<div dir="ltr"><div>Ok I did not see your ultra fast reply, thanks a lot : I immediately correct my configure line !<br></div>Natacha <br></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Apr 14, 2016 at 5:41 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:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Configure Options: --configModules=PETSc.Configure --optionsModule=config.compilerOptions --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 --with-ssl=0 --with-mpi=1 --with-debugging=1 --PETSC_ARCH=linux-metis --with-scalapack-lib=/usr/lib/libscalapack-openmpi.so --with-blacs-lib=/usr/lib/libblacs-openmpi.so --with-metis-lib="[~/dev/codeaster-prerequisites/v13/prerequisites/Metis_aster-510_aster/lib/libmetis.a,~/dev/codeaster-prerequisites/v13/prerequisites/Metis_aster-510_aster/lib/libGKlib.a]" --with-metis-include=~/dev/codeaster-prerequisites/v13/prerequisites/Metis_aster-510_aster/include<br>
<br>
A couple of issues:<br>
- there is no more blacs option [as latest scalapack bundles blacs inside scalapack]<br>
- configure doesn't understsnad '~'<br>
<br>
<br>
So Try:<br>
<br>
--with-scalapack-lib="-lscalapack-openmpi -lblacs-openmpi"<br>
--with-metis-lib="-L/home/H03755/dev/codeaster-prerequisites/v13/prerequisites/Metis_aster-510_aster/lib -lmetis.a -lGKlib"<br>
--with-metis-include=/home/H03755/dev/codeaster-prerequisites/v13/prerequisites/Metis_aster-510_aster/include<br>
<br>
You would also need the petsc configure option --with-shared-libraries=0<br>
[to be able to build petsc with these static libraries that are not likely compiled with -fPIC option]<br>
<span class="HOEnZb"><font color="#888888"><br>
Satish<br>
</font></span><div class="HOEnZb"><div class="h5"><br>
On Thu, 14 Apr 2016, Natacha BEREUX 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 etc)<br>
> > :<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 `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 `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 `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 `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 `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 `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 `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 `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 `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 `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>
</div></div></blockquote></div><br></div>