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

Thu Aug 22 18:13:45 CDT 2019

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