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 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. >> Actually, besides the previous discussions on this thread, this problem is documented in the OMPI FAQ: http://www.open-mpi.org/faq/?category=sm#poor-sm-btl-performance >> 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 > I agree that it is bad. Perhaps unusual also, but not unheard of. If these nodes are diskless, I guess that the cluster vendor would probably recommend mounting /tmp as a tmpfs / ramfs (in RAM / shared memory). That is what is usually done in diskless computers, right? Why some installations mount /tmp over the network is unclear. I guess OpenMPI is not alone in using /tmp for to store temporary and readily accessible stuff, which, given its name, /tmp is supposed to do. So, it is not a matter of OMPI enforcing it. However, reducing the dependence on /tmp, may be a plus anyway. > >> >> 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 > > _______________________________________________ > 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
