Hi. The pbsdsh tool is great. I ran an interactive qsub session
(qsub -I -lnodes=2:ppn=12) and then rand the pbsdsh tool like this:
[rsvancara@node164 ~]$ /usr/local/bin/pbsdsh -h node164 printenv
PATH=/bin:/usr/bin
LANG=C
PBS_O_HOME=/home/admins/rsvancara
PBS_O_LANG=en_US.UTF-8
PBS_O_LOGNAME=rsvancara
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
PBS_O_MAIL=/var/spool/mail/rsvancara
PBS_O_SHELL=/bin/bash
PBS_SERVER=mgt1.wsuhpc.edu
PBS_O_WORKDIR=/home/admins/rsvancara/TEST
PBS_O_QUEUE=batch
PBS_O_HOST=login1
HOME=/home/admins/rsvancara
PBS_JOBNAME=STDIN
PBS_JOBID=1672.mgt1.wsuhpc.edu
PBS_QUEUE=batch
PBS_JOBCOOKIE=50E4985E63684BA781EE9294F21EE25E
PBS_NODENUM=0
PBS_TASKNUM=146
PBS_MOMPORT=15003
PBS_NODEFILE=/var/spool/torque/aux//1672.mgt1.wsuhpc.edu
PBS_VERSION=TORQUE-2.4.7
PBS_VNODENUM=0
PBS_ENVIRONMENT=PBS_BATCH
ENVIRONMENT=BATCH
[rsvancara@node164 ~]$ /usr/local/bin/pbsdsh -h node163 printenv
PATH=/bin:/usr/bin
LANG=C
PBS_O_HOME=/home/admins/rsvancara
PBS_O_LANG=en_US.UTF-8
PBS_O_LOGNAME=rsvancara
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
PBS_O_MAIL=/var/spool/mail/rsvancara
PBS_O_SHELL=/bin/bash
PBS_SERVER=mgt1.wsuhpc.edu
PBS_O_WORKDIR=/home/admins/rsvancara/TEST
PBS_O_QUEUE=batch
PBS_O_HOST=login1
HOME=/home/admins/rsvancara
PBS_JOBNAME=STDIN
PBS_JOBID=1672.mgt1.wsuhpc.edu
PBS_QUEUE=batch
PBS_JOBCOOKIE=50E4985E63684BA781EE9294F21EE25E
PBS_NODENUM=1
PBS_TASKNUM=147
PBS_MOMPORT=15003
PBS_VERSION=TORQUE-2.4.7
PBS_VNODENUM=12
PBS_ENVIRONMENT=PBS_BATCH
ENVIRONMENT=BATCH
So one thing that strikes me as bad is the LD_LIBRARY_PATH does not
appear available. Attempted to run mpiexec like this and it fails.
[rsvancara@node164 ~]$ /usr/local/bin/pbsdsh -h node163
/home/software/mpi/intel/openmpi-1.4.3/bin/mpiexec hostname
/home/software/mpi/intel/openmpi-1.4.3/bin/mpiexec: error while
loading shared libraries: libimf.so: cannot open shared object file:
No such file or directory
pbsdsh: task 12 exit status 127
[rsvancara@node164 ~]$ /usr/local/bin/pbsdsh -h node164
/home/software/mpi/intel/openmpi-1.4.3/bin/mpiexec hostname
/home/software/mpi/intel/openmpi-1.4.3/bin/mpiexec: error while
loading shared libraries: libimf.so: cannot open shared object file:
No such file or directory
pbsdsh: task 0 exit status 127
If this is how the openmpi processes are being launched, then it is no
wonder they are failing and the LD_LIBRARY_PATH error message is
indeed somewhat accurate.
So the next question is how to I ensure that this information is
available to pbsdsh?
Thanks,
Randall
On Mon, Mar 21, 2011 at 11:24 AM, Randall Svancara <rsvanc...@gmail.com> wrote:
> 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/
>
--
Randall Svancara
http://knowyourlinux.com/
