The $PATH and $LD_LIBRARY_PATH seem to be correct, as does module list. I will try to hear back from our particular cluster people, otherwise I will try using the latest version. This is old government software, significant parts are written in fortran77 for example, typically upgrading to a new version breaks it. It was looking for mpich, hence the link, but a long time ago I gave it openmpi instead as recommended and that worked, so I suppose it's less persnickety about the mpi version than some other things. The most current version installed is openmpi/1.6.5-intel(default). Thanks again.
[bl10@login2 ~]$ echo $PATH /home/bl10/rlib/deps/bin:/opt/apps/netcdf/4.1.3/bin:/opt/apps/netcdf/4.1.3/deps/hdf5/1.8.7/bin:/opt/apps/openmpi/retired/1.4.4-intel/bin:/opt/apps/pgi/11.7/linux86-64/11.7/bin:/opt/apps/python3/3.2.1/bin:/opt/apps/intel/2013.1.039/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/ibutils/bin:/opt/apps/moab/current/bin:/projects/dsc1/apps/cmaq/deps/ioapi-kiran/3.1/bin:/home/bl10/bin [bl10@login2 ~]$ echo $LD_LIBRARY_PATH /home/bl10/rlib/deps/lib:/projects/dsc1/apps/cmaq/deps/netcdf/4.1.3-intel/lib:/opt/apps/netcdf/4.1.3/lib:/opt/apps/netcdf/4.1.3/deps/hdf5/1.8.7/lib:/opt/apps/netcdf/4.1.3/deps/szip/2.1/lib:/opt/apps/openmpi/retired/1.4.4-intel/lib:/opt/apps/intel/2011.0.013/mkl/lib/intel64:/opt/apps/intel/2013.1.039/mkl/lib/intel64:/opt/apps/intel/2013.1.039/lib/intel64 [bl10@login2 ~]$ 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@login2 ~]$ On Fri, May 16, 2014 at 5:46 PM, Gus Correa <g...@ldeo.columbia.edu> 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 Most likely the module openmpi/1.4.4 is out of date.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.boissonnea...@calculquebec.ca >> <mailto:maxime.boissonnea...@calculquebec.ca>> 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 <b...@rice.edu >>> <mailto:b...@rice.edu>> 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 >>>> us...@open-mpi.org <mailto:us...@open-mpi.org> >>>> http://www.open-mpi.org/mailman/listinfo.cgi/users >>>> >>> >>> >>> >>> _______________________________________________ >>> users mailing list >>> us...@open-mpi.org <mailto:us...@open-mpi.org> >>> 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 >> us...@open-mpi.org <mailto:us...@open-mpi.org> >> >> http://www.open-mpi.org/mailman/listinfo.cgi/users >> >> >> >> >> -- >> --Ben L >> >> >> _______________________________________________ >> users mailing list >> us...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/users >> >> > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users > > -- --Ben L
