[petsc-users] errors when using elemental with petsc3.10.5

[Balay, Satish]

> ./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
> >>>> petsc-maint at mcs.anl.gov
> >>>>
> >>>> 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
> >>>>>>
> 
> 
>