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

Balay, Satish balay at mcs.anl.gov
Thu Aug 22 18:48:01 CDT 2019 

Compilers are supposed to prefer libraries in specified -L path before system stuff.

>>>>>>
balay at 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 at 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 <petsc-users at mcs.anl.gov> 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
> >>>>>> 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
> >>>>>>>> 
> >> 
> >> 
> >> 
>

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