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Subject: Re: [OMPI users] help me please, about Open MPI
From: Ilmar Wilbers (ilmarw_at_[hidden])
Date: 2008-06-17 13:20:19


TMPDIR should be a single directory:
export TMPDIR=/tmp

It should not be a list of directories seperated by a ':'.

"setenv TMPDIR /tmp" (or "setenv TMPDIR
/local2/pbs/myname/37911.hpc-cluster") would hence be the correct line.

After setting the variable, try
'cd $TMPDIR'
'touch test'

to verify that you have writing permissions.

ilmar

Tony Smith wrote:
> thanks,
> I added "setenv TMPDIR /tmp:$TMPDIR" in my job script file.
>
> so , echo $TMPDIR :
>
> /tmp:/local2/pbs/myname/37911.hpc-cluster
>
> but the same errors.
>
> thanks
>
>
> > From: jsquyres_at_[hidden]
> > To: users_at_[hidden]
> > Date: Tue, 17 Jun 2008 11:55:05 -0400
> > Subject: Re: [OMPI users] help me please, about Open MPI
> >
> > Sure, that configure line should be fine. But that's a different
> > issue than the permissions on your temp directories. The environment
> > variables I was asking about are what are set at run time -- not when
> > you configure/build OMPI.
> >
> > If you're using Torque, I *believe* that it sets TMPDIR in its jobs --
> > you might want to check (I don't use Torque on a day-to-day basis, so
> > I don't remember offhand).
> >
> >
> > On Jun 17, 2008, at 11:52 AM, Tony Smith wrote:
> >
> > > thanks,
> > >
> > > My configure :
> > > ./configure --prefix=/ptmp/myname/openmpi --enable-static --disable-
> > > shared
> > > CC=icc CXX=icpc F77=ifort FC=ifort --with-gm=/opt/gm
> > > -with-tm=/usr/spool/PBS/
> > > is that correct ?
> > >
> > > thanks
> > >
> > >
> > > > From: jsquyres_at_[hidden]
> > > > To: users_at_[hidden]
> > > > Date: Tue, 17 Jun 2008 10:35:06 -0400
> > > > Subject: Re: [OMPI users] help me please, about Open MPI
> > > >
> > > > What are the exact permissions on /tmp? They should likely be 1777.
> > > >
> > > > Do you have the TMPDIR or TMP environment variables set? If so, is
> > > > that directory also world-writable? (if set, these will override the
> > > > default location of /tmp)
> > > >
> > > > The error you are seeing (session directory failed) usually has to
> > > do
> > > > with ORTE not being able to create a session directory for the user.
> > > >
> > > >
> > > >
> > > > On Jun 17, 2008, at 10:27 AM, Tony Smith wrote:
> > > >
> > > > > thanks,
> > > > > I changed /tmp and /ptmp and its sub directories to writable .
> > > > >
> > > > > But , the same errors.
> > > > >
> > > > > thanks,
> > > > >
> > > > >
> > > > > > From: jsquyres_at_[hidden]
> > > > > > To: users_at_[hidden]
> > > > > > Date: Tue, 17 Jun 2008 09:10:18 -0400
> > > > > > Subject: Re: [OMPI users] help me please, about Open MPI
> > > > > >
> > > > > > Is /tmp writable on your compute nodes?
> > > > > >
> > > > > >
> > > > > > On Jun 16, 2008, at 1:49 PM, Tony Smith wrote:
> > > > > >
> > > > > > > Dear Sir:
> > > > > > >
> > > > > > > thanks.
> > > > > > > I have changed it to its absolute path:
> > > > > > > /ptmp/myname/openmpi123/ompi123_install/bin/mpirun -np 8 /
> > > ptmp/
> > > > > > > myname/openmpi123/openmpi-1.2.3/examples/hello_c
> > > > > > >
> > > > > > > But I still got the error :
> > > > > > > ====================================================
> > > > > > > [hpc-cluster-38 :32635] [0,0,0] ORTE_ERROR_LOG: Error in file
> > > > > > >
> > > > > > > runtime/orte_init_stage1.c at line 626
> > > > > > >
> > > > >
> > >
> --------------------------------------------------------------------------
> > > > > > > It looks like orte_init failed for some reason; your parallel
> > > > > > > process is
> > > > > > > likely to abort. There are many reasons that a parallel
> > > process
> > > > > can
> > > > > > > fail during orte_init; some of which are due to
> > > configuration or
> > > > > > > environment problems. This failure appears to be an internal
> > > > > failure;
> > > > > > > here's some additional information (which may only be relevant
> > > > > to an
> > > > > > > Open MPI developer):
> > > > > > >
> > > > > > > orte_session_dir failed
> > > > > > > --> Returned value -1 instead of ORTE_SUCCESS
> > > > > > >
> > > > > > >
> > > > >
> > >
> --------------------------------------------------------------------------
> > > > > > > [hpc-cluster-38 :32635] [0,0,0] ORTE_ERROR_LOG: Error in file
> > > > > > >
> > > > > > > runtime/orte_system_init.c at line 42
> > > > > > > [hpc-cluster-38 :32635] [0,0,0] ORTE_ERROR_LOG: Error in file
> > > > > > >
> > > > > > > runtime/orte_init.c at line 52
> > > > > > >
> > > > >
> > >
> --------------------------------------------------------------------------
> > > > > > > Open RTE was unable to initialize properly. The error occured
> > > > > while
> > > > > > > attempting to orte_init(). Returned value -1 instead of
> > > > > ORTE_SUCCESS.
> > > > > > >
> > > > >
> > >
> --------------------------------------------------------------------------
> > > > > > >
> > > > > > > ====================================
> > > > > > >
> > > > > > > I can not find the file "runtime/orte_init_stage1.c"
> > > > > > >
> > > > > > > It seems that ORTE is not initialized .
> > > > > > > I have built OPEN MPI and installed it correctly .
> > > > > > >
> > > > > > > Why ?
> > > > > > >
> > > > > > > thanks a lot ,
> > > > > > >
> > > > > > > June 16 2008
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > > Date: Mon, 16 Jun 2008 19:05:06 +0200
> > > > > > > > From: gentryx_at_[hidden]
> > > > > > > > To: users_at_[hidden]
> > > > > > > > Subject: Re: [OMPI users] help me please, about Open MPI
> > > > > > > >
> > > > > > > > Dear Mister Smith,
> > > > > > > >
> > > > > > > > Thank you for installing Open MPI.
> > > > > > > >
> > > > > > > > On 12:51 Mon 16 Jun , Tony Smith wrote:
> > > > > > > > > I have changed PATH and LD_LIBRARY_PATH:
> > > > > > > >
> > > > > > > > Please be aware that you have to make those changes within
> > > > > your job
> > > > > > > > script. Otherwise they will only affect your local shell.
> > > > > > > >
> > > > > > > > > But, how can I make sure that the application is run by
> > > Open
> > > > > MPI
> > > > > > > not by mpich-
> > > > > > > >
> > > > > > > > You could enforce a certain mpirun by using its absolute
> > > path,
> > > > > e.g
> > > > > > > > "/ptmp/myname/openmpi123/ompi123_install/bin/mpirun foo"
> > > > > instead of
> > > > > > > > just "mpirun foo".
> > > > > > > >
> > > > > > > > > I deleted /opt/mpich-gm/bin from PATH and added
> > > > > > > >
> > > > > > > > You should not need to delete, just add in front of MPICH.
> > > > > > > >
> > > > > > > > > Would you please help me with that ?
> > > > > > > >
> > > > > > > > I utterly hope I just did.
> > > > > > > >
> > > > > > > > Most sincerely yours ;-)
> > > > > > > > -Andreas
> > > > > > > >
> > > > > > > >
> > > > > > > > --
> > > > > > > > ============================================
> > > > > > > > Andreas Schäfer
> > > > > > > > Cluster and Metacomputing Working Group
> > > > > > > > Friedrich-Schiller-Universität Jena, Germany
> > > > > > > > PGP/GPG key via keyserver
> > > > > > > > I'm a bright... http://www.the-brights.net
> > > > > > > > ============================================
> > > > > > > >
> > > > > > > > (\___/)
> > > > > > > > (+'.'+)
> > > > > > > > (")_(")
> > > > > > > > This is Bunny. Copy and paste Bunny into your
> > > > > > > > signature to help him gain world domination!
> > > > > > >
> > > > > > > Now you can invite friends from Facebook and other groups to
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> > > > > > > _______________________________________________
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> > > > > >
> > > > > >
> > > > > > --
> > > > > > Jeff Squyres
> > > > > > Cisco Systems
> > > > > >
> > > > > >
> > > > > > _______________________________________________
> > > > > > users mailing list
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> > > > > > http://www.open-mpi.org/mailman/listinfo.cgi/users
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> > > >
> > > > --
> > > > Jeff Squyres
> > > > Cisco Systems
> > > >
> > > >
> > > > _______________________________________________
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> > Cisco Systems
> >
> >
> > _______________________________________________
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