Re: [OMPI users] gfortran bindings apparently not built on mac os leopard

Brian W. Barrett Wed, 18 Jun 2008 09:56:26 -0400

Thanks for adding the section, but the information contained within iswrong (as was the information in this e-mail thread). OS X essentially*always* adds a -rpath to both executables depending on libraries andlibraries depending on other libraries. There is no need to setLD_LIBRARY_PATH, which on OS X is only used by the linker at link time andby dlopen, but not the linker at run time. Setting DYLD_LIBRARY_PATH isnot only unnecessary, but considered harmful. There are very fewsituations where one would need to set DYLD_LIBRARY_PATH, and they shouldnever be part of a production environment.

If you built Open MPI as a set of static libraries, there is a librarysearch order problem (which neither of the two LIBRARY_PATH variables willsolve) in that OS X searches the entire library path for a shared libraryof the specified name, then searches the entire library path again for astatic library of the specified name. Since /usr/lib/libmpi.dylib wouldthen always be found before <my install/lib/libmpi.a, you'd have aproblem. An easy workaround is to add -Wl,-search_paths_first to the linkline when linking MPI applications. I'd accomplish this by adding thefollowing to OMPI's configure:


  --with-wrapper-ldflags="-Wl,-search_paths_first"

Getting back to the original problem, unless the user already has setDYLD_LIBRARY_PATH (which they shouldn't do), there is no need to modifyDYLD_LIBRARY_PATH for OMPI to work properly (even with the systeminstalled version in /usr/lib). We should not mention DYLD_LIBRARY_PATHin the FAQ. If we do mention it, it should only be to say that it shouldnot be set.


Brian


On Wed, 18 Jun 2008, Jeff Squyres wrote:

FWIW, I added this issue to the FAQ under the "OS X" section to make it alittle easier to find.


On Jun 17, 2008, at 5:17 PM, Jeff Squyres wrote:

Sorry for not replying earlier -- glad you figured it out.

Yes, if you didn't also reset the LIBRARY_PATH, the "wrong" libmpi (andfriends) will get picked up, and it will therefore use the hard-codeddirectory path in those "wrong" libraries to find the wrapper data textfiles (the ones without Fortran support).



On Jun 17, 2008, at 4:15 PM, Weirs, V Gregory wrote:


Alright, I’m an idiot. I didn’t adjust my DYLD_LIBRARY_PATH.
Sorry about that-
Greg

On 6/17/08 7:08 AM, "Jeff Squyres" <jsquy...@cisco.com> wrote:

This is pretty odd.

What files do you see in $prefix/share/openmpi/mpi*txt?

What do you see from:

  grep required_file $prefix/share/openmpi/mpi*txt



On Jun 16, 2008, at 2:12 PM, Weirs, V Gregory wrote:


Dave Gunter:

According to ./configure —help, by default  —enable-mpi-f77 and —
enable-mpi-f90 are set. Also, ompi_info (see output in run_output in
the tarball) seems to indicate they are there. I rebuilt with them
just to be sure, and got the same results.


Doug Reeder:
In my run_output file, you can see results of ‘which mpif77’ that
shows I am using the version I built. (current is a symlink to 1.2.6-
gcc4.0). In any case, I get the same results with the absolute path /
usr/local/openmpi/1.2.6-4.0/bin/mpif77.


Thanks,
Greg

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Today's Topics:

   1. Re: gfortran bindings apparently not built on mac os
leopard
      (David Gunter)
   2. Re: gfortran bindings apparently not built on mac os
leopard
      (Doug Reeder)
   3. Re: gfortran bindings apparently not built on mac os
leopard
      (Doug Reeder)
   4. help me please, about Open MPI (Tony Smith)
   5. Re: help me please, about Open MPI (Andreas Sch?fer)


----------------------------------------------------------------------

Message: 1
Date: Mon, 16 Jun 2008 10:37:22 -0600
From: David Gunter <d...@lanl.gov>
Subject: Re: [OMPI users] gfortran bindings apparently not built on
        mac os  leopard
To: Open MPI Users <us...@open-mpi.org>
Message-ID: <4683c284-4fef-45ca-a2bc-8be91a439...@lanl.gov>
Content-Type: text/plain; charset="windows-1252"; Format="flowed";
        DelSp="yes"

I believe you still must add "--enable-f77" and "--enable-f90" to the
OMPI configure line in addition to setting the FC and F77 env
variables.

-david
--
David Gunter
HPC-3: Parallel Tools Team
Los Alamos National Laboratory

On Jun 16, 2008, at 10:25 AM, Weirs, V Gregory wrote:

>
>
> I am having trouble building mpif77/mpif90 with gfortran on Mac OS
> 10.5. Or maybe just running. The configure, make all, and make
> install seemed to go just fine, finding my gfortran and apparently
> using it, but the scripts mpif77 and mpif90 give the error that my
> openmpi was not built with fortran bindings. Mpicc and mpicxx don?t
> give this error.  Ompi_info says the f77 and f90 bindings were
built.
>
> I know that OS X 10.5 comes with openmpi mpicc and mpicxx installed,
> but not fortran bindings, and I was careful to put the openmpi I
> built first in the path.
>
> Some run output (mpif77 ?version, ompi_info), config.log,
> configure.log, make.out, make-install.out are in the attached
tarball.
>
> Any clues?
>
> Thanks,
> Greg
>
>
> --
> V. Gregory Weirs
> Sandia National Laboratories                vgwe...@sandia.gov
> P.O.Box 5800, MS 0378                        phone: 505 845 2032
> Albuquerque, NM 87185-0378              fax: 505 284 0154
> <dig.tar.gz>_______________________________________________
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users

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Message: 2
Date: Mon, 16 Jun 2008 09:32:21 -0700
From: Doug Reeder <d...@rain.org>
Subject: Re: [OMPI users] gfortran bindings apparently not built on
        mac os  leopard
To: Open MPI Users <us...@open-mpi.org>
Message-ID: <5047581c-f2e2-473b-8576-3e11f0d54...@rain.org>
Content-Type: text/plain; charset="windows-1252"; Format="flowed";
        DelSp="yes"

Greg,

If you use the absolute path names to run your mpif77 and mpif90 what
output do you get. In spite of the results from which mpif77, the
outputs from mpif77 and mpif90 look suspiciously like the outputs
from the apple supplied versions in /usr/bin.

Doug Reeder
On Jun 16, 2008, at 9:25 AM, Weirs, V Gregory wrote:

>
>
> I am having trouble building mpif77/mpif90 with gfortran on Mac OS
> 10.5. Or maybe just running. The configure, make all, and make
> install seemed to go just fine, finding my gfortran and apparently
> using it, but the scripts mpif77 and mpif90 give the error that my
> openmpi was not built with fortran bindings. Mpicc and mpicxx don?t
> give this error.  Ompi_info says the f77 and f90 bindings were
built.
>
> I know that OS X 10.5 comes with openmpi mpicc and mpicxx
> installed, but not fortran bindings, and I was careful to put the
> openmpi I built first in the path.
>
> Some run output (mpif77 ?version, ompi_info), config.log,
> configure.log, make.out, make-install.out are in the attached
tarball.
>
> Any clues?
>
> Thanks,
> Greg
>
>
> --
> V. Gregory Weirs
> Sandia National Laboratories                vgwe...@sandia.gov
> P.O.Box 5800, MS 0378                        phone: 505 845 2032
> Albuquerque, NM 87185-0378              fax: 505 284 0154
> <dig.tar.gz>
> _______________________________________________
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users

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Message: 3
Date: Mon, 16 Jun 2008 09:42:55 -0700
From: Doug Reeder <d...@rain.org>
Subject: Re: [OMPI users] gfortran bindings apparently not built on
        mac os  leopard
To: Open MPI Users <us...@open-mpi.org>
Message-ID: <08b5c06d-8b64-4189-adae-e9fbe6be5...@rain.org>
Content-Type: text/plain; charset="windows-1252"; Format="flowed";
        DelSp="yes"

Greg,

In your run_output file you don't appear to be using the openmpi
versions that you built. From your make-install.out file it looks
like your versions are in /usr/local/openmpi/1.2.6-gcc4.0/bin. You
need to use that absolute path or prepend that path to your PATH
environment variable.

Doug Reeder
On Jun 16, 2008, at 9:25 AM, Weirs, V Gregory wrote:

>
>
> I am having trouble building mpif77/mpif90 with gfortran on Mac OS
> 10.5. Or maybe just running. The configure, make all, and make
> install seemed to go just fine, finding my gfortran and apparently
> using it, but the scripts mpif77 and mpif90 give the error that my
> openmpi was not built with fortran bindings. Mpicc and mpicxx don?t
> give this error.  Ompi_info says the f77 and f90 bindings were
built.
>
> I know that OS X 10.5 comes with openmpi mpicc and mpicxx
> installed, but not fortran bindings, and I was careful to put the
> openmpi I built first in the path.
>
> Some run output (mpif77 ?version, ompi_info), config.log,
> configure.log, make.out, make-install.out are in the attached
tarball.
>
> Any clues?
>
> Thanks,
> Greg
>
>
> --
> V. Gregory Weirs
> Sandia National Laboratories                vgwe...@sandia.gov
> P.O.Box 5800, MS 0378                        phone: 505 845 2032
> Albuquerque, NM 87185-0378              fax: 505 284 0154
> <dig.tar.gz>
> _______________________________________________
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users

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Message: 4
Date: Mon, 16 Jun 2008 12:51:31 -0400
From: Tony Smith <dtustu...@hotmail.com>
Subject: [OMPI users] help me please, about Open MPI
To: <us...@open-mpi.org>
Message-ID: <bay104-w32bc5d00da99730856fd48fd...@phx.gbl>
Content-Type: text/plain; charset="windows-1252"





Dear Sir:



I am trying to install Open MPI on a cluster that has been installed
with mpich-

gm  MPI.



I have followed the steps on your website.

I can compile and run the Hello_c application correctly.



But, how can I make sure that the application is run by Open MPI not
by mpich-

gm MPI ?



I have changed PATH and LD_LIBRARY_PATH:



I deleted /opt/mpich-gm/bin from PATH and added

/ptmp/myname/openmpi123/ompi123_install/bin/ into PATH.



LD_LIBRARY_PATH=/ptmp/myname/openmpi123/ompi123_install/lib



And then, I got



-bash-3.00$ which mpirun
/ptmp/myname/openmpi123/ompi123_install/bin/mpirun



In my job script , I used



"time mpirun -np 16  /ptmp/jxding/openmpi123/openmpi-1.2.3/examples/
hello_c"

Then I added "which mpirun" in my job script, and then submited my
job to the
cluster , I got :
====================================

/opt/mpich-gm/bin/mpirun
Hello, world, I am 0 of 1
Hello, world, I am 0 of 1
Hello, world, I am 0 of 1
Hello, world, I am 0 of 1
Hello, world, I am 0 of 1
Hello, world, I am 0 of 1
Hello, world, I am 0 of 1
Hello, world, I am 0 of 1
Hello, world, I am 0 of 1
Hello, world, I am 0 of 1
Hello, world, I am 0 of 1
Hello, world, I am 0 of 1
Hello, world, I am 0 of 1
Hello, world, I am 0 of 1
Hello, world, I am 0 of 1
Hello, world, I am 0 of 1
0.117u 0.165s 0:09.54 2.8%      0+0k 0+0io 0pf+0w

====================================

So , it means that the application is still using MPICH-GM not Open
MPI.

Would you please help me with that ?


thanks,



Tony



June 16  2008
_________________________________________________________________
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Message: 5
Date: Mon, 16 Jun 2008 19:05:06 +0200
From: Andreas Sch?fer <gent...@gmx.de>
Subject: Re: [OMPI users] help me please, about Open MPI
To: Open MPI Users <us...@open-mpi.org>
Message-ID: <20080616170506.gb7...@hex.inf-ra.uni-jena.de>
Content-Type: text/plain; charset="iso-8859-1"

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


--
============================================
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Cluster and Metacomputing Working Group
Friedrich-Schiller-Universit?t Jena, Germany
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--
V. Gregory Weirs
Sandia National Laboratories                vgwe...@sandia.gov
P.O.Box 5800, MS 0378                        phone: 505 845 2032
Albuquerque, NM 87185-0378              fax: 505 284 0154
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--
Jeff Squyres
Cisco Systems


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--
V. Gregory Weirs
Sandia National Laboratories                vgwe...@sandia.gov
P.O.Box 5800, MS 0378                        phone: 505 845 2032
Albuquerque, NM 87185-0378              fax: 505 284 0154
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Cisco Systems


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Re: [OMPI users] gfortran bindings apparently not built on mac os leopard

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