From: John P. <pet...@cf...> - 2007-07-02 19:40:53
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Have you been able to install 2.3.3 anywhere besides your /home dir? I tried to play along with their game: the configure script detects if you are root and doesn't let you continue... so I build it in my home directory and tried 'make install' as root. Only problem is 'make install' is horribly broken. It doesn't copy over any of the external packages and it doesn't change the petscconf make vars over from the build dir to the install dir. I resorted to commenting out the checks for root from the python code and Makefiles (yay open source!) so I could just build and install the damn thing in the same place. -J Derek Gaston writes: > On 7/2/07, John Peterson <pet...@cf...> wrote: > > The only other option would be to build mpich outside petsc again -- > > this is the approach we have used in the past. > > This is what I currently do... build mpich myself and then build > petsc, specifying the --mpi-dir or --mpi-libs and --mpi-include > options (depending on the machine). > > It seems to work just fine for me. > > Derek > > > > > > > > > > > > > Derek Gaston writes: > > > Are there tangible advantages of 2.3.3? I'm doing a lot of runs right > > > now... and if there is some huge speedup offered then it might be > > > worth the pain to upgrade Petsc.... > > > > > > Derek > > > > > > On 7/2/07, John Peterson <pet...@cf...> wrote: > > > > Roy, > > > > > > > > I can confirm that your changes work (i.e. compile) with my copy of > > > > Petsc 2.3.3 at home. I'm still working out the installation for the > > > > CFDLab...it seems the easiest way may be to have petsc download > > > > mpich and the blas itself using PETSc's configure options. Any > > > > objections to doing this in the cfdlab? > > > > > > > > -John > > > > > > > > > > > > Roy Stogner writes: > > > > > On Mon, 2 Jul 2007, Tahar Amari wrote: > > > > > > > > > > > I tried with your new files > > > > > > > > > > > > ./configure --enable-laspack --enable-petsc --disable-shared > > > > > > --with-mpi-dir=/usr/local/mpich > > > > > > --with-blas-lapack=/Library/Frameworks/Intel_MKL.framework/Versions/9.0/lib/32/ > > > > > > --enable-mpi > > > > > > > > > > > > and then make > > > > > > and then I got the error > > > > > > > > > > > > src/numerics/petsc_vector.C:30:22: error: parallel.h: No such file or > > > > > > directory > > > > > > > > > > I was afraid of that; there are too many changes in CVS to just copy a > > > > > file or two back to 0.6.0. You'll need to download the whole CVS > > > > > libMesh. > > > > > --- > > > > > Roy > > |
From: Derek G. <fri...@gm...> - 2007-07-02 19:48:00
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I've never done "make install" with petsc. In their documentation it tells you to copy the source directory to where you want to install it and run ./configure and then "make all test" and that's it. What I do is something like this: tar -zxvf petsc-whatever mv petsc-whatever /home/drgasto/roots/x86_64/local/petsc cd /home/drgasto/roots/x86_64/local/petsc ./configure --with-options export PETSC_DIR=/home/drgasto/roots/x86_64/local/petsc export PETSC_ARCH=linux-gnu-opt (both of those exports it tells you at the end of configure) make all make test (I like to do these seperately) Now petsc is "installed" in /home/drgasto/roots/x86_64/local/petsc there is no need to do a "make install".... But maybe I'm misunderstanding you. Derek On 7/2/07, John Peterson <pet...@cf...> wrote: > Have you been able to install 2.3.3 anywhere besides your /home dir? > > I tried to play along with their game: the configure script detects > if you are root and doesn't let you continue... so I build it in > my home directory and tried 'make install' as root. Only problem > is 'make install' is horribly broken. It doesn't copy over any > of the external packages and it doesn't change the petscconf make > vars over from the build dir to the install dir. > > I resorted to commenting out the checks for root from the python > code and Makefiles (yay open source!) so I could just build and > install the damn thing in the same place. > > -J > > Derek Gaston writes: > > On 7/2/07, John Peterson <pet...@cf...> wrote: > > > The only other option would be to build mpich outside petsc again -- > > > this is the approach we have used in the past. > > > > This is what I currently do... build mpich myself and then build > > petsc, specifying the --mpi-dir or --mpi-libs and --mpi-include > > options (depending on the machine). > > > > It seems to work just fine for me. > > > > Derek > > > > > > > > > > > > > > > > > > > > > > Derek Gaston writes: > > > > Are there tangible advantages of 2.3.3? I'm doing a lot of runs right > > > > now... and if there is some huge speedup offered then it might be > > > > worth the pain to upgrade Petsc.... > > > > > > > > Derek > > > > > > > > On 7/2/07, John Peterson <pet...@cf...> wrote: > > > > > Roy, > > > > > > > > > > I can confirm that your changes work (i.e. compile) with my copy of > > > > > Petsc 2.3.3 at home. I'm still working out the installation for the > > > > > CFDLab...it seems the easiest way may be to have petsc download > > > > > mpich and the blas itself using PETSc's configure options. Any > > > > > objections to doing this in the cfdlab? > > > > > > > > > > -John > > > > > > > > > > > > > > > Roy Stogner writes: > > > > > > On Mon, 2 Jul 2007, Tahar Amari wrote: > > > > > > > > > > > > > I tried with your new files > > > > > > > > > > > > > > ./configure --enable-laspack --enable-petsc --disable-shared > > > > > > > --with-mpi-dir=/usr/local/mpich > > > > > > > --with-blas-lapack=/Library/Frameworks/Intel_MKL.framework/Versions/9.0/lib/32/ > > > > > > > --enable-mpi > > > > > > > > > > > > > > and then make > > > > > > > and then I got the error > > > > > > > > > > > > > > src/numerics/petsc_vector.C:30:22: error: parallel.h: No such file or > > > > > > > directory > > > > > > > > > > > > I was afraid of that; there are too many changes in CVS to just copy a > > > > > > file or two back to 0.6.0. You'll need to download the whole CVS > > > > > > libMesh. > > > > > > --- > > > > > > Roy > > > > |
From: John P. <pet...@cf...> - 2007-07-02 19:57:09
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Derek Gaston writes: > I've never done "make install" with petsc. In their documentation it > tells you to copy the source directory to where you want to install it > and run ./configure and then "make all test" and that's it. > > What I do is something like this: > tar -zxvf petsc-whatever > mv petsc-whatever /home/drgasto/roots/x86_64/local/petsc > cd /home/drgasto/roots/x86_64/local/petsc > ./configure --with-options > export PETSC_DIR=/home/drgasto/roots/x86_64/local/petsc > export PETSC_ARCH=linux-gnu-opt > (both of those exports it tells you at the end of configure) > make all > make test (I like to do these seperately) > > Now petsc is "installed" in /home/drgasto/roots/x86_64/local/petsc > there is no need to do a "make install".... > > But maybe I'm misunderstanding you. Right, but if you want to install for the CFDLab, you need to do the same process above in /usr/local or /cfdlab/Petsc, or whatever, and you need to be root. Unfortunately, the 2.3.3 scripts exit if they detect that you are root: they want you to compile in your home dir and then 'make install' as root. I have no problem with that approach, as long as make install actually generates a usable install :) -J |
From: Tahar A. <am...@cp...> - 2007-07-02 19:53:27
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Roy, I followed your suggestion dowload the cvs version configure with sudo ./configure --enable-laspack --enable-petsc --disable-shared --=20 with-mpi-dir=3D/usr/local/mpich --with-blas-lapack=3D/Library/Frameworks/=20= Intel_MKL.framework/Versions/9.0/lib/32/ --enable-mpi The library was succesfully built However I did make run_examples and got the error [Imac-Intel-de-Tahar-Amari:/usr/local/libmesh] amari% sudo make =20 run_examples Password: Compiling C++ (in optimized mode) ex0.C... g++ -DNDEBUG -O2 -felide-constructors -funroll-loops -fstrict-=20 aliasing -Wdisabled-optimization /Library/Frameworks/=20 Intel_MKL.framework/Headers -I/usr/local/libmesh/include/base -I/usr/=20 local/libmesh/include/enums -I/usr/local/libmesh/include/fe -I/usr/=20 local/libmesh/include/geom -I/usr/local/libmesh/include/mesh -I/usr/=20 local/libmesh/include/numerics -I/usr/local/libmesh/include/=20 partitioning -I/usr/local/libmesh/include/quadrature -I/usr/local/=20 libmesh/include/solvers -I/usr/local/libmesh/include/utils -I/usr/=20 local/libmesh/contrib/boost -I/usr/local/libmesh/contrib/laspack -I/=20 usr/local/libmesh/contrib/parmetis/Lib -I/usr/local/libmesh/contrib/=20 metis/Lib -I/usr/local/libmesh/contrib/sfcurves -I/usr/local/libmesh/=20 contrib/gzstream -I/usr/local/libmesh/contrib/gmv -I/usr/local/=20 libmesh/contrib/tetgen -I/usr/local/libmesh/contrib/triangle -I/usr/=20 local/petsc/include -I/usr/local/petsc/bmake/macx -I/usr/local/=20 mpich/include -I/usr/local/libmesh/include/base -I/usr/local/=20 libmesh/include/enums -I/usr/local/libmesh/include/fe -I/usr/local/=20 libmesh/include/geom -I/usr/local/libmesh/include/mesh -I/usr/local/=20 libmesh/include/numerics -I/usr/local/libmesh/include/partitioning -I/=20= usr/local/libmesh/include/quadrature -I/usr/local/libmesh/include/=20 solvers -I/usr/local/libmesh/include/utils -I/usr/local/libmesh/=20 contrib/boost -I/usr/local/libmesh/contrib/laspack -I/usr/local/=20 libmesh/contrib/parmetis/Lib -I/usr/local/libmesh/contrib/metis/Lib -=20 I/usr/local/libmesh/contrib/sfcurves -I/usr/local/libmesh/contrib/=20 gzstream -I/usr/local/libmesh/contrib/gmv -I/usr/local/libmesh/=20 contrib/tetgen -I/usr/local/libmesh/contrib/triangle -I/usr/local/=20 petsc/include -I/usr/local/petsc/bmake/macx -I/usr/local/mpich/=20 include -c ex0.C -o ex0.i686-apple-darwin8.10.1.opt.o i686-apple-darwin8-g++-4.0.1: /Library/Frameworks/Intel_MKL.framework/=20= Headers: linker input file unused because linking not done Linking ex0-opt... /usr/bin/ld: Undefined symbols: _MPI_Wtime _MPI_Alltoall collect2: ld returned 1 exit status make[2]: *** [ex0-opt] Error 1 make[1]: *** [run] Error 1 make: *** [run_examples] Error 2 I looked at Make.common and got for MPI # (only explicitly defined when PETSc is absent, otherwise snooped =20 from PETSc) MPI_IMPL =3D petsc_snooped MPI_INCLUDE =3D MPI_LIB =3D Is there something wrong somewhere else please ? Many thanks Tahar -------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 47 53 fax: 33 1 69 33 30 08 email: <mailto:am...@cp...> URL : http://www.cpht.polytechnique.fr/cpht/amari Le 2 juil. 07 =E0 20:00, Roy Stogner a =E9crit : > On Mon, 2 Jul 2007, Tahar Amari wrote: > >> I tried with your new files >> >> ./configure --enable-laspack --enable-petsc --disable-shared --=20 >> with-mpi-dir=3D/usr/local/mpich --with-blas-lapack=3D/Library/=20 >> Frameworks/Intel_MKL.framework/Versions/9.0/lib/32/ --enable-mpi >> >> and then make >> and then I got the error >> >> src/numerics/petsc_vector.C:30:22: error: parallel.h: No such file =20= >> or directory > > I was afraid of that; there are too many changes in CVS to just copy a > file or two back to 0.6.0. You'll need to download the whole CVS > libMesh. > --- > Roy |
From: John P. <pet...@cf...> - 2007-07-02 20:01:20
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Tahar Amari writes: > Roy, > > I followed your suggestion > > dowload the cvs version > configure with > sudo ./configure --enable-laspack --enable-petsc --disable-shared -- > with-mpi-dir=/usr/local/mpich --with-blas-lapack=/Library/Frameworks/ > Intel_MKL.framework/Versions/9.0/lib/32/ --enable-mpi > > > The library was succesfully built > > However I did make run_examples and got the error > > I looked at Make.common and got for MPI > > # (only explicitly defined when PETSc is absent, otherwise snooped > from PETSc) > MPI_IMPL = petsc_snooped > MPI_INCLUDE = > MPI_LIB = The problem might be that PETSc is not correctly setting MPI_LIB and thus libmesh cannot snoop it. Check your $PETSC_DIR/bmake/$PETSC_ARCH/petscconf file. Is MPI_LIB undefined? You should see a line like MPI_LIB = where it is blank. If so, you could try adding it by hand, or compiling libmesh with the mpiCC compilers and see if that gets you the right link line. If you want to add it by hand, you have to do something like MPI_LIB = -Wl,-rpath,/path/to/mpi/lib -L /path/to/mpi/lib -lmpich -John |
From: Roy S. <roy...@ic...> - 2007-07-02 20:11:14
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On Mon, 2 Jul 2007, Tahar Amari wrote: > sudo ./configure --enable-laspack --enable-petsc --disable-shared > --with-mpi-dir=/usr/local/mpich Shouldn't that argument be "--with-mpi", not "--with-mpi-dir"? Check "./configure --help". It could be that libMesh is only falling back on trying to snoop PETSc's MPI variables because you haven't really told libMesh where to find MPI itself. > --with-blas-lapack=/Library/Frameworks/Intel_MKL.framework/Versions/9.0/lib/32/ I don't think our configure script accepts "--with-blas-lapack" at all; whatever linear algebra code your version of laspack and/or petsc was built with, that's what gets used. --- Roy |
From: Tahar A. <am...@cp...> - 2007-07-02 21:33:52
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Hi Roy, Thanks a lot for noticing this > > Shouldn't that argument be "--with-mpi", not "--with-mpi-dir"? Check > "./configure --help". It could be that libMesh is only falling back > on trying to snoop PETSc's MPI variables because you haven't really > told libMesh where to find MPI itself. > >> --with-blas-lapack=/Library/Frameworks/Intel_MKL.framework/ >> Versions/9.0/lib/32/ > > I don't think our configure script accepts "--with-blas-lapack" at > all; whatever linear algebra code your version of laspack and/or petsc > was built with, that's what gets used. > --- > Roy I did it removing what you suggested to remove. It built oK ./configure --enable-laspack --enable-petsc --disable-shared --with- mpi=/usr/local/mpich --enable-mpi but the example gave [Imac-Intel-de-Tahar-Amari:/usr/local/libmesh] amari% sudo make run_examples Compiling C++ (in optimized mode) ex0.C... g++ -DNDEBUG -O2 -felide-constructors -funroll-loops -fstrict- aliasing -Wdisabled-optimization /Library/Frameworks/ Intel_MKL.framework/Headers -I/usr/local/libmesh/include/base -I/usr/ local/libmesh/include/enums -I/usr/local/libmesh/include/fe -I/usr/ local/libmesh/include/geom -I/usr/local/libmesh/include/mesh -I/usr/ local/libmesh/include/numerics -I/usr/local/libmesh/include/ partitioning -I/usr/local/libmesh/include/quadrature -I/usr/local/ libmesh/include/solvers -I/usr/local/libmesh/include/utils -I/usr/ local/libmesh/contrib/boost -I/usr/local/libmesh/contrib/laspack -I/ usr/local/libmesh/contrib/parmetis/Lib -I/usr/local/libmesh/contrib/ metis/Lib -I/usr/local/libmesh/contrib/sfcurves -I/usr/local/libmesh/ contrib/gzstream -I/usr/local/libmesh/contrib/gmv -I/usr/local/ libmesh/contrib/tetgen -I/usr/local/libmesh/contrib/triangle -I/usr/ local/petsc/include -I/usr/local/petsc/bmake/macx -I/usr/local/ mpich/include -I/usr/local/libmesh/include/base -I/usr/local/ libmesh/include/enums -I/usr/local/libmesh/include/fe -I/usr/local/ libmesh/include/geom -I/usr/local/libmesh/include/mesh -I/usr/local/ libmesh/include/numerics -I/usr/local/libmesh/include/partitioning -I/ usr/local/libmesh/include/quadrature -I/usr/local/libmesh/include/ solvers -I/usr/local/libmesh/include/utils -I/usr/local/libmesh/ contrib/boost -I/usr/local/libmesh/contrib/laspack -I/usr/local/ libmesh/contrib/parmetis/Lib -I/usr/local/libmesh/contrib/metis/Lib - I/usr/local/libmesh/contrib/sfcurves -I/usr/local/libmesh/contrib/ gzstream -I/usr/local/libmesh/contrib/gmv -I/usr/local/libmesh/ contrib/tetgen -I/usr/local/libmesh/contrib/triangle -I/usr/local/ petsc/include -I/usr/local/petsc/bmake/macx -I/usr/local/mpich/ include -c ex0.C -o ex0.i686-apple-darwin8.10.1.opt.o i686-apple-darwin8-g++-4.0.1: /Library/Frameworks/Intel_MKL.framework/ Headers: linker input file unused because linking not done Linking ex0-opt... /usr/bin/ld: Undefined symbols: _MPI_Wtime _MPI_Alltoall collect2: ld returned 1 exit status make[2]: *** [ex0-opt] Error 1 make[1]: *** [run] Error 1 make: *** [run_examples] Error 2 So, what is wrong now please ? Tahar |
From: Tahar A. <am...@cp...> - 2007-07-02 21:37:17
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Hi John I opened the file > $PETSC_DIR/bmake/$PETSC_ARCH/petscconf and found MPI_LIB =3D -L/usr/local/mpich/lib -L/usr/local/mpich/lib -lfmpich -=20 lmpich -lpmpich -lmpich -lpmpich -lpmpich So , is what you thought really happening ? Tahar -------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 47 53 fax: 33 1 69 33 30 08 email: <mailto:am...@cp...> URL : http://www.cpht.polytechnique.fr/cpht/amari Le 2 juil. 07 =E0 22:01, John Peterson a =E9crit : > Tahar Amari writes: >> Roy, >> >> I followed your suggestion >> >> dowload the cvs version >> configure with >> sudo ./configure --enable-laspack --enable-petsc --disable-shared -- >> with-mpi-dir=3D/usr/local/mpich = --with-blas-lapack=3D/Library/Frameworks/ >> Intel_MKL.framework/Versions/9.0/lib/32/ --enable-mpi >> >> >> The library was succesfully built >> >> However I did make run_examples and got the error >> >> I looked at Make.common and got for MPI >> >> # (only explicitly defined when PETSc is absent, otherwise snooped >> from PETSc) >> MPI_IMPL =3D petsc_snooped >> MPI_INCLUDE =3D >> MPI_LIB =3D > > The problem might be that PETSc is not correctly setting MPI_LIB and > thus libmesh cannot snoop it. Check your $PETSC_DIR/bmake/=20 > $PETSC_ARCH/petscconf > file. Is MPI_LIB undefined? You should see a line like > > MPI_LIB =3D > > where it is blank. If so, you could try adding it by hand, or > compiling libmesh with the mpiCC compilers and see if that gets you > the right link line. If you want to add it by hand, you have to do > something like > > MPI_LIB =3D -Wl,-rpath,/path/to/mpi/lib -L /path/to/mpi/lib -lmpich > > -John > > |
From: John P. <pet...@cf...> - 2007-07-02 21:44:18
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Tahar Amari writes: > Hi John >=20 > I opened the file >=20 > > $PETSC=5FDIR/bmake/$PETSC=5FARCH/petscconf >=20 > and found >=20 > MPI=5FLIB =3D -L/usr/local/mpich/lib -L/usr/local/mpich/lib -lfmpich= -=20 > lmpich -lpmpich -lmpich -lpmpich -lpmpich >=20 >=20 > So , is what you thought really happening =3F Well, it's not blank as I had guessed, and it doesn't really look "wrong", just a little strange. The library names shouldn't be repeated multiple times like that. And note that if you are linking against shared (.so) libraries, "/usr/local/mpich/lib" must be in your LD=5FLIBRARY=5FPATH, or whatever the equivalent is on Mac OSX. -J > Tahar > -------------------------------------------- > T. Amari > Centre de Physique Theorique > Ecole Polytechnique > 91128 Palaiseau Cedex France > tel : 33 1 69 33 47 53 > fax: 33 1 69 33 30 08 > email: <mailto:am...@cp...> > URL : http://www.cpht.polytechnique.fr/cpht/amari >=20 > Le 2 juil. 07 =E0 22:01, John Peterson a =E9crit : >=20 > > Tahar Amari writes: > >> Roy, > >> > >> I followed your suggestion > >> > >> dowload the cvs version > >> configure with > >> sudo ./configure --enable-laspack --enable-petsc --disable-shared= -- > >> with-mpi-dir=3D/usr/local/mpich --with-blas-lapack=3D/Library/Fra= meworks/ > >> Intel=5FMKL.framework/Versions/9.0/lib/32/ --enable-mpi > >> > >> > >> The library was succesfully built > >> > >> However I did make run=5Fexamples and got the error > >> > >> I looked at Make.common and got for MPI > >> > >> # (only explicitly defined when PETSc is absent, otherwise snoope= d > >> from PETSc) > >> MPI=5FIMPL =3D petsc=5Fsnooped > >> MPI=5FINCLUDE =3D > >> MPI=5FLIB =3D > > > > The problem might be that PETSc is not correctly setting MPI=5FLIB= and > > thus libmesh cannot snoop it. Check your $PETSC=5FDIR/bmake/=20 > > $PETSC=5FARCH/petscconf > > file. Is MPI=5FLIB undefined=3F You should see a line like > > > > MPI=5FLIB =3D > > > > where it is blank. If so, you could try adding it by hand, or > > compiling libmesh with the mpiCC compilers and see if that gets yo= u > > the right link line. If you want to add it by hand, you have to d= o > > something like > > > > MPI=5FLIB =3D -Wl,-rpath,/path/to/mpi/lib -L /path/to/mpi/lib -lmp= ich > > > > -John > > > > >=20 |
From: Roy S. <roy...@ic...> - 2007-07-02 22:07:03
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On Mon, 2 Jul 2007, John Peterson wrote: > Tahar Amari writes: > > Hi John > > > > I opened the file > > > > > $PETSC_DIR/bmake/$PETSC_ARCH/petscconf > > > > and found > > > > MPI_LIB = -L/usr/local/mpich/lib -L/usr/local/mpich/lib -lfmpich - > > lmpich -lpmpich -lmpich -lpmpich -lpmpich > > > > So , is what you thought really happening ? > > Well, it's not blank as I had guessed, and it doesn't really look > "wrong", just a little strange. The library names shouldn't be > repeated multiple times like that. And note that if you are > linking against shared (.so) libraries, "/usr/local/mpich/lib" > must be in your LD_LIBRARY_PATH, or whatever the equivalent is > on Mac OSX. But the MPI_LIB variable in PETSc still isn't being used correctly by libMesh, right? The MPI_LIB and MPI_INCLUDE variables in Make.common are blank? First try copying the PETSc versions of those variables and see what happens. The multiple library names are PETSc's problem, and won't hurt anything. And with --disable-shared the library path isn't a problem. Let's first see if hand-setting the MPI variables in Make.common fixes things, and if so then we can try and figure out why they aren't being autodetected by either snooping PETSc or by manually setting an MPI directory. --- Roy |
From: Tahar A. <am...@cp...> - 2007-07-02 22:39:31
|
Hi Roy, I followed your suggestion I changed Make.common and put by hand # MPI configuration # (only explicitly defined when PETSc is absent, otherwise snooped =20 from PETSc) MPI_IMPL =3D petsc_snooped MPI_INCLUDE =3D $(MPICHINC) MPI_LIB =3D $(MPICHLIB) (where the environment variables are picked from my .cshrc) The example seems link with mpi (for me mpich) but have now a =20 different problem : [Imac-Intel-de-Tahar-Amari:/usr/local/libmesh] amari% sudo make =20 run_examples Password: Compiling C++ (in optimized mode) ex0.C... g++ -DNDEBUG -O2 -felide-constructors -funroll-loops -fstrict-=20 aliasing -Wdisabled-optimization /Library/Frameworks/=20 Intel_MKL.framework/Headers -I/usr/local/libmesh/include/base -I/usr/=20 local/libmesh/include/enums -I/usr/local/libmesh/include/fe -I/usr/=20 local/libmesh/include/geom -I/usr/local/libmesh/include/mesh -I/usr/=20 local/libmesh/include/numerics -I/usr/local/libmesh/include/=20 partitioning -I/usr/local/libmesh/include/quadrature -I/usr/local/=20 libmesh/include/solvers -I/usr/local/libmesh/include/utils -I/usr/=20 local/libmesh/contrib/boost -I/usr/local/libmesh/contrib/laspack -I/=20 usr/local/libmesh/contrib/parmetis/Lib -I/usr/local/libmesh/contrib/=20 metis/Lib -I/usr/local/libmesh/contrib/sfcurves -I/usr/local/libmesh/=20 contrib/gzstream -I/usr/local/libmesh/contrib/gmv -I/usr/local/=20 libmesh/contrib/tetgen -I/usr/local/libmesh/contrib/triangle -I/usr/=20 local/petsc/include -I/usr/local/petsc/bmake/macx -I/usr/local/=20 mpich/include -I/usr/local/libmesh/include/base -I/usr/local/=20 libmesh/include/enums -I/usr/local/libmesh/include/fe -I/usr/local/=20 libmesh/include/geom -I/usr/local/libmesh/include/mesh -I/usr/local/=20 libmesh/include/numerics -I/usr/local/libmesh/include/partitioning -I/=20= usr/local/libmesh/include/quadrature -I/usr/local/libmesh/include/=20 solvers -I/usr/local/libmesh/include/utils -I/usr/local/libmesh/=20 contrib/boost -I/usr/local/libmesh/contrib/laspack -I/usr/local/=20 libmesh/contrib/parmetis/Lib -I/usr/local/libmesh/contrib/metis/Lib -=20 I/usr/local/libmesh/contrib/sfcurves -I/usr/local/libmesh/contrib/=20 gzstream -I/usr/local/libmesh/contrib/gmv -I/usr/local/libmesh/=20 contrib/tetgen -I/usr/local/libmesh/contrib/triangle -I/usr/local/=20 petsc/include -I/usr/local/petsc/bmake/macx -I/usr/local/mpich/=20 include -c ex0.C -o ex0.i686-apple-darwin8.10.1.opt.o i686-apple-darwin8-g++-4.0.1: /Library/Frameworks/Intel_MKL.framework/=20= Headers: linker input file unused because linking not done Linking ex0-opt... g++ -DNDEBUG -O2 -felide-constructors -funroll-loops -fstrict-=20 aliasing -Wdisabled-optimization ex0.i686-apple-darwin8.10.1.opt.o -=20 o ex0-opt /usr/local/libmesh/lib/i686-apple-darwin8.10.1_opt/=20 libmesh.a -L/usr/local/petsc/lib/macx -lpetscsnes -lpetscksp -=20 lpetscdm -lpetscmat -lpetscvec -lpetscsnes -lpetsc -L/usr/local/mpich/=20= lib -L/usr/local/mpich/lib -lfmpich -lmpich -lpmpich -lmpich -lpmpich =20= -lpmpich -L/Library/Frameworks/Intel_MKL.framework/Libraries/32 -L/=20 Library/Frameworks/Intel_MKL.framework/Libraries/32 -lmkl_lapack -=20 lmkl_ia32 -lguide -lz -L/usr/local/libmesh/contrib/lib/i686-apple-=20 darwin8.10.1_opt -lgzstream -llaspack -lmetis -lparmetis -lsfcurves -=20 ltetgen -ltriangle -lgmv -lz -L/usr/local/mpich/lib -lmpich -=20 lmpichcxx -lpmpich -lfmpich -lmpichf90 *************************************************************** * Running Example ./ex0-opt *************************************************************** dyld: Library not loaded: libguide.dylib Referenced from: /usr/local/libmesh/examples/ex0/./ex0-opt Reason: image not found make[2]: *** [run] Trace/BPT trap make[1]: *** [run] Error 1 make: *** [run_examples] Error 2 I guess "lguide" is a library for Shared memory management on Mac ? =20 is it right ? Thanks a lot for your help Tahar -------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 47 53 fax: 33 1 69 33 30 08 email: <mailto:am...@cp...> URL : http://www.cpht.polytechnique.fr/cpht/amari Le 3 juil. 07 =E0 00:06, Roy Stogner a =E9crit : > On Mon, 2 Jul 2007, John Peterson wrote: > >> Tahar Amari writes: >> > Hi John >> > >> > I opened the file >> > >> > > $PETSC_DIR/bmake/$PETSC_ARCH/petscconf >> > >> > and found >> > >> > MPI_LIB =3D -L/usr/local/mpich/lib -L/usr/local/mpich/lib -lfmpich = - >> > lmpich -lpmpich -lmpich -lpmpich -lpmpich >> > >> > So , is what you thought really happening ? >> >> Well, it's not blank as I had guessed, and it doesn't really look >> "wrong", just a little strange. The library names shouldn't be >> repeated multiple times like that. And note that if you are >> linking against shared (.so) libraries, "/usr/local/mpich/lib" >> must be in your LD_LIBRARY_PATH, or whatever the equivalent is >> on Mac OSX. > > But the MPI_LIB variable in PETSc still isn't being used correctly by > libMesh, right? The MPI_LIB and MPI_INCLUDE variables in Make.common > are blank? First try copying the PETSc versions of those variables > and see what happens. > > The multiple library names are PETSc's problem, and won't hurt > anything. And with --disable-shared the library path isn't a problem. > Let's first see if hand-setting the MPI variables in Make.common fixes > things, and if so then we can try and figure out why they aren't being > autodetected by either snooping PETSc or by manually setting an MPI > directory. > --- > Roy |
From: Roy S. <roy...@ic...> - 2007-07-02 23:10:01
|
On Tue, 3 Jul 2007, Tahar Amari wrote: > The example seems link with mpi (for me mpich) but have now a different > problem : > > Linking ex0-opt... > g++ -DNDEBUG -O2 -felide-constructors -funroll-loops -fstrict-aliasing > -Wdisabled-optimization ex0.i686-apple-darwin8.10.1.opt.o -o ex0-opt > /usr/local/libmesh/lib/i686-apple-darwin8.10.1_opt/libmesh.a > -L/usr/local/petsc/lib/macx -lpetscsnes -lpetscksp -lpetscdm -lpetscmat > -lpetscvec -lpetscsnes -lpetsc -L/usr/local/mpich/lib -L/usr/local/mpich/lib > -lfmpich -lmpich -lpmpich -lmpich -lpmpich -lpmpich > -L/Library/Frameworks/Intel_MKL.framework/Libraries/32 > -L/Library/Frameworks/Intel_MKL.framework/Libraries/32 -lmkl_lapack > -lmkl_ia32 -lguide -lz > -L/usr/local/libmesh/contrib/lib/i686-apple-darwin8.10.1_opt -lgzstream > -llaspack -lmetis -lparmetis -lsfcurves -ltetgen -ltriangle -lgmv -lz > -L/usr/local/mpich/lib -lmpich -lmpichcxx -lpmpich -lfmpich -lmpichf90 > *************************************************************** > * Running Example ./ex0-opt > *************************************************************** > dyld: Library not loaded: libguide.dylib > Referenced from: /usr/local/libmesh/examples/ex0/./ex0-opt > Reason: image not found > make[2]: *** [run] Trace/BPT trap > make[1]: *** [run] Error 1 > make: *** [run_examples] Error 2 > > > > I guess "lguide" is a library for Shared memory management on Mac ? is it > right ? I don't know what it is, but it's got to be Mac specific, because there's no libguide on my system. "dyld" sounds like it's the Mac dynamic linker, but I'm not sure why your system would be trying to use dynamically linked libraries after you've configured with --disable-shared. Perhaps you need to configure MPICH and PETSc to use static libraries as well? --- Roy |
From: Tahar A. <am...@cp...> - 2007-07-03 09:32:17
|
Hello, Because of libguide.dylib problem that I cannot solve right now, I decided to try to buiild libmesh in serial. sudo ./configure --enable-laspack --disable-petsc --disable-shared --=20 disable-parmetis --disable-mpi It builds but then when I build the examples I get [Imac-Intel-de-Tahar-Amari:/usr/local/libmesh] amari% sudo make =20 run_examples Password: Compiling C++ (in optimized mode) ex0.C... i686-apple-darwin8-g++-4.0.1: /Library/Frameworks/Intel_MKL.framework/=20= Headers: linker input file unused because linking not done Linking ex0-opt... g++ -DNDEBUG -O2 -felide-constructors -funroll-loops -fstrict-=20 aliasing -Wdisabled-optimization ex0.i686-apple-darwin8.10.1.opt.o -=20 o ex0-opt /usr/local/libmesh/lib/i686-apple-darwin8.10.1_opt/=20 libmesh.a -L/usr/local/libmesh/contrib/lib/i686-apple-=20 darwin8.10.1_opt -lgzstream -llaspack -lmetis -lsfcurves -ltetgen -=20 ltriangle -lgmv -lz *************************************************************** * Running Example ./ex0-opt *************************************************************** *************************************************************** * Done Running Example ./ex0-opt *************************************************************** Compiling C++ (in optimized mode) ex1.C... i686-apple-darwin8-g++-4.0.1: /Library/Frameworks/Intel_MKL.framework/=20= Headers: linker input file unused because linking not done Linking ex1-opt... g++ -DNDEBUG -O2 -felide-constructors -funroll-loops -fstrict-=20 aliasing -Wdisabled-optimization ex1.i686-apple-darwin8.10.1.opt.o -=20 o ex1-opt /usr/local/libmesh/lib/i686-apple-darwin8.10.1_opt/=20 libmesh.a -L/usr/local/libmesh/contrib/lib/i686-apple-=20 darwin8.10.1_opt -lgzstream -llaspack -lmetis -lsfcurves -ltetgen -=20 ltriangle -lgmv -lz *************************************************************** * Running Example ./ex1-opt -d 3 ../../reference_elements/3D/=20 one_hex27.xda *************************************************************** Mesh Information: mesh_dimension()=3D3 spatial_dimension()=3D3 n_nodes()=3D27 n_elem()=3D1 n_local_elem()=3D1 n_active_elem()=3D1 n_subdomains()=3D1 n_processors()=3D1 processor_id()=3D0 *************************************************************** * Done Running Example ./ex1-opt -d 3 ../../reference_elements/3D/=20 one_hex27.xda *************************************************************** Compiling C++ (in optimized mode) ex2.C... i686-apple-darwin8-g++-4.0.1: /Library/Frameworks/Intel_MKL.framework/=20= Headers: linker input file unused because linking not done Linking ex2-opt... /usr/bin/ld: Undefined symbols: _gzclose _gzopen _gzread _gzseek _gzwrite collect2: ld returned 1 exit status make[2]: *** [ex2-opt] Error 1 make[1]: *** [run] Error 1 make: *** [run_examples] Error 2 I do not have any idea where now these symbols might come from ? Many thanks for help Tahar -------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 47 53 fax: 33 1 69 33 30 08 email: <mailto:am...@cp...> URL : http://www.cpht.polytechnique.fr/cpht/amari Le 3 juil. 07 =E0 01:11, John Peterson a =E9crit : > Tahar Amari writes: >> Hi Roy, >> >> I followed your suggestion >> >> >> I changed Make.common and put by hand >> >> >> # MPI configuration >> # (only explicitly defined when PETSc is absent, otherwise snooped >> from PETSc) >> MPI_IMPL =3D petsc_snooped >> MPI_INCLUDE =3D $(MPICHINC) >> MPI_LIB =3D $(MPICHLIB) >> >> >> (where the environment variables are picked from my .cshrc) >> >> The example seems link with mpi (for me mpich) but have now a >> different problem : >> *************************************************************** >> * Running Example ./ex0-opt >> *************************************************************** >> dyld: Library not loaded: libguide.dylib >> Referenced from: /usr/local/libmesh/examples/ex0/./ex0-opt >> Reason: image not found >> make[2]: *** [run] Trace/BPT trap >> make[1]: *** [run] Error 1 >> make: *** [run_examples] Error 2 >> >> >> >> I guess "lguide" is a library for Shared memory management on Mac ? >> is it right ? > > I don't think so. libguide is distributed with the Intel MKL on my > system, but I don't know exactly what it's used for. > > -J |
From: Tahar A. <am...@cp...> - 2007-07-03 15:30:23
|
Hello John, I went to the directory of ex2 and modified the Makefile adding -lz to the link. IIt works. What do you think of the strategy ? Does it mean that the library built setting is OK and I just have to modify the makefiles of my codes to make them work in case I need some precise library ? Regarding petsc. As I told you I have not been able to make it work with libmesh. the libguide.dyld problem was not solved Either I do not use MKL on mac and then I have some other libraries =20 missing with laspack download for libmesh Or I use MKL but I do not have a precise way to tell the compiler to =20 use only the static libraries libguide.dyld is in a directory with the the static libraries and =20 pestsc onllly ask for either one blas-lapack-dir or one blas-lapack-lib . I would really enjoy making petsc work with libmesh ! Thanks a lot again Tahar -------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 47 53 fax: 33 1 69 33 30 08 email: <mailto:am...@cp...> URL : http://www.cpht.polytechnique.fr/cpht/amari Le 3 juil. 07 =E0 17:12, John Peterson a =E9crit : > Tahar Amari writes: >> Hello, >> >> Because of libguide.dylib problem that I cannot solve right now, >> I decided to try to buiild libmesh in serial. >> >> sudo ./configure --enable-laspack --disable-petsc --disable-shared -- >> disable-parmetis --disable-mpi >> >> It builds but then when I build the examples I get >> >> >> Compiling C++ (in optimized mode) ex2.C... >> i686-apple-darwin8-g++-4.0.1: /Library/Frameworks/=20 >> Intel_MKL.framework/ >> Headers: linker input file unused because linking not done >> Linking ex2-opt... >> /usr/bin/ld: Undefined symbols: >> _gzclose >> _gzopen >> _gzread >> _gzseek >> _gzwrite >> collect2: ld returned 1 exit status >> make[2]: *** [ex2-opt] Error 1 >> make[1]: *** [run] Error 1 >> make: *** [run_examples] Error 2 >> >> >> I do not have any idea where now these symbols might come from ? > > They come from libz.so, and are used for writing/reading compressed > streams. If ldd is available on your system, ldd ex2-opt will quickly > tell you what dynamically-linked libraries are not found. > > -J |
From: Derek G. <fri...@gm...> - 2007-07-03 15:45:55
|
Hey Tahar... you know you can load Linux on that Mac right? Might save you a lot of trouble ;-) After just going through some similar issues with getting libMesh to compile and run in parallel on a Sun Solaris machine... 1. If you find that you need to add libraries to the link line, edit Make.common in the root directory... and add them in there. If you do that, all of the examples use Make.common to build so you don't have to modify each individually. Also, any of your own programs can also import the info from Make.common and use the variables. 2. As for dynamic linking petsc... I had to build a _staticly_ linked version of Petsc before it would work on the Sun. I kept getting odd linking errors like yours. I still built Mpich with dynamic linking (and of course libmesh as well)... but I just built Petsc as static (look at ./configure --help for more info on how to do that). Good luck! Derek On 7/3/07, Tahar Amari <am...@cp...> wrote: > Hello John, > > I went to the directory of ex2 and modified the Makefile > adding -lz to the link. > IIt works. > > What do you think of the strategy ? > > Does it mean that the library built setting is OK and I just have to > modify the makefiles of my codes to make them work in case I need > some precise library ? > > > Regarding petsc. As I told you I have not been able to make it work with > libmesh. > > the libguide.dyld problem was not solved > > > > > Either I do not use MKL on mac and then I have some other libraries missi= ng > with laspack download > > for libmesh > > Or I use MKL but I do not have a precise way to tell the compiler to use > only the static libraries > > libguide.dyld is in a directory with the the static libraries and pestsc > onllly ask for either > > one blas-lapack-dir or one blas-lapack-lib . > > > > > I would really enjoy making petsc work with libmesh ! > > > > > Thanks a lot again > > > > > Tahar > > > > > > > > -------------------------------------------- > > T. Amari > > Centre de Physique Theorique > > Ecole Polytechnique > > 91128 Palaiseau Cedex France > > tel : 33 1 69 33 47 53 > > fax: 33 1 69 33 30 08 > > email: <mailto:am...@cp...> > > URL : http://www.cpht.polytechnique.fr/cpht/amari > > Le 3 juil. 07 =E0 17:12, John Peterson a =E9crit : > > Tahar Amari writes: > Hello, > > Because of libguide.dylib problem that I cannot solve right now, > I decided to try to buiild libmesh in serial. > > sudo ./configure --enable-laspack --disable-petsc --disable-shared -- > disable-parmetis --disable-mpi > > It builds but then when I build the examples I get > > > Compiling C++ (in optimized mode) ex2.C... > i686-apple-darwin8-g++-4.0.1: > /Library/Frameworks/Intel_MKL.framework/ > Headers: linker input file unused because linking not done > Linking ex2-opt... > /usr/bin/ld: Undefined symbols: > _gzclose > _gzopen > _gzread > _gzseek > _gzwrite > collect2: ld returned 1 exit status > make[2]: *** [ex2-opt] Error 1 > make[1]: *** [run] Error 1 > make: *** [run_examples] Error 2 > > > I do not have any idea where now these symbols might come from ? > > They come from libz.so, and are used for writing/reading compressed > streams. If ldd is available on your system, ldd ex2-opt will quickly > tell you what dynamically-linked libraries are not found. > > -J > > ------------------------------------------------------------------------- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > Libmesh-users mailing list > Lib...@li... > https://lists.sourceforge.net/lists/listinfo/libmesh-users > > |
From: Tahar A. <am...@cp...> - 2007-07-03 16:04:39
|
Hi Derek Thank you very much for those ideas. I actually like very much mac OS and we have developped so many applications on this OS which do not have problems, and you know how that it is not easy to change .... It is now about 6 years that I have installed mpich, lam, on my various macs and link with them with our codes. The same way it is about 4 years I am using petsc (with mpich) on several applications we have developped and this work well on the mac. I usually do not use high level libraries but we develop ours. Libmesh is the first high level library we want to use, SO I am sure =20= you understand that we would rather like to make it work on my mac OS and not change the OS. As I said in my first email, when we were not able to install libmesh on the mac (we first make it work on linux) we spent some time to rewrite all the libmesh fucntions we were actually using, =20 classes ... keeping the same names . Since we wanted to make some mesh refinement, some parallelization, =20 when I saw libmesh working with the libraries that I already use on our macs (mpich, petsc ....), I thought it will be worth to come back to libmesh which does a lot of nice and powerful things ! libmesh It is a very nice library, and I do not want to give up ! Tahar -------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 47 53 fax: 33 1 69 33 30 08 email: <mailto:am...@cp...> URL : http://www.cpht.polytechnique.fr/cpht/amari Le 3 juil. 07 =E0 17:45, Derek Gaston a =E9crit : > Hey Tahar... you know you can load Linux on that Mac right? Might > save you a lot of trouble ;-) > > After just going through some similar issues with getting libMesh to > compile and run in parallel on a Sun Solaris machine... > > 1. If you find that you need to add libraries to the link line, edit > Make.common in the root directory... and add them in there. If you do > that, all of the examples use Make.common to build so you don't have > to modify each individually. Also, any of your own programs can also > import the info from Make.common and use the variables. > > 2. As for dynamic linking petsc... I had to build a _staticly_ linked > version of Petsc before it would work on the Sun. I kept getting odd > linking errors like yours. I still built Mpich with dynamic linking > (and of course libmesh as well)... but I just built Petsc as static > (look at ./configure --help for more info on how to do that). > > Good luck! > Derek > > On 7/3/07, Tahar Amari <am...@cp...> wrote: >> Hello John, >> >> I went to the directory of ex2 and modified the Makefile >> adding -lz to the link. >> IIt works. >> >> What do you think of the strategy ? >> >> Does it mean that the library built setting is OK and I just have to >> modify the makefiles of my codes to make them work in case I need >> some precise library ? >> >> >> Regarding petsc. As I told you I have not been able to make it =20 >> work with >> libmesh. >> >> the libguide.dyld problem was not solved >> >> >> >> >> Either I do not use MKL on mac and then I have some other =20 >> libraries missing >> with laspack download >> >> for libmesh >> >> Or I use MKL but I do not have a precise way to tell the compiler =20 >> to use >> only the static libraries >> >> libguide.dyld is in a directory with the the static libraries and =20 >> pestsc >> onllly ask for either >> >> one blas-lapack-dir or one blas-lapack-lib . >> >> >> >> >> I would really enjoy making petsc work with libmesh ! >> >> >> >> >> Thanks a lot again >> >> >> >> >> Tahar >> >> >> >> >> >> >> >> -------------------------------------------- >> >> T. Amari >> >> Centre de Physique Theorique >> >> Ecole Polytechnique >> >> 91128 Palaiseau Cedex France >> >> tel : 33 1 69 33 47 53 >> >> fax: 33 1 69 33 30 08 >> >> email: <mailto:am...@cp...> >> >> URL : http://www.cpht.polytechnique.fr/cpht/amari >> >> Le 3 juil. 07 =E0 17:12, John Peterson a =E9crit : >> >> Tahar Amari writes: >> Hello, >> >> Because of libguide.dylib problem that I cannot solve right now, >> I decided to try to buiild libmesh in serial. >> >> sudo ./configure --enable-laspack --disable-petsc --disable-shared -- >> disable-parmetis --disable-mpi >> >> It builds but then when I build the examples I get >> >> >> Compiling C++ (in optimized mode) ex2.C... >> i686-apple-darwin8-g++-4.0.1: >> /Library/Frameworks/Intel_MKL.framework/ >> Headers: linker input file unused because linking not done >> Linking ex2-opt... >> /usr/bin/ld: Undefined symbols: >> _gzclose >> _gzopen >> _gzread >> _gzseek >> _gzwrite >> collect2: ld returned 1 exit status >> make[2]: *** [ex2-opt] Error 1 >> make[1]: *** [run] Error 1 >> make: *** [run_examples] Error 2 >> >> >> I do not have any idea where now these symbols might come from ? >> >> They come from libz.so, and are used for writing/reading compressed >> streams. If ldd is available on your system, ldd ex2-opt will =20 >> quickly >> tell you what dynamically-linked libraries are not found. >> >> -J >> >> ---------------------------------------------------------------------=20= >> ---- >> This SF.net email is sponsored by DB2 Express >> Download DB2 Express C - the FREE version of DB2 express and take >> control of your XML. No limits. Just data. Click to get it now. >> http://sourceforge.net/powerbar/db2/ >> _______________________________________________ >> Libmesh-users mailing list >> Lib...@li... >> https://lists.sourceforge.net/lists/listinfo/libmesh-users >> >> |
From: Tahar A. <am...@cp...> - 2007-07-04 14:00:55
|
Dear Colleagues, If anyone made progress on the front line of installing libmesh on mac-intel os x with petsc, mpich, ... Please let me know what are the correct intruction to do it. Best regards Tahar -------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 47 53 fax: 33 1 69 33 30 08 email: <mailto:am...@cp...> URL : http://www.cpht.polytechnique.fr/cpht/amari Le 3 juil. 07 =E0 01:11, John Peterson a =E9crit : > Tahar Amari writes: >> Hi Roy, >> >> I followed your suggestion >> >> >> I changed Make.common and put by hand >> >> >> # MPI configuration >> # (only explicitly defined when PETSc is absent, otherwise snooped >> from PETSc) >> MPI_IMPL =3D petsc_snooped >> MPI_INCLUDE =3D $(MPICHINC) >> MPI_LIB =3D $(MPICHLIB) >> >> >> (where the environment variables are picked from my .cshrc) >> >> The example seems link with mpi (for me mpich) but have now a >> different problem : >> *************************************************************** >> * Running Example ./ex0-opt >> *************************************************************** >> dyld: Library not loaded: libguide.dylib >> Referenced from: /usr/local/libmesh/examples/ex0/./ex0-opt >> Reason: image not found >> make[2]: *** [run] Trace/BPT trap >> make[1]: *** [run] Error 1 >> make: *** [run_examples] Error 2 >> >> >> >> I guess "lguide" is a library for Shared memory management on Mac ? >> is it right ? > > I don't think so. libguide is distributed with the Intel MKL on my > system, but I don't know exactly what it's used for. > > -J |
From: Tahar A. <am...@cp...> - 2007-07-02 15:48:14
|
The problem I have now with PETSc 2.3.2 is that unlike PETSc 2.3.3 =20 that I installed with option ./config/configure.py PETSC_ARCH=3Dmacx CC=3Dgcc FC=3Difort = --with-mpi-dir=3D/=20 usr/local/mpich --with-blas-lapack-dir=3D/Library/Frameworks/=20 Intel_MKL.framework/Libraries/32 --download-parmetis=3D1, it seems that PETSc 2.3.2 does not understand --download-parmetis=3D1 =20= since =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=20 =3D=3D=3D=3D=3D=3D=3D=3D=3D = =20 Configuring and =20 compiling ParMetis; this may take several =20 minutes =20= =20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=20 =3D=3D=3D=3D=3D=3D=3D=3D=3D = =20 SECTION: configure in =20 externalpackages/ParMetis from make(externalpackages/ParMetis/make.py:=20= 143) at Mon Jul 2 17:02:06 =20 2007 =20 Compilers: C Compiler: gcc -fPIC -Wall -Wwrite-strings -Wno-long-=20 double -Wno-strict-aliasing -g3 Fortran Compiler: ifort -fPIC -g Linkers: Shared linker: gcc -dynamiclib -single_module -undefined =20 dynamic_lookup -multiply_defined suppress -fPIC -Wall -Wwrite-=20 strings -Wno-long-double -Wno-strict-aliasing -g3 Dynamic linker: gcc -bundle -undefined dynamic_lookup -=20 multiply_defined suppress -fPIC -Wall -Wwrite-strings -Wno-long-=20 double -Wno-strict-aliasing -g3 MPI: Includes: ['/usr/local/mpich/include'] Library: ['/usr/local/mpich/lib/libfmpich.a', 'libmpich.a', =20 'libpmpich.a', 'libmpich.a', 'libpmpich.a', 'libpmpich.a'] SECTION: buildDynamicLibraries in externalpackages/ParMetis from make=20 (python/BuildSystem/maker.py:545) at Mon Jul 2 17:02:06 =20 2007 =20 ************************************************************************=20= ********* UNABLE to CONFIGURE with GIVEN OPTIONS (see =20 configure.log for details): ------------------------------------------------------------------------=20= --------------- Error running configure on ParMetis: /usr/bin/ld: can't locate file =20 for: -lmetis collect2: ld returned 1 exit status So may be I should wait for new version of libmesh compatible with =20 PETSc 2.3.3. When do you think this could be OK ? Many thanks Tahar -------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 47 53 fax: 33 1 69 33 30 08 email: <mailto:am...@cp...> URL : http://www.cpht.polytechnique.fr/cpht/amari Le 2 juil. 07 =E0 16:34, Roy Stogner a =E9crit : > On Mon, 2 Jul 2007, Tahar Amari wrote: > >> Do you mean that I have to install PETSc 2.3.2 on my system or can >> let libmesh installing it as optional package, but in this case how >> can I tell libmesh to install PETSc 2.3.2 ? Will it be default ? > > You'll have to install PETSc before configuring libMesh, and make sure > the PETSC_ARCH and PETSC_DIR variables correctly identify the 2.3.2 > version whenever you configure (and probably whenever you compile or > run) libMesh. > > We'll have PETSc 2.3.3 supported in the CVS version of libMesh > shortly, but I can't guess how long it will be before there's a stable > 0.6.1 libMesh release supporting it, and unless you're enjoying this > process of diagnosing and correcting strange compiler errors I don't > recommend you using the CVS libMesh. > --- > Roy |
From: Mike <mik...@gm...> - 2007-07-01 22:11:33
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Hi Tahar, I have susccesfully built libmesh a few months ago on Mac OS X 10.4 runing on a PPC G4 powerbook. It took me a couple of goes to figure out the correct config options, (but that was mostly for me to get infinite elements and complex numbers). I used Laspack instaed of Petsc and ignored all the parallel stuff. Mike On 01/07/07, Tahar Amari <am...@cp...> wrote: > Dear Colleagues, > > In 2004 I spent several days trying to build libmesh on mac os x for one of > our finite element project. > It was impossible . I sent several emails with no real help from your team. > We decided to code by ourself . > > 3 year afters, I have a mac intel, and seeing advertising from you about > "extreme portability" of libmesh, > I decided to try again building libmesh on mac os x 10.4.9 > > I tried almost all the ./connfigure --enable , disable combinaison, and the > make phase always died > with error. > > So I am surprised that there is even not a line on your web page, suggering > what are the options > build in 10 minutes your library. > > Why is this please ? > > Is there any one who happened to have build libmesh on mac os x ? > > So why keeping Mac OS on the list of targeted platform of libmesh please ? > > Many thanks for some hints > > Sincerely > > Tahar > > > > > -------------------------------------------- > > T. Amari > > Directeur de recherche au CNRS > > Centre de Physique Theorique > > Ecole Polytechnique > > 91128 Palaiseau Cedex France > > tel : 33 1 69 33 47 53 > > fax: 33 1 69 33 30 08 > > email: <mailto:am...@cp...> > > URL : http://www.cpht.polytechnique.fr/cpht/amari > > ------------------------------------------------------------------------- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > Libmesh-users mailing list > Lib...@li... > https://lists.sourceforge.net/lists/listinfo/libmesh-users > > -- Dr Mike Kidner Acoustics Vibration & Control Group School of Mechnical Engineering University of Adelaide |
From: Tahar A. <am...@cp...> - 2007-07-01 22:18:08
|
Hi Mike Many thanks for this reply. I actually tried what Ben suggested me which was to keep only Laspack to have the linear part working. But it seems it does not work still. Have you seen my reply about Ben suggestion ? Thank you very much again Tahar -------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 47 53 fax: 33 1 69 33 30 08 email: <mailto:am...@cp...> URL : http://www.cpht.polytechnique.fr/cpht/amari Le 2 juil. 07 =E0 00:11, Mike a =E9crit : > Hi Tahar, > I have susccesfully built libmesh a few months ago on Mac OS X 10.4 > runing on a PPC G4 powerbook. It took me a couple of goes to figure > out the correct config options, (but that was mostly for me to get > infinite elements and complex numbers). > > I used Laspack instaed of Petsc and ignored all the parallel stuff. > > Mike > > > > On 01/07/07, Tahar Amari <am...@cp...> wrote: >> Dear Colleagues, >> >> In 2004 I spent several days trying to build libmesh on mac os x =20 >> for one of >> our finite element project. >> It was impossible . I sent several emails with no real help from =20 >> your team. >> We decided to code by ourself . >> >> 3 year afters, I have a mac intel, and seeing advertising from you =20= >> about >> "extreme portability" of libmesh, >> I decided to try again building libmesh on mac os x 10.4.9 >> >> I tried almost all the ./connfigure --enable , disable =20 >> combinaison, and the >> make phase always died >> with error. >> >> So I am surprised that there is even not a line on your web page, =20 >> suggering >> what are the options >> build in 10 minutes your library. >> >> Why is this please ? >> >> Is there any one who happened to have build libmesh on mac os x ? >> >> So why keeping Mac OS on the list of targeted platform of libmesh =20 >> please ? >> >> Many thanks for some hints >> >> Sincerely >> >> Tahar >> >> >> >> >> -------------------------------------------- >> >> T. Amari >> >> Directeur de recherche au CNRS >> >> Centre de Physique Theorique >> >> Ecole Polytechnique >> >> 91128 Palaiseau Cedex France >> >> tel : 33 1 69 33 47 53 >> >> fax: 33 1 69 33 30 08 >> >> email: <mailto:am...@cp...> >> >> URL : http://www.cpht.polytechnique.fr/cpht/amari >> >> ---------------------------------------------------------------------=20= >> ---- >> This SF.net email is sponsored by DB2 Express >> Download DB2 Express C - the FREE version of DB2 express and take >> control of your XML. No limits. Just data. Click to get it now. >> http://sourceforge.net/powerbar/db2/ >> _______________________________________________ >> Libmesh-users mailing list >> Lib...@li... >> https://lists.sourceforge.net/lists/listinfo/libmesh-users >> >> > > > --=20 > Dr Mike Kidner > Acoustics Vibration & Control Group > School of Mechnical Engineering > University of Adelaide |
From: Mike <mik...@gm...> - 2007-07-01 22:32:53
Attachments:
config.log
|
Hi Tahar, I saw the reply , but I don't know enough to understand it! Attached is my config.log, maybe if you try these options you'll get something that will build. Otherwise it may be something to do with 10.3. I used libmesh-0.6.0-rc2 Cheers Mike On 02/07/07, Tahar Amari <am...@cp...> wrote: > Hi Mike > > Many thanks for this reply. > I actually tried what Ben suggested me which was to keep only Laspack > to have the linear part working. > But it seems it does not work still. > Have you seen my reply about Ben suggestion ? > > Thank you very much again > > Tahar > > > -------------------------------------------- > > T. Amari > > Centre de Physique Theorique > > Ecole Polytechnique > > 91128 Palaiseau Cedex France > > tel : 33 1 69 33 47 53 > > fax: 33 1 69 33 30 08 > > email: <mailto:am...@cp...> > > URL : http://www.cpht.polytechnique.fr/cpht/amari > > Le 2 juil. 07 =E0 00:11, Mike a =E9crit : > > > Hi Tahar, > I have susccesfully built libmesh a few months ago on Mac OS X 10.4 > runing on a PPC G4 powerbook. It took me a couple of goes to figure > out the correct config options, (but that was mostly for me to get > infinite elements and complex numbers). > > I used Laspack instaed of Petsc and ignored all the parallel stuff. > > Mike > > > > On 01/07/07, Tahar Amari <am...@cp...> wrote: > Dear Colleagues, > > In 2004 I spent several days trying to build libmesh on mac os x for one = of > our finite element project. > It was impossible . I sent several emails with no real help from your tea= m. > We decided to code by ourself . > > 3 year afters, I have a mac intel, and seeing advertising from you about > "extreme portability" of libmesh, > I decided to try again building libmesh on mac os x 10.4.9 > > I tried almost all the ./connfigure --enable , disable combinaison, and = the > make phase always died > with error. > > So I am surprised that there is even not a line on your web page, suggeri= ng > what are the options > build in 10 minutes your library. > > Why is this please ? > > Is there any one who happened to have build libmesh on mac os x ? > > So why keeping Mac OS on the list of targeted platform of libmesh please = ? > > Many thanks for some hints > > Sincerely > > Tahar > > > > > -------------------------------------------- > > T. Amari > > Directeur de recherche au CNRS > > Centre de Physique Theorique > > Ecole Polytechnique > > 91128 Palaiseau Cedex France > > tel : 33 1 69 33 47 53 > > fax: 33 1 69 33 30 08 > > email: <mailto:am...@cp...> > > URL : http://www.cpht.polytechnique.fr/cpht/amari > > ------------------------------------------------------------------------- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > Libmesh-users mailing list > Lib...@li... > https://lists.sourceforge.net/lists/listinfo/libmesh-users > > > > > > -- > Dr Mike Kidner > Acoustics Vibration & Control Group > School of Mechnical Engineering > University of Adelaide > --=20 Dr Mike Kidner Acoustics Vibration & Control Group School of Mechnical Engineering University of Adelaide |
From: Tahar A. <am...@cp...> - 2007-07-02 08:59:50
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Hi Mike Thanks a lot for your suggestion. Please note that I just tried first Jon 's one and it appeared to work well . Many thanks again Tahar -------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 47 53 fax: 33 1 69 33 30 08 email: <mailto:am...@cp...> URL : http://www.cpht.polytechnique.fr/cpht/amari Le 2 juil. 07 =E0 00:32, Mike a =E9crit : > Hi Tahar, > I saw the reply , but I don't know enough to understand it! > > Attached is my config.log, maybe if you try these options you'll get > something that will build. Otherwise it may be something to do with > 10.3. > > I used libmesh-0.6.0-rc2 > > Cheers > Mike > > > On 02/07/07, Tahar Amari <am...@cp...> wrote: >> Hi Mike >> >> Many thanks for this reply. >> I actually tried what Ben suggested me which was to keep only Laspack >> to have the linear part working. >> But it seems it does not work still. >> Have you seen my reply about Ben suggestion ? >> >> Thank you very much again >> >> Tahar >> >> >> -------------------------------------------- >> >> T. Amari >> >> Centre de Physique Theorique >> >> Ecole Polytechnique >> >> 91128 Palaiseau Cedex France >> >> tel : 33 1 69 33 47 53 >> >> fax: 33 1 69 33 30 08 >> >> email: <mailto:am...@cp...> >> >> URL : http://www.cpht.polytechnique.fr/cpht/amari >> >> Le 2 juil. 07 =E0 00:11, Mike a =E9crit : >> >> >> Hi Tahar, >> I have susccesfully built libmesh a few months ago on Mac OS X 10.4 >> runing on a PPC G4 powerbook. It took me a couple of goes to figure >> out the correct config options, (but that was mostly for me to get >> infinite elements and complex numbers). >> >> I used Laspack instaed of Petsc and ignored all the parallel stuff. >> >> Mike >> >> >> >> On 01/07/07, Tahar Amari <am...@cp...> wrote: >> Dear Colleagues, >> >> In 2004 I spent several days trying to build libmesh on mac os x =20 >> for one of >> our finite element project. >> It was impossible . I sent several emails with no real help from =20 >> your team. >> We decided to code by ourself . >> >> 3 year afters, I have a mac intel, and seeing advertising from you =20= >> about >> "extreme portability" of libmesh, >> I decided to try again building libmesh on mac os x 10.4.9 >> >> I tried almost all the ./connfigure --enable , disable =20 >> combinaison, and the >> make phase always died >> with error. >> >> So I am surprised that there is even not a line on your web page, =20 >> suggering >> what are the options >> build in 10 minutes your library. >> >> Why is this please ? >> >> Is there any one who happened to have build libmesh on mac os x ? >> >> So why keeping Mac OS on the list of targeted platform of libmesh =20 >> please ? >> >> Many thanks for some hints >> >> Sincerely >> >> Tahar >> >> >> >> >> -------------------------------------------- >> >> T. Amari >> >> Directeur de recherche au CNRS >> >> Centre de Physique Theorique >> >> Ecole Polytechnique >> >> 91128 Palaiseau Cedex France >> >> tel : 33 1 69 33 47 53 >> >> fax: 33 1 69 33 30 08 >> >> email: <mailto:am...@cp...> >> >> URL : http://www.cpht.polytechnique.fr/cpht/amari >> >> ---------------------------------------------------------------------=20= >> ---- >> This SF.net email is sponsored by DB2 Express >> Download DB2 Express C - the FREE version of DB2 express and take >> control of your XML. No limits. Just data. Click to get it now. >> http://sourceforge.net/powerbar/db2/ >> _______________________________________________ >> Libmesh-users mailing list >> Lib...@li... >> https://lists.sourceforge.net/lists/listinfo/libmesh-users >> >> >> >> >> >> -- >> Dr Mike Kidner >> Acoustics Vibration & Control Group >> School of Mechnical Engineering >> University of Adelaide >> > > > --=20 > Dr Mike Kidner > Acoustics Vibration & Control Group > School of Mechnical Engineering > University of Adelaide > <config.log> |
From: John P. <pet...@cf...> - 2007-07-02 14:13:04
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Tahar Amari writes: > Hi John, > > Thanks a lot . > > >> --SInce I disabled petsc, does it mean that there is no chance for me > >> to use > >> petsc ? > > > > Yes, that's usually what that means... > > Do you think I will never be able to use petsc ? This is a pity. > If you *want* to use petsc, why are you disabling it? I think someone already suggested: use a version of PETSc prior to 2.3.3 until we properly support the latest PETSc. > > > What does Make.common show for the MPI variables? > > > > MPI_IMPL = > > MPI_INCLUDE = > > MPI_LIB = > > > > > # MPI configuration > # (only explicitly defined when PETSc is absent, otherwise snooped > from PETSc) > MPI_IMPL = built-in > MPI_INCLUDE = > MPI_LIB = > > > Does this mean somethiing to you ? It means that MPI was not found in any of the "standard" places, but the configure test somehow found it could compile the test program: #include <mpi.h> int main() { int np; MPI_Comm_size (MPI_COMM_WORLD, &np); return 0; } Unfortunately, this branch of the configure test does not set any of the MPI_LIB variables. This means you can't link any of the example programs. If you know where your MPI installation is located, try doing ./configure --with-mpi=/path/to/mpi (along with all the other options we already discussed) and seeing if your MPI_LIB and MPI_INCLUDE are then set correctly. -J |
From: Tahar A. <am...@cp...> - 2007-07-02 14:20:37
|
Sorry our emails cross . As you can see , in my previous email I enabled petsc , and put the =20 correct path for mpi ... as you suggested it, but I got the error I sent you. Tahar -------------------------------------------- T. Amari Centre de Physique Theorique Ecole Polytechnique 91128 Palaiseau Cedex France tel : 33 1 69 33 47 53 fax: 33 1 69 33 30 08 email: <mailto:am...@cp...> URL : http://www.cpht.polytechnique.fr/cpht/amari Le 2 juil. 07 =E0 16:12, John Peterson a =E9crit : > Tahar Amari writes: >> Hi John, >> >> Thanks a lot . >> >>>> --SInce I disabled petsc, does it mean that there is no chance =20 >>>> for me >>>> to use >>>> petsc ? >>> >>> Yes, that's usually what that means... >> >> Do you think I will never be able to use petsc ? This is a pity. >> > > If you *want* to use petsc, why are you disabling it? I think someone > already suggested: use a version of PETSc prior to 2.3.3 until we =20 > properly > support the latest PETSc. > >> >>> What does Make.common show for the MPI variables? >>> >>> MPI_IMPL =3D >>> MPI_INCLUDE =3D >>> MPI_LIB =3D >> >> >> >> >> # MPI configuration >> # (only explicitly defined when PETSc is absent, otherwise snooped >> from PETSc) >> MPI_IMPL =3D built-in >> MPI_INCLUDE =3D >> MPI_LIB =3D >> >> >> Does this mean somethiing to you ? > > It means that MPI was not found in any of the "standard" places, but > the configure test somehow found it could compile the test program: > > #include <mpi.h> > int main() > { > int np; MPI_Comm_size (MPI_COMM_WORLD, &np); > return 0; > } > > > Unfortunately, this branch of the configure test does not set any of > the MPI_LIB variables. This means you can't link any of the example > programs. If you know where your MPI installation is located, try > doing ./configure --with-mpi=3D/path/to/mpi (along with all the other > options we already discussed) and seeing if your MPI_LIB and =20 > MPI_INCLUDE > are then set correctly. > > -J |
From: John P. <pet...@cf...> - 2007-07-02 14:25:14
|
Tahar Amari writes: > Sorry our emails cross . > > As you can see , in my previous email I enabled petsc , and put the > correct path for mpi ... > as you suggested it, but I got the error I sent you. Quoting myself: > I think someone already suggested: use a version of PETSc prior to > 2.3.3 until we properly support the latest PETSc. This is just a rough guess but it appears that SNESSetMonitor became SNESMonitorSet in petsc 2.3.3. I'm working on this fix today. -John |