finalize
themselves. My guess is that is the source - would help us target the problem.
On Mar 20, 2014, at 9:00 PM, Beichuan Yan wrote:
> Here is an example of my data measured in seconds:
>
> communication overhead = commuT + migraT + print, compuT is
> computational cost, tot
Hi Rob,
As you pointed out in April that there are many cases that could arouse
ADIOI_Set_lock error. My code writes to a file at a location specified by a
shared file pointer (it is a blocking and collective call):
MPI_File_write_ordered(contactFile, const_cast (inf.str().c_str()),
length, MP
08:49
To: us...@open-mpi.org
Subject: Re: [OMPI users] File locking in ADIO, OpenMPI 1.6.4
On 09/17/2014 05:46 PM, Beichuan Yan wrote:
> Hi Rob,
>
> As you pointed out in April that there are many cases that could
> arouse ADIOI_Set_lock error. My code writes to a file at a location
>
"
mpirun $TCP -hostfile $PBS_NODEFILE -np 8 ./paraEllip3d input.txt
3. Then I turned to Intel MPI, which surprisingly starts and runs my job
correctly each time (though it is a little slower than OpenMPI, maybe 15%
slower, but it works each time).
Can you please advise? Many thanks.
Sincerely,
Beichuan Yan
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
Thanks. Yes I am asking sysadmin to install the libibverbs-devel, which has not
been installed.
It appears that Open MPI 1.6.5 does not need the verbs.h, but 1.7.4 does need
it?
Beichuan
-Original Message-
From: users [mailto:users-boun...@open-mpi.org] On Behalf Of Jeff Squyres
(jsq
hostfile $PBS_NODEFILE ./paraEllip3d input.txt
So I am wondering if Open MPI has any problem/solution with the shared-memory
transfer?
Thanks,
Beichuan
-Original Message-
From: Beichuan Yan
Sent: Sunday, March 02, 2014 00:56
To: 'Open MPI Users'
Subject: RE: [OMPI users] O
I agree there are two cases for pure-MPI mode: 1. Job fails with no apparent
reason; 2 job complains shared-memory file on network file system, which can
be resolved by " export TMPDIR=/home/yanb/tmp", /home/yanb/tmp is my local
directory. The default TMPDIR points to a Lustre directory.
There
March 03, 2014 16:57
To: Open MPI Users
Subject: Re: [OMPI users] OpenMPI job initializing problem
How about setting TMPDIR to a local filesystem?
On Mar 3, 2014, at 3:43 PM, Beichuan Yan wrote:
> I agree there are two cases for pure-MPI mode: 1. Job fails with no apparent
> reason; 2 jo
TMPDIR is on Lustre (did you say this?, anyway I don't
remember) you could perhaps try to force it to /tmp:
export TMPDIR=/tmp,
If the cluster nodes are diskfull /tmp is likely to exist and be local to the
cluster nodes.
[But the cluster nodes may be diskless ... :( ]
I hope this helps,
system administrator of this machine.
Gus Correa
On 03/03/2014 07:43 PM, Beichuan Yan wrote:
> Gus,
>
> I am using this system:
> http://centers.hpc.mil/systems/unclassified.html#Spirit. I don't know exactly
> configurations of the file system. Here is the output
y) common problems.
**
I hope this helps,
Gus Correa
On 03/03/2014 10:13 PM, Beichuan Yan wrote:
> 1. info from a compute node
> -bash-4.1$ hostname
> r32i1n1
> -bash-4.1$ df -h /home
> FilesystemSize Used Avail Use% Mounted on
> 10.148.18.45@o2ib:10.148.18.46@o2ib
lete OFED installation, some that
were not mounting shared file systems properly, etc.
[I didn't administer that one!]
Hopefully that is not the problem you are facing, but verbose output
may help anyways.
I hope this helps,
Gus Correa
On 03/06/2014 01:49 PM, Beichuan Yan wrote:
> 1.
14 03:35 PM, Beichuan Yan wrote:
> Gus,
>
> Yes, 10.148.0.0/16 is the IB subnet.
>
> I did try others but none worked:
> #export
> TCP="--mca btl sm,openib"
> No run, no output
If I remember right, and unless this changed in recent OMPI vervsions, you also
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
oblem
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/users/2011/11/17688.php
> The correct
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/users/2011/11/17688.php
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
[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
[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
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