Compilers are supposed to prefer libraries in specified -L path before system stuff.
>>>>>> balay@es^~ $ ls /usr/lib/lib*metis* /usr/lib/libmetis.a /usr/lib/libmetis.so.3.1 /usr/lib/libparmetis.so@ /usr/lib/libscotchmetis-5.1.so /usr/lib/libscotchmetis.so@ /usr/lib/libmetis.so@ /usr/lib/libparmetis.a /usr/lib/libparmetis.so.3.1 /usr/lib/libscotchmetis.a balay@es^~ $ <<<< And we have these files installed and they don't cause problems. And its not always practical to uninstall system stuff [esp on multi-user machines] Satish On Thu, 22 Aug 2019, Smith, Barry F. wrote: > > You have a copy of parmetis installed in /usr/lib this is a systems > directory and many compilers and linkers automatically find libraries in that > location and it is often difficult to avoid have the compilers/linkers use > these. In general you never want to install external software such as > parmetis, PETSc, MPI, etc in systems directories (/usr/ and /usr/local) > > You should delete this library (and the includes in /usr/include) > > Barry > > > > > > On Aug 22, 2019, at 5:17 PM, Balay, Satish via petsc-users > > <[email protected]> wrote: > > > > > >> ./ex19: symbol lookup error: /usr/lib/libparmetis.so: undefined symbol: > >> ompi_mpi_comm_world > > > > For some reason the wrong parmetis library is getting picked up. I don't > > know why. > > > > Can you copy/paste the log from the following? > > > > cd src/snes/examples/tutorials > > make PETSC_DIR=/home/lailai/nonroot/petsc/petsc3.11.3_intel19_mpich3.3 ex19 > > ldd ex19 > > > > cd > > /home/lailai/nonroot/petsc/petsc3.11.3_intel19_mpich3.3/pet3.11.3-intel19-mpich3.3/lib > > ldd *.so > > > > Satish > > > > On Thu, 22 Aug 2019, Lailai Zhu via petsc-users wrote: > > > >> hi, Satish, > >> > >> as you have suggested, i compiled a new version using 3.11.3, > >> it compiles well, the errors occur in checking. i also attach > >> the errors of check. thanks very much, > >> > >> lailai > >> > >> On 8/22/19 4:16 PM, Balay, Satish wrote: > >>> Any reason for using petsc-3.10.5 and not latest petsc-3.11? > >>> > >>> I suggest starting from scatch and rebuilding. > >>> > >>> And if you still have issues - send corresponding configure.log and > >>> make.log > >>> > >>> Satish > >>> > >>> On Thu, 22 Aug 2019, Lailai Zhu via petsc-users wrote: > >>> > >>>> sorry, Satish, > >>>> > >>>> but it does not seem to solve the problem. > >>>> > >>>> best, > >>>> lailai > >>>> > >>>> On 8/22/19 12:41 AM, Balay, Satish wrote: > >>>>> Can you run 'make' again and see if this error goes away? > >>>>> > >>>>> Satish > >>>>> > >>>>> On Wed, 21 Aug 2019, Lailai Zhu via petsc-users wrote: > >>>>> > >>>>>> hi, Satish, > >>>>>> i tried to do it following your suggestion, i get the following errors > >>>>>> when > >>>>>> installing. > >>>>>> here is my configuration, > >>>>>> > >>>>>> any ideas? > >>>>>> > >>>>>> best, > >>>>>> lailai > >>>>>> > >>>>>> ./config/configure.py --with-c++-support --known-mpi-shared-libraries=1 > >>>>>> --with-batch=0 --with-mpi=1 --with-debugging=0 CXXOPTFLAGS="-g -O3" > >>>>>> COPTFLAGS="-O3 -ip -axCORE-AVX2 -xSSE4.2" FOPTFLAGS="-O3 -ip > >>>>>> -axCORE-AVX2 > >>>>>> -xSSE4.2" --with-blas-lapack-dir=/opt/intel/mkl --download-elemental=1 > >>>>>> --download-blacs=1 --download-scalapack=1 --download-hypre=1 > >>>>>> --download-plapack=1 --with-cc=mpicc --with-cxx=mpic++ > >>>>>> --with-fc=mpifort > >>>>>> --download-amd=1 --download-anamod=1 --download-blopex=1 > >>>>>> --download-dscpack=1 --download-sprng=1 --download-superlu=1 > >>>>>> --with-cxx-dialect=C++11 --download-metis --download-parmetis > >>>>>> > >>>>>> > >>>>>> > >>>>>> pet3.10.5-intel19-mpich3.3/obj/mat/impls/sbaij/seq/sbaij.o: In function > >>>>>> `MatCreate_SeqSBAIJ': > >>>>>> sbaij.c:(.text+0x1bc45): undefined reference to > >>>>>> `MatConvert_SeqSBAIJ_Elemental' > >>>>>> ld: pet3.10.5-intel19-mpich3.3/obj/mat/impls/sbaij/seq/sbaij.o: > >>>>>> relocation > >>>>>> R_X86_64_PC32 against undefined hidden symbol > >>>>>> `MatConvert_SeqSBAIJ_Elemental' > >>>>>> can not be used when making a shared object > >>>>>> ld: final link failed: Bad value > >>>>>> gmakefile:86: recipe for target > >>>>>> 'pet3.10.5-intel19-mpich3.3/lib/libpetsc.so.3.10.5' failed > >>>>>> make[2]: *** [pet3.10.5-intel19-mpich3.3/lib/libpetsc.so.3.10.5] Error > >>>>>> 1 > >>>>>> make[2]: Leaving directory > >>>>>> '/usr/nonroot/petsc/petsc3.10.5_intel19_mpich3.3' > >>>>>> ........................../petsc3.10.5_intel19_mpich3.3/lib/petsc/conf/rules:81: > >>>>>> recipe for target 'gnumake' failed > >>>>>> make[1]: *** [gnumake] Error 2 > >>>>>> make[1]: Leaving directory > >>>>>> '/usr/nonroot/petsc/petsc3.10.5_intel19_mpich3.3' > >>>>>> **************************ERROR************************************* > >>>>>> Error during compile, check > >>>>>> pet3.10.5-intel19-mpich3.3/lib/petsc/conf/make.log > >>>>>> Send it and pet3.10.5-intel19-mpich3.3/lib/petsc/conf/configure.log > >>>>>> to > >>>>>> [email protected] > >>>>>> > >>>>>> On 8/21/19 10:58 PM, Balay, Satish wrote: > >>>>>>> To install elemental - you use: --download-elemental=1 [not > >>>>>>> --download-elemental-commit=v0.87.7] > >>>>>>> > >>>>>>> Satish > >>>>>>> > >>>>>>> > >>>>>>> On Wed, 21 Aug 2019, Lailai Zhu via petsc-users wrote: > >>>>>>> > >>>>>>>> hi, dear petsc developers, > >>>>>>>> > >>>>>>>> I am having a problem when using the external solver elemental. > >>>>>>>> I installed petsc3.10.5 version with the flag > >>>>>>>> --download-elemental-commit=v0.87.7 > >>>>>>>> the installation seems to be ok. However, it seems that i may not be > >>>>>>>> able > >>>>>>>> to use the elemental solver though. > >>>>>>>> > >>>>>>>> I followed this page > >>>>>>>> https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MATELEMENTAL.html > >>>>>>>> to interface the elemental solver, namely, > >>>>>>>> MatSetType(A,MATELEMENTAL); > >>>>>>>> or set it via the command line '*-mat_type elemental*', > >>>>>>>> > >>>>>>>> in either case, i will get the following error, > >>>>>>>> > >>>>>>>> [0]PETSC ERROR: --------------------- Error Message > >>>>>>>> -------------------------------------------------------------- > >>>>>>>> [0]PETSC ERROR: Unknown type. Check for miss-spelling or missing > >>>>>>>> package: > >>>>>>>> http://www.mcs.anl.gov/petsc/documentation/installation.html#external > >>>>>>>> [0]PETSC ERROR: Unknown Mat type given: elemental > >>>>>>>> [0]PETSC ERROR: See > >>>>>>>> http://www.mcs.anl.gov/petsc/documentation/faq.html > >>>>>>>> for > >>>>>>>> trouble shooting. > >>>>>>>> [0]PETSC ERROR: Petsc Release Version 3.10.5, Mar, 28, 2019 > >>>>>>>> > >>>>>>>> May i ask whether there will be a way or some specific petsc versions > >>>>>>>> that > >>>>>>>> are > >>>>>>>> able to use the elemental solver? > >>>>>>>> > >>>>>>>> Thanks in advance, > >>>>>>>> > >>>>>>>> best, > >>>>>>>> lailai > >>>>>>>> > >> > >> > >> >
