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Subject: Re: [OMPI users] openmpi configuration error?
From: Gus Correa (gus_at_[hidden])
Date: 2014-05-16 19:29:54


On 05/16/2014 07:09 PM, Ben Lash wrote:
> The $PATH and $LD_LIBRARY_PATH seem to be correct, as does module list.
> I will try to hear back from our particular cluster people, otherwise I
> will try using the latest version. This is old government software,
> significant parts are written in fortran77 for example, typically
> upgrading to a new version breaks it. It was looking for mpich, hence
> the link, but a long time ago I gave it openmpi instead as recommended
> and that worked, so I suppose it's less persnickety about the mpi
> version than some other things. The most current version installed
> is openmpi/1.6.5-intel(default). Thanks again.
>

We have code here that has been recompiled (some with modifications,
some not) with OpenMPI since 1.2.8 with no problems.
MPI is a standard, both OpenMPI and MPICH follow the standard (except
perhaps for very dusty corners or latest greatest MPI 3 features).
If your code compiled with 1.4.4, it should (better) do with 1.6.5.
Fortran77 shouldn't be an issue.

I agree, the PATH and LD_LIBRARY_PATH point to the "retired" directory.
Many things may have happened, though, say, the "retired" directory may
not be complete, or may not have been installed on all cluster nodes,
or (if not really re-installed) probably points to the original
(pre-retirement) directories that no longer exist.
Rather than sorting this out, I think you have a better shot using
Open MPI 1.6.5.
Just load the module and try to recompile the code.
(Probably just
module swap openmpi/1.4.4-intel openmpi/1.6.5-intel)

You may need to tweak with the Makefile, if it hardwires
the MPI wrappers/binary location, or the library and include paths.
Some do, some don't.

Gus Correa

> [bl10_at_login2 ~]$ echo $PATH
> /home/bl10/rlib/deps/bin:/opt/apps/netcdf/4.1.3/bin:/opt/apps/netcdf/4.1.3/deps/hdf5/1.8.7/bin:/opt/apps/openmpi/retired/1.4.4-intel/bin:/opt/apps/pgi/11.7/linux86-64/11.7/bin:/opt/apps/python3/3.2.1/bin:/opt/apps/intel/2013.1.039/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/ibutils/bin:/opt/apps/moab/current/bin:/projects/dsc1/apps/cmaq/deps/ioapi-kiran/3.1/bin:/home/bl10/bin
>
> [bl10_at_login2 ~]$ echo $LD_LIBRARY_PATH
> /home/bl10/rlib/deps/lib:/projects/dsc1/apps/cmaq/deps/netcdf/4.1.3-intel/lib:/opt/apps/netcdf/4.1.3/lib:/opt/apps/netcdf/4.1.3/deps/hdf5/1.8.7/lib:/opt/apps/netcdf/4.1.3/deps/szip/2.1/lib:/opt/apps/openmpi/retired/1.4.4-intel/lib:/opt/apps/intel/2011.0.013/mkl/lib/intel64:/opt/apps/intel/2013.1.039/mkl/lib/intel64:/opt/apps/intel/2013.1.039/lib/intel64
>
> [bl10_at_login2 ~]$ module list
> Currently Loaded Modulefiles:
> 1) intel/2013.1.039 2) python3/3.2.1 3) pgi/11.7
> 4) openmpi/1.4.4-intel 5) netcdf/4.1.3
> [bl10_at_login2 ~]$
>
>
>
>
> On Fri, May 16, 2014 at 5:46 PM, Gus Correa <gus_at_[hidden]
> <mailto:gus_at_[hidden]>> wrote:
>
> On 05/16/2014 06:26 PM, Ben Lash wrote:
>
> I'm not sure I have the ability to implement a different module
> management system, I am using a university cluster. We have a module
> system, and I am beginning to suspect that maybe it wasn't updated
> during the upgrade. I have
> module list
> ..other modules....openmpi/1.4.4
> Perhaps this is still trying to go to the old source location?
> How would
> I check? Is there an easy way around it if it is wrong? Thanks
> again!
>
>
> Most likely the module openmpi/1.4.4 is out of date.
> You can check it with
> echo $PATH
> If it doesn't point to the "retired" directory, then it is probably
> out of date.
>
> Why don't you try to recompile the code
> with the current Open MPI installed in the cluster?
>
> module avail
> will show everyting, and you can pick the latest, load it,
> and try to recompile the program with that.
>
> Gus Correa
>
>
> On Fri, May 16, 2014 at 5:07 PM, Maxime Boissonneault
> <maxime.boissonneault@__calculquebec.ca
> <mailto:maxime.boissonneault_at_[hidden]>
> <mailto:maxime.boissonneault@__calculquebec.ca
> <mailto:maxime.boissonneault_at_[hidden]>>> wrote:
>
> Instead of using the outdated and not maintained Module
> environment,
> why not use Lmod :
> https://www.tacc.utexas.edu/__tacc-projects/lmod
> <https://www.tacc.utexas.edu/tacc-projects/lmod>
>
> It is a drop-in replacement for Module environment that
> supports all
> of their features and much, much more, such as :
> - module hierarchies
> - module properties and color highlighting (we use it to
> higlight
> bioinformatic modules or tools for example)
> - module caching (very useful for a parallel filesystem
> with tons of
> modules)
> - path priorities (useful to make sure personal modules take
> precendence over system modules)
> - export module tree to json
>
> It works like a charm, understand both TCL and Lua modules
> and is
> actively developped and debugged. There are litteraly new
> features
> every month or so. If it does not do what you want, odds
> are that
> the developper will add it shortly (I've had it happen).
>
> Maxime
>
> Le 2014-05-16 17:58, Douglas L Reeder a écrit :
>
> Ben,
>
> You might want to use module (source forge) to manage
> paths to
> different mpi implementations. It is fairly easy to set
> up and
> very robust for this type of problem. You would remove
> contentious
> application paths from you standard PATH and then use
> module to
> switch them in and out as needed.
>
> Doug Reeder
> On May 16, 2014, at 3:39 PM, Ben Lash <bl10_at_[hidden]
> <mailto:bl10_at_[hidden]>
> <mailto:bl10_at_[hidden] <mailto:bl10_at_[hidden]>>> wrote:
>
> My cluster has just upgraded to a new version of
> MPI, and I'm
> using an old one. It seems that I'm having trouble
> compiling due
> to the compiler wrapper file moving (full error here:
> http://pastebin.com/EmwRvCd9)
> "Cannot open configuration file
>
> /opt/apps/openmpi/1.4.4-intel/__share/openmpi/mpif90-wrapper-__data.txt"
>
> I've found the file on the cluster at
>
> /opt/apps/openmpi/retired/1.4.__4-intel/share/openmpi/mpif90-__wrapper-data.txt
> How do I tell the old mpi wrapper where this file is?
> I've already corrected one link to mpich ->
> /opt/apps/openmpi/retired/1.4.__4-intel/, which is
> in the software
> I'm trying to recompile's lib folder
> (/home/bl10/CMAQv5.0.1/lib/__x86_64/ifort). Thanks
> for any ideas. I
> also tried changing $pkgdatadir based on what I
> read here:
> http://www.open-mpi.org/faq/?__category=mpi-apps#default-__wrapper-compiler-flags
> <http://www.open-mpi.org/faq/?category=mpi-apps#default-wrapper-compiler-flags>
>
>
> Thanks.
>
> --Ben L
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>
> --
> ------------------------------__---
> Maxime Boissonneault
> Analyste de calcul - Calcul Québec, Université Laval
> Ph. D. en physique
>
>
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> --
> --Ben L
>
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> --
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