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

Thu Apr 14 10:57:16 CDT 2016

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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