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Subject: Re: [OMPI users] Unable to find the following executable
From: Tushar Andriyas (thugnomics28_at_[hidden])
Date: 2010-11-21 16:24:07


The same TCP connection if I run on the other cluster UINTA,
I get the following error log

mca/pls/tm/pls_tm_module.c at line 572
[uinta-0039:14508] [0,0,0] ORTE_ERROR_LOG: Timeout in file
../../../../../orte/\
mca/errmgr/hnp/errmgr_hnp.c at line 90
[uinta-0039:14508] [0,0,0] ORTE_ERROR_LOG: Timeout in file
../../../../orte/mca\
/pls/base/pls_base_orted_cmds.c at line 188
[uinta-0039:14508] [0,0,0] ORTE_ERROR_LOG: Timeout in file
../../../../../orte/\
mca/pls/tm/pls_tm_module.c at line 603
--------------------------------------------------------------------------
mpirun was unable to cleanly terminate the daemons for this job. Returned
value\
 Timeout instead of ORTE_SUCCESS.
--------------------------------------------------------------------------
[uinta-0039:14510] OOB: Connection to HNP lost
[uinta-0038:15165] OOB: Connection to HNP lost

On Sat, Nov 20, 2010 at 5:35 PM, Tushar Andriyas <thugnomics28_at_[hidden]>wrote:

> I tried out the TCP connection and here is what the error file came out as.
>
>
>
> [wasatch-29:05042] [0,0,0] ORTE_ERROR_LOG: Timeout in file
> ../../../../orte/mca\
> /pls/base/pls_base_orted_cmds.c at line 275
> [wasatch-29:05042] [0,0,0] ORTE_ERROR_LOG: Timeout in file
> ../../../../../orte/\
> mca/pls/tm/pls_tm_module.c at line 572
> [wasatch-29:05042] [0,0,0] ORTE_ERROR_LOG: Timeout in file
> ../../../../../orte/\
> mca/errmgr/hnp/errmgr_hnp.c at line 90
> [wasatch-29:05042] [0,0,0] ORTE_ERROR_LOG: Timeout in file
> ../../../../orte/mca\
> /pls/base/pls_base_orted_cmds.c at line 188
> [wasatch-29:05042] [0,0,0] ORTE_ERROR_LOG: Timeout in file
> ../../../../../orte/\
> mca/pls/tm/pls_tm_module.c at line 603
> --------------------------------------------------------------------------
> mpirun was unable to cleanly terminate the daemons for this job. Returned
> value\
> Timeout instead of ORTE_SUCCESS.
> --------------------------------------------------------------------------
> [wasatch-29:05044] OOB: Connection to HNP lost
>
>
>
>
> On Sat, Nov 20, 2010 at 2:03 PM, Addepalli, Srirangam V <
> srirangam.v.addepalli_at_[hidden]> wrote:
>
>> mpirun --mca btl self,sm,tcp --mca btl_base_verbose 30 -np 8
>> /home/A00945081/SWMF_v2.3/run/SWMF.exe > run.log
>>
>> to run using tcp interface in job submission script.
>>
>> Rangam
>> _______________________________________
>> From: users-bounces_at_[hidden] [users-bounces_at_[hidden]] On Behalf
>> Of Tushar Andriyas [thugnomics28_at_[hidden]]
>> Sent: Saturday, November 20, 2010 1:36 PM
>> To: Open MPI Users
>> Subject: Re: [OMPI users] Unable to find the following executable
>>
>> Ya sure, here is the list
>>
>>
>> Open MPI: 1.2.7
>> Open MPI SVN revision: r19401
>> Open RTE: 1.2.7
>> Open RTE SVN revision: r19401
>> OPAL: 1.2.7
>> OPAL SVN revision: r19401
>> Prefix: /opt/libraries/openmpi/openmpi-1.2.7-pgi
>> Configured architecture: x86_64-unknown-linux-gnu
>> Configured by: A00017402
>> Configured on: Thu Sep 18 15:00:05 MDT 2008
>> Configure host: volvox.hpc.usu.edu<http://volvox.hpc.usu.edu>
>> Built by: A00017402
>> Built on: Thu Sep 18 15:20:06 MDT 2008
>> Built host: volvox.hpc.usu.edu<http://volvox.hpc.usu.edu>
>> C bindings: yes
>> C++ bindings: yes
>> Fortran77 bindings: yes (all)
>> Fortran90 bindings: yes
>> Fortran90 bindings size: large
>> C compiler: pgcc
>> C compiler absolute: /opt/apps/pgi/linux86-64/7.2/bin/pgcc
>> C++ compiler: pgCC
>> C++ compiler absolute: /opt/apps/pgi/linux86-64/7.2/bin/pgCC
>> Fortran77 compiler: pgf77
>> Fortran77 compiler abs: /opt/apps/pgi/linux86-64/7.2/bin/pgf77
>> Fortran90 compiler: pgf90
>> Fortran90 compiler abs: /opt/apps/pgi/linux86-64/7.2/bin/pgf90
>> C profiling: yes
>> C++ profiling: yes
>> Fortran77 profiling: yes
>> Fortran90 profiling: yes
>> C++ exceptions: no
>> Thread support: posix (mpi: no, progress: no)
>> Internal debug support: no
>> MPI parameter check: runtime
>> Memory profiling support: no
>> Memory debugging support: no
>> libltdl support: yes
>> Heterogeneous support: yes
>> mpirun default --prefix: no
>> MCA backtrace: execinfo (MCA v1.0, API v1.0, Component v1.2.7)
>> MCA memory: ptmalloc2 (MCA v1.0, API v1.0, Component v1.2.7)
>> MCA paffinity: linux (MCA v1.0, API v1.0, Component v1.2.7)
>> MCA maffinity: first_use (MCA v1.0, API v1.0, Component v1.2.7)
>> MCA maffinity: libnuma (MCA v1.0, API v1.0, Component v1.2.7)
>> MCA timer: linux (MCA v1.0, API v1.0, Component v1.2.7)
>> MCA installdirs: env (MCA v1.0, API v1.0, Component v1.2.7)
>> MCA installdirs: config (MCA v1.0, API v1.0, Component v1.2.7)
>> MCA allocator: basic (MCA v1.0, API v1.0, Component v1.0)
>> MCA allocator: bucket (MCA v1.0, API v1.0, Component v1.0)
>> MCA coll: basic (MCA v1.0, API v1.0, Component v1.2.7)
>> MCA coll: self (MCA v1.0, API v1.0, Component v1.2.7)
>> MCA coll: sm (MCA v1.0, API v1.0, Component v1.2.7)
>> MCA coll: tuned (MCA v1.0, API v1.0, Component v1.2.7)
>> MCA io: romio (MCA v1.0, API v1.0, Component v1.2.7)
>> MCA mpool: rdma (MCA v1.0, API v1.0, Component v1.2.7)
>> MCA mpool: sm (MCA v1.0, API v1.0, Component v1.2.7)
>> MCA pml: cm (MCA v1.0, API v1.0, Component v1.2.7)
>> MCA pml: ob1 (MCA v1.0, API v1.0, Component v1.2.7)
>> MCA bml: r2 (MCA v1.0, API v1.0, Component v1.2.7)
>> MCA rcache: vma (MCA v1.0, API v1.0, Component v1.2.7)
>> MCA btl: gm (MCA v1.0, API v1.0.1, Component v1.2.7)
>> MCA btl: self (MCA v1.0, API v1.0.1, Component v1.2.7)
>> MCA btl: sm (MCA v1.0, API v1.0.1, Component v1.2.7)
>> MCA btl: tcp (MCA v1.0, API v1.0.1, Component v1.0)
>> MCA topo: unity (MCA v1.0, API v1.0, Component v1.2.7)
>> MCA osc: pt2pt (MCA v1.0, API v1.0, Component v1.2.7)
>> MCA errmgr: hnp (MCA v1.0, API v1.3, Component v1.2.7)
>> MCA errmgr: orted (MCA v1.0, API v1.3, Component v1.2.7)
>> MCA errmgr: proxy (MCA v1.0, API v1.3, Component v1.2.7)
>> MCA gpr: null (MCA v1.0, API v1.0, Component v1.2.7)
>> MCA gpr: proxy (MCA v1.0, API v1.0, Component v1.2.7)
>> MCA gpr: replica (MCA v1.0, API v1.0, Component v1.2.7)
>> MCA iof: proxy (MCA v1.0, API v1.0, Component v1.2.7)
>> MCA iof: svc (MCA v1.0, API v1.0, Component v1.2.7)
>> MCA ns: proxy (MCA v1.0, API v2.0, Component v1.2.7)
>> MCA ns: replica (MCA v1.0, API v2.0, Component v1.2.7)
>> MCA oob: tcp (MCA v1.0, API v1.0, Component v1.0)
>> MCA ras: dash_host (MCA v1.0, API v1.3, Component v1.2.7)
>> MCA ras: gridengine (MCA v1.0, API v1.3, Component v1.2.7)
>> MCA ras: localhost (MCA v1.0, API v1.3, Component v1.2.7)
>> MCA ras: slurm (MCA v1.0, API v1.3, Component v1.2.7)
>> MCA ras: tm (MCA v1.0, API v1.3, Component v1.2.7)
>> MCA rds: hostfile (MCA v1.0, API v1.3, Component v1.2.7)
>> MCA rds: proxy (MCA v1.0, API v1.3, Component v1.2.7)
>> MCA rds: resfile (MCA v1.0, API v1.3, Component v1.2.7)
>> MCA rmaps: round_robin (MCA v1.0, API v1.3, Component
>> v1.2.7)
>> MCA rmgr: proxy (MCA v1.0, API v2.0, Component v1.2.7)
>> MCA rmgr: urm (MCA v1.0, API v2.0, Component v1.2.7)
>> MCA rml: oob (MCA v1.0, API v1.0, Component v1.2.7)
>> MCA pls: gridengine (MCA v1.0, API v1.3, Component v1.2.7)
>> MCA pls: proxy (MCA v1.0, API v1.3, Component v1.2.7)
>> MCA pls: rsh (MCA v1.0, API v1.3, Component v1.2.7)
>> MCA pls: slurm (MCA v1.0, API v1.3, Component v1.2.7)
>> MCA pls: tm (MCA v1.0, API v1.3, Component v1.2.7)
>> MCA sds: env (MCA v1.0, API v1.0, Component v1.2.7)
>> MCA sds: pipe (MCA v1.0, API v1.0, Component v1.2.7)
>> MCA sds: seed (MCA v1.0, API v1.0, Component v1.2.7)
>> MCA sds: singleton (MCA v1.0, API v1.0, Component v1.2.7)
>> MCA sds: slurm (MCA v1.0, API v1.0, Component v1.2.7)
>>
>> How do you invoke tcp? I no for sure that the launcher on the clusters is
>> torque.
>>
>> Tushar
>>
>> On Sat, Nov 20, 2010 at 11:28 AM, Addepalli, Srirangam V <
>> srirangam.v.addepalli_at_[hidden]<mailto:srirangam.v.addepalli_at_[hidden]>>
>> wrote:
>> Hello Tushar,
>> Can you send me the output of ompi_info.
>> Have you tried using just tcp instead of IB to narrow down.
>> Rangam
>>
>> #!/bin/sh
>> #PBS -V
>> #PBS -q wasatch
>> #PBS -N SWMF
>> #PBS -l nodes=1:ppn=8
>> # change to the run directory
>> #cd $SWMF_v2.3/run
>> cat `echo ${PBS_NODEFILE}` > list_of_nodes
>>
>> mpirun --mca btl self,sm,tcp --mca btl_base_verbose 30 -np 8
>> /home/A00945081/SWMF_v2.3/run/SWMF.exe > run.log
>>
>>
>> ________________________________________
>> From: users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]> [
>> users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]>] On Behalf
>> Of Tushar Andriyas [thugnomics28_at_[hidden]<mailto:thugnomics28_at_[hidden]
>> >]
>> Sent: Saturday, November 20, 2010 12:11 PM
>> To: Open MPI Users
>> Subject: Re: [OMPI users] Unable to find the following executable
>>
>> Rangam,
>>
>> It does not want to run at all. Attached is the log file from the batch
>> file run u sent.
>>
>> On Sat, Nov 20, 2010 at 10:32 AM, Addepalli, Srirangam V <
>> srirangam.v.addepalli_at_[hidden]<mailto:srirangam.v.addepalli_at_[hidden]
>> ><mailto:srirangam.v.addepalli_at_[hidden]<mailto:
>> srirangam.v.addepalli_at_[hidden]>>> wrote:
>> Hello Tushar,
>> MPIRUN is not able to spawn processes on the node allocated. This should
>> help
>>
>> #!/bin/sh
>> #PBS -V
>> #PBS -q wasatch
>> #PBS -N SWMF
>> #PBS -l nodes=2:ppn=8
>> # change to the run directory
>> #cd $SWMF_v2.3/run
>> cat `echo ${PBS_NODEFILE}` > list_of_nodes
>> mpirun -np 8 /home/A00945081/SWMF_v2.3/run/SWMF.exe > run.log
>>
>>
>> Rangam
>>
>>
>> ________________________________________
>> From: users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]
>> ><mailto:users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]>> [
>> users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]><mailto:
>> users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]>>] On Behalf
>> Of Tushar Andriyas [thugnomics28_at_[hidden]<mailto:thugnomics28_at_[hidden]
>> ><mailto:thugnomics28_at_[hidden]<mailto:thugnomics28_at_[hidden]>>]
>> Sent: Saturday, November 20, 2010 10:48 AM
>> To: Open MPI Users
>> Subject: Re: [OMPI users] Unable to find the following executable
>>
>> Hi Rangam,
>>
>> I ran the batch file that you gave and have attached the error file. Also,
>> since the WASATCH cluster is kind of small, people usually run on UINTA. So,
>> if possible could you look at the uinta error files?
>> Tushar
>>
>> On Fri, Nov 19, 2010 at 12:31 PM, Addepalli, Srirangam V <
>> srirangam.v.addepalli_at_[hidden]<mailto:srirangam.v.addepalli_at_[hidden]
>> ><mailto:srirangam.v.addepalli_at_[hidden]<mailto:
>> srirangam.v.addepalli_at_[hidden]>><mailto:srirangam.v.addepalli_at_[hidden]
>> <mailto:srirangam.v.addepalli_at_[hidden]><mailto:
>> srirangam.v.addepalli_at_[hidden]<mailto:srirangam.v.addepalli_at_[hidden]>>>>
>> wrote:
>> Hello Tushar,
>> After looking at the log files you attached it appears that there are
>> multiple issues.
>>
>> [0,1,11]: Myrinet/GM on host wasatch-55 was unable to find any NICs.
>> Another transport will be used instead, although this may result in
>> lower performance.
>>
>> Usually they occur if there is a mismatch in mpirun version and mca blt
>> selection. I suggest the following order to check if the job actually works
>> on a single node
>>
>> #!/bin/sh
>> #PBS -V
>> #PBS -q wasatch
>> #PBS -N SWMF
>> #PBS -l nodes=2:ppn=8
>> # change to the run directory
>> #cd $SWMF_v2.3/run
>> cat `echo ${PBS_NODEFILE}` > list_of_nodes
>> mpirun -np 8 -machinefile list_of_nodes
>> /home/A00945081/SWMF_v2.3/run/SWMF.exe > run.log
>>
>>
>> Rangam
>>
>>
>> ________________________________________
>> From: users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]
>> ><mailto:users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]
>> >><mailto:users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]
>> ><mailto:users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]>>>
>> [users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]><mailto:
>> users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]>><mailto:
>> users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]><mailto:
>> users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]>>>] On
>> Behalf Of Tushar Andriyas [thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]>><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]>>>]
>> Sent: Friday, November 19, 2010 1:11 PM
>> To: Open MPI Users
>> Subject: Re: [OMPI users] Unable to find the following executable
>>
>> Hey Rangam,
>>
>> I tried out the batch script and the error file comes out empty and the
>> output file has /home/A00945081/SWM_v2.3/run/SWMF.exe (WHEN RUN ON A SINGLE
>> MACHINE) and the same with multiple machines in the run. So, does that mean
>> that the exe is auto mounted ? What should I do next?
>>
>> Tushar
>>
>> On Fri, Nov 19, 2010 at 10:05 AM, Addepalli, Srirangam V <
>> srirangam.v.addepalli_at_[hidden]<mailto:srirangam.v.addepalli_at_[hidden]
>> ><mailto:srirangam.v.addepalli_at_[hidden]<mailto:
>> srirangam.v.addepalli_at_[hidden]>><mailto:srirangam.v.addepalli_at_[hidden]
>> <mailto:srirangam.v.addepalli_at_[hidden]><mailto:
>> srirangam.v.addepalli_at_[hidden]<mailto:srirangam.v.addepalli_at_[hidden]
>> >>><mailto:srirangam.v.addepalli_at_[hidden]<mailto:
>> srirangam.v.addepalli_at_[hidden]><mailto:srirangam.v.addepalli_at_[hidden]
>> <mailto:srirangam.v.addepalli_at_[hidden]>><mailto:
>> srirangam.v.addepalli_at_[hidden]<mailto:srirangam.v.addepalli_at_[hidden]
>> ><mailto:srirangam.v.addepalli_at_[hidden]<mailto:
>> srirangam.v.addepalli_at_[hidden]>>>>> wrote:
>> Hello Tushar,
>>
>> Try the following script.
>>
>> #!/bin/sh
>> #PBS -V
>> #PBS -q wasatch
>> #PBS -N SWMF
>> #PBS -l nodes=1:ppn=8
>> # change to the run directory
>> #cd $SWMF_v2.3/run
>> cat `echo ${PBS_NODEFILE}` > list_of_nodes
>>
>>
>>
>>
>> The objective is to check if your user directories are auto mounted on
>> compute nodes and are available during run time.
>>
>> If the job returns information about SWMF.exe then it can be safely
>> assumed that user directories are being auto mounted.
>>
>> Rangam
>>
>>
>>
>> ________________________________________
>> From: users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]
>> ><mailto:users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]
>> >><mailto:users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]
>> ><mailto:users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]
>> >>><mailto:users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]
>> ><mailto:users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]
>> >><mailto:users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]
>> ><mailto:users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]>>>>
>> [users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]><mailto:
>> users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]>><mailto:
>> users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]><mailto:
>> users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]>>><mailto:
>> users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]><mailto:
>> users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]>><mailto:
>> users-bounce!
>> s_at_[hidden]<mailto:users-bounces_at_[hidden]><mailto:
>> users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]>>>>] On
>> Behalf Of Tushar Andriyas [thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]>><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]>>><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]>><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]>>>>]
>> Sent: Friday, November 19, 2010 8:35 AM
>> To: Open MPI Users
>> Subject: Re: [OMPI users] Unable to find the following executable
>>
>> It just gives back the info on folders in my home directory. Dont get me
>> wrong but i m kinda new in this. So, could u type out d full command which i
>> need to give?
>>
>> Tushar
>>
>> On Thu, Nov 18, 2010 at 8:35 AM, Ralph Castain <rhc_at_[hidden]<mailto:
>> rhc_at_[hidden]><mailto:rhc_at_[hidden]<mailto:rhc_at_[hidden]
>> >><mailto:rhc_at_[hidden]<mailto:rhc_at_[hidden]><mailto:
>> rhc_at_[hidden]<mailto:rhc_at_[hidden]>>><mailto:rhc_at_[hidden]
>> <mailto:rhc_at_[hidden]><mailto:rhc_at_[hidden]<mailto:rhc_at_[hidden]
>> >><mailto:rhc_at_[hidden]<mailto:rhc_at_[hidden]><mailto:
>> rhc_at_[hidden]<mailto:rhc_at_[hidden]>>>><mailto:rhc_at_[hidden]
>> <mailto:rhc_at_[hidden]><mailto:rhc_at_[hidden]<mailto:rhc_at_[hidden]
>> >><mailto:rhc_at_[hidden]<mailto:rhc_at_[hidden]><mailto:
>> rhc_at_[hidden]<mailto:rhc_at_[hidden]>>><mailto:rhc_at_[hidden]
>> <mailto:rhc_at_[hidden]><mailto:rhc_at_[hidden]<mailto:rhc_at_[hidden]
>> >><mailto:rhc_at_[hidden]<mailto:rhc_at_[hidden]><mailto:
>> rhc_at_[hidden]<mailto:rhc_at_[hidden]>>>>>> wrote:
>> You can qsub a simple "ls" on that path - that will tell you if the path
>> is valid on all machines in that allocation.
>>
>> What typically happens is that home directories aren't remotely mounted,
>> or are mounted on a different location.
>>
>>
>> On Thu, Nov 18, 2010 at 8:31 AM, Tushar Andriyas <thugnomics28_at_[hidden]
>> <mailto:thugnomics28_at_[hidden]><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]>><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]>>><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]>><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]>>>><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]>><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]>>><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]>><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]><mailto:thugnomics28@!
>> gmail.com<mailto:thugnomics28_at_[hidden]>>>>>> wrote:
>> no its not in the same directory as SWMF. I guess the path is the same
>> since all the machines in a cluster are configured d same way. How do I know
>> if this is not the case?
>>
>>
>> On Thu, Nov 18, 2010 at 8:25 AM, Ralph Castain <rhc_at_[hidden]<mailto:
>> rhc_at_[hidden]><mailto:rhc_at_[hidden]<mailto:rhc_at_[hidden]
>> >><mailto:rhc_at_[hidden]<mailto:rhc_at_[hidden]><mailto:
>> rhc_at_[hidden]<mailto:rhc_at_[hidden]>>><mailto:rhc_at_[hidden]
>> <mailto:rhc_at_[hidden]><mailto:rhc_at_[hidden]<mailto:rhc_at_[hidden]
>> >><mailto:rhc_at_[hidden]<mailto:rhc_at_[hidden]><mailto:
>> rhc_at_[hidden]<mailto:rhc_at_[hidden]>>>><mailto:rhc_at_[hidden]
>> <mailto:rhc_at_[hidden]><mailto:rhc_at_[hidden]<mailto:rhc_at_[hidden]
>> >><mailto:rhc_at_[hidden]<mailto:rhc_at_[hidden]><mailto:
>> rhc_at_[hidden]<mailto:rhc_at_[hidden]>>><mailto:rhc_at_[hidden]
>> <mailto:rhc_at_[hidden]><mailto:rhc_at_[hidden]<mailto:rhc_at_[hidden]
>> >><mailto:rhc_at_[hidden]<mailto:rhc_at_[hidden]><mailto:
>> rhc_at_[hidden]<mailto:rhc_at_[hidden]>>>>>> wrote:
>> Is you "hello world" test program in the same directory as SWMF? Is it
>> possible that the path you are specifying is not available on all of the
>> remote machines? That's the most common problem we see.
>>
>>
>> On Thu, Nov 18, 2010 at 7:59 AM, Tushar Andriyas <thugnomics28_at_[hidden]
>> <mailto:thugnomics28_at_[hidden]><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]>><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]>>><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]>><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]>>>><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]>><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]>>><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]>><mailto:thugnomics28_at_[hidden]<mailto:
>> thugnomics28_at_[hidden]><mailto:thugnomics28@!
>> gmail.com<mailto:thugnomics28_at_[hidden]>>>>>> wrote:
>> Hi there,
>>
>> Thanks for the expedite reply. The thing is that although the mpirun is
>> setup correctly (since a simple hello world works), when I run the main
>> SWMF.exe executable, the cluster machines somehow fail to find the
>> executable (SWMF.exe).
>>
>> So, I have attached the sample error file from one of the runs
>> (SWMF.e143438) and also the MAKEFILES so that you could better gauge the
>> problem. The makefiles have Linux as the OS and pgf90 as compiler with
>> mpif90 as the linker. I am using openmpi-1.2.7-pgi. Job is submitted using a
>> batch file (job.bats) and the scheduler is Torque (version I am not sure but
>> I can see three on the machines viz 2.0.0, 2.2.1, 2.5.2).
>>
>> I have also attached an error file from one of the clusters (WASATCH viz
>> SWMF.e143439) and UINTA (SWMF.e143440) with the whole path of the exe as
>> Srirangam mentioned as follows (in the batch file).
>>
>> mpirun --prefix /opt/libraries/openmpi/openmpi-1.2.7-pgi
>> /home/A00945081/SWMF_v2.3/run/SWMF.exe > runlog_`date +%y%m%d%H%M`
>>
>> I have tried both mpirun and mpiexec but nothing seems to work.
>>
>> Tushar
>>
>>
>> On Wed, Nov 17, 2010 at 8:12 PM, Addepalli, Srirangam V <
>> srirangam.v.addepalli_at_[hidden]<mailto:srirangam.v.addepalli_at_[hidden]
>> ><mailto:srirangam.v.addepalli_at_[hidden]<mailto:
>> srirangam.v.addepalli_at_[hidden]>><mailto:srirangam.v.addepalli_at_[hidden]
>> <mailto:srirangam.v.addepalli_at_[hidden]><mailto:
>> srirangam.v.addepalli_at_[hidden]<mailto:srirangam.v.addepalli_at_[hidden]
>> >>><mailto:srirangam.v.addepalli_at_[hidden]<mailto:
>> srirangam.v.addepalli_at_[hidden]><mailto:srirangam.v.addepalli_at_[hidden]
>> <mailto:srirangam.v.addepalli_at_[hidden]>><mailto:
>> srirangam.v.addepalli_at_[hidden]<mailto:srirangam.v.addepalli_at_[hidden]
>> ><mailto:srirangam.v.addepalli_at_[hidden]<mailto:
>> srirangam.v.addepalli_at_[hidden]>>>><mailto:srirangam.v.addepalli_at_[hidden]
>> <mailto:srirangam.v.addepalli_at_[hidden]><mailto:
>> srirangam.v.addepalli_at_[hidden]<mailto:srirangam.v.addepalli_at_[hidden]
>> >><mailto:srirangam.v.addepalli_at_[hidden]<mailto:
>> srirangam.v.addepalli_at_[hidden]><mailto:srirangam.v.addepalli_at_[hidden]
>> <mailto:srirangam.v.addepalli_at_[hidden]>>><mailto:srirangam.v.addepalli@!
>> ttu.edu<mailto:srirangam.v.addepalli_at_[hidden]><mailto:
>> srirangam.v.addepalli_at_[hidden]<mailto:srirangam.v.addepalli_at_[hidden]
>> >><mailto:srirangam.v.addepalli_at_[hidden]<mailto:
>> srirangam.v.addepalli_at_[hidden]><mailto:srirangam.v.addepalli_at_[hidden]
>> <mailto:srirangam.v.addepalli_at_[hidden]>>>>>> wrote:
>> Hello Tushar,
>> Have you tried supplying the full path of the executable just to check ?
>> Rangam
>> ________________________________________
>> From: users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]
>> ><mailto:users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]
>> >><mailto:users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]
>> ><mailto:users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]
>> >>><mailto:users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]
>> ><mailto:users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]
>> >><mailto:users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]
>> ><mailto:users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]
>> >>>><mailto:users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]
>> ><mailto:users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]
>> >><mailto:users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]
>> ><mailto:users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]
>> >>><mailto:users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]
>> ><mailto:users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]
>> >><mailto:users-!
>> bounces_at_[hidden]<mailto:users-bounces_at_[hidden]><mailto:
>> users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]>>>>> [
>> users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]><mailto:
>> users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]>><mailto:
>> users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]><mailto:
>> users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]>>><mailto:
>> users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]><mailto:
>> users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]>><mailto:
>> users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]><mailto:
>> users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]>>>><mailto:
>> users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]><mailto:
>> users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]>><mailto:
>> users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]><mailto:
>> users-bounces_at_[hidden]<mailto:users-bounces_at_[hidden]>>><mailto:
>> users-bounce<mailto:!
>> users-bounce>!
>> s_at_[hidden]<mailto:s_at_[hidden]><mailto:users-bounces_at_[hidden]
>> <mailto:users-bounces_at_[hidden]>><mailto:users-bounces_at_[hidden]
>> <mailto:users-bounces_at_[hidden]><mailto:users-bounces_at_[hidden]
>> <mailto:users-bounces_at_[hidden]>>>>>] On Behalf Of Tushar Andriyas [
>> thugnomics28_at_[hidden]<mailto:thugnomics28_at_[hidden]><mailto:
>> thugnomics28_at_[hidden]<mailto:thugnomics28_at_[hidden]>><mailto:
>> thugnomics28_at_[hidden]<mailto:thugnomics28_at_[hidden]><mailto:
>> thugnomics28_at_[hidden]<mailto:thugnomics28_at_[hidden]>>><mailto:
>> thugnomics28_at_[hidden]<mailto:thugnomics28_at_[hidden]><mailto:
>> thugnomics28_at_[hidden]<mailto:thugnomics28_at_[hidden]>><mailto:
>> thugnomics28_at_[hidden]<mailto:thugnomics28_at_[hidden]><mailto:
>> thugnomics28_at_[hidden]<mailto:thugnomics28_at_[hidden]>>>><mailto:
>> thugnomics28_at_[hidden]<mailto:thugnomics28_at_[hidden]><mailto:
>> thugnomics28_at_[hidden]<mailto:thugnomics28_at_[hidden]>><mailto:
>> thugnomics28_at_[hidden]<mailto:thugnomics28_at_[hidden]><mailto:
>> thugnomics28_at_[hidden]<mailt!
>> o:thugnomics28_at_[hidden] <o%3Athugnomics28_at_[hidden]>>>><mailto:
>> thugnomics28_at_[hidden]<mailto:thugnomics28_at_[hidden]><mailto:
>> thugnomics28_at_[hidden]<mailto:thugnomics28_at_[hidden]>><mailto:
>> thugnomics28_at_[hidden]<mailto:thugnomics28_at_[hidden]><mailto:
>> thugnomics28_at_[hidden]<mailto:thugnomics28_at_[hidden]>>>>>]
>> Sent: Wednesday, November 17, 2010 8:49 PM
>> To: users_at_[hidden]<mailto:users_at_[hidden]><mailto:
>> users_at_[hidden]<mailto:users_at_[hidden]>><mailto:users_at_[hidden]
>> <mailto:users_at_[hidden]><mailto:users_at_[hidden]<mailto:
>> users_at_[hidden]>>><mailto:users_at_[hidden]<mailto:users_at_[hidden]
>> ><mailto:users_at_[hidden]<mailto:users_at_[hidden]>><mailto:
>> users_at_[hidden]<mailto:users_at_[hidden]><mailto:users_at_[hidden]
>> <mailto:users_at_[hidden]>>>><mailto:users_at_[hidden]<mailto:
>> users_at_[hidden]><mailto:users_at_[hidden]<mailto:users_at_[hidden]
>> >><mailto:users_at_[hidden]<mailto:users_at_[hidden]><mailto:
>> users_at_[hidden]<mailto:users_at_[hidden]>>><mailto:users_at_[hidden]
>> <mailto:users_at_[hidden]><mailto:users_at_[hidden]<mailto:
>> users_at_[hidden]>><mailto:users_at_[hidden]<mailto:users_at_[hidden]
>> ><mailto:users_at_[hidden]<mailto:users_at_[hidden]>>>>>
>> Subject: [OMPI users] Unable to find the following executable
>>
>> Hi there,
>>
>> I am new to using mpi commands and was stuck in problem with running a
>> code. When I submit my job through a batch file, the job exits with the
>> message that the executable could not be found on the machines. I have tried
>> a lot of options such as PBS -V and so on on but the problem persists. If
>> someone is interested, I can send the full info on the cluster, the compiler
>> and openmpi settings and other stuff. BTW the launcher is torque (which you
>> might have guessed). The code does not have a forum so I am in a deep mire.
>>
>> Thanks,
>> Tushar
>>
>> _______________________________________________
>> users mailing list
>> users_at_[hidden]<mailto:users_at_[hidden]><mailto:users_at_[hidden]
>> <mailto:users_at_[hidden]>><mailto:users_at_[hidden]<mailto:
>> users_at_[hidden]><mailto:users_at_[hidden]<mailto:users_at_[hidden]
>> >>><mailto:users_at_[hidden]<mailto:users_at_[hidden]><mailto:
>> users_at_[hidden]<mailto:users_at_[hidden]>><mailto:users_at_[hidden]
>> <mailto:users_at_[hidden]><mailto:users_at_[hidden]<mailto:
>> users_at_[hidden]>>>><mailto:users_at_[hidden]<mailto:
>> users_at_[hidden]><mailto:users_at_[hidden]<mailto:users_at_[hidden]
>> >><mailto:users_at_[hidden]<mailto:users_at_[hidden]><mailto:
>> users_at_[hidden]<mailto:users_at_[hidden]>>><mailto:users_at_[hidden]
>> <mailto:users_at_[hidden]><mailto:users_at_[hidden]<mailto:
>> users_at_[hidden]>><mailto:users_at_[hidden]<mailto:users_at_[hidden]
>> ><mailto:users_at_[hidden]<mailto:users_at_[hidden]>>>>>
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>>
>> _______________________________________________
>> users mailing list
>> users_at_[hidden]<mailto:users_at_[hidden]><mailto:users_at_[hidden]
>> <mailto:users_at_[hidden]>><mailto:users_at_[hidden]<mailto:
>> users_at_[hidden]><mailto:users_at_[hidden]<mailto:users_at_[hidden]
>> >>><mailto:users_at_[hidden]<mailto:users_at_[hidden]><mailto:
>> users_at_[hidden]<mailto:users_at_[hidden]>><mailto:users_at_[hidden]
>> <mailto:users_at_[hidden]><mailto:users_at_[hidden]<mailto:
>> users_at_[hidden]>>>><mailto:users_at_[hidden]<mailto:
>> users_at_[hidden]><mailto:users_at_[hidden]<mailto:users_at_[hidden]
>> >><mailto:users_at_[hidden]<mailto:users_at_[hidden]><mailto:
>> users_at_[hidden]<mailto:users_at_[hidden]>>><mailto:users_at_[hidden]
>> <mailto:users_at_[hidden]><mailto:users_at_[hidden]<mailto:
>> users_at_[hidden]>><mailto:users_at_[hidden]<mailto:users_at_[hidden]
>> ><mailto:users_at_[hidden]<mailto:users_at_[hidden]>>>>>
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>>
>> _______________________________________________
>> users mailing list
>> users_at_[hidden]<mailto:users_at_[hidden]><mailto:users_at_[hidden]
>> <mailto:users_at_[hidden]>><mailto:users_at_[hidden]<mailto:
>> users_at_[hidden]><mailto:users_at_[hidden]<mailto:users_at_[hidden]
>> >>><mailto:users_at_[hidden]<mailto:users_at_[hidden]><mailto:
>> users_at_[hidden]<mailto:users_at_[hidden]>><mailto:users_at_[hidden]
>> <mailto:users_at_[hidden]><mailto:users_at_[hidden]<mailto:
>> users_at_[hidden]>>>><mailto:users_at_[hidden]<mailto:
>> users_at_[hidden]><mailto:users_at_[hidden]<mailto:users_at_[hidden]
>> >><mailto:users_at_[hidden]<mailto:users_at_[hidden]><mailto:
>> users_at_[hidden]<mailto:users_at_[hidden]>>><mailto:users_at_[hidden]
>> <mailto:users_at_[hidden]><mailto:users_at_[hidden]<mailto:
>> users_at_[hidden]>><mailto:users_at_[hidden]<mailto:users_at_[hidden]
>> ><mailto:users_at_[hidden]<mailto:users_at_[hidden]>>>>>
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>>
>> _______________________________________________
>> users mailing list
>> users_at_[hidden]<mailto:users_at_[hidden]><mailto:users_at_[hidden]
>> <mailto:users_at_[hidden]>><mailto:users_at_[hidden]<mailto:
>> users_at_[hidden]><mailto:users_at_[hidden]<mailto:users_at_[hidden]
>> >>><mailto:users_at_[hidden]<mailto:users_at_[hidden]><mailto:
>> users_at_[hidden]<mailto:users_at_[hidden]>><mailto:users_at_[hidden]
>> <mailto:users_at_[hidden]><mailto:users_at_[hidden]<mailto:
>> users_at_[hidden]>>>><mailto:users_at_[hidden]<mailto:
>> users_at_[hidden]><mailto:users_at_[hidden]<mailto:users_at_[hidden]
>> >><mailto:users_at_[hidden]<mailto:users_at_[hidden]><mailto:
>> users_at_[hidden]<mailto:users_at_[hidden]>>><mailto:users_at_[hidden]
>> <mailto:users_at_[hidden]><mailto:users_at_[hidden]<mailto:
>> users_at_[hidden]>><mailto:users_at_[hidden]<mailto:users_at_[hidden]
>> ><mailto:users_at_[hidden]<mailto:users_at_[hidden]>>>>>
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>>
>> _______________________________________________
>> users mailing list
>> users_at_[hidden]<mailto:users_at_[hidden]><mailto:users_at_[hidden]
>> <mailto:users_at_[hidden]>><mailto:users_at_[hidden]<mailto:
>> users_at_[hidden]><mailto:users_at_[hidden]<mailto:users_at_[hidden]
>> >>><mailto:users_at_[hidden]<mailto:users_at_[hidden]><mailto:
>> users_at_[hidden]<mailto:users_at_[hidden]>><mailto:users_at_[hidden]
>> <mailto:users_at_[hidden]><mailto:users_at_[hidden]<mailto:
>> users_at_[hidden]>>>><mailto:users_at_[hidden]<mailto:
>> users_at_[hidden]><mailto:users_at_[hidden]<mailto:users_at_[hidden]
>> >><mailto:users_at_[hidden]<mailto:users_at_[hidden]><mailto:
>> users_at_[hidden]<mailto:users_at_[hidden]>>><mailto:users_at_[hidden]
>> <mailto:users_at_[hidden]><mailto:users_at_[hidden]<mailto:
>> users_at_[hidden]>><mailto:users_at_[hidden]<mailto:users_at_[hidden]
>> ><mailto:users_at_[hidden]<mailto:users_at_[hidden]>>>>>
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>>
>> _______________________________________________
>> users mailing list
>> users_at_[hidden]<mailto:users_at_[hidden]><mailto:users_at_[hidden]
>> <mailto:users_at_[hidden]>><mailto:users_at_[hidden]<mailto:
>> users_at_[hidden]><mailto:users_at_[hidden]<mailto:users_at_[hidden]
>> >>><mailto:users_at_[hidden]<mailto:users_at_[hidden]><mailto:
>> users_at_[hidden]<mailto:users_at_[hidden]>><mailto:users_at_[hidden]
>> <mailto:users_at_[hidden]><mailto:users_at_[hidden]<mailto:
>> users_at_[hidden]>>>>
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>>
>> _______________________________________________
>> users mailing list
>> users_at_[hidden]<mailto:users_at_[hidden]><mailto:users_at_[hidden]
>> <mailto:users_at_[hidden]>><mailto:users_at_[hidden]<mailto:
>> users_at_[hidden]><mailto:users_at_[hidden]<mailto:users_at_[hidden]
>> >>>
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>>
>> _______________________________________________
>> users mailing list
>> users_at_[hidden]<mailto:users_at_[hidden]><mailto:users_at_[hidden]
>> <mailto:users_at_[hidden]>>
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>>
>> _______________________________________________
>> users mailing list
>> users_at_[hidden]<mailto: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
>>
>
>