[Pkg-scicomp-devel] Bug#522287: Bug#522287: Bug#522287: [petsc] fail to execute code linked with petsc

Adam C Powell IV hazelsct at debian.org
Wed May 13 14:20:24 UTC 2009 

Oops.  Forgot to check pkg-scicomp svn *before* uploading.  Christophe,
I'll add your change as -3.  Sorry about that!

-Adam

On Wed, 2009-05-13 at 09:33 -0400, Adam C Powell IV wrote:
> tags 522287 -unreproducible
> thanks
> 
> Hmm, make testexamples is not working for me either now, so I'm going to
> disable the "dynamic" libraries.  I'll test in a few minutes, and upload
> sometime today with fixes for this and a bunch of other bugs.
> 
> -Adam
> 
> On Wed, 2009-05-13 at 08:50 -0400, Adam C Powell IV wrote:
> > I see.  This is very annoying.  I generally have to jump through a
> > couple of hoops to make this work with each new version, and thought I
> > had it working fine...
> > 
> > Can you try building/running the tests as described in README.Debian?
> > It's pretty easy, just install petsc3.0.0-doc, unpack src.tar.gz, cd to
> > it and "make testexamples".
> > 
> > If that works, maybe this is a C++ issue...
> > 
> > Thanks,
> > Adam
> > 
> > On Wed, 2009-05-13 at 10:32 +0200, Johannes Ring wrote:
> > > Hi,
> > > 
> > > I have the same problem as Christophe. I created a makefile for
> > > Christophe's simple code (t.cpp) by adapting one of the makefiles from the
> > > PETSc examples. My makefile looks like this:
> > > 
> > > include ${PETSC_DIR}/conf/base
> > > t: t.o  chkopts
> > >         -${CLINKER} -o t t.o ${PETSC_LIB}
> > >         ${RM} -f t.o
> > > 
> > > Compiling works fine:
> > > 
> > > $ PETSC_DIR=/usr/lib/petsc PETSC_ARCH=linux-gnu-c-opt make t
> > > mpicc -o t.o -c -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -O
> > > -I/usr/lib/petsc/linux-gnu-c-opt/include -I/usr/lib/petsc/include
> > > -I/usr/lib/openmpi/include -I/usr/lib/openmpi/lib -I/usr/include
> > > -I/usr/include/spooles -I/usr/include/superlu -I/usr/include/suitesparse
> > > -D__SDIR__="" t.cpp
> > > mpicc -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -O  -o t t.o
> > > -L/usr/lib/petsc/linux-gnu-c-opt/lib -L/usr/lib/petsc/linux-gnu-c-opt/lib
> > > -lpetscts -lpetscsnes -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetsc
> > >      -lX11 -L/usr/lib -lHYPRE -lmpi_cxx -lstdc++ -lspooles -lsuperlu
> > > -lumfpack -lamd -llapack -lblas -L/usr/lib/openmpi/lib
> > > -L/usr/lib/gcc/i486-linux-gnu/4.3.3 -L/lib -ldl -lmpi -lopen-rte
> > > -lopen-pal -lnsl -lutil -lgcc_s -lpthread -lmpi_f90 -lmpi_f77
> > > -lgfortranbegin -lgfortran -lm -lm -L/usr/lib/gcc/i486-linux-gnu -lm -lm
> > > -ldl -lmpi -lopen-rte -lopen-pal -lnsl -lutil -lgcc_s -lpthread -lmpi_f90
> > > -lmpi_f77 -lgfortranbegin -lgfortran -lm -lm -lm -lm
> > > -L/usr/lib/openmpi/lib -L/usr/lib/gcc/i486-linux-gnu/4.3.3 -L/lib -ldl
> > > -lmpi -lopen-rte -lopen-pal -lnsl -lutil -lgcc_s -lpthread -lmpi_f90
> > > -lmpi_f77 -lgfortranbegin -lgfortran -lm -lm -L/usr/lib/gcc/i486-linux-gnu
> > > -lm -lm -lmpi_cxx -lstdc++ -lmpi_cxx -lstdc++ -ldl -lmpi -lopen-rte
> > > -lopen-pal -lnsl -lutil -lgcc_s -lpthread -ldl
> > > /bin/rm -f -f t.o
> > > 
> > > Running the program produces this output:
> > > 
> > > $ ./t
> > > [0]PETSC ERROR: --------------------- Error Message
> > > ------------------------------------
> > > [0]PETSC ERROR: Unable to open file!
> > > [0]PETSC ERROR: Unable to locate PETSc dynamic library
> > >  You cannot move the dynamic libraries!!
> > > [0]PETSC ERROR:
> > > ------------------------------------------------------------------------
> > > [0]PETSC ERROR: Petsc Release Version 3.0.0, Patch 0, Fri Dec 19 22:02:38
> > > CST 2008
> > > [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> > > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> > > [0]PETSC ERROR: See docs/index.html for manual pages.
> > > [0]PETSC ERROR:
> > > ------------------------------------------------------------------------
> > > [0]PETSC ERROR: ./t on a linux-gnu named debian-vmware by johannr Wed May
> > > 13 11:15:48 2009
> > > [0]PETSC ERROR: Libraries linked from
> > > /build/buildd-petsc_3.0.0.dfsg-1-i386-lmxbUJ/petsc-3.0.0.dfsg/linux-gnu-c-opt/lib
> > > [0]PETSC ERROR: Configure run at Mon Mar 30 23:54:34 2009
> > > [0]PETSC ERROR: Configure options --with-shared --with-dynamic
> > > --with-debugging=0 --useThreads 0 --with-mpi-dir=/usr/lib/openmpi
> > > --with-mpi-shared=1 --with-blas-lib=-lblas --with-lapack-lib=-llapack
> > > --with-umfpack=1 --with-umfpack-include=/usr/include/suitesparse
> > > --with-umfpack-lib="[/usr/lib/libumfpack.so,/usr/lib/libamd.so]"
> > > --with-superlu=1 --with-superlu-include=/usr/include/superlu
> > > --with-superlu-lib=/usr/lib/libsuperlu.so --with-spooles=1
> > > --with-spooles-include=/usr/include/spooles
> > > --with-spooles-lib=/usr/lib/libspooles.so --with-hypre=1
> > > --with-hypre-dir=/usr
> > > [0]PETSC ERROR:
> > > ------------------------------------------------------------------------
> > > [0]PETSC ERROR: PetscInitialize_DynamicLibraries() line 97 in
> > > src/sys/dll/reg.c
> > > [0]PETSC ERROR: PetscInitialize() line 581 in src/sys/objects/pinit.c
> > > 
> > > 
> > > Best regards,
> > > 
> > > Johannes
> > > 
> > > On Tue, May 12, 2009 21:02, Christophe Prud'homme wrote:
> > > > Hi Adam
> > > >
> > > > thanks for the heads up :)
> > > >
> > > > until 3.0 I never had to set PETSC_DIR  and PETSC_ARCH, it was working
> > > > out of the box.
> > > > The other problem is that it affects slepc too.
> > > > What I do at the moment is use 2.3.3 which works without problems, I
> > > > just had to recompile with the newest openmpi
> > > >
> > > > I will look again into this, I am pretty sure I went down the road of
> > > > setting these PETSC variables, I will do that again.
> > > >
> > > > Best regards
> > > > C.
> > > >
> > > > On Tue, May 12, 2009 at 2:27 PM, Adam C Powell IV <hazelsct at debian.org>
> > > > wrote:
> > > >> severity 522287 important
> > > >> tags 522287 unreproducible
> > > >> thanks
> > > >>
> > > >> Hi Christophe,
> > > >>
> > > >> Sorry about the delay, I'm accustomed to getting bugs via email, and
> > > >> only just subscribed to the PTS.
> > > >>
> > > >> I'm afraid I can't reproduce this.  Did you set PETSC_DIR and PETSC_ARCH
> > > >> as described in README.Debian?  I'm afraid PETSc is picky about this.
> > > >>
> > > >> Can you test it as described in README.Debian, by unpacking src.tar.gz
> > > >> test files in the -doc package?
> > > >>
> > > >> Thanks,
> > > >> -Adam
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