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

Thu Apr 14 11:07:56 CDT 2016

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
> >> >
> >>
> >
> >
> 