Great. Thanks very much for the assistance!
Best,
Todd
On Wed, Aug 19, 2009 at 7:54 AM, Jack Howarth <[email protected]>wrote:
> Todd,
> The latest openmpi packaging in fink now contains the
> missing symlinks so that the renamed mpi compiler wrappers
> can be invoked directly. Yes, installing openmpi creates
> symlinks for the original names of the mpi compiler wrappers.
> Jack
>
> On Tue, Aug 18, 2009 at 09:08:55PM -0500, Todd Krause wrote:
> > Howdy Jack,
> >
> > Ah, okay; sorry, my bad. You're right: now when I execute make, but with
> > "mpicc" in the makefile rather than "om-mpicc", the program compiles.
> And I
> > get
> >
> > 08:53 PM btpro:Gadget2> which mpicc
> > /sw/bin/mpicc
> >
> > Before this wasn't the case: typing "which mpicc" returned
> > "/usr/bin/mpicc". Was this change brought about by installing
> > "openmpi-dev"? (I obviously don't know what that last package does; but
> > that was the only difference between this last time and the time earlier
> > today that I installed "openmpi".)
> >
> > ... well, now that I got the program to run by typing
> >
> > > om-mpirun -np 2 ./Gadget2 paramfile
> >
> > I think I'm more confused. Perhaps my earlier error was only at runtime,
> > trying to use "mpirun" (which had worked previously) rather than
> > "om-mpirun".
> >
> > So at this point, in principle, I could use "mpicc" indifferently, then,
> > say, type either "lam-mpirun" or "om-mpirun" later on to run a given
> > program?
> >
> > Thanks,
> > Todd
> >
> > On Tue, Aug 18, 2009 at 7:28 PM, Jack Howarth <[email protected]
> >wrote:
> >
> > > On Tue, Aug 18, 2009 at 06:24:46PM -0500, Todd Krause 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
> > > >
> > >
> > > Ah, your problem is that you are attempting to execute om-mpicc
> directly.
> > > The openmpi compiler is looking for a wrapper file based on its
> filename.
> > > Remember that the om- prefixed compilers were never intended to be used
> > > directly but through the symlinks installed by openmpi-dev. You can use
> > > the utilities like om-mpirun directly though without installing
> > > openmpi-dev.
> > > I would rather not add in symlinks for compiler wrappers under the om-
> > > names since I really don't want to support that usage. Most folks will
> > > likely use either lammpi or openmpi so just install the -dev of one
> > > and leave it in place.
> > > Jack
> > >
> > > > (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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