[CIG-SHORT] missing installation files v1.8
Brad Aagaard
baagaard at usgs.gov
Fri Jun 5 17:00:16 PDT 2015
Birendra,
This is an MPI issue. Some likely explanations inclide MPI is not
configured correctly for the hardware, the MPI implementation it is
trying to use is not the one with which PyLith was built, and the
environment is inconsistent.
If this is a cluster, I suggest contacting the admin and getting help
verifying your environment and that you are using the correct MPI
implementation.
If it is a desktop, then there are likely multiple MPI implementations
installed. Make sure your environment is setup to use one and only one
implementation consistently across the entire PyLith build.
Regards,
Brad
On 06/05/2015 04:48 PM, Birendra jha wrote:
> Brad
>
> One of the tests is failing:
>
> make[7]: Entering directory `/galileo/home/usera06agi/a06agi25/build/pylith/pylith-build/unittests/libtests/bc'
> --------------------------------------------------------------------------
> Error obtaining unique transport key from ORTE (orte_precondition_transports not present in
> the environment).
>
> Local host: node171
> --------------------------------------------------------------------------
> --------------------------------------------------------------------------
> It looks like MPI_INIT failed for some reason; your parallel process is
> likely to abort. There are many reasons that a parallel process can
> fail during MPI_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):
>
> PML add procs failed
> --> Returned "Error" (-1) instead of "Success" (0)
> --------------------------------------------------------------------------
> [node171:2483] *** An error occurred in MPI_Init_thread
> [node171:2483] *** on a NULL communicator
> [node171:2483] *** Unknown error
> [node171:2483] *** MPI_ERRORS_ARE_FATAL: your MPI job will now abort
> --------------------------------------------------------------------------
> An MPI process is aborting at a time when it cannot guarantee that all
> of its peer processes in the job will be killed properly. You should
> double check that everything has shut down cleanly.
>
> Reason: Before MPI_INIT completed
> Local host: node171
> PID: 2483
> --------------------------------------------------------------------------
> FAIL: testbc
>
>
> Any suggestions?
>
> Birendra
>
> --------------------------------------------
> On Fri, 6/5/15, Brad Aagaard <baagaard at usgs.gov> wrote:
>
> Subject: Re: [CIG-SHORT] missing installation files v1.8
> To: cig-short at geodynamics.org
> Date: Friday, June 5, 2015, 12:53 PM
>
> Birendra,
>
> https://geodynamics.org/cig/software/spatialdata/
>
> I updated the package entry on
> geodynamics.org, so now this shows up
> under
> "Computational Science" and it is no longer
> hidden.
>
> Thanks for pointing
> this out!
>
> Cheers,
> Brad
>
> On
> 06/05/2015 09:41 AM, Birendra jha wrote:
> > Brad
> >
> > Thanks. Quick question: where can I find
> spatialdata? It's neither on geodynamics nor on geoweb
> website.
> >
> >
> regards
> > Birendra
> >
> --------------------------------------------
> > On Thu, 6/4/15, Brad Aagaard <baagaard at usgs.gov>
> wrote:
> >
> > Subject: Re: [CIG-SHORT]
> missing installation files v1.8
> > To: cig-short at geodynamics.org
> > Date: Thursday, June 4, 2015,
> 12:29 PM
> >
> > Birendra,
> >
> > The
> configure line to nemesis
> > is missing CC=mpicc
> CXX=mpicxx
> >
> > This was added on Nov 30,
> 2012
> > (https://github.com/geodynamics/pylith_installer/commit/3d75ee30dc708622244324b1a537f6e0a4db4b9b),
> >
> > which
> may have been a patch after the
> > installer version you are
> using.
> >
> > Note that we have a complete
> history of the
> > commits for
> the installer
> > via Git, but
> we
> > only have a complete
> history of the installer tags going
> > back to v1.9.0-2 when we
> started tagging things
> > in
> Git.
> >
> > There are a number
> > of patches that have been
> made to the installer since
> > v1.8.0 was released. A few of
> these fix
> > problems while
> others are more
> > cosmetic
> or
> > update to new verions
> of dependencies.
> >
> > If you encounter additional
> problems, I suggest
> > you
> download the current
> > installer and do a
> > diff of the Makefile or
> peruse the commits of the
> > installer Git repo and cherry
> pick the
> > appropriate
> updates.
> >
> > Regards,
> > Brad
> >
> >
> > On
> 06/04/2015
> > 08:33 AM,
> Birendra jha wrote:
> > >
> Brad
> > >
> > > I am getting missing
> > MPI library error:
> > >
> > >
> > configure: downloading
> missing Python dependencies
> > > configure: building
> Python dependencies
> > >
> checking for egg-related flags... ok
> > > checking for library
> containing
> > MPI_Init...
> no
> > > configure: error:
> MPI
> > library not found
> > > make[3]: Entering
> > directory
> > `/galileo/home/usera06agi/a06agi25/build/pylith/nemesis-build'
> > >
> > > I have attached
> > nemesis-build/config.log and
> build/pylith/config.log
> > >
> > > I have added openmpi
> > in the path:
> > > [a06agi25 at node171
> > nemesis-build]$ which
> mpicc
> > >
> > /developers/devenv/prod/opt/compilers/openmpi/1.6.4/gnu--4.7.2/bin/mpicc
> > >
> > > So I don't
> > understand why it calls gcc
> instead of mpicc in the nemesis
> > config.log:
> > >
> > >
> > configure:4206: checking for
> library containing MPI_Init
> > > configure:4237: gcc -o
> conftest -g -O2
> > -I/galileo/home/usera06agi/a06agi25/pylith/include
> > -L/galileo/home/usera06agi/a06agi25/pylith/lib
> > conftest.c
> > >
> > >
> > Thanks
> > > Birendra
> > >
> > --------------------------------------------
> > > On Tue, 5/26/15, Brad
> Aagaard <baagaard at usgs.gov>
> > wrote:
> > >
> > > Subject:
> Re: [CIG-SHORT]
> > missing
> installation files v1.8
> > > To: cig-short at geodynamics.org
> > > Date:
> Tuesday, May 26, 2015,
> > 2:32 PM
> > >
> > > Birendra,
> > >
> > > It is
> > looking for merlin,
> > > which
> > was not migrated over to the
> "new"
> > > geodynamics
> website because
> > it is no
> longer
> > > needed
> by
> > pythia (or
> > > supported).
> You
> > can
> > > get merlin
> from
> > > https://pypi.python.org/pypi/merlin/1.0
> > >
> > > Regards,
> > > Brad
> > >
> > >
> > > On
> > 05/26/2015 11:23 AM, Birendra
> jha wrote:
> > > > Hi
> Brad
> > > >
> > > > I am
> getting error
> > during
> 'make'
> > > at
> > nemesis:
> > > >
> > > >
> > > configure:
> downloading
> > missing Python
> dependencies
> > > >
> configure: error: in
> > > `/galileo/home/usera06agi/a06agi25/build/pylith/nemesis-build':
> > > >
> configure: error: cannot
> > download missing
> > > Python
> > dependencies
> > > >
> > > > I have
> attached
> > build/pyith/config.log and
> > > build/pylith/nemesis-build/config.log
> > > >
> > > > Any
> help will be
> > > appreciated.
> > > >
> Birendra
> > > >
> > > >
> > > --------------------------------------------
> > > > On
> Fri, 5/15/15, Brad
> > Aagaard
> <baagaard at usgs.gov>
> > > wrote:
> > > >
> > > > Subject:
> > Re: [CIG-SHORT]
> > > missing
> > installation files v1.8
> > > > To:
> cig-short at geodynamics.org
> > > > Date:
> > Friday, May 15, 2015,
> > > 10:48 AM
> > > >
> > > > Birendra,
> > > >
> > > > CIG
> his
> > > migrated
> the files to
> > > > a
> > > new
> webserver
> > > > http://geoweb.cse.ucdavis.edu/~buildbot/deps
> > > >
> > > > Regards,
> > > > Brad
> > > >
> > > >
> > > > On
> > > > 05/15/2015
> > 06:26 AM, Birendra
> > > jha
> > wrote:
> > > > >
> > Hello
> > > developers
> > > > >
> > > > >
> I am
> > trying to install
> > > pylith-1.8.0
> using
> > > > the
> > > installer
> and I get 404
> > error.
> > > > >
> > > > >
> > Downloading
> > > cppunit-1.12.1.tar.gz
> from
> > > > http://geodynamics.org/~buildbot/deps.
> > > > >
> > > > --2015-05-15
> > 15:22:04-- http://geodynamics.org/~buildbot/deps/cppunit-1.12.1.tar.gz
> > > > >
> > Resolving
> > > geodynamics.org
> > > > (geodynamics.org)...
> > > 128.120.246.102,
> > > > 2607:f810:c20:1c:a800:ff:fe59:2234
> > > > >
> > > > Connecting
> > to
> > > geodynamics.org
> > > > (geodynamics.org)|128.120.246.102|:80...
> > > connected.
> > > > >
> > HTTP
> > > request
> sent,
> > awaiting
> response...
> > > > 404
> Not
> > Found
> > > > >
> > 2015-05-15 15:22:05
> > > ERROR
> > > > 404:
> Not
> > Found.
> > > > >
> > > > >
> I
> > > > understand
> > that latest
> > > version
> is
> > recommended but I
> need
> > > > this
> > version because of some
> > > earlier
> work. Where can I
> > get
> > > > these
> files
> > now?
> > > > >
> > > > >
> > > > Thanks
> > > > >
> > Birendra
> > > > >
> > > > _______________________________________________
> > > > >
> > CIG-SHORT mailing
> > > list
> > > > >
> CIG-SHORT at geodynamics.org
> > > > >
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
> > > > >
> > > >
> > > > _______________________________________________
> > > > CIG-SHORT
> > mailing list
> > > > CIG-SHORT at geodynamics.org
> > > > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
> > > >
> > > >
> > > >
> > > >
> > > _______________________________________________
> > > >
> CIG-SHORT mailing
> > list
> > > > CIG-SHORT at geodynamics.org
> > > > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
> > > >
> > >
> > > _______________________________________________
> > > CIG-SHORT
> mailing list
> > > CIG-SHORT at geodynamics.org
> > > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
> > >
> > >
> > >
> > >
> > _______________________________________________
> > > CIG-SHORT mailing
> list
> > > CIG-SHORT at geodynamics.org
> > > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
> > >
> >
> > _______________________________________________
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> > CIG-SHORT at geodynamics.org
> > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
> >
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> > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
> >
>
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