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Subject: Re: [OMPI users] OpenMPI job initializing problem
From: Beichuan Yan (beichuan.yan_at_[hidden])
Date: 2014-03-20 12:48:50


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 solution here is get your sys admin to make /tmp local. Making /tmp NFS mounted across multiple nodes is a major "faux pas" in the Linux world - it should never be done, for the reasons stated by Jeff.

my comment: for most clusters I have used, /tmp is NOT local. Open MPI community may not enforce it.

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 backed in a real filesystem. So the issue goes away.

my comment: up to OMPI v1.7.4, this shmem issue is still there. However, it is resolved in OMPI v1.7.5rc5. This is surprising.

Anyway, OMPI v1.7.5rc5 works well for multi-processes-on-one-node (shmem) mode on Spirit. There is no need to tune TCP or IB parameters to use it. My code just runs well:

My test data takes 20 minutes to run with OMPI v1.7.4, but needs less than 1 minute with OMPI v1.7.5rc5. I don't know what the magic is. I am wondering when OMPI v1.7.5 final will be released.

I will update performance comparison between Intel MPI and Open MPI.

Thanks,
Beichuan

-----Original Message-----
From: users [mailto:users-bounces_at_[hidden]] 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 none worked.
>
> I just found, with exact the same code, data and job settings, a job can really run one day while cannot the other day. It is NOT repeatable. I don't know what the problem is: hardware? OpenMPI? PBS Pro?
>
> Anyway, I may have to give up using OpenMPI on that system and switch to IntelMPI which always work.
>
> Thanks,
> Beichuan

Well, this machine may have been setup to run only Intel MPI (DAPL?) and SGI MPI.
It is a pity that it doesn't seem to work with OpenMPI.

In any case, good luck with your research project.

Gus Correa

>
> -----Original Message-----
> From: users [mailto:users-bounces_at_[hidden]] 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:
>> 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 need "self":
>
> -mca btl sm,openib,self
>
> Alternatively, you could rule out tcp:
>
> -mca btl ^tcp
>
>>
>> #export
>> TCP="--mca btl sm,openib --mca btl_tcp_if_include 10.148.0.0/16"
>> No run, no output
>>
> > Beichuan
>
> Likewise, "self" is missing here.
>
> Also, I don't know if you can ask for openib and also add --mca btl_tcp_if_include 10.148.0.0/16.
> Note that one turns off tcp (I think), whereas the other requests a
> tcp interface (or that the IB interface with IPoIB functionality).
> That combination sounds weird to me.
> The OMPI developers may clarify if this is valid syntax/syntax combination.
>
> I would try simply -mca btl sm,openib,self, which is likely to give
> you the IB transport with verbs, plus shared memory intra-node, plus
> the
> (mandatory?) self (loopback interface?).
> In my experience, this will also help identify any malfunctioning IB HCA in the nodes (with a failure/error message).
>
>
> I hope it helps,
> Gus Correa
>
>
>>
>> -----Original Message-----
>> From: users [mailto:users-bounces_at_[hidden]] 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 using OMPI 1.6.5 or 1.7.4, right?
>>
>> It looks like the problem now is performance, right?
>>
>> System load affects performance, but unless the network is overwhelmed, or perhaps the Lustre file system is hanging or too slow, I would think that a walltime increase from 1min to 10min is not related to system load, but something else.
>>
>> Do you remember the setup that gave you 1min walltime?
>> Was it the same that you sent below?
>> Do you happen to know which nodes?
>> Are you sharing nodes with other jobs, or are you running alone on the nodes?
>> Sharing with other processes may slow down your job.
>> If you request all cores in the node, PBS should give you a full node (unless they tricked PBS to think the nodes have more cores than they actually do).
>> How do you request the nodes in your #PBS directives?
>> Do you request nodes and ppn, or do you request procs?
>>
>> I suggest that you do:
>> cat $PBS_NODEFILE
>> in your PBS script, just to document which nodes are actually given to you.
>>
>> Also helpful to document/troubleshoot is to add -v and -tag-output to your mpiexec command line.
>>
>>
>> The difference in walltime could be due to some malfunction of IB HCAs on the nodes, for instance.
>> Since you are allowing (if I remember right) the use of TCP, OpenMPI will try to use any interfaces that you did not rule out.
>> If your mpiexec command line doesn't make any restriction, it will use anything available, if I remember right.
>> (Jeff will correct me in the next second.) If your mpiexec command line has mca btl_tcp_if_include 10.148.0.0/16 it will use the 10.148.0.0/16 subnet in with TCP transport, I think.
>> (Jeff will cut my list subscription after that one, for spreading
>> misinformation.)
>>
>> In either case my impression is that you may have left a door open to the use of non-IB (and non-IB-verbs) transport.
>>
>> Is 10.148.0.0/16 the an Infiniband subnet or an Ethernet subnet?
>>
>> Did you remeber Jeff's suggestion from a while ago to avoid TCP (over Ethernet or over IB), and stick to IB verbs?
>>
>>
>> Is 10.148.0.0/16 the IB or the Ethernet subnet?
>>
>> On 03/02/2014 02:38 PM, Jeff Squyres (jsquyres) wrote:
>> > Both 1.6.x and 1.7.x/1.8.x will need verbs.h to use the native verbs
>> > network stack.
>> >
>> > You can use emulated TCP over IB (e.g., using the OMPI TCP BTL), but
>> > it's nowhere near as fast/efficient the native verbs network stack.
>> >
>>
>>
>> You could force the use of IB verbs with
>>
>> -mca btl ^tcp
>>
>> or with
>>
>> -mca btl sm,openib,self
>>
>> on the mpiexec command line.
>>
>> In this case, if any of the IB HCAs on the nodes is bad, the job will
>> abort with an error message, instead of running too slow (if it is
>> using other networks).
>>
>> There are also ways to tell OMPI to do a more verbose output, that
>> may perhaps help diagnose the problem.
>> ompi_info | grep verbose
>> may give some hints (I confess I don't remember them).
>>
>>
>> Believe me, this did happen to me, i.e., to run MPI programs in a
>> cluster that had all sorts of non-homogeneous nodes, some with faulty
>> IB HCAs, some with incomplete 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. For $TMPDIR and $TCP, there are four combinations by commenting on/off (note the system's default TMPDIR=/work3/yanb):
>>> export TMPDIR=/work1/home/yanb/tmp
>>> TCP="--mca btl_tcp_if_include 10.148.0.0/16"
>>>
>>> 2. I tested the 4 combinations for OpenMPI 1.6.5 and OpenMPI 1.7.4 respectively for the pure-MPI mode (no OPENMP threads; 8 nodes, each node runs 16 processes). The results are weird: of all 8 cases, only TWO of them can run, but run so slow:
>>>
>>> OpenMPI 1.6.5:
>>> export TMPDIR=/work1/home/yanb/tmp
>>> TCP="--mca btl_tcp_if_include 10.148.0.0/16"
>>> Warning: shared-memory, /work1/home/yanb/tmp/ Run, take 10 minutes,
>>> slow
>>>
>>> OpenMPI 1.7.4:
>>> #export TMPDIR=/work1/home/yanb/tmp
>>> #TCP="--mca btl_tcp_if_include 10.148.0.0/16"
>>> Warning: shared-memory /work3/yanb/605832.SPIRIT/ Run, take 10
>>> minutess, slow
>>>
>>> So you see, a) openmpi 1.6.5 and 1.7.4 need different settings to
>>> run;
>> b) whether specifying TMPDIR, I got the shared memory warning.
>>>
>>> 3. But a few days ago, OpenMPI 1.6.5 worked great and took only 1
>>> minute
>> (now it takes 10 minutes). I am so confused by the results.
>> Does the system loading level or fluctuation or PBS pro affect
>> OpenMPI performance?
>>>
>>> Thanks,
>>> Beichuan
>>>
>>> -----Original Message-----
>>> From: users [mailto:users-bounces_at_[hidden]] 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?
>>>
>>> Also, "mount" shows only /work[1-4], not the other
>>> 7 CWFS panfs (Panasas?), which apparently are not available in the compute nodes/blades.
>>>
>>> I presume you have access and are using only some of the /work[1-4]
>>> (lustre) file systems for all your MPI and other software installation, right? Not the panfs, right?
>>>
>>> Awkward that it doesn't work, because lustre is supposed to be a parallel file system, highly available to all nodes (assuming it is mounted on all nodes).
>>>
>>> It also shows a small /tmp with a tmpfs file system, which is volatile, in memory:
>>>
>>> http://en.wikipedia.org/wiki/Tmpfs
>>>
>>> I would guess they don't let you write there, so TMPDIR=/tmp may not be a possible option, but this is just a wild guess.
>>> Or maybe OMPI requires an actual non-volatile file system to write its shared memory auxiliary files and other stuff that normally goes on /tmp? [Jeff, Ralph, help!!] I kind of remember some old discussion on this list about this, but maybe it was in another list.
>>>
>>> [You could ask the sys admin about this, and perhaps what he
>>> recommends to use to replace /tmp.]
>>>
>>> Just in case they may have some file system mount point mixup, you could try perhaps TMPDIR=/work1/yanb/tmp (rather than /home) You could also try TMPDIR=/work3/yanb/tmp, as if I remember right this is another file system you have access to (not sure anymore, it may have been in the previous emails).
>>> Either way, you may need to create the tmp directory beforehand.
>>>
>>> **
>>>
>>> Any chances that this is an environment mixup?
>>>
>>> Say, that you may be inadvertently using the SGI-MPI mpiexec Using a /full/path/to/mpiexec in your job may clarify this.
>>>
>>> "which mpiexec" will tell, but since the environment on the compute nodes may not be exactly the same as in the login node, it may not be reliable information.
>>>
>>> Or perhaps you may not be pointing to the OMPI libraries?
>>> Are you exporting PATH and LD_LIBRARY_PATH on .bashrc/.tcshrc, with the OMPI items (bin and lib) *PREPENDED* (not appended), so as to take precedence over other possible/SGI/pre-existent MPI items?
>>>
>>> Those are pretty (ugly) 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
>>>> Filesystem Size Used Avail Use% Mounted on
>>>> 10.148.18.45_at_o2ib:10.148.18.46_at_o2ib:/fs1
>>>> 1.2P 136T 1.1P 12% /work1 -bash-4.1$
>>>> mount devpts on /dev/pts type devpts (rw,gid=5,mode=620) tmpfs on
>>>> /tmp type tmpfs (rw,size=150m) none on /proc/sys/fs/binfmt_misc
>>>> type binfmt_misc
>>>> (rw) cpuset on /dev/cpuset type cpuset (rw)
>>>> 10.148.18.45_at_o2ib:10.148.18.46_at_o2ib:/fs1 on /work1 type lustre
>>>> (rw,flock)
>>>> 10.148.18.76_at_o2ib:10.148.18.164_at_o2ib:/fs2 on /work2 type lustre
>>>> (rw,flock)
>>>> 10.148.18.104_at_o2ib:10.148.18.165_at_o2ib:/fs3 on /work3 type lustre
>>>> (rw,flock)
>>>> 10.148.18.132_at_o2ib:10.148.18.133_at_o2ib:/fs4 on /work4 type lustre
>>>> (rw,flock)
>>>>
>>>>
>>>> 2. For "export TMPDIR=/home/yanb/tmp", I created it beforehand, and I did see mpi-related temporary files there when the job gets started.
>>>>
>>>> -----Original Message-----
>>>> From: users [mailto:users-bounces_at_[hidden]] 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 site says the computer is an SGI ICE X.
>>>> I am not familiar to it, so what follows are guesses.
>>>>
>>>> The SGI site brochure suggests that the nodes/blades have local disks:
>>>> https://www.sgi.com/pdfs/4330.pdf
>>>>
>>>> The file systems prefixed with IP addresses (work[1-4]) and with panfs (cwfs and CWFS[1-6]) and a colon (:) are shared exports (not local), but not necessarily NFS (panfs may be Panasas?).
>>>> From this output it is hard to tell where /home is, but I would guess it is also shared (not local).
>>>> Maybe "df -h /home" will tell. Or perhaps "mount".
>>>>
>>>> You may be logged in to a login/service node, so although it does have a /tmp (your ls / shows tmp), this doesn't guarantee that the compute nodes/blades also do.
>>>>
>>>> Since your jobs failed when you specified TMPDIR=/tmp, I would guess /tmp doesn't exist on the nodes/blades, or is not writable.
>>>>
>>>> Did you try to submit a job with, say, "mpiexec -np 16 ls -ld /tmp"?
>>>> This should tell if /tmp exists on the nodes, if it is writable.
>>>>
>>>> A stupid question:
>>>> When you tried your job with this:
>>>>
>>>> export TMPDIR=/home/yanb/tmp
>>>>
>>>> Did you create the directory /home/yanb/tmp beforehand?
>>>>
>>>> Anyway, you may need to ask the help of a 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 of "df -h":
>>>>> Filesystem Size Used Avail Use% Mounted on
>>>>> /dev/sda6 919G 16G 857G 2% /
>>>>> tmpfs 32G 0 32G 0% /dev/shm
>>>>> /dev/sda5 139M 33M 100M 25% /boot
>>>>> adfs3v-s:/adfs3/hafs14
>>>>> 6.5T 678G 5.5T 11% /scratch
>>>>> adfs3v-s:/adfs3/hafs16
>>>>> 6.5T 678G 5.5T 11% /var/spool/mail
>>>>> 10.148.18.45_at_o2ib:10.148.18.46_at_o2ib:/fs1
>>>>> 1.2P 136T 1.1P 12% /work1
>>>>> 10.148.18.132_at_o2ib:10.148.18.133_at_o2ib:/fs4
>>>>> 1.2P 793T 368T 69% /work4
>>>>> 10.148.18.104_at_o2ib:10.148.18.165_at_o2ib:/fs3
>>>>> 1.2P 509T 652T 44% /work3
>>>>> 10.148.18.76_at_o2ib:10.148.18.164_at_o2ib:/fs2
>>>>> 1.2P 521T 640T 45% /work2
>>>>> panfs://172.16.0.10/CWFS
>>>>> 728T 286T 443T 40% /p/cwfs
>>>>> panfs://172.16.1.61/CWFS1
>>>>> 728T 286T 443T 40% /p/CWFS1
>>>>> panfs://172.16.0.210/CWFS2
>>>>> 728T 286T 443T 40% /p/CWFS2
>>>>> panfs://172.16.1.125/CWFS3
>>>>> 728T 286T 443T 40% /p/CWFS3
>>>>> panfs://172.16.1.224/CWFS4
>>>>> 728T 286T 443T 40% /p/CWFS4
>>>>> panfs://172.16.1.224/CWFS5
>>>>> 728T 286T 443T 40% /p/CWFS5
>>>>> panfs://172.16.1.224/CWFS6
>>>>> 728T 286T 443T 40% /p/CWFS6
>>>>> panfs://172.16.1.224/CWFS7
>>>>> 728T 286T 443T 40% /p/CWFS7
>>>>>
>>>>> 1. My home directory is /home/yanb.
>>>>> My simulation files are located at /work3/yanb.
>>>>> The default TMPDIR set by system is just /work3/yanb
>>>>>
>>>>> 2. I did try not to set TMPDIR and let it default, which is just case 1 and case 2.
>>>>> Case1: #export TMPDIR=/home/yanb/tmp
>>>>> TCP="--mca btl_tcp_if_include 10.148.0.0/16"
>>>>> It gives no apparent reason.
>>>>> Case2: #export TMPDIR=/home/yanb/tmp
>>>>> #TCP="--mca btl_tcp_if_include 10.148.0.0/16"
>>>>> It gives warning of shared memory file on network file system.
>>>>>
>>>>> 3. With "export TMPDIR=/tmp", the job gives the same, no apparent reason.
>>>>>
>>>>> 4. FYI, "ls /" gives:
>>>>> ELT apps cgroup hafs1 hafs12 hafs2 hafs5 hafs8 home lost+found mnt p root selinux tftpboot var work3
>>>>> admin bin dev hafs10 hafs13 hafs3 hafs6 hafs9 lib media net panfs sbin srv tmp work1 work4
>>>>> app boot etc hafs11 hafs15 hafs4 hafs7 hafs_x86_64 lib64 misc opt proc scratch sys usr work2 workspace
>>>>>
>>>>> Beichuan
>>>>>
>>>>> -----Original Message-----
>>>>> From: users [mailto:users-bounces_at_[hidden]] 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 perhaps Lustre (which you may have mentioned before, I don't remember).
>>>>>
>>>>> Maybe "df -h" will show what is local what is not.
>>>>> It works for NFS, it prefixes file systems with the server name, but I don't know about Lustre.
>>>>>
>>>>> Did you try just not to set TMPDIR and let it default?
>>>>> If the default 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,
>>>>> Gus 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-bounces_at_[hidden]] 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 setting TMPDIR to a local filesystem?
>>>>>>
>>>>>>
>>>>>> On Mar 3, 2014, at 3:43 PM, Beichuan Yan<beichuan.yan_at_[hidden]> 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/yanb/tmp", /home/yanb/tmp is my local directory. The default TMPDIR points to a Lustre directory.
>>>>>>>
>>>>>>> There is no any other output. I checked my job with "qstat -n" and found that processes were actually not started on compute nodes even though PBS Pro has "started" my job.
>>>>>>>
>>>>>>> Beichuan
>>>>>>>
>>>>>>>> 3. Then I test pure-MPI mode: OPENMP is turned off, and each compute node runs 16 processes (clearly shared-memory of MPI is used). Four combinations of "TMPDIR" and "TCP" are tested:
>>>>>>>> case 1:
>>>>>>>> #export TMPDIR=/home/yanb/tmp
>>>>>>>> TCP="--mca btl_tcp_if_include 10.148.0.0/16"
>>>>>>>> mpirun $TCP -np 64 -npernode 16 -hostfile $PBS_NODEFILE
>>>>>>>> ./paraEllip3d input.txt
>>>>>>>> output:
>>>>>>>> Start Prologue v2.5 Mon Mar 3 15:47:16 EST 2014 End Prologue
>>>>>>>> v2.5 Mon Mar 3 15:47:16 EST 2014
>>>>>>>> -bash: line 1: 448597 Terminated /var/spool/PBS/mom_priv/jobs/602244.service12.SC
>>>>>>>> Start Epilogue v2.5 Mon Mar 3 15:50:51 EST 2014 Statistics
>>>>>>>> cpupercent=0,cput=00:00:00,mem=7028kb,ncpus=128,vmem=495768kb,w
>>>>>>>> all
>>>>>>>> t
>>>>>>>> i
>>>>>>>> m
>>>>>>>> e
>>>>>>>> =00:03:24 End Epilogue v2.5 Mon Mar 3 15:50:52 EST 2014
>>>>>>>
>>>>>>> It looks like you have two general cases:
>>>>>>>
>>>>>>> 1. The job fails for no apparent reason (like above), or 2. The
>>>>>>> job complains that your TMPDIR is on a shared filesystem
>>>>>>>
>>>>>>> Right?
>>>>>>>
>>>>>>> I think the real issue, then, is to figure out why your jobs are failing with no output.
>>>>>>>
>>>>>>> Is there anything in the stderr output?
>>>>>>>
>>>>>>> --
>>>>>>> Jeff Squyres
>>>>>>> jsquyres_at_[hidden]
>>>>>>> For corporate legal information go to:
>>>>>>> http://www.cisco.com/web/about/doing_business/legal/cri/
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> users mailing list
>>>>>>> users_at_[hidden]
>>>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>>>>> _______________________________________________
>>>>>>> users mailing list
>>>>>>> users_at_[hidden]
>>>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Jeff Squyres
>>>>>> jsquyres_at_[hidden]
>>>>>> For corporate legal information go to:
>>>>>> http://www.cisco.com/web/about/doing_business/legal/cri/
>>>>>>
>>>>>> _______________________________________________
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