on a separate core. It worked but do not ask me why :-)

Patrick

Le 24/04/2020 à 20:28, Riebs, Andy via users a écrit :
Prentice, have you tried something trivial, like "srun -N3 hostname", to rule 
out non-OMPI problems?

Andy

-Original Message-
From: users [mailto:users-boun...@lists.open-mpi.org] On Behalf Of Prentice 
Bisbal via users
Sent: Friday, April 24, 2020 2:19 PM
To: Ralph Castain mailto:r...@open-mpi.org>>; Open MPI Users 
mailto:users@lists.open-mpi.org>>
Cc: Prentice Bisbal mailto:pbis...@pppl.gov>>
Subject: Re: [OMPI users] [External] Re: Can't start jobs with srun.

Okay. I've got Slurm built with pmix support:

$ srun --mpi=list
srun: MPI types are...
srun: none
srun: pmix_v3
srun: pmi2
srun: openmpi
srun: pmix

But now when I try to launch a job with srun, the job appears to be
running, but doesn't do anything - it just hangs in the running state
but doesn't do anything. Any ideas what could be wrong, or how to debug
this?

I'm also asking around on the Slurm mailing list, too

Prentice

On 4/23/20 3:03 PM, Ralph Castain wrote:
You can trust the --mpi=list. The problem is likely that OMPI wasn't configured 
--with-pmi2


On Apr 23, 2020, at 11:59 AM, Prentice Bisbal via users 
mailto:users@lists.open-mpi.org>> wrote:

--mpi=list shows pmi2 and openmpi as valid values, but if I set --mpi= to 
either of them, my job still fails. Why is that? Can I not trust the output of 
--mpi=list?

Prentice

On 4/23/20 10:43 AM, Ralph Castain via users wrote:
No, but you do have to explicitly build OMPI with non-PMIx support if that is 
what you are going to use. In this case, you need to configure OMPI 
--with-pmi2=

You can leave off the path if Slurm (i.e., just "--with-pmi2") was installed in 
a standard location as we should find it there.


On Apr 23, 2020, at 7:39 AM, Prentice Bisbal via users 
mailto:users@lists.open-mpi.org>> wrote:

It looks like it was built with PMI2, but not PMIx:

$ srun --mpi=list
srun: MPI types are...
srun: none
srun: pmi2
srun: openmpi

I did launch the job with srun --mpi=pmi2 

Does OpenMPI 4 need PMIx specifically?


On 4/23/20 10:23 AM, Ralph Castain via users wrote:
Is Slurm built with PMIx support? Did you tell srun to use it?


On Apr 23, 2020, at 7:00 AM, Prentice Bisbal via users 
mailto:users@lists.open-mpi.org>> wrote:

I'm using OpenMPI 4.0.3 with Slurm 19.05.5  I'm testing the software with a 
very simple hello, world MPI program that I've used reliably for years. When I 
submit the job through slurm and use srun to launch the job, I get these errors:

*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
***and potentially your MPI job)
[dawson029.pppl.gov:26070<http://dawson029.pppl.gov:26070>] Local abort before 
MPI_INIT completed completed successfully, but am not able to aggregate error 
messages,

Re: [OMPI users] Can't start jobs with srun.

2020-04-27 Thread Riebs, Andy via users 
Y’know, a quick check on versions and PATHs might be a good idea here. I 
suggest something like

$ srun  -N3  ompi_info  |&  grep  "MPI repo"

to confirm that all nodes are running the same version of OMPI.

From: users [mailto:users-boun...@lists.open-mpi.org] On Behalf Of Prentice 
Bisbal via users
Sent: Monday, April 27, 2020 10:25 AM
To: users@lists.open-mpi.org
Cc: Prentice Bisbal 
Subject: Re: [OMPI users] [External] Re: Can't start jobs with srun.


Ralph,

PMI2 support works just fine. It's just PMIx that seems to be the problem.

We rebuilt Slurm with PMIx 3.1.5, but the problem persists. I've opened a 
ticket with Slurm support to see if it's a problem on Slurm's end.

Prentice
On 4/26/20 2:12 PM, Ralph Castain via users wrote:
It is entirely possible that the PMI2 support in OMPI v4 is broken - I doubt it 
is used or tested very much as pretty much everyone has moved to PMIx. In fact, 
we completely dropped PMI-1 and PMI-2 from OMPI v5 for that reason.

I would suggest building Slurm with PMIx v3.1.5 
(https://github.com/openpmix/openpmix/releases/tag/v3.1.5) as that is what OMPI 
v4 is using, and launching with "srun --mpi=pmix_v3"



On Apr 26, 2020, at 10:07 AM, Patrick Bégou via users 
mailto:users@lists.open-mpi.org>> wrote:

I have also this problem on servers I'm benching at DELL's lab with
OpenMPI-4.0.3. I've tried  a new build of OpenMPI with "--with-pmi2". No
change.
Finally my work around in the slurm script was to launch my code with
mpirun. As mpirun was only finding one slot per nodes I have used
"--oversubscribe --bind-to core" and checked that every process was
binded on a separate core. It worked but do not ask me why :-)

Patrick

Le 24/04/2020 à 20:28, Riebs, Andy via users a écrit :

Prentice, have you tried something trivial, like "srun -N3 hostname", to rule 
out non-OMPI problems?

Andy

-Original Message-
From: users [mailto:users-boun...@lists.open-mpi.org] On Behalf Of Prentice 
Bisbal via users
Sent: Friday, April 24, 2020 2:19 PM
To: Ralph Castain mailto:r...@open-mpi.org>>; Open MPI Users 
mailto:users@lists.open-mpi.org>>
Cc: Prentice Bisbal mailto:pbis...@pppl.gov>>
Subject: Re: [OMPI users] [External] Re: Can't start jobs with srun.

Okay. I've got Slurm built with pmix support:

$ srun --mpi=list
srun: MPI types are...
srun: none
srun: pmix_v3
srun: pmi2
srun: openmpi
srun: pmix

But now when I try to launch a job with srun, the job appears to be
running, but doesn't do anything - it just hangs in the running state
but doesn't do anything. Any ideas what could be wrong, or how to debug
this?

I'm also asking around on the Slurm mailing list, too

Prentice

On 4/23/20 3:03 PM, Ralph Castain wrote:

You can trust the --mpi=list. The problem is likely that OMPI wasn't configured 
--with-pmi2



On Apr 23, 2020, at 11:59 AM, Prentice Bisbal via users 
mailto:users@lists.open-mpi.org>> wrote:

--mpi=list shows pmi2 and openmpi as valid values, but if I set --mpi= to 
either of them, my job still fails. Why is that? Can I not trust the output of 
--mpi=list?

Prentice

On 4/23/20 10:43 AM, Ralph Castain via users wrote:

No, but you do have to explicitly build OMPI with non-PMIx support if that is 
what you are going to use. In this case, you need to configure OMPI 
--with-pmi2=

You can leave off the path if Slurm (i.e., just "--with-pmi2") was installed in 
a standard location as we should find it there.



On Apr 23, 2020, at 7:39 AM, Prentice Bisbal via users 
mailto:users@lists.open-mpi.org>> wrote:

It looks like it was built with PMI2, but not PMIx:

$ srun --mpi=list
srun: MPI types are...
srun: none
srun: pmi2
srun: openmpi

I did launch the job with srun --mpi=pmi2 

Does OpenMPI 4 need PMIx specifically?


On 4/23/20 10:23 AM, Ralph Castain via users wrote:

Is Slurm built with PMIx support? Did you tell srun to use it?



On Apr 23, 2020, at 7:00 AM, Prentice Bisbal via users 
mailto:users@lists.open-mpi.org>> wrote:

I'm using OpenMPI 4.0.3 with Slurm 19.05.5  I'm testing the software with a 
very simple hello, world MPI program that I've used reliably for years. When I 
submit the job through slurm and use srun to launch the job, I get these errors:

*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
***and potentially your MPI job)
[dawson029.pppl.gov:26070<http://dawson029.pppl.gov:26070>] Local abort before 
MPI_INIT completed completed successfully, but am not able to aggregate error 
messages, and not able to guarantee that all other processes were killed!
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
***and potentially your MPI job)
[dawson029.pppl.gov:26076<http://dawson029.pppl.gov:26076>] Local abort before 
MPI_INIT completed completed succ

Re: [OMPI users] Can't start jobs with srun.

2020-04-24 Thread Riebs, Andy via users 
Prentice, have you tried something trivial, like "srun -N3 hostname", to rule 
out non-OMPI problems?

Andy

-Original Message-
From: users [mailto:users-boun...@lists.open-mpi.org] On Behalf Of Prentice 
Bisbal via users
Sent: Friday, April 24, 2020 2:19 PM
To: Ralph Castain ; Open MPI Users 
Cc: Prentice Bisbal 
Subject: Re: [OMPI users] [External] Re: Can't start jobs with srun.

Okay. I've got Slurm built with pmix support:

$ srun --mpi=list
srun: MPI types are...
srun: none
srun: pmix_v3
srun: pmi2
srun: openmpi
srun: pmix

But now when I try to launch a job with srun, the job appears to be 
running, but doesn't do anything - it just hangs in the running state 
but doesn't do anything. Any ideas what could be wrong, or how to debug 
this?

I'm also asking around on the Slurm mailing list, too

Prentice

On 4/23/20 3:03 PM, Ralph Castain wrote:
> You can trust the --mpi=list. The problem is likely that OMPI wasn't 
> configured --with-pmi2
>
>
>> On Apr 23, 2020, at 11:59 AM, Prentice Bisbal via users 
>>  wrote:
>>
>> --mpi=list shows pmi2 and openmpi as valid values, but if I set --mpi= to 
>> either of them, my job still fails. Why is that? Can I not trust the output 
>> of --mpi=list?
>>
>> Prentice
>>
>> On 4/23/20 10:43 AM, Ralph Castain via users wrote:
>>> No, but you do have to explicitly build OMPI with non-PMIx support if that 
>>> is what you are going to use. In this case, you need to configure OMPI 
>>> --with-pmi2=
>>>
>>> You can leave off the path if Slurm (i.e., just "--with-pmi2") was 
>>> installed in a standard location as we should find it there.
>>>
>>>
 On Apr 23, 2020, at 7:39 AM, Prentice Bisbal via users 
  wrote:

 It looks like it was built with PMI2, but not PMIx:

 $ srun --mpi=list
 srun: MPI types are...
 srun: none
 srun: pmi2
 srun: openmpi

 I did launch the job with srun --mpi=pmi2 

 Does OpenMPI 4 need PMIx specifically?


 On 4/23/20 10:23 AM, Ralph Castain via users wrote:
> Is Slurm built with PMIx support? Did you tell srun to use it?
>
>
>> On Apr 23, 2020, at 7:00 AM, Prentice Bisbal via users 
>>  wrote:
>>
>> I'm using OpenMPI 4.0.3 with Slurm 19.05.5  I'm testing the software 
>> with a very simple hello, world MPI program that I've used reliably for 
>> years. When I submit the job through slurm and use srun to launch the 
>> job, I get these errors:
>>
>> *** An error occurred in MPI_Init
>> *** on a NULL communicator
>> *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
>> ***and potentially your MPI job)
>> [dawson029.pppl.gov:26070] Local abort before MPI_INIT completed 
>> completed successfully, but am not able to aggregate error messages, and 
>> not able to guarantee that all other processes were killed!
>> *** An error occurred in MPI_Init
>> *** on a NULL communicator
>> *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
>> ***and potentially your MPI job)
>> [dawson029.pppl.gov:26076] Local abort before MPI_INIT completed 
>> completed successfully, but am not able to aggregate error messages, and 
>> not able to guarantee that all other processes were killed!
>>
>> If I run the same job, but use mpiexec or mpirun instead of srun, the 
>> jobs run just fine. I checked ompi_info to make sure OpenMPI was 
>> compiled with  Slurm support:
>>
>> $ ompi_info | grep slurm
>>Configure command line: 
>> '--prefix=/usr/pppl/intel/2019-pkgs/openmpi-4.0.3' 
>> '--disable-silent-rules' '--enable-shared' '--with-pmix=internal' 
>> '--with-slurm' '--with-psm'
>>   MCA ess: slurm (MCA v2.1.0, API v3.0.0, Component 
>> v4.0.3)
>>   MCA plm: slurm (MCA v2.1.0, API v2.0.0, Component 
>> v4.0.3)
>>   MCA ras: slurm (MCA v2.1.0, API v2.0.0, Component 
>> v4.0.3)
>>MCA schizo: slurm (MCA v2.1.0, API v1.0.0, Component 
>> v4.0.3)
>>
>> Any ideas what could be wrong? Do you need any additional information?
>>
>> Prentice
>>
>

Re: [OMPI users] **URGENT: Error during testing

2019-08-19 Thread Riebs, Andy via users 
Is there any chance that the fact that Riddhi appears to be trying to execute 
an uncompiled hello.c could be the problem here?

From: users [mailto:users-boun...@lists.open-mpi.org] On Behalf Of Jeff Squyres 
(jsquyres) via users
Sent: Monday, August 19, 2019 2:05 PM
To: Open MPI User's List 
Cc: Jeff Squyres (jsquyres) 
Subject: Re: [OMPI users] **URGENT: Error during testing

Can you provide some more details?

https://www.open-mpi.org/community/help/



On Aug 19, 2019, at 1:18 PM, Riddhi A Mehta via users 
mailto:users@lists.open-mpi.org>> wrote:

Hello

My name is Riddhi and I am a Graduate Research Assistant in the Dept. of 
Physics & Astronomy at Purdue University. About a month ago I correctly 
configured openmpi on my mac and the ‘mpirun -np 2 ./hello.c’ ran correctly. 
But today, it gave me the following error:


[Riddhis-MacBook-Air.local:89582] [[56525,0],0] ORTE_ERROR_LOG: Bad parameter 
in file orted/pmix/pmix_server.c at line 262
[Riddhis-MacBook-Air.local:89582] [[56525,0],0] ORTE_ERROR_LOG: Bad parameter 
in file ess_hnp_module.c at line 667
--
It looks like orte_init failed for some reason; your parallel process is
likely to abort.  There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems.  This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):

  pmix server init failed
  --> Returned value Bad parameter (-5) instead of ORTE_SUCCESS

I tried to google this error and the only thing I found was to change the 
TMPDIR name to a shorter name. But I don’t think I understand what it’s asking 
me to do. Kindly help since I am not able to understand what went wrong in one 
month and mpirun stopped working.

Thank you

Riddhi Mehta
Research Group: Maxim Lyutikov, Theoretical High Energy Astrophysics
Dept. of Physics & Astronomy
Purdue University

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Jeff Squyres
jsquy...@cisco.com



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