On Mar 20, 2014, at 9:48 AM, Beichuan Yan <beichuan....@colorado.edu> 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 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.

We don't enforce anything, but /tmp being network mounted is a VERY unusual 
situation in the cluster world, and highly unrecommended


> 
> 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-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 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-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:
>>> 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-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 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-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?
>>>> 
>>>> 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@o2ib:10.148.18.46@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@o2ib:10.148.18.46@o2ib:/fs1 on /work1 type lustre
>>>>> (rw,flock)
>>>>> 10.148.18.76@o2ib:10.148.18.164@o2ib:/fs2 on /work2 type lustre
>>>>> (rw,flock)
>>>>> 10.148.18.104@o2ib:10.148.18.165@o2ib:/fs3 on /work3 type lustre
>>>>> (rw,flock)
>>>>> 10.148.18.132@o2ib:10.148.18.133@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-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 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@o2ib:10.148.18.46@o2ib:/fs1
>>>>>>                           1.2P  136T  1.1P  12% /work1
>>>>>> 10.148.18.132@o2ib:10.148.18.133@o2ib:/fs4
>>>>>>                           1.2P  793T  368T  69% /work4
>>>>>> 10.148.18.104@o2ib:10.148.18.165@o2ib:/fs3
>>>>>>                           1.2P  509T  652T  44% /work3
>>>>>> 10.148.18.76@o2ib:10.148.18.164@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-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 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-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 setting TMPDIR to a local filesystem?
>>>>>>> 
>>>>>>> 
>>>>>>> On Mar 3, 2014, at 3:43 PM, Beichuan Yan<beichuan....@colorado.edu>     
>>>>>>>   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
>>>>>>>> jsquy...@cisco.com
>>>>>>>> For corporate legal information go to:
>>>>>>>> http://www.cisco.com/web/about/doing_business/legal/cri/
>>>>>>>> 
>>>>>>>> _______________________________________________
>>>>>>>> users mailing list
>>>>>>>> us...@open-mpi.org
>>>>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>>>>>> _______________________________________________
>>>>>>>> users mailing list
>>>>>>>> us...@open-mpi.org
>>>>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>>>>> 
>>>>>>> 
>>>>>>> --
>>>>>>> Jeff Squyres
>>>>>>> jsquy...@cisco.com
>>>>>>> For corporate legal information go to:
>>>>>>> http://www.cisco.com/web/about/doing_business/legal/cri/
>>>>>>> 
>>>>>>> _______________________________________________
>>>>>>> users mailing list
>>>>>>> us...@open-mpi.org
>>>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>>>>> _______________________________________________
>>>>>>> users mailing list
>>>>>>> us...@open-mpi.org
>>>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>>>> 
>>>>>> _______________________________________________
>>>>>> users mailing list
>>>>>> us...@open-mpi.org
>>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>>>> _______________________________________________
>>>>>> users mailing list
>>>>>> us...@open-mpi.org
>>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>>> 
>>>>> _______________________________________________
>>>>> users mailing list
>>>>> us...@open-mpi.org
>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>>> _______________________________________________
>>>>> users mailing list
>>>>> us...@open-mpi.org
>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>> 
>>>> _______________________________________________
>>>> users mailing list
>>>> us...@open-mpi.org
>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>> _______________________________________________
>>>> users mailing list
>>>> us...@open-mpi.org
>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>> 
>>> _______________________________________________
>>> users mailing list
>>> us...@open-mpi.org
>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>> _______________________________________________
>>> users mailing list
>>> us...@open-mpi.org
>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>> 
>> _______________________________________________
>> users mailing list
>> us...@open-mpi.org
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>> _______________________________________________
>> users mailing list
>> us...@open-mpi.org
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
> 
> _______________________________________________
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users
> _______________________________________________
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users

Reply via email to