-mpi.org] On Behalf Of Ralph Castain
Sent: Friday, March 21, 2014 07:06
To: Open MPI Users
Subject: Re: [OMPI users] OpenMPI job initializing problem
One thing to check would be the time spent between MPI_Init and MPI_Finalize -
i.e., see if the time difference is caused by differences in init and
tion and computation
> measured by MPI_Wtime calls, but the wall time reported by PBS pro is larger.
>
>
> -Original Message-
> From: users [mailto:users-boun...@open-mpi.org] On Behalf Of Gus Correa
> Sent: Thursday, March 20, 2014 15:08
> To: Open MPI Users
> Sub
[mailto:users-boun...@open-mpi.org] On Behalf Of Gus Correa
Sent: Thursday, March 20, 2014 15:08
To: Open MPI Users
Subject: Re: [OMPI users] OpenMPI job initializing problem
On 03/20/2014 04:48 PM, Beichuan Yan wrote:
> Ralph and Noam,
>
> Thanks for the clarifications, they are important.
I could
[mailto:users-boun...@open-mpi.org] On Behalf Of Beichuan Yan
Sent: Thursday, March 20, 2014 15:15
To: Open MPI Users
Subject: Re: [OMPI users] OpenMPI job initializing problem
As for the performance, my 4-node (64-processes) 3-hour job indicates Intel MPI
and OpenMPI have close benchmarks. Intel
Squyres
(jsquyres)
Sent: Thursday, March 20, 2014 11:15
To: Open MPI Users
Subject: Re: [OMPI users] OpenMPI job initializing problem
On Mar 20, 2014, at 12:48 PM, Beichuan Yan wrote:
> 2. http://www.open-mpi.org/community/lists/users/2011/11/17684.php
> In the upcoming OMPI v1.7, we revamp
users-boun...@open-mpi.org] On Behalf Of Ralph Castain
Sent: Thursday, March 20, 2014 12:13
To: Open MPI Users
Subject: Re: [OMPI users] OpenMPI job initializing problem
On Mar 20, 2014, at 9:48 AM, Beichuan Yan wrote:
Hi,
Today I tested OMPI v1.7.5rc5 and surprisingly, it works like a charm
Good for me to read it.
-Original Message-
From: users [mailto:users-boun...@open-mpi.org] On Behalf Of Gus Correa
Sent: Thursday, March 20, 2014 15:00
To: Open MPI Users
Subject: Re: [OMPI users] OpenMPI job initializing problem
On 03/20/2014 02:13 PM, Ralph Castain wrote:
>
> On
en MPI.
Thanks,
Beichuan
-Original Message-
From: users [mailto:users-boun...@open-mpi.org] On Behalf Of Gus Correa
Sent: Friday, March 07, 2014 18:41
To: Open MPI Users
Subject: Re: [OMPI users] OpenMPI job initializing problem
On 03/06/2014 04:52 PM, Beichuan Yan wrote:
No, I did all these and n
; Is this /tmp at compute node a local directory? I don't know how to tell it.
>
> Thanks,
> Beichuan
>
>
>
> -Original Message-
> From: users [mailto:users-boun...@open-mpi.org] On Behalf Of Ralph Castain
> Sent: Thursday, March 20, 2014 12:13
> To: O
at compute node a local directory? I don't know how to tell it.
Thanks,
Beichuan
-Original Message-
From: users [mailto:users-boun...@open-mpi.org] On Behalf Of Ralph Castain
Sent: Thursday, March 20, 2014 12:13
To: Open MPI Users
Subject: Re: [OMPI users] OpenMPI job initializing pr
On Mar 20, 2014, at 2:13 PM, Ralph Castain wrote:
>
> On Mar 20, 2014, at 9:48 AM, Beichuan Yan wrote:
>
>> Hi,
>>
>> Today I tested OMPI v1.7.5rc5 and surprisingly, it works like a charm!
>>
>> I found discussions related to this issue:
>>
>> 1. http://www.open-mpi.org/community/lists/user
--Original Message-
> From: users [mailto:users-boun...@open-mpi.org] On Behalf Of Gus Correa
> Sent: Friday, March 07, 2014 18:41
> To: Open MPI Users
> Subject: Re: [OMPI users] OpenMPI job initializing problem
>
> On 03/06/2014 04:52 PM, Beichuan Yan wrote:
>> No, I did
On Mar 20, 2014, at 12:48 PM, Beichuan Yan wrote:
> 2. http://www.open-mpi.org/community/lists/users/2011/11/17684.php
> In the upcoming OMPI v1.7, we revamped the shared memory setup code such that
> it'll actually use /dev/shm properly, or use some other mechanism other than
> a mmap file bac
Correa
Sent: Friday, March 07, 2014 18:41
To: Open MPI Users
Subject: Re: [OMPI users] OpenMPI job initializing problem
On 03/06/2014 04:52 PM, Beichuan Yan wrote:
> No, I did all these and none worked.
>
> I just found, with exact the same code, data and job settings, a job can
> rea
r research project.
Gus Correa
-Original Message-
From: users [mailto:users-boun...@open-mpi.org] On Behalf Of Gus Correa
Sent: Thursday, March 06, 2014 13:51
To: Open MPI Users
Subject: Re: [OMPI users] OpenMPI job initializing problem
On 03/06/2014 03:35 PM, Beichuan Yan wrote:
that system and switch to
IntelMPI which always work.
Thanks,
Beichuan
-Original Message-
From: users [mailto:users-boun...@open-mpi.org] On Behalf Of Gus Correa
Sent: Thursday, March 06, 2014 13:51
To: Open MPI Users
Subject: Re: [OMPI users] OpenMPI job initializing problem
On 03/06/20
I hope it helps,
Gus Correa
-Original Message-
From: users [mailto:users-boun...@open-mpi.org] On Behalf Of Gus Correa
Sent: Thursday, March 06, 2014 13:16
To: Open MPI Users
Subject: Re: [OMPI users] OpenMPI job initializing problem
Hi Beichuan
So, it looks like that now the program run
o:users-boun...@open-mpi.org] On Behalf Of Gus Correa
Sent: Thursday, March 06, 2014 13:16
To: Open MPI Users
Subject: Re: [OMPI users] OpenMPI job initializing problem
Hi Beichuan
So, it looks like that now the program runs, even though with specific settings
depending on whether you're
the results.
Does the system loading level or fluctuation or PBS pro affect OpenMPI
performance?
Thanks,
Beichuan
-Original Message-
From: users [mailto:users-boun...@open-mpi.org] On Behalf Of Gus Correa
Sent: Tuesday, March 04, 2014 08:48
To: Open MPI Users
Subject: Re: [OMPI users]
ks,
Beichuan
-Original Message-
From: users [mailto:users-boun...@open-mpi.org] On Behalf Of Gus Correa
Sent: Tuesday, March 04, 2014 08:48
To: Open MPI Users
Subject: Re: [OMPI users] OpenMPI job initializing problem
Hi Beichuan
So, from "df" it looks like /home is /work1, right?
s Correa
On 03/03/2014 07:10 PM, Beichuan Yan wrote:
How to set TMPDIR to a local filesystem? Is /home/yanb/tmp a local filesystem?
I don't know how to tell a directory is local file system or network file
system.
-Original Message-
From: users [mailto:users-boun...@open-mpi.org] O
al Message-
From: users [mailto:users-boun...@open-mpi.org] On Behalf Of Gus Correa
Sent: Monday, March 03, 2014 18:23
To: Open MPI Users
Subject: Re: [OMPI users] OpenMPI job initializing problem
Hi Beichuan
OK, it says "unclassified.html", so I presume it is not a problem.
The web si
v tmp work1 work4
appboot etc hafs11 hafs15 hafs4 hafs7 hafs_x86_64 lib64 misc
opt proc scratch sys usr work2 workspace
Beichuan
-Original Message-
From: users [mailto:users-boun...@open-mpi.org] On Behalf Of Gus Correa
Sent: Monday, March 03, 2014
rs [mailto:users-boun...@open-mpi.org] On Behalf Of Gus Correa
Sent: Monday, March 03, 2014 17:24
To: Open MPI Users
Subject: Re: [OMPI users] OpenMPI job initializing problem
Hi Beichuan
If you are using the university cluster, chances are that /home is not local,
but on an NFS share, or perhap
ectory is local file system or network file
system.
-Original Message-
From: users [mailto:users-boun...@open-mpi.org] On Behalf Of Jeff Squyres
(jsquyres)
Sent: Monday, March 03, 2014 16:57
To: Open MPI Users
Subject: Re: [OMPI users] OpenMPI job initializing problem
How about settin
Hi
If I remember right, there were issues in the past with setting TMPDIR
on an NFS share. Maybe the same problem happens on Lustre?
http://arc.liv.ac.uk/pipermail/gridengine-users/2009-November/027767.html
FWIW, we leave it to the default local /tmp, and it works.
Gus Correa
On 03/03/2014 0
March 03, 2014 16:57
To: Open MPI Users
Subject: Re: [OMPI users] OpenMPI job initializing problem
How about setting TMPDIR to a local filesystem?
On Mar 3, 2014, at 3:43 PM, Beichuan Yan wrote:
> I agree there are two cases for pure-MPI mode: 1. Job fails with no apparent
> reason; 2 jo
How about setting TMPDIR to a local filesystem?
On Mar 3, 2014, at 3:43 PM, Beichuan Yan wrote:
> I agree there are two cases for pure-MPI mode: 1. Job fails with no apparent
> reason; 2 job complains shared-memory file on network file system, which can
> be resolved by " export TMPDIR=/home
I agree there are two cases for pure-MPI mode: 1. Job fails with no apparent
reason; 2 job complains shared-memory file on network file system, which can
be resolved by " export TMPDIR=/home/yanb/tmp", /home/yanb/tmp is my local
directory. The default TMPDIR points to a Lustre directory.
There
On Mar 3, 2014, at 1:48 PM, Beichuan Yan wrote:
> 1. After sysadmin installed libibverbs-devel package, I build Open MPI 1.7.4
> successfully with the command:
> ./configure
> --prefix=/work4/projects/openmpi/openmpi-1.7.4-gcc-compilers-4.7.3
> --with-tm=/opt/pbs/default --with-verbs=/hafs_x86
hostfile $PBS_NODEFILE ./paraEllip3d input.txt
So I am wondering if Open MPI has any problem/solution with the shared-memory
transfer?
Thanks,
Beichuan
-Original Message-
From: Beichuan Yan
Sent: Sunday, March 02, 2014 00:56
To: 'Open MPI Users'
Subject: RE: [OMPI users] O
-mpi.org] On Behalf Of Jeff Squyres
> (jsquyres)
> Sent: Sunday, March 02, 2014 11:44
> To: Open MPI Users
> Subject: Re: [OMPI users] OpenMPI job initializing problem
>
> On Mar 2, 2014, at 10:18 AM, Gustavo Correa wrote:
>
>> Make sure you have any ofed/openib "d
(jsquyres)
Sent: Sunday, March 02, 2014 11:44
To: Open MPI Users
Subject: Re: [OMPI users] OpenMPI job initializing problem
On Mar 2, 2014, at 10:18 AM, Gustavo Correa wrote:
> Make sure you have any ofed/openib "devel" packages installed, in case
> they exist and yum lists them.
On Mar 2, 2014, at 10:18 AM, Gustavo Correa wrote:
> Make sure you have any ofed/openib "devel" packages installed,
> in case they exist and yum lists them.
> This may be a possible reason for missing header files.
+1
Look for libibverbs-devel.
--
Jeff Squyres
jsquy...@cisco.com
For corpora
simple ok (unspecified)
>>> checking --with-verbs-libdir value... sanity check ok (/usr/lib64)
>>> configure: WARNING: Could not find verbs.h in the usual locations under
>>> configure: error: Cannot continue
>>>
>>> Our system is Red
Cannot continue
>>
>> Our system is Red Hat 6.4. Do we need to install more packages of
>> Infiniband? Can you please advise?
>>
>> Thanks,
>> Beichuan Yan
>>
>>
>> -Original Message-
>> From: users [mailto:users-boun...@open-mpi.org]
not find verbs.h in the usual locations under
> configure: error: Cannot continue
>
> Our system is Red Hat 6.4. Do we need to install more packages of Infiniband?
> Can you please advise?
>
> Thanks,
> Beichuan Yan
>
>
> -----Original Message-
> From: users [m
nue
Our system is Red Hat 6.4. Do we need to install more packages of Infiniband?
Can you please advise?
Thanks,
Beichuan Yan
-Original Message-
From: users [mailto:users-boun...@open-mpi.org] On Behalf Of Gus Correa
Sent: Friday, February 28, 2014 15:59
To: Open MPI Users
Subject: Re: [OMP
HI Beichuan
To add to what Ralph said,
the RHEL OpenMPI package probably wasn't built with
with PBS Pro support either.
Besides, OMPI 1.5.4 (RHEL version) is old.
**
You will save yourself time and grief if you read the installation FAQs,
before you install from the source tarball:
http://www.
Almost certainly, the redhat package wasn't built with matching infiniband
support and so we aren't picking it up. I'd suggest downloading the latest
1.7.4 or 1.7.5 nightly tarball, or even the latest 1.6 tarball if you want the
stable release, and build it yourself so you *know* it was built fo
Hi there,
I am running jobs on clusters with Infiniband connection. They installed
OpenMPI v1.5.4 via REDHAT 6 yum package). My problem is that although my jobs
gets queued and started by PBS PRO quickly, most of the time they don't really
run (occasionally they really run) and give error info
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