[MITgcm-support] Myrinet, PGI, & mac

Mon Nov 16 02:32:14 EST 2009

Hi Amato,
I am no specialist for this, but what makes we wonder are warnings  
like this:
> cat main.F | ../../../tools/set64bitConst.sh | pgcpp -DALLOW_USE_MPI  
> -DALWAYS_USE_MPI -DHAVE_SYSTEM -DHAVE_FDATE -DHAVE_ETIME -DHAVE_CLOC  
> -DHAVE_SETRLSTK -DHAVE_SIGREG -DHAVE_STAT -I/common/netcdf-4.0.1 >  
> main.for
> pgcpp-Warning-No files to process
> mpif90   -c main.for
> PGF90-W-0006-Input file empty (main.for)
These warning seem to appear for each file that is processed. In the  
end the main program is not available (as f90main complains, this is  
not a MITgcm routine, only something that invokes the main program  
"MAIN", which you'll find in "eesupp/scr/main.F").

You seem to have fundamental problem in the way the sources are  
processed, so that already in the CPP step (.F -> .for) there is  
nothing in either the *.F or the *.for files. Maybe you can verify  
that by having a look at some *.for files. They should be the same as  
the *.F files, except that all the CPP-flags have been evaluated and  
the header-files are included. You probably need to specify special  
flags for pgcpp? Or are symbolic links treated in a funny way on your  
system? (I once had problems with symbolic links and MacOS in  
different contexts).

Further, but I think that that may be unrelated, you're MPI paths  
don't seem to show up in the make.log, probably because you overwrite  
them in the optfile. It should look like this

#- for MPI:
MPI_INC_DIR="/common/mpich2-mx-1.1.1p1..5/src/include"
#-- for NetCDF:
NETCDF_INCDIR="/common/netcdf-4.0.1"
# and then
INCLUDES="-I$NETCDF_INCDIR -I$MPI_INC_DIR"
# or
INCLUDEDIRS="$NETCDF_INCDIR $MPI_INC_DIR"
# this is only for netcdf
LIBS="-L/common/netcdf-4.0.1/libsrc"

Again, a problem to fix once your are able to get any executable: in  
your genmake2, you get a message, that you cannot compile netcdf  
files. After the genmake2 step (or make makefile) you can check in  
genmake_warnings, what the specific error messages related to this are.

Martin

PS. If I can get access to that machine (I know that that's not always  
possible, certainly not a my institute) I might be able to figure out  
what's going myself.

On Nov 16, 2009, at 4:01 AM, Amato Evan wrote:

> Hi Martin,
>
> Firstly, thank you so much for the help!  I have posted my working  
> optfile, and the output from "genmake" and "make" here:
> http://trane.evsc.virginia.edu/mitgcm/
>
> If you have a second, please let me know if anything is obviously  
> amiss here. I am getting in touch with PGI support about compiling  
> the MITgcm, so once I have my optfile (and flags) down I will  
> definitely submit for inclusion in the repository.
>
> Sincerely,
> Amato
>
> On Nov 14, 2009, at 4:54 AM, Martin Losch wrote:
>
>> Amato,
>>
>> I would expect that with a working mpi-installation, you shouldn't
>> have these problems.
>> You are using mpif90 for compiling and linking, so that the library
>> paths to the mpi libs should already be included; the only thing that
>> you need is the path to the mpi-header files (because the makefile
>> first produces *.f files with $(CPP) and not $(FC), the INCLUDES is
>> passed to $(CPP)). I assume it's this: "/common/mpich2-mx-1.1.1p1..5/
>> src/include" (it should show up somewhere in mpif90). So your  
>> settings
>> look good to me.
>> You seem to get as far as the link step (because the only error
>> message you report is "ld: ..."), so that I think it has to do with
>> the library paths. For more help you'd need to give more details,  
>> e.g.
>> 1. the complete build options file
>> 2. output of genmake2 (and genmake_warnings, if available after
>> running genmake2)
>> 3. full error messages of the make step
>>
>> BTW: Once you have managed to get the model compiled and running, it
>> would be nice if you can share the successful build_options file, and
>> we can add it to the repository.
>>
>> Martin
>>
>> On Nov 13, 2009, at 10:33 PM, Amato Evan wrote:
>>
>>> Good afternoon!
>>>
>>> I'm new to HPC, MPI, PGI, MX, MPD, MITgcm... And just about any
>>> fancy acronym
>>> you can think of. Although I've gotten the MITgcm running on a  
>>> macbook
>>> pro, trying to do this on a cluster is much more involved! I am  
>>> trying
>>> to compile the verification/exp2 code on:
>>>
>>> -An eight node Xserve cluster with Myrinet MPI comms
>>> -mpich2-mx compiled with pgcc/pgf95/pgcpp
>>>
>>> I am pretty sure that mpicc etc is working since I can run IMB-MPI1
>>> codes.  But trying to compile the MITgcm is a total disaster! I am
>>> getting "ld: symbol(s) not found" errors on "Make" although I  
>>> think I
>>> am including paths to my mpi and pgi libs.  Can anyone with a  
>>> similar
>>> setup post an optfile?
>>>
>>> Some of my (sloppy) settings are:
>>>
>>> CPP='pgcpp'
>>> FC='mpif90'
>>> CC='mpicc'
>>> LINK='mpif90'
>>> INCLUDES='-I/usr/local/include -I/common/usr/local/include -I/ 
>>> common/
>>> mpich2-mx-1.1.1p1..5/src/include'
>>> INCLUDEFILES='-I/usr/local/include -I/common/usr/local/include -I/
>>> common/mpich2-mx-1.1.1p1..5/src/include'
>>> LIBS='-L/usr/local/lib -L/common/mpich2-mx-1.1.1p1..5/src/binding/
>>> f90 -
>>> L/common/usr/local/lib'
>>>
>>> Thanks for the help!!!
>>>
>>> Sincerely,
>>> Amato
>>> _______________________________________________
>>> MITgcm-support mailing list
>>> MITgcm-support at mitgcm.org
>>> http://mitgcm.org/mailman/listinfo/mitgcm-support
>>
>>
>> _______________________________________________
>> MITgcm-support mailing list
>> MITgcm-support at mitgcm.org
>> http://mitgcm.org/mailman/listinfo/mitgcm-support
>
> ---
> Amato Evan
> Asst. Professor
> Dept. of Environmental Sciences
> University of Virginia
> 434.243.7711
> aevan at virginia.edu
> http://trane.evsc.virginia.edu
>
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