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

Mon Apr 18 10:19:07 CDT 2016

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 ?

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.

What is the good practice ?

Best regards
Natacha

On Thu, Apr 14, 2016 at 6:07 PM, Satish Balay <balay at mcs.anl.gov> 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 <
> natacha.bereux at gmail.com>
> > 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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