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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