Does this crash on a PETSc example that uses elemental? For example run
src/ksp/ksp/examples/tests/ex40.c: with the arguments -pc_type lu -pc_factor_mat_solver_type elemental To get the stack trace Add the command line option -start_in_debugger noxterm when you run your program and when it starts up type c (for continue) when it crashes type bt (for backtrace) send all the output. Barry > On Aug 22, 2019, at 7:54 PM, Matthew Knepley <knep...@gmail.com> wrote: > > On Thu, Aug 22, 2019 at 8:45 PM Lailai Zhu via petsc-users > <petsc-users@mcs.anl.gov> wrote: > 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. > > It would be really helpful to get a stack trace from the debugger. > > Thanks, > > Matt > > > On 8/22/19 8:03 PM, Smith, Barry F. wrote: > > > >> On Aug 22, 2019, at 6:48 PM, Balay, Satish <ba...@mcs.anl.gov> wrote: > >> > >> Compilers are supposed to prefer libraries in specified -L path before > >> system stuff. > > Suppose to. > > > >> balay@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@es^~ $ > > This is really bad system management, there is no reason for them to be > > there nor should they be there. > > > > bsmith@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@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@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-ma...@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 > >>>>>>>>>>> > >>>>> > >>>>> > > > > -- > What most experimenters take for granted before they begin their experiments > is infinitely more interesting than any results to which their experiments > lead. > -- Norbert Wiener > > https://www.cse.buffalo.edu/~knepley/