<div dir="ltr"><div>Sorry, do not take into account my last email. <br></div><div>I made some progress and I am now able to configure  PETSc with a pre-installed version of metis.<br><br> Problems come when I try to configure PETSc with MUMPS <br> <br></div><div>My command line is<br> ./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<br></div><div><br>where METIS_PRE and MUMPS_PRE are the path to the local installs of metis and mumps)<br></div><div><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 command line<br>collect2: error: ld returned 1 exit status<br><br><br></div><div>Would you have any idea of its meaning ? <br><br></div><div>The configure.log is attached <br></div><div>Thanks a lot if you can help me  !<br></div><div>Natacha <br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Apr 14, 2016 at 5:19 PM, Natacha BEREUX <span dir="ltr"><<a href="mailto:natacha.bereux@gmail.com" target="_blank">natacha.bereux@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Hi Satish <br></div><div>thanks a lot for the answer. Unfortunately, it does not work yet. <br></div><div>More precisely :<br> --download-mumps works fine (and every --download-package option works perfectly). I am then able to compile a PETSc library.<br></div><div>--with-package-lib=/usr/lib/libscalapack-openmpi.so or more generally --with-package-lib=libXXXX.so also works <br><br></div><div>But I would like to use  static librairies, preinstalled on my computer ... and  this fails.<br></div><div><br></div><div>For the moment I gave up compiling with MUMPS, and I am  instead trying to compile with Metis 5. <br></div><div>I have a preinstalled version in a some directory lets say metis_dir <br></div><div>I try <br>-with-metis-lib=[metis_dir/lib/libmetis.a, metis_dir/lib/libGKlib.a] --with-metis-include=metis_dir/include<br></div><div>this fails  (see the attached config.log)<br></div><div>-with-metis-dir=metis_dir also fails <br></div><div>Is there a problem with static librairies ? <br><span class="HOEnZb"><font color="#888888"><br></font></span></div><span class="HOEnZb"><font color="#888888"><div>Natacha <br></div><div><br></div></font></span></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Apr 12, 2016 at 6:19 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"><span>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 its<br>
> prerequisites).<br>
> More precisely I would like PETSc to use a pre-installed version of MUMPS.<br>
><br>
> Petsc downloads and compiles the prerequisites (parmetis, scalapack etc) :<br>
> this works fine.<br>
<br>
</span>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>
<span><br>
><br>
> I define MUMPS location by --with-mumps-dir=top-directory of MUMPS install,<br>
> but the<br>
> configure step  fails with the followiing message:<br>
><br>
> UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log for 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>
</span>Executing: mpicc -show<br>
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<br>
                  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"<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 -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<br>
Possible ERROR while running linker: exit code 256<br>
stderr:<br>
/home/H03755/Librairies/Mumps_MPI/lib/libdmumps.a(dlr_stats.o): In function `__dmumps_lr_stats_MOD_update_flop_stats_lrb_product':<br>
dlr_stats.F:(.text+0x3079): undefined reference to `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 `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 function `__dmumps_lr_stats_MOD_update_flop_stats_trsm':<br>
dlr_stats.F:(.text+0x33a9): undefined reference to `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 `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 function `__dmumps_lr_stats_MOD_update_flop_stats_panel':<br>
dlr_stats.F:(.text+0x3576): undefined reference to `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 `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 function `__dmumps_lr_stats_MOD_update_flop_stats_demote':<br>
dlr_stats.F:(.text+0x36ac): undefined reference to `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 `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 function `__dmumps_lr_stats_MOD_update_flop_stats_cb_demote':<br>
dlr_stats.F:(.text+0x37c1): undefined reference to `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 function `__dmumps_lr_stats_MOD_update_flop_stats_cb_promote':<br>
dlr_stats.F:(.text+0x3839): undefined reference to `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 `__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 option<br>
LIBS=-lgomp<br>
<br>
Wrt and PTSCOTCH stuff depending upon how its installed we'll have to figureout<br>
how to specify it.<br>
<br>
Its best to specify all the packages [mumps and its dependencies] you 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>
</blockquote></div><br></div>
</div></div></blockquote></div><br></div>