[petsc-users] Compiling petsc with a user-defined MUMPS directory

Thu Apr 14 10:59:23 CDT 2016

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 <balay at mcs.anl.gov> 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 <balay at mcs.anl.gov> 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
> > > >
> > >
> >
>
>
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