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

Mon Apr 18 10:52:06 CDT 2016

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 <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
> > > >> >
> > > >>
> > > >
> > > >
> > >
> >
> >
> 