Ok I did not see your ultra fast reply, thanks a lot : I immediately correct my configure line ! Natacha
On Thu, Apr 14, 2016 at 5:41 PM, Satish Balay <[email protected]> wrote: > Configure Options: --configModules=PETSc.Configure > --optionsModule=config.compilerOptions --with-cc=mpicc --with-cxx=mpicxx > --with-fc=mpif90 --with-ssl=0 --with-mpi=1 --with-debugging=1 > --PETSC_ARCH=linux-metis > --with-scalapack-lib=/usr/lib/libscalapack-openmpi.so > --with-blacs-lib=/usr/lib/libblacs-openmpi.so > --with-metis-lib="[~/dev/codeaster-prerequisites/v13/prerequisites/Metis_aster-510_aster/lib/libmetis.a,~/dev/codeaster-prerequisites/v13/prerequisites/Metis_aster-510_aster/lib/libGKlib.a]" > --with-metis-include=~/dev/codeaster-prerequisites/v13/prerequisites/Metis_aster-510_aster/include > > A couple of issues: > - there is no more blacs option [as latest scalapack bundles blacs inside > scalapack] > - configure doesn't understsnad '~' > > > So Try: > > --with-scalapack-lib="-lscalapack-openmpi -lblacs-openmpi" > --with-metis-lib="-L/home/H03755/dev/codeaster-prerequisites/v13/prerequisites/Metis_aster-510_aster/lib > -lmetis.a -lGKlib" > > --with-metis-include=/home/H03755/dev/codeaster-prerequisites/v13/prerequisites/Metis_aster-510_aster/include > > You would also need the petsc configure option --with-shared-libraries=0 > [to be able to build petsc with these static libraries that are not likely > compiled with -fPIC option] > > Satish > > On Thu, 14 Apr 2016, Natacha BEREUX 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 > > > > > > > > > > >
