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 >>>>>>>> >> >> >>
