Sorry, I should've replied to all. Please see the response below.
Thanks,
Todd
On Tue, Aug 18, 2009 at 6:24 PM, Todd Krause <[email protected]>wrote:
> Hi Jack,
>
> Thanks for the quick reply. I went through the procedure you mentioned
> (adding a "fink selfupdate" between the two steps to make sure fink didn't
> try to install openmpi *again* --- I missed that the first time, and fink
> aborted). Unfortunately I still have the same error when I try to use make:
>
> 06:09 PM btpro:Gadget2> make -f
> ../bobtodd_tests/milos_test01/makefiles/makefile.milos01
>
> om-mpicc -O3 -Wall -DUNEQUALSOFTENINGS -DPEANOHILBERT -DWALLCLOCK
> -DSYNCHRONIZATION -DISOTHERM_EQS -I/sw/include -I/sw/include -I/sw/include
> -c -o main.o main.c
> Cannot open configuration file
> /sw/share/doc/openmpi/openmpi/om-mpicc-wrapper-data.txt
> Error parsing data file om-mpicc: Not found
> make: *** [main.o] Error 243
> 06:10 PM btpro:Gadget2> which om-mpicc
> /sw/bin/om-mpicc
>
> To give you an idea of what the makefile contains, the relevant section is
>
> ifeq ($(SYSTYPE),"bobtoddpro")
> CC = om-mpicc
> OPTIMIZE = -O3 -Wall
> GSL_INCL = -I/sw/include
> GSL_LIBS = -L/sw/lib
> FFTW_INCL= -I/sw/include
> FFTW_LIBS= -L/sw/lib
> #MPICHLIB = -L/usr/local/mpich2/mpich2-1.0.5p4/install/lib -lmpich
> #MPICHINCL = -I/usr/local/mpich2/mpich2-1.0.5p4/install/include
> HDF5INCL = -I/sw/include
> HDF5LIB = -L/sw/lib -lhdf5 -lz -Wl#,"-R /sw/lib"
> endif
>
> (this worked fine before, when I just had mpicc... it picked up openmpi's
> commands fine; but I understand you renamed them to coexist with lam-mpi...
> is there really a reason to keep lam-mpi around, since they stopped
> development and moved to openmpi? Just asking...). The problem seems to be
> that the system is looking for a file
> "/sw/share/doc/openmpi/openmpi/xxxxxx-wrapper-data.txt", where "xxxxxx"
> should be the same as what I've set CC to; but it finds nothing with
> "om-mpicc-...". Here's the contents of that directory on my system:
>
> 06:10 PM btpro:Gadget2> ls /sw/share/doc/openmpi/openmpi/
> amca-param-sets/ help-orte-iof.txt
> help-coll-sync.txt help-orte-odls-base.txt
> help-dash-host.txt help-orte-ps.txt
> help-ess-base.txt help-orte-rmaps-base.txt
> help-hostfile.txt help-orte-rmaps-rr.txt
> help-mca-base.txt help-orte-rmaps-seq.txt
> help-mca-bml-r2.txt help-orte-runtime.txt
> help-mca-coll-base.txt help-orte-snapc-base.txt
> help-mca-param.txt help-orted.txt
> help-mpi-api.txt help-orterun.txt
> help-mpi-btl-base.txt help-plm-base.txt
> help-mpi-errors.txt help-plm-rsh.txt
> help-mpi-runtime.txt help-plm-slurm.txt
> help-mpool-base.txt help-ras-base.txt
> help-odls-default.txt help-ras-slurm.txt
> help-ompi-crcp-base.txt help-rmaps_rank_file.txt
> help-ompi-dpm-base.txt mpic++-vt-wrapper-data.txt
> help-ompi-dpm-orte.txt mpic++-wrapper-data.txt
> help-ompi-pubsub-orte.txt mpicc-vt-wrapper-data.txt
> help-ompi-server.txt mpicc-wrapper-data.txt
> help-ompi_info.txt mpicxx-vt-wrapper-data.txt@
> help-opal-carto-file.txt mpicxx-wrapper-data.txt@
> help-opal-crs-base.txt mpif77-vt-wrapper-data.txt
> help-opal-crs-none.txt mpif77-wrapper-data.txt
> help-opal-runtime.txt mpif90-vt-wrapper-data.txt
> help-opal-util.txt mpif90-wrapper-data.txt
> help-opal-wrapper.txt opalc++-wrapper-data.txt
> help-orte-clean.txt opalcc-wrapper-data.txt
> help-orte-filem-base.txt ortec++-wrapper-data.txt
> help-orte-filem-rsh.txt ortecc-wrapper-data.txt
> 06:12 PM btpro:Gadget2>
>
> From my current understanding, it seems that these filenames would be fine
> if "om-mpicc" were still named "mpicc"; but since the change, the filenames
> don't match what the wrapper's expecting.
>
> So does that mean I just have to go into that directory and change all the
> filenames by hand? As a general policy, I try not to change things in /sw
> by hand if I don't have to, for fear of messing things up....
>
> Thanks,
> Todd
>
>
> On Tue, Aug 18, 2009 at 4:53 PM, Jack Howarth <[email protected]>wrote:
>
>> Doh. I misread your message. This is a glitch from earlier attempts
>> at supporting openmpi on case-sensitive filesystems. There were some
>> problems with the logic which caused the previous openmpi package to
>> nuke the files in the newly installed one. These issues are all
>> resolved in the current openmpi packaging and all you need to do is
>> execute...
>>
>> fink reinstall openmpi
>> fink reinstall openmpi-dev
>>
>> to restore the missing files.
>> Jack
>> ps I didn't realize at the time that the PostRmScript of the previously
>> installed package would be executing after the installation of the
>> new upgrade package. I assumed that it would be executing only after
>> the original packages files were removed but not before the new packages
>> files were installed. Or is that a bug in fink?
>>
>> On Tue, Aug 18, 2009 at 02:58:31PM -0400, Alexander Hansen wrote:
>> > -----BEGIN PGP SIGNED MESSAGE-----
>> > Hash: SHA1
>> >
>> > Todd Krause wrote:
>> > > Hi,
>> > >
>> > > I recently installed the fftw-mpi package, which in turn required
>> > > installation of the openmpi package (fine in my book). After finally
>> > > realizing that fink named the new openmpi commands in /sw/bin to have
>> > > "om-" prefixes, I ran make to compile the code Gadget-2, and received
>> > > the following error:
>> > >
>> > > 01:03 PM btpro:Gadget2> make -f
>> > > ../bobtodd_tests/milos_test01/makefiles/makefile.milos01
>> > > om-mpicc -O3 -Wall -DUNEQUALSOFTENINGS -DPEANOHILBERT -DWALLCLOCK
>> > > -DSYNCHRONIZATION -DISOTHERM_EQS -I/sw/include -I/sw/include
>> > > -I/sw/include -c -o main.o main.c
>> > > Cannot open configuration file
>> > > /sw/share/doc/openmpi/openmpi/om-mpicc-wrapper-data.txt
>> > > Error parsing data file om-mpicc: Not found
>> > > make: *** [main.o] Error 243
>> > > 01:03 PM btpro:Gadget2> which om-mpicc
>> > > /sw/bin/om-mpicc
>> > >
>> > > Interestingly, the last time I made Gadget-2, I didn't need to use
>> > > "om-mpicc"; simply "mpicc" seemed to find my /sw/bin/mpicc (which was
>> > > openmpi) without problems. Since then, unfortunately, I had to remove
>> > > fink and start from scratch, and this time I realized everything's
>> > > called "om-xxxxx". I found a similar error in an earlier exchange on
>> > > the fink listserve:
>> > >
>> > >
>> http://www.opensubscriber.com/message/[email protected]/7238283.html
>> > >
>> > > the relevant part of which is the following
>> > >
>> > > -------------- begin quoted text ---------------
>> > > The first problem was a file which the executable needed, that had an
>> > > unexpected name:
>> > >
>> > > ----
>> > >
>> > > nell:~/tmp/tst barnes$ om-mpif77
>> > > Cannot open configuration file
>> > > /sw/share/doc/openmpi/openmpi/om-mpif77-wrapper-data.txt
>> > > Error parsing data file om-mpif77: Not found
>> > >
>> > > nell:~/tmp/tst barnes$ sudo cp
>> > > /sw/share/doc/openmpi/openmpi/mpif77-wrapper-data.txt
>> > > /sw/share/doc/openmpi/openmpi/om-mpif77-wrapper-data.txt
>> > >
>> > > nell:~/tmp/tst barnes$ ls -l /sw/share/doc/openmpi/openmpi/*77*
>> > > -rw-r--r-- 1 root admin 668 Jul 26 18:42
>> > > /sw/share/doc/openmpi/openmpi/mpif77-wrapper-data.txt
>> > > -rw-r--r-- 1 root admin 668 Jul 26 18:49
>> > > /sw/share/doc/openmpi/openmpi/om-mpif77-wrapper-data.txt
>> > >
>> > > nell:~/tmp/tst barnes$ om-mpif77
>> > > gfortran: no input files
>> > >
>> > > -----
>> > > There were many other similar .txt files which probably also need
>> > > renaming.
>> > > So that's fixed with a kludge, but now it's having trouble finding
>> > > libraries
>> > > which do exist (perhaps the same .so vs .dynlib problem?):
>> > >
>> > > /usr/bin/ld: can't locate file for: -lmpi_f77
>> > > collect2: ld returned 1 exit status
>> > > make: *** [table.x] Error 1
>> > >
>> > > -------------- end quoted text ----------------
>> > >
>> > > So my question is this: I can find the relevant data files, and I
>> could
>> > > rename them all to have the "om-" prefix, but is there a better fix so
>> > > that I don't have to go through all that and muck around in /sw?
>> > > Moreover, it seems like I'll have to do that for each wrapper I use
>> > > (om-mpic++ next, then om-mpif77 if I have to use Fortran, etc.). And
>> in
>> > > the end, even that will only get me to the library error, according to
>> > > the above email. Is there a resolution to this problem that I failed
>> to
>> > > find?
>> > >
>> > > Thanks very much,
>> > > Todd
>> > >
>> > >
>> >
>> > I'll cc the maintainer for the first part.
>> >
>> > As for the the library linker issue above, it's hard to say without
>> > seeing what is being fed to ld. However, it may be as simple as not
>> > having '-L/sw/lib/openmpi' before '-lmpi_f77', since libmpi_f77.dylib is
>> > not in ld's default search path. How to fix this depends on what the
>> > package you're building supports.
>> > - --
>> > Alexander Hansen
>> > Fink User Liaison
>> > -----BEGIN PGP SIGNATURE-----
>> > Version: GnuPG v1.4.9 (Darwin)
>> > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
>> >
>> > iEYEARECAAYFAkqK+dcACgkQB8UpO3rKjQ/5/ACfZlj4yC6vQ3koohwp+a8/sjdF
>> > YBYAnRwM8jlk1vlNUu1ouDk51Di8LIsQ
>> > =8Oat
>> > -----END PGP SIGNATURE-----
>>
>
>
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