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

Lailai Zhu julyzll06 at gmail.com
Thu Aug 22 19:44:12 CDT 2019 

Thank you guys,  after i remove the system's metis-related things,
it compiles well and go through the check. however when i try to
use the elemental solver, it still does not work out. i basically get
the segmentation fault error, which does not appear when i use
the standard dense matrix and jacobi sovers. thanks in advance,

best,
lailai

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, 
probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see 
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS 
X to find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, 
and run
[0]PETSC ERROR: to get more information on the crash.


On 8/22/19 8:03 PM, Smith, Barry F. wrote:
>
>> On Aug 22, 2019, at 6:48 PM, Balay, Satish <balay at mcs.anl.gov> wrote:
>>
>> Compilers are supposed to prefer libraries in specified -L path before system stuff.
>    Suppose to.
>
>> 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^~ $
>    This is really bad system management, there is no reason for them to be there nor should they be there.
>
> bsmith at es:~$ ldd /usr/lib/libparmetis.so.3.1
> 	linux-vdso.so.1 =>  (0x00007fff9115e000)
> 	libmpi.so.1 => /usr/lib/libmpi.so.1 (0x00007faf95f87000)
> 	libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007faf95c81000)
> 	libmetis.so.3.1 => /usr/lib/libmetis.so.3.1 (0x00007faf95a34000)
> 	libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007faf9566b000)
> 	libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007faf95468000)
> 	libhwloc.so.5 => /usr/lib/x86_64-linux-gnu/libhwloc.so.5 (0x00007faf95228000)
> 	libltdl.so.7 => /usr/lib/x86_64-linux-gnu/libltdl.so.7 (0x00007faf9501e000)
> 	libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007faf94e00000)
> 	/lib64/ld-linux-x86-64.so.2 (0x00007faf9654e000)
> 	libnuma.so.1 => /soft/com/packages/pgi/19.3/linux86-64/19.3/lib/libnuma.so.1 (0x00007faf94bf5000)
> 	libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007faf949f1000)
>
> You have something in /usr/lib referring to something in /soft/com/packages/pgi/  ??
>
> and of course that refers back to
>
> bsmith at es:~$ ls -l /soft/com/packages/pgi/19.3/linux86-64/19.3/lib/libnuma.so.1
> lrwxrwxrwx 1 fritz voice 38 Mar 29 15:59 /soft/com/packages/pgi/19.3/linux86-64/19.3/lib/libnuma.so.1 -> /usr/lib/x86_64-linux-gnu/libnuma.so.1
>
> I stand by my statement, it is bad policy to put any stuff like this in system directories.
>
>
>> <<<<
>>
>> 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]
>    I agree it is not always practical or possible to remove them.
>
>    barry
>
>> 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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