Ok, these are good things to check. I am going to follow through with
this in the next hour after our GPFS upgrade. Thanks!!!
On Mon, Mar 21, 2011 at 11:14 AM, Brock Palen <bro...@umich.edu> wrote:
> On Mar 21, 2011, at 1:59 PM, Jeff Squyres wrote:
>
>> I no longer run Torque on my cluster, so my Torqueology is pretty rusty --
>> but I think there's a Torque command to launch on remote nodes. tmrsh or
>> pbsrsh or something like that...?
>
> pbsdsh
> If TM is working pbsdsh should work fine.
>
> Torque+OpenMPI has been working just fine for us.
> Do you have libtorque on all your compute hosts? You should see it open on
> all hosts if it works.
>
>>
>> Try that and make sure it works. Open MPI should be using the same API as
>> that command under the covers.
>>
>> I also have a dim recollection that the TM API support library(ies?) may not
>> be installed by default. You may have to ensure that they're available on
>> all nodes...?
>>
>>
>> On Mar 21, 2011, at 1:53 PM, Randall Svancara wrote:
>>
>>> I am not sure if there is any extra configuration necessary for torque
>>> to forward the environment. I have included the output of printenv
>>> for an interactive qsub session. I am really at a loss here because I
>>> never had this much difficulty making torque run with openmpi. It has
>>> been mostly a good experience.
>>>
>>> Permissions of /tmp
>>>
>>> drwxrwxrwt 4 root root 140 Mar 20 08:57 tmp
>>>
>>> mpiexec hostname single node:
>>>
>>> [rsvancara@login1 ~]$ qsub -I -lnodes=1:ppn=12
>>> qsub: waiting for job 1667.mgt1.wsuhpc.edu to start
>>> qsub: job 1667.mgt1.wsuhpc.edu ready
>>>
>>> [rsvancara@node100 ~]$ mpiexec hostname
>>> node100
>>> node100
>>> node100
>>> node100
>>> node100
>>> node100
>>> node100
>>> node100
>>> node100
>>> node100
>>> node100
>>> node100
>>>
>>> mpiexec hostname two nodes:
>>>
>>> [rsvancara@node100 ~]$ mpiexec hostname
>>> [node100:09342] plm:tm: failed to poll for a spawned daemon, return
>>> status = 17002
>>> --------------------------------------------------------------------------
>>> A daemon (pid unknown) died unexpectedly on signal 1 while attempting to
>>> launch so we are aborting.
>>>
>>> There may be more information reported by the environment (see above).
>>>
>>> This may be because the daemon was unable to find all the needed shared
>>> libraries on the remote node. You may set your LD_LIBRARY_PATH to have the
>>> location of the shared libraries on the remote nodes and this will
>>> automatically be forwarded to the remote nodes.
>>> --------------------------------------------------------------------------
>>> --------------------------------------------------------------------------
>>> mpiexec noticed that the job aborted, but has no info as to the process
>>> that caused that situation.
>>> --------------------------------------------------------------------------
>>> --------------------------------------------------------------------------
>>> mpiexec was unable to cleanly terminate the daemons on the nodes shown
>>> below. Additional manual cleanup may be required - please refer to
>>> the "orte-clean" tool for assistance.
>>> --------------------------------------------------------------------------
>>> node99 - daemon did not report back when launched
>>>
>>>
>>> MPIexec on one node with one cpu:
>>>
>>> [rsvancara@node164 ~]$ mpiexec printenv
>>> OMPI_MCA_orte_precondition_transports=5fbd0d3c8e4195f1-80f964226d1575ea
>>> MODULE_VERSION_STACK=3.2.8
>>> MANPATH=/home/software/mpi/intel/openmpi-1.4.3/share/man:/home/software/intel/Compiler/11.1/075/man/en_US:/home/software/intel/Compiler/11.1/075/mkl/man/en_US:/home/software/intel/Compiler/11.1/075/mkl/../man/en_US:/home/software/Modules/3.2.8/share/man:/usr/share/man
>>> HOSTNAME=node164
>>> PBS_VERSION=TORQUE-2.4.7
>>> TERM=xterm
>>> SHELL=/bin/bash
>>> HISTSIZE=1000
>>> PBS_JOBNAME=STDIN
>>> PBS_ENVIRONMENT=PBS_INTERACTIVE
>>> PBS_O_WORKDIR=/home/admins/rsvancara
>>> PBS_TASKNUM=1
>>> USER=rsvancara
>>> LD_LIBRARY_PATH=/home/software/mpi/intel/openmpi-1.4.3/lib:/home/software/intel/Compiler/11.1/075/lib/intel64:/home/software/intel/Compiler/11.1/075/ipp/em64t/sharedlib:/home/software/intel/Compiler/11.1/075/mkl/lib/em64t:/home/software/intel/Compiler/11.1/075/tbb/intel64/cc4.1.0_libc2.4_kernel2.6.16.21/lib:/home/software/intel/Compiler/11.1/075/lib
>>> LS_COLORS=no=00:fi=00:di=00;34:ln=00;36:pi=40;33:so=00;35:bd=40;33;01:cd=40;33;01:or=01;05;37;41:mi=01;05;37;41:ex=00;32:*.cmd=00;32:*.exe=00;32:*.com=00;32:*.btm=00;32:*.bat=00;32:*.sh=00;32:*.csh=00;32:*.tar=00;31:*.tgz=00;31:*.arj=00;31:*.taz=00;31:*.lzh=00;31:*.zip=00;31:*.z=00;31:*.Z=00;31:*.gz=00;31:*.bz2=00;31:*.bz=00;31:*.tz=00;31:*.rpm=00;31:*.cpio=00;31:*.jpg=00;35:*.gif=00;35:*.bmp=00;35:*.xbm=00;35:*.xpm=00;35:*.png=00;35:*.tif=00;35:
>>> PBS_O_HOME=/home/admins/rsvancara
>>> CPATH=/home/software/intel/Compiler/11.1/075/ipp/em64t/include:/home/software/intel/Compiler/11.1/075/mkl/include:/home/software/intel/Compiler/11.1/075/tbb/include
>>> PBS_MOMPORT=15003
>>> PBS_O_QUEUE=batch
>>> NLSPATH=/home/software/intel/Compiler/11.1/075/lib/intel64/locale/%l_%t/%N:/home/software/intel/Compiler/11.1/075/ipp/em64t/lib/locale/%l_%t/%N:/home/software/intel/Compiler/11.1/075/mkl/lib/em64t/locale/%l_%t/%N:/home/software/intel/Compiler/11.1/075/idb/intel64/locale/%l_%t/%N
>>> MODULE_VERSION=3.2.8
>>> MAIL=/var/spool/mail/rsvancara
>>> PBS_O_LOGNAME=rsvancara
>>> PATH=/home/software/mpi/intel/openmpi-1.4.3/bin:/home/software/intel/Compiler/11.1/075/bin/intel64:/home/software/Modules/3.2.8/bin:/bin:/usr/bin:/usr/lpp/mmfs/bin
>>> PBS_O_LANG=en_US.UTF-8
>>> PBS_JOBCOOKIE=D52DE562B685A462849C1136D6B581F9
>>> INPUTRC=/etc/inputrc
>>> PWD=/home/admins/rsvancara
>>> _LMFILES_=/home/software/Modules/3.2.8/modulefiles/modules:/home/software/Modules/3.2.8/modulefiles/null:/home/software/modulefiles/intel/11.1.075:/home/software/modulefiles/openmpi/1.4.3_intel
>>> PBS_NODENUM=0
>>> LANG=C
>>> MODULEPATH=/home/software/Modules/versions:/home/software/Modules/$MODULE_VERSION/modulefiles:/home/software/modulefiles
>>> LOADEDMODULES=modules:null:intel/11.1.075:openmpi/1.4.3_intel
>>> PBS_O_SHELL=/bin/bash
>>> PBS_SERVER=mgt1.wsuhpc.edu
>>> PBS_JOBID=1670.mgt1.wsuhpc.edu
>>> SHLVL=1
>>> HOME=/home/admins/rsvancara
>>> INTEL_LICENSES=/home/software/intel/Compiler/11.1/075/licenses:/opt/intel/licenses
>>> PBS_O_HOST=login1
>>> DYLD_LIBRARY_PATH=/home/software/intel/Compiler/11.1/075/tbb/intel64/cc4.1.0_libc2.4_kernel2.6.16.21/lib
>>> PBS_VNODENUM=0
>>> LOGNAME=rsvancara
>>> PBS_QUEUE=batch
>>> MODULESHOME=/home/software/mpi/intel/openmpi-1.4.3
>>> LESSOPEN=|/usr/bin/lesspipe.sh %s
>>> PBS_O_MAIL=/var/spool/mail/rsvancara
>>> G_BROKEN_FILENAMES=1
>>> PBS_NODEFILE=/var/spool/torque/aux//1670.mgt1.wsuhpc.edu
>>> PBS_O_PATH=/home/software/mpi/intel/openmpi-1.4.3/bin:/home/software/intel/Compiler/11.1/075/bin/intel64:/home/software/Modules/3.2.8/bin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/lpp/mmfs/bin
>>> module=() { eval `/home/software/Modules/$MODULE_VERSION/bin/modulecmd
>>> bash $*`
>>> }
>>> _=/home/software/mpi/intel/openmpi-1.4.3/bin/mpiexec
>>> OMPI_MCA_orte_local_daemon_uri=3236233216.0;tcp://172.20.102.82:33559;tcp://172.40.102.82:33559
>>> OMPI_MCA_orte_hnp_uri=3236233216.0;tcp://172.20.102.82:33559;tcp://172.40.102.82:33559
>>> OMPI_MCA_mpi_yield_when_idle=0
>>> OMPI_MCA_orte_app_num=0
>>> OMPI_UNIVERSE_SIZE=1
>>> OMPI_MCA_ess=env
>>> OMPI_MCA_orte_ess_num_procs=1
>>> OMPI_COMM_WORLD_SIZE=1
>>> OMPI_COMM_WORLD_LOCAL_SIZE=1
>>> OMPI_MCA_orte_ess_jobid=3236233217
>>> OMPI_MCA_orte_ess_vpid=0
>>> OMPI_COMM_WORLD_RANK=0
>>> OMPI_COMM_WORLD_LOCAL_RANK=0
>>> OPAL_OUTPUT_STDERR_FD=19
>>>
>>> MPIExec with -mca plm rsh:
>>>
>>> [rsvancara@node164 ~]$ mpiexec -mca plm rsh -mca orte_tmpdir_base
>>> /fastscratch/admins/tmp hostname
>>> node164
>>> node164
>>> node164
>>> node164
>>> node164
>>> node164
>>> node164
>>> node164
>>> node164
>>> node164
>>> node164
>>> node164
>>> node163
>>> node163
>>> node163
>>> node163
>>> node163
>>> node163
>>> node163
>>> node163
>>> node163
>>> node163
>>> node163
>>> node163
>>>
>>>
>>> On Mon, Mar 21, 2011 at 9:22 AM, Ralph Castain <r...@open-mpi.org> wrote:
>>>> Can you run anything under TM? Try running "hostname" directly from Torque
>>>> to see if anything works at all.
>>>>
>>>> The error message is telling you that the Torque daemon on the remote node
>>>> reported a failure when trying to launch the OMPI daemon. Could be that
>>>> Torque isn't setup to forward environments so the OMPI daemon isn't
>>>> finding required libs. You could directly run "printenv" to see how your
>>>> remote environ is being setup.
>>>>
>>>> Could be that the tmp dir lacks correct permissions for a user to create
>>>> the required directories. The OMPI daemon tries to create a session
>>>> directory in the tmp dir, so failure to do so would indeed cause the
>>>> launch to fail. You can specify the tmp dir with a cmd line option to
>>>> mpirun. See "mpirun -h" for info.
>>>>
>>>>
>>>> On Mar 21, 2011, at 12:21 AM, Randall Svancara wrote:
>>>>
>>>>> I have a question about using OpenMPI and Torque on stateless nodes.
>>>>> I have compiled openmpi 1.4.3 with --with-tm=/usr/local
>>>>> --without-slurm using intel compiler version 11.1.075.
>>>>>
>>>>> When I run a simple "hello world" mpi program, I am receiving the
>>>>> following error.
>>>>>
>>>>> [node164:11193] plm:tm: failed to poll for a spawned daemon, return
>>>>> status = 17002
>>>>> --------------------------------------------------------------------------
>>>>> A daemon (pid unknown) died unexpectedly on signal 1 while attempting to
>>>>> launch so we are aborting.
>>>>>
>>>>> There may be more information reported by the environment (see above).
>>>>>
>>>>> This may be because the daemon was unable to find all the needed shared
>>>>> libraries on the remote node. You may set your LD_LIBRARY_PATH to have the
>>>>> location of the shared libraries on the remote nodes and this will
>>>>> automatically be forwarded to the remote nodes.
>>>>> --------------------------------------------------------------------------
>>>>> --------------------------------------------------------------------------
>>>>> mpiexec noticed that the job aborted, but has no info as to the process
>>>>> that caused that situation.
>>>>> --------------------------------------------------------------------------
>>>>> --------------------------------------------------------------------------
>>>>> mpiexec was unable to cleanly terminate the daemons on the nodes shown
>>>>> below. Additional manual cleanup may be required - please refer to
>>>>> the "orte-clean" tool for assistance.
>>>>> --------------------------------------------------------------------------
>>>>> node163 - daemon did not report back when launched
>>>>> node159 - daemon did not report back when launched
>>>>> node158 - daemon did not report back when launched
>>>>> node157 - daemon did not report back when launched
>>>>> node156 - daemon did not report back when launched
>>>>> node155 - daemon did not report back when launched
>>>>> node154 - daemon did not report back when launched
>>>>> node152 - daemon did not report back when launched
>>>>> node151 - daemon did not report back when launched
>>>>> node150 - daemon did not report back when launched
>>>>> node149 - daemon did not report back when launched
>>>>>
>>>>>
>>>>> But if I include:
>>>>>
>>>>> -mca plm rsh
>>>>>
>>>>> The job runs just fine.
>>>>>
>>>>> I am not sure what the problem is with torque or openmpi that prevents
>>>>> the process from launching on remote nodes. I have posted to the
>>>>> torque list and someone suggested that it may be temporary directory
>>>>> space that can be causing issues. I have 100MB allocated to /tmp
>>>>>
>>>>> Any ideas as to why I am having this problem would be appreciated.
>>>>>
>>>>>
>>>>> --
>>>>> Randall Svancara
>>>>> http://knowyourlinux.com/
>>>>> _______________________________________________
>>>>> 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
>>>>
>>>
>>>
>>>
>>> --
>>> Randall Svancara
>>> http://knowyourlinux.com/
>>>
>>> _______________________________________________
>>> 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
>
--
Randall Svancara
http://knowyourlinux.com/
