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
Built by: A00017402
Built on: Thu Sep 18 15:20:06 MDT 2008
Built host: 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.addepa...@ttu.edu> 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-boun...@open-mpi.org [users-boun...@open-mpi.org] On Behalf Of
> Tushar Andriyas [thugnomic...@gmail.com]
> 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.addepa...@ttu.edu<mailto:srirangam.v.addepa...@ttu.edu>>
> 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-boun...@open-mpi.org<mailto:users-boun...@open-mpi.org> [
> users-boun...@open-mpi.org<mailto:users-boun...@open-mpi.org>] On Behalf
> Of Tushar Andriyas [thugnomic...@gmail.com<mailto:thugnomic...@gmail.com>]
> 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.addepa...@ttu.edu<mailto:srirangam.v.addepa...@ttu.edu
> ><mailto:srirangam.v.addepa...@ttu.edu<mailto:
> srirangam.v.addepa...@ttu.edu>>> 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-boun...@open-mpi.org<mailto:users-boun...@open-mpi.org
> ><mailto:users-boun...@open-mpi.org<mailto:users-boun...@open-mpi.org>> [
> users-boun...@open-mpi.org<mailto:users-boun...@open-mpi.org><mailto:
> users-boun...@open-mpi.org<mailto:users-boun...@open-mpi.org>>] On Behalf
> Of Tushar Andriyas [thugnomic...@gmail.com<mailto:thugnomic...@gmail.com
> ><mailto:thugnomic...@gmail.com<mailto:thugnomic...@gmail.com>>]
> 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.addepa...@ttu.edu<mailto:srirangam.v.addepa...@ttu.edu
> ><mailto:srirangam.v.addepa...@ttu.edu<mailto:
> srirangam.v.addepa...@ttu.edu>><mailto:srirangam.v.addepa...@ttu.edu
> <mailto:srirangam.v.addepa...@ttu.edu><mailto:
> srirangam.v.addepa...@ttu.edu<mailto:srirangam.v.addepa...@ttu.edu>>>>
> 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-boun...@open-mpi.org<mailto:users-boun...@open-mpi.org
> ><mailto:users-boun...@open-mpi.org<mailto:users-boun...@open-mpi.org
> >><mailto:users-boun...@open-mpi.org<mailto:users-boun...@open-mpi.org
> ><mailto:users-boun...@open-mpi.org<mailto:users-boun...@open-mpi.org>>> [
> users-boun...@open-mpi.org<mailto:users-boun...@open-mpi.org><mailto:
> users-boun...@open-mpi.org<mailto:users-boun...@open-mpi.org>><mailto:
> users-boun...@open-mpi.org<mailto:users-boun...@open-mpi.org><mailto:
> users-boun...@open-mpi.org<mailto:users-boun...@open-mpi.org>>>] On Behalf
> Of Tushar Andriyas [thugnomic...@gmail.com<mailto:thugnomic...@gmail.com
> ><mailto:thugnomic...@gmail.com<mailto:thugnomic...@gmail.com>><mailto:
> thugnomic...@gmail.com<mailto:thugnomic...@gmail.com><mailto:
> thugnomic...@gmail.com<mailto:thugnomic...@gmail.com>>>]
> 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 <r...@open-mpi.org<mailto:
> r...@open-mpi.org><mailto:r...@open-mpi.org<mailto:r...@open-mpi.org
> >><mailto:r...@open-mpi.org<mailto:r...@open-mpi.org><mailto:
> r...@open-mpi.org<mailto:r...@open-mpi.org>>><mailto:r...@open-mpi.org
> <mailto:r...@open-mpi.org><mailto:r...@open-mpi.org<mailto:r...@open-mpi.org
> >><mailto:r...@open-mpi.org<mailto:r...@open-mpi.org><mailto:
> r...@open-mpi.org<mailto:r...@open-mpi.org>>>>> 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 <thugnomic...@gmail.com
> <mailto:thugnomic...@gmail.com><mailto:thugnomic...@gmail.com<mailto:
> thugnomic...@gmail.com>><mailto:thugnomic...@gmail.com<mailto:
> thugnomic...@gmail.com><mailto:thugnomic...@gmail.com<mailto:
> thugnomic...@gmail.com>>><mailto:thugnomic...@gmail.com<mailto:
> thugnomic...@gmail.com><mailto:thugnomic...@gmail.com<mailto:
> thugnomic...@gmail.com>><mailto:thugnomic...@gmail.com<mailto:
> thugnomic...@gmail.com><mailto:thugnomic...@gmail.com<mailto:
> thugnomic...@gmail.com>>>>> 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 <r...@open-mpi.org<mailto:
> r...@open-mpi.org><mailto:r...@open-mpi.org<mailto:r...@open-mpi.org
> >><mailto:r...@open-mpi.org<mailto:r...@open-mpi.org><mailto:
> r...@open-mpi.org<mailto:r...@open-mpi.org>>><mailto:r...@open-mpi.org
> <mailto:r...@open-mpi.org><mailto:r...@open-mpi.org<mailto:r...@open-mpi.org
> >><mailto:r...@open-mpi.org<mailto:r...@open-mpi.org><mailto:
> r...@open-mpi.org<mailto:r...@open-mpi.org>>>>> 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 <thugnomic...@gmail.com
> <mailto:thugnomic...@gmail.com><mailto:thugnomic...@gmail.com<mailto:
> thugnomic...@gmail.com>><mailto:thugnomic...@gmail.com<mailto:
> thugnomic...@gmail.com><mailto:thugnomic...@gmail.com<mailto:
> thugnomic...@gmail.com>>><mailto:thugnomic...@gmail.com<mailto:
> thugnomic...@gmail.com><mailto:thugnomic...@gmail.com<mailto:
> thugnomic...@gmail.com>><mailto:thugnomic...@gmail.com<mailto:
> thugnomic...@gmail.com><mailto:thugnomic...@gmail.com<mailto:
> thugnomic...@gmail.com>>>>> 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.addepa...@ttu.edu<mailto:srirangam.v.addepa...@ttu.edu
> ><mailto:srirangam.v.addepa...@ttu.edu<mailto:
> srirangam.v.addepa...@ttu.edu>><mailto:srirangam.v.addepa...@ttu.edu
> <mailto:srirangam.v.addepa...@ttu.edu><mailto:
> srirangam.v.addepa...@ttu.edu<mailto:srirangam.v.addepa...@ttu.edu
> >>><mailto:srirangam.v.addepa...@ttu.edu<mailto:
> srirangam.v.addepa...@ttu.edu><mailto:srirangam.v.addepa...@ttu.edu
> <mailto:srirangam.v.addepa...@ttu.edu>><mailto:
> srirangam.v.addepa...@ttu.edu<mailto:srirangam.v.addepa...@ttu.edu
> ><mailto:srirangam.v.addepa...@ttu.edu<mailto:
> srirangam.v.addepa...@ttu.edu>>>>> wrote:
> Hello Tushar,
> Have you tried supplying the full path of the executable just to check ?
> Rangam
> ________________________________________
> From: users-boun...@open-mpi.org<mailto:users-boun...@open-mpi.org
> ><mailto:users-boun...@open-mpi.org<mailto:users-boun...@open-mpi.org
> >><mailto:users-boun...@open-mpi.org<mailto:users-boun...@open-mpi.org
> ><mailto:users-boun...@open-mpi.org<mailto:users-boun...@open-mpi.org
> >>><mailto:users-boun...@open-mpi.org<mailto:users-boun...@open-mpi.org
> ><mailto:users-boun...@open-mpi.org<mailto:users-boun...@open-mpi.org
> >><mailto:users-boun...@open-mpi.org<mailto:users-boun...@open-mpi.org
> ><mailto:users-boun...@open-mpi.org<mailto:users-boun...@open-mpi.org>>>>
> [users-boun...@open-mpi.org<mailto:users-boun...@open-mpi.org><mailto:
> users-boun...@open-mpi.org<mailto:users-boun...@open-mpi.org>><mailto:
> users-boun...@open-mpi.org<mailto:users-boun...@open-mpi.org><mailto:
> users-boun...@open-mpi.org<mailto:users-boun...@open-mpi.org>>><mailto:
> users-boun...@open-mpi.org<mailto:users-boun...@open-mpi.org><mailto:
> users-boun...@open-mpi.org<mailto:users-boun...@open-mpi.org>><mailto:
> users-bounce!
> s...@open-mpi.org<mailto:users-boun...@open-mpi.org><mailto:
> users-boun...@open-mpi.org<mailto:users-boun...@open-mpi.org>>>>] On
> Behalf Of Tushar Andriyas [thugnomic...@gmail.com<mailto:
> thugnomic...@gmail.com><mailto:thugnomic...@gmail.com<mailto:
> thugnomic...@gmail.com>><mailto:thugnomic...@gmail.com<mailto:
> thugnomic...@gmail.com><mailto:thugnomic...@gmail.com<mailto:
> thugnomic...@gmail.com>>><mailto:thugnomic...@gmail.com<mailto:
> thugnomic...@gmail.com><mailto:thugnomic...@gmail.com<mailto:
> thugnomic...@gmail.com>><mailto:thugnomic...@gmail.com<mailto:
> thugnomic...@gmail.com><mailto:thugnomic...@gmail.com<mailto:
> thugnomic...@gmail.com>>>>]
> Sent: Wednesday, November 17, 2010 8:49 PM
> To: us...@open-mpi.org<mailto:us...@open-mpi.org><mailto:
> us...@open-mpi.org<mailto:us...@open-mpi.org>><mailto:us...@open-mpi.org
> <mailto:us...@open-mpi.org><mailto:us...@open-mpi.org<mailto:
> us...@open-mpi.org>>><mailto:us...@open-mpi.org<mailto:us...@open-mpi.org
> ><mailto:us...@open-mpi.org<mailto:us...@open-mpi.org>><mailto:
> us...@open-mpi.org<mailto:us...@open-mpi.org><mailto:us...@open-mpi.org
> <mailto:us...@open-mpi.org>>>>
> 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
>
> _______________________________________________
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