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Subject: Re: [OMPI users] openmpi configuration error?
From: Ben Lash (bl10_at_[hidden])
Date: 2014-05-16 19:09:38


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.

[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]> 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 Most likely the module openmpi/1.4.4 is out of date.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_at_[hidden]
>> <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
>>
>> 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]>> 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
>>>>
>>>>
>>>> Thanks.
>>>>
>>>> --Ben L
>>>> _______________________________________________
>>>> users mailing list
>>>> users_at_[hidden] <mailto:users_at_[hidden]>
>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> users mailing list
>>> users_at_[hidden] <mailto:users_at_[hidden]>
>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>
>>
>>
>> --
>> ---------------------------------
>> Maxime Boissonneault
>> Analyste de calcul - Calcul Québec, Université Laval
>> Ph. D. en physique
>>
>>
>> _______________________________________________
>> users mailing list
>> users_at_[hidden] <mailto:users_at_[hidden]>
>>
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>>
>>
>>
>> --
>> --Ben L
>>
>>
>> _______________________________________________
>> users mailing list
>> users_at_[hidden]
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>>
> _______________________________________________
> users mailing list
> users_at_[hidden]
> http://www.open-mpi.org/mailman/listinfo.cgi/users
>
>

-- 
--Ben L