Same with parmetis. On Mon, 18 Apr 2016, Natacha BEREUX wrote:
> Hello Satish, > thank you very much for yor advices. They were very helpful ! > > The configure step finally succeeds if I use the following configure line: > ./configure --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 --with-mpi=1 > --with-debugging=0 --PETSC_ARCH=linux-metis-mumps > --with-scalapack-lib="-lscalapack-openmpi -lblacs-openmpi > -lblacsF77init-openmpi -lblacsCinit-openmpi" > --with-metis-lib="-L/home/H03755/dev/codeaster-prerequisites/v13/prerequisites/Metis_aster-510_aster/lib > -lmetis -lGKlib" > --with-metis-include=/home/H03755/dev/codeaster-prerequisites/v13/prerequisites/Metis_aster-510_aster/include > --with-mumps-lib="-L/home/H03755/dev/codeaster-prerequisites/v13/prerequisites/Mumps-501_consortium_aster5/MPI/lib > -lzmumps -ldmumps -lmumps_common -lpord > -L/home/H03755/dev/codeaster-prerequisites/v13/prerequisites/Scotch_aster-604_aster1/lib > -lesmumps -lscotch -lscotcherr -lscotcherrexit > -L/home/H03755/dev/codeaster-prerequisites/v13/prerequisites/Metis_aster-510_aster/lib > -lmetis" > --with-mumps-include=/home/H03755/dev/codeaster-prerequisites/v13/prerequisites/Mumps-501_consortium_aster5/MPI/include > --with-blas-lapack-lib="-llapack -lopenblas" > --download-ptscotch=/home/H03755/Librairies/scotch_6.0.3.tar.gz LIBS=-lgomp > > I have to specify scotch shared libraries (-lscotch -lscotcherr > -lscotcherrexit ) and metis shared library in --with-mumps-lib option > otherwise the test (on dmump) in configure fails. > Is it OK to do so ? Hm - its best to avoid duplication of libraries. i.e specifying scotch via mumps-libs and also via --download-ptscotch will cause problems. Why not specify scotch with --with-ptscotch-include,--with-ptscotch-lib options? > > I also tried to use the following shorter line > > ./configure --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 > --with-mpi=1 --with-debugging=0 --PETSC_ARCH=linux-mumps- > --with-scalapack-lib="-lscalapack-openmpi -lblacs-openmpi > -lblacsF77init-openmpi -lblacsCinit-openmpi" > --with-mumps-lib="-L/home/H03755/dev/codeaster-prerequisites/v13/prerequisites/Mumps-501_consortium_aster5/MPI/lib > -lzmumps -ldmumps -lmumps_common -lpord > -L/home/H03755/dev/codeaster-prerequisites/v13/prerequisites/Scotch_aster-604_aster1/lib > -lesmumps -lscotch -lscotcherr -lscotcherrexit > -L/home/H03755/dev/codeaster-prerequisites/v13/prerequisites/Metis_aster-510_aster/lib > -lmetis" > --with-mumps-include=/home/H03755/dev/codeaster-prerequisites/v13/prerequisites/Mumps-501_consortium_aster5/MPI/include > --with-blas-lapack-lib="-llapack -lopenblas" > --download-ptscotch=/home/H03755/Librairies/scotch_6.0.3.tar.gz LIBS=-lgomp > > I do not use --with-metis-lib/--with-metis-include. > I wonder if this is authorized : the libraries are given with the > --with-mumps-lib, but the include are not defined. This is fine. [except for the dupliation of ptscotch] > > What is the good practice ? Either is work - but its best to specify each package with its own options listed by configure. The issues usually are: - Is this package primarily a depencency of an externalpakage or if there is a petsc interface to it? For ex: PETSc has interface to mumps, parmetis - but not scalapack. So if you club parmetis into mumps-libs then petsc interface to parmetis would not be enabled. If you are not using this feature - it doesn't matter if its not enabled. - does this externalpakage also require the includes in the public interface? If dmumps_c.h requires metis.h [when mumps is built with metis] - then you might have to specify metis include also with --with-mumps-include. Otherwise - it doesn't matter. - are there bugs in petsc configure that can trigger wrong error checks? Because mumps depends on scalapack, and optionally on metis,parmetis,ptscotch [i.e only one of them is required - but not all] - there is an error-check in configure to make sure atleast one of them is specified for --download-mumps. Perhaps this check should not trigger error for user built mumps. Did you build MUMPS with both metis, ptscotch? [and not parmetis?] Satish > > Best regards > Natacha > > > > > > On Thu, Apr 14, 2016 at 6:07 PM, Satish Balay <[email protected]> wrote: > > > you'll have to roll-in the --with-blacs-lib option into > > --with-scalapack-lib option > > > > Satish > > > > On Thu, 14 Apr 2016, Natacha BEREUX wrote: > > > > > Sorry, do not take into account my last email. > > > I made some progress and I am now able to configure PETSc with a > > > pre-installed version of metis. > > > > > > Problems come when I try to configure PETSc with MUMPS > > > > > > My command line is > > > ./configure --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 > > > --with-ssl=0 --with-mpi=1 --with-debugging=1 > > > --PETSC_ARCH=linux-metis-mumps > > > --with-scalapack-lib=/usr/lib/libscalapack-openmpi.so > > > > > --with-blacs-lib=[/usr/lib/libblacs-openmpi.so,/usr/lib/libblacsCinit-openmpi.so,/usr/lib/libblacsF77init-openmpi.so] > > > > > --with-metis-lib=[${METIS_PRE}/lib/libmetis.a,${METIS_PRE}/lib/libGKlib.a] > > > --with-metis-include=$METIS_PRE/include > > > > > --with-mumps-lib=[$MUMPS_PRE/lib/libdmumps.a,$MUMPS_PRE/lib/libmumps_common.a,$MUMPS_PRE/lib/libpord.a] > > > --with-mumps-include=$MUMPS_PRE/include > > > > > > where METIS_PRE and MUMPS_PRE are the path to the local installs of metis > > > and mumps) > > > > > > I get (at least) the following error > > > /libdmumps.a(dend_driver.o): undefined reference to symbol > > 'blacs_gridexit_' > > > /usr/lib/libblacs-openmpi.so.1: error adding symbols: DSO missing from > > > command line > > > collect2: error: ld returned 1 exit status > > > > > > > > > Would you have any idea of its meaning ? > > > > > > The configure.log is attached > > > Thanks a lot if you can help me ! > > > Natacha > > > > > > On Thu, Apr 14, 2016 at 5:19 PM, Natacha BEREUX < > > [email protected]> > > > wrote: > > > > > > > Hi Satish > > > > thanks a lot for the answer. Unfortunately, it does not work yet. > > > > More precisely : > > > > --download-mumps works fine (and every --download-package option works > > > > perfectly). I am then able to compile a PETSc library. > > > > --with-package-lib=/usr/lib/libscalapack-openmpi.so or more generally > > > > --with-package-lib=libXXXX.so also works > > > > > > > > But I would like to use static librairies, preinstalled on my computer > > > > ... and this fails. > > > > > > > > For the moment I gave up compiling with MUMPS, and I am instead > > trying to > > > > compile with Metis 5. > > > > I have a preinstalled version in a some directory lets say metis_dir > > > > I try > > > > -with-metis-lib=[metis_dir/lib/libmetis.a, metis_dir/lib/libGKlib.a] > > > > --with-metis-include=metis_dir/include > > > > this fails (see the attached config.log) > > > > -with-metis-dir=metis_dir also fails > > > > Is there a problem with static librairies ? > > > > > > > > Natacha > > > > > > > > > > > > On Tue, Apr 12, 2016 at 6:19 PM, Satish Balay <[email protected]> > > wrote: > > > > > > > >> On Tue, 12 Apr 2016, Natacha BEREUX wrote: > > > >> > > > >> > Hello, > > > >> > I am trying to compile Petsc (3.6.3) with external packages (MUMPS > > and > > > >> its > > > >> > prerequisites). > > > >> > More precisely I would like PETSc to use a pre-installed version of > > > >> MUMPS. > > > >> > > > > >> > Petsc downloads and compiles the prerequisites (parmetis, scalapack > > > >> etc) : > > > >> > this works fine. > > > >> > > > >> What metis/parmetis/slcalapack is this MUMPS installed with? > > > >> > > > >> What version of MUMPS did you install? > > > >> > > > >> Why could you not use --download-mumps? > > > >> > > > >> Using a different metis/parmetis/slcalapack to install MUMPS - and > > > >> then specifying --download-metis --download-parmetis > > > >> --download-scalapack [i.e different versions/builds of the same > > > >> libraries] can result in conflcits. > > > >> > > > >> > > > > >> > I define MUMPS location by --with-mumps-dir=top-directory of MUMPS > > > >> install, > > > >> > but the > > > >> > configure step fails with the followiing message: > > > >> > > > > >> > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for > > > >> details): > > > >> > --with-mumps-dir=/home/H03755/Librairies/Mumps_MPI did not work > > > >> > > > > >> > I do not understand what is wrong. > > > >> > I have attached the configure.log file. > > > >> > > > > >> > Any hint would be greatly appreciated ! > > > >> > > > >> >>>> > > > >> Executing: mpicc -show > > > >> stdout: gcc -I/usr/lib/openmpi/include > > -I/usr/lib/openmpi/include/openmpi > > > >> -pthread -L/usr//lib -L/usr/lib/openmpi/lib -lmpi -ldl -lhwloc > > > >> Defined make macro "MPICC_SHOW" to "gcc > > > >> -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -pthread > > > >> -L/usr//lib -L/usr/lib/openmpi/lib -lmpi -ldl -lhwloc" > > > >> <<<< > > > >> Ok - so you are using system openmpi with gcc. > > > >> > > > >> > > > >> >>>> > > > >> Executing: mpicc -o /tmp/petsc-0u_4WI/config.libraries/conftest > > -fPIC > > > >> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -O > > > >> /tmp/petsc-0u_4WI/config.libraries/conftest.o > > > >> -Wl,-rpath,/home/H03755/Librairies/Mumps_MPI/lib > > > >> -L/home/H03755/Librairies/Mumps_MPI/lib -lcmumps -ldmumps -lsmumps > > -lzmumps > > > >> -lmumps_common -lpord > > > >> > > -Wl,-rpath,/home/H03755/Librairies/petsc-3.6.3/linux-debug-mumps-ext/lib > > > >> -L/home/H03755/Librairies/petsc-3.6.3/linux-debug-mumps-ext/lib > > -lscalapack > > > >> -llapack -lblas -Wl,-rpath,/usr/lib/openmpi/lib -L/usr/lib/openmpi/lib > > > >> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.9 > > > >> -L/usr/lib/gcc/x86_64-linux-gnu/4.9 > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu > > > >> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu > > > >> -L/lib/x86_64-linux-gnu -lmpi_f90 -lmpi_f77 -lgfortran -lm > > > >> -Wl,-rpath,/usr/lib/openmpi/lib > > > >> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.9 > > > >> -Wl,-rpath,/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu > > > >> -lgfortran -lm -lquadmath -lm -llapack -lblas > > > >> -Wl,-rpath,/usr/lib/openmpi/lib -L/usr/lib/openmpi/lib > > > >> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.9 > > > >> -L/usr/lib/gcc/x86_64-linux-gnu/4.9 > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu > > > >> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu > > > >> -L/lib/x86_64-linux-gnu -lmpi_f90 -lmpi_f77 -lgfortran -lm > > > >> -Wl,-rpath,/usr/lib/openmpi/lib > > > >> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.9 > > > >> -Wl,-rpath,/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu > > > >> -lgfortran -lm -lquadmath -lm > > > >> > > -Wl,-rpath,/home/H03755/Librairies/petsc-3.6.3/linux-debug-mumps-ext/lib > > > >> -L/home/H03755/Librairies/petsc-3.6.3/linux-debug-mumps-ext/lib > > -lparmetis > > > >> > > -Wl,-rpath,/home/H03755/Librairies/petsc-3.6.3/linux-debug-mumps-ext/lib > > > >> -L/home/H03755/Librairies/petsc-3.6.3/linux-debug-mumps-ext/lib > > -lmetis -lm > > > >> -lm -Wl,-rpath,/usr/lib/openmpi/lib -L/usr/lib/openmpi/lib > > > >> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.9 > > > >> -L/usr/lib/gcc/x86_64-linux-gnu/4.9 > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu > > > >> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu > > > >> -L/lib/x86_64-linux-gnu -Wl,-rpath,/usr/lib/x86_64-linux-gnu > > > >> -L/usr/lib/x86_64-linux-gnu -ldl -lmpi -lhwloc -lgcc_s -lpthread -ldl > > > >> Possible ERROR while running linker: exit code 256 > > > >> stderr: > > > >> /home/H03755/Librairies/Mumps_MPI/lib/libdmumps.a(dlr_stats.o): In > > > >> function `__dmumps_lr_stats_MOD_update_flop_stats_lrb_product': > > > >> dlr_stats.F:(.text+0x3079): undefined reference to > > > >> `GOMP_critical_name_start' > > > >> dlr_stats.F:(.text+0x30fa): undefined reference to > > > >> `GOMP_critical_name_end' > > > >> dlr_stats.F:(.text+0x310e): undefined reference to > > > >> `GOMP_critical_name_start' > > > >> dlr_stats.F:(.text+0x318f): undefined reference to > > > >> `GOMP_critical_name_end' > > > >> /home/H03755/Librairies/Mumps_MPI/lib/libdmumps.a(dlr_stats.o): In > > > >> function `__dmumps_lr_stats_MOD_update_flop_stats_trsm': > > > >> dlr_stats.F:(.text+0x33a9): undefined reference to > > > >> `GOMP_critical_name_start' > > > >> dlr_stats.F:(.text+0x33f9): undefined reference to > > > >> `GOMP_critical_name_end' > > > >> dlr_stats.F:(.text+0x340a): undefined reference to > > > >> `GOMP_critical_name_start' > > > >> dlr_stats.F:(.text+0x345a): undefined reference to > > > >> `GOMP_critical_name_end' > > > >> /home/H03755/Librairies/Mumps_MPI/lib/libdmumps.a(dlr_stats.o): In > > > >> function `__dmumps_lr_stats_MOD_update_flop_stats_panel': > > > >> dlr_stats.F:(.text+0x3576): undefined reference to > > > >> `GOMP_critical_name_start' > > > >> dlr_stats.F:(.text+0x35a7): undefined reference to > > > >> `GOMP_critical_name_end' > > > >> dlr_stats.F:(.text+0x35b8): undefined reference to > > > >> `GOMP_critical_name_start' > > > >> dlr_stats.F:(.text+0x35e9): undefined reference to > > > >> `GOMP_critical_name_end' > > > >> /home/H03755/Librairies/Mumps_MPI/lib/libdmumps.a(dlr_stats.o): In > > > >> function `__dmumps_lr_stats_MOD_update_flop_stats_demote': > > > >> dlr_stats.F:(.text+0x36ac): undefined reference to > > > >> `GOMP_critical_name_start' > > > >> dlr_stats.F:(.text+0x36ce): undefined reference to > > > >> `GOMP_critical_name_end' > > > >> dlr_stats.F:(.text+0x36df): undefined reference to > > > >> `GOMP_critical_name_start' > > > >> dlr_stats.F:(.text+0x3701): undefined reference to > > > >> `GOMP_critical_name_end' > > > >> /home/H03755/Librairies/Mumps_MPI/lib/libdmumps.a(dlr_stats.o): In > > > >> function `__dmumps_lr_stats_MOD_update_flop_stats_cb_demote': > > > >> dlr_stats.F:(.text+0x37c1): undefined reference to > > > >> `GOMP_critical_name_start' > > > >> dlr_stats.F:(.text+0x37e3): undefined reference to > > > >> `GOMP_critical_name_end' > > > >> /home/H03755/Librairies/Mumps_MPI/lib/libdmumps.a(dlr_stats.o): In > > > >> function `__dmumps_lr_stats_MOD_update_flop_stats_cb_promote': > > > >> dlr_stats.F:(.text+0x3839): undefined reference to > > > >> `GOMP_critical_name_start' > > > >> dlr_stats.F:(.text+0x3856): undefined reference to > > > >> `GOMP_critical_name_end' > > > >> /home/H03755/Librairies/Mumps_MPI/lib/libdmumps.a(dana_lr.o): In > > function > > > >> `__dmumps_ana_lr_MOD_mumps_scotch_kway': > > > >> dana_lr.F:(.text+0x115): undefined reference to `scotchfgraphbuild_' > > > >> dana_lr.F:(.text+0x131): undefined reference to `scotchfstratinit_' > > > >> dana_lr.F:(.text+0x151): undefined reference to `scotchfgraphpart_' > > > >> dana_lr.F:(.text+0x15e): undefined reference to `scotchfstratexit_' > > > >> dana_lr.F:(.text+0x16b): undefined reference to `scotchfgraphexit_' > > > >> <snip> > > > >> > > > >> > > > >> Looks like this MUMPS is built with ptscotch and openmp. > > > >> > > > >> You can specify -lgomp for openmp. This can be done with the configure > > > >> option > > > >> LIBS=-lgomp > > > >> > > > >> Wrt and PTSCOTCH stuff depending upon how its installed we'll have to > > > >> figureout > > > >> how to specify it. > > > >> > > > >> Its best to specify all the packages [mumps and its dependencies] you > > > >> built manually with the options: > > > >> > > > >> --with-package-include --with-package-lib > > > >> > > > >> Satish > > > >> > > > >> > Best regards, > > > >> > > > > >> > Natacha > > > >> > > > > >> > > > > > > > > > > > > > > > >
