<div dir="ltr"><div><div><div>Hello Satish, <br></div>thank you very much for yor advices. They were very helpful !<br></div><br>The configure step finally succeeds if I use the following configure line:<br>./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<br></div> <div class="gmail_extra"><br></div><div class="gmail_extra">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.<br></div><div class="gmail_extra">Is it OK to do so ? <br><br></div><div class="gmail_extra">I also tried to use the following shorter line <br><br></div><div class="gmail_extra"> ./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<br></div><div class="gmail_extra"><br>I do not use --with-metis-lib/--with-metis-include. <br></div><div class="gmail_extra">I wonder if this is authorized : the libraries are given with the --with-mumps-lib, but the include are not defined. </div><div class="gmail_extra"><br>What is the good practice ? <br><br></div><div class="gmail_extra">Best regards <br></div><div class="gmail_extra">Natacha <br></div><div class="gmail_extra"><br><br><br><br><br><div class="gmail_quote">On Thu, Apr 14, 2016 at 6:07 PM, Satish Balay <span dir="ltr"><<a href="mailto:balay@mcs.anl.gov" target="_blank">balay@mcs.anl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">you'll have to roll-in the --with-blacs-lib option into --with-scalapack-lib option<br>
<span class=""><font color="#888888"><br>
Satish<br>
</font></span><div class=""><div class="h5"><br>
On Thu, 14 Apr 2016, Natacha BEREUX wrote:<br>
<br>
> Sorry, do not take into account my last email.<br>
> I made some progress and I am now able to configure PETSc with a<br>
> pre-installed version of metis.<br>
><br>
> Problems come when I try to configure PETSc with MUMPS<br>
><br>
> My command line is<br>
> ./configure --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90<br>
> --with-ssl=0 --with-mpi=1 --with-debugging=1<br>
> --PETSC_ARCH=linux-metis-mumps<br>
> --with-scalapack-lib=/usr/lib/libscalapack-openmpi.so<br>
> --with-blacs-lib=[/usr/lib/libblacs-openmpi.so,/usr/lib/libblacsCinit-openmpi.so,/usr/lib/libblacsF77init-openmpi.so]<br>
> --with-metis-lib=[${METIS_PRE}/lib/libmetis.a,${METIS_PRE}/lib/libGKlib.a]<br>
> --with-metis-include=$METIS_PRE/include<br>
> --with-mumps-lib=[$MUMPS_PRE/lib/libdmumps.a,$MUMPS_PRE/lib/libmumps_common.a,$MUMPS_PRE/lib/libpord.a]<br>
> --with-mumps-include=$MUMPS_PRE/include<br>
><br>
> where METIS_PRE and MUMPS_PRE are the path to the local installs of metis<br>
> and mumps)<br>
><br>
> I get (at least) the following error<br>
> /libdmumps.a(dend_driver.o): undefined reference to symbol 'blacs_gridexit_'<br>
> /usr/lib/libblacs-openmpi.so.1: error adding symbols: DSO missing from<br>
> command line<br>
> collect2: error: ld returned 1 exit status<br>
><br>
><br>
> Would you have any idea of its meaning ?<br>
><br>
> The configure.log is attached<br>
> Thanks a lot if you can help me !<br>
> Natacha<br>
><br>
> On Thu, Apr 14, 2016 at 5:19 PM, Natacha BEREUX <<a href="mailto:natacha.bereux@gmail.com">natacha.bereux@gmail.com</a>><br>
> wrote:<br>
><br>
> > Hi Satish<br>
> > thanks a lot for the answer. Unfortunately, it does not work yet.<br>
> > More precisely :<br>
> > --download-mumps works fine (and every --download-package option works<br>
> > perfectly). I am then able to compile a PETSc library.<br>
> > --with-package-lib=/usr/lib/libscalapack-openmpi.so or more generally<br>
> > --with-package-lib=libXXXX.so also works<br>
> ><br>
> > But I would like to use static librairies, preinstalled on my computer<br>
> > ... and this fails.<br>
> ><br>
> > For the moment I gave up compiling with MUMPS, and I am instead trying to<br>
> > compile with Metis 5.<br>
> > I have a preinstalled version in a some directory lets say metis_dir<br>
> > I try<br>
> > -with-metis-lib=[metis_dir/lib/libmetis.a, metis_dir/lib/libGKlib.a]<br>
> > --with-metis-include=metis_dir/include<br>
> > this fails (see the attached config.log)<br>
> > -with-metis-dir=metis_dir also fails<br>
> > Is there a problem with static librairies ?<br>
> ><br>
> > Natacha<br>
> ><br>
> ><br>
> > On Tue, Apr 12, 2016 at 6:19 PM, Satish Balay <<a href="mailto:balay@mcs.anl.gov">balay@mcs.anl.gov</a>> wrote:<br>
> ><br>
> >> On Tue, 12 Apr 2016, Natacha BEREUX wrote:<br>
> >><br>
> >> > Hello,<br>
> >> > I am trying to compile Petsc (3.6.3) with external packages (MUMPS and<br>
> >> its<br>
> >> > prerequisites).<br>
> >> > More precisely I would like PETSc to use a pre-installed version of<br>
> >> MUMPS.<br>
> >> ><br>
> >> > Petsc downloads and compiles the prerequisites (parmetis, scalapack<br>
> >> etc) :<br>
> >> > this works fine.<br>
> >><br>
> >> What metis/parmetis/slcalapack is this MUMPS installed with?<br>
> >><br>
> >> What version of MUMPS did you install?<br>
> >><br>
> >> Why could you not use --download-mumps?<br>
> >><br>
> >> Using a different metis/parmetis/slcalapack to install MUMPS - and<br>
> >> then specifying --download-metis --download-parmetis<br>
> >> --download-scalapack [i.e different versions/builds of the same<br>
> >> libraries] can result in conflcits.<br>
> >><br>
> >> ><br>
> >> > I define MUMPS location by --with-mumps-dir=top-directory of MUMPS<br>
> >> install,<br>
> >> > but the<br>
> >> > configure step fails with the followiing message:<br>
> >> ><br>
> >> > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for<br>
> >> details):<br>
> >> > --with-mumps-dir=/home/H03755/Librairies/Mumps_MPI did not work<br>
> >> ><br>
> >> > I do not understand what is wrong.<br>
> >> > I have attached the configure.log file.<br>
> >> ><br>
> >> > Any hint would be greatly appreciated !<br>
> >><br>
> >> >>>><br>
> >> Executing: mpicc -show<br>
> >> stdout: gcc -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi<br>
> >> -pthread -L/usr//lib -L/usr/lib/openmpi/lib -lmpi -ldl -lhwloc<br>
> >> Defined make macro "MPICC_SHOW" to "gcc<br>
> >> -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -pthread<br>
> >> -L/usr//lib -L/usr/lib/openmpi/lib -lmpi -ldl -lhwloc"<br>
> >> <<<<<br>
> >> Ok - so you are using system openmpi with gcc.<br>
> >><br>
> >><br>
> >> >>>><br>
> >> Executing: mpicc -o /tmp/petsc-0u_4WI/config.libraries/conftest -fPIC<br>
> >> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -O<br>
> >> /tmp/petsc-0u_4WI/config.libraries/conftest.o<br>
> >> -Wl,-rpath,/home/H03755/Librairies/Mumps_MPI/lib<br>
> >> -L/home/H03755/Librairies/Mumps_MPI/lib -lcmumps -ldmumps -lsmumps -lzmumps<br>
> >> -lmumps_common -lpord<br>
> >> -Wl,-rpath,/home/H03755/Librairies/petsc-3.6.3/linux-debug-mumps-ext/lib<br>
> >> -L/home/H03755/Librairies/petsc-3.6.3/linux-debug-mumps-ext/lib -lscalapack<br>
> >> -llapack -lblas -Wl,-rpath,/usr/lib/openmpi/lib -L/usr/lib/openmpi/lib<br>
> >> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.9<br>
> >> -L/usr/lib/gcc/x86_64-linux-gnu/4.9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu<br>
> >> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu<br>
> >> -L/lib/x86_64-linux-gnu -lmpi_f90 -lmpi_f77 -lgfortran -lm<br>
> >> -Wl,-rpath,/usr/lib/openmpi/lib<br>
> >> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.9<br>
> >> -Wl,-rpath,/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu<br>
> >> -lgfortran -lm -lquadmath -lm -llapack -lblas<br>
> >> -Wl,-rpath,/usr/lib/openmpi/lib -L/usr/lib/openmpi/lib<br>
> >> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.9<br>
> >> -L/usr/lib/gcc/x86_64-linux-gnu/4.9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu<br>
> >> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu<br>
> >> -L/lib/x86_64-linux-gnu -lmpi_f90 -lmpi_f77 -lgfortran -lm<br>
> >> -Wl,-rpath,/usr/lib/openmpi/lib<br>
> >> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.9<br>
> >> -Wl,-rpath,/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu<br>
> >> -lgfortran -lm -lquadmath -lm<br>
> >> -Wl,-rpath,/home/H03755/Librairies/petsc-3.6.3/linux-debug-mumps-ext/lib<br>
> >> -L/home/H03755/Librairies/petsc-3.6.3/linux-debug-mumps-ext/lib -lparmetis<br>
> >> -Wl,-rpath,/home/H03755/Librairies/petsc-3.6.3/linux-debug-mumps-ext/lib<br>
> >> -L/home/H03755/Librairies/petsc-3.6.3/linux-debug-mumps-ext/lib -lmetis -lm<br>
> >> -lm -Wl,-rpath,/usr/lib/openmpi/lib -L/usr/lib/openmpi/lib<br>
> >> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.9<br>
> >> -L/usr/lib/gcc/x86_64-linux-gnu/4.9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu<br>
> >> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu<br>
> >> -L/lib/x86_64-linux-gnu -Wl,-rpath,/usr/lib/x86_64-linux-gnu<br>
> >> -L/usr/lib/x86_64-linux-gnu -ldl -lmpi -lhwloc -lgcc_s -lpthread -ldl<br>
> >> Possible ERROR while running linker: exit code 256<br>
> >> stderr:<br>
> >> /home/H03755/Librairies/Mumps_MPI/lib/libdmumps.a(dlr_stats.o): In<br>
> >> function `__dmumps_lr_stats_MOD_update_flop_stats_lrb_product':<br>
> >> dlr_stats.F:(.text+0x3079): undefined reference to<br>
> >> `GOMP_critical_name_start'<br>
> >> dlr_stats.F:(.text+0x30fa): undefined reference to<br>
> >> `GOMP_critical_name_end'<br>
> >> dlr_stats.F:(.text+0x310e): undefined reference to<br>
> >> `GOMP_critical_name_start'<br>
> >> dlr_stats.F:(.text+0x318f): undefined reference to<br>
> >> `GOMP_critical_name_end'<br>
> >> /home/H03755/Librairies/Mumps_MPI/lib/libdmumps.a(dlr_stats.o): In<br>
> >> function `__dmumps_lr_stats_MOD_update_flop_stats_trsm':<br>
> >> dlr_stats.F:(.text+0x33a9): undefined reference to<br>
> >> `GOMP_critical_name_start'<br>
> >> dlr_stats.F:(.text+0x33f9): undefined reference to<br>
> >> `GOMP_critical_name_end'<br>
> >> dlr_stats.F:(.text+0x340a): undefined reference to<br>
> >> `GOMP_critical_name_start'<br>
> >> dlr_stats.F:(.text+0x345a): undefined reference to<br>
> >> `GOMP_critical_name_end'<br>
> >> /home/H03755/Librairies/Mumps_MPI/lib/libdmumps.a(dlr_stats.o): In<br>
> >> function `__dmumps_lr_stats_MOD_update_flop_stats_panel':<br>
> >> dlr_stats.F:(.text+0x3576): undefined reference to<br>
> >> `GOMP_critical_name_start'<br>
> >> dlr_stats.F:(.text+0x35a7): undefined reference to<br>
> >> `GOMP_critical_name_end'<br>
> >> dlr_stats.F:(.text+0x35b8): undefined reference to<br>
> >> `GOMP_critical_name_start'<br>
> >> dlr_stats.F:(.text+0x35e9): undefined reference to<br>
> >> `GOMP_critical_name_end'<br>
> >> /home/H03755/Librairies/Mumps_MPI/lib/libdmumps.a(dlr_stats.o): In<br>
> >> function `__dmumps_lr_stats_MOD_update_flop_stats_demote':<br>
> >> dlr_stats.F:(.text+0x36ac): undefined reference to<br>
> >> `GOMP_critical_name_start'<br>
> >> dlr_stats.F:(.text+0x36ce): undefined reference to<br>
> >> `GOMP_critical_name_end'<br>
> >> dlr_stats.F:(.text+0x36df): undefined reference to<br>
> >> `GOMP_critical_name_start'<br>
> >> dlr_stats.F:(.text+0x3701): undefined reference to<br>
> >> `GOMP_critical_name_end'<br>
> >> /home/H03755/Librairies/Mumps_MPI/lib/libdmumps.a(dlr_stats.o): In<br>
> >> function `__dmumps_lr_stats_MOD_update_flop_stats_cb_demote':<br>
> >> dlr_stats.F:(.text+0x37c1): undefined reference to<br>
> >> `GOMP_critical_name_start'<br>
> >> dlr_stats.F:(.text+0x37e3): undefined reference to<br>
> >> `GOMP_critical_name_end'<br>
> >> /home/H03755/Librairies/Mumps_MPI/lib/libdmumps.a(dlr_stats.o): In<br>
> >> function `__dmumps_lr_stats_MOD_update_flop_stats_cb_promote':<br>
> >> dlr_stats.F:(.text+0x3839): undefined reference to<br>
> >> `GOMP_critical_name_start'<br>
> >> dlr_stats.F:(.text+0x3856): undefined reference to<br>
> >> `GOMP_critical_name_end'<br>
> >> /home/H03755/Librairies/Mumps_MPI/lib/libdmumps.a(dana_lr.o): In function<br>
> >> `__dmumps_ana_lr_MOD_mumps_scotch_kway':<br>
> >> dana_lr.F:(.text+0x115): undefined reference to `scotchfgraphbuild_'<br>
> >> dana_lr.F:(.text+0x131): undefined reference to `scotchfstratinit_'<br>
> >> dana_lr.F:(.text+0x151): undefined reference to `scotchfgraphpart_'<br>
> >> dana_lr.F:(.text+0x15e): undefined reference to `scotchfstratexit_'<br>
> >> dana_lr.F:(.text+0x16b): undefined reference to `scotchfgraphexit_'<br>
> >> <snip><br>
> >><br>
> >><br>
> >> Looks like this MUMPS is built with ptscotch and openmp.<br>
> >><br>
> >> You can specify -lgomp for openmp. This can be done with the configure<br>
> >> option<br>
> >> LIBS=-lgomp<br>
> >><br>
> >> Wrt and PTSCOTCH stuff depending upon how its installed we'll have to<br>
> >> figureout<br>
> >> how to specify it.<br>
> >><br>
> >> Its best to specify all the packages [mumps and its dependencies] you<br>
> >> built manually with the options:<br>
> >><br>
> >> --with-package-include --with-package-lib<br>
> >><br>
> >> Satish<br>
> >><br>
> >> > Best regards,<br>
> >> ><br>
> >> > Natacha<br>
> >> ><br>
> >><br>
> ><br>
> ><br>
><br>
<br>
</div></div></blockquote></div><br></div></div>