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

Thu Apr 14 10:19:45 CDT 2016

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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