Re: [petsc-users] errors when using elemental with petsc3.10.5
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 wrote: > > On Thu, Aug 22, 2019 at 8:45 PM Lailai Zhu via petsc-users > 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 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 => (0x7fff9115e000) > > libmpi.so.1 => /usr/lib/libmpi.so.1 (0x7faf95f87000) > > libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x7faf95c81000) > > libmetis.so.3.1 => /usr/lib/libmetis.so.3.1 (0x7faf95a34000) > > libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x7faf9566b000) > > libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 > > (0x7faf95468000) > > libhwloc.so.5 => /usr/lib/x86_64-linux-gnu/libhwloc.so.5 > > (0x7faf95228000) > > libltdl.so.7 => /usr/lib/x86_64-linux-gnu/libltdl.so.7 > > (0x7faf9501e000) > > libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 > > (0x7faf94e0) > > /lib64/ld-linux-x86-64.so.2 (0x7faf9654e000) > > libnuma.so.1 => > > /soft/com/packages/pgi/19.3/linux86-64/19.3/lib/libnuma.so.1 > > (0x7faf94bf5000) > > libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x7faf949f1000) > > > > 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 > 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? > >
Re: [petsc-users] errors when using elemental with petsc3.10.5
On Fri, 23 Aug 2019, Smith, Barry F. via petsc-users wrote: > bsmith@es:~$ ldd /usr/lib/libparmetis.so.3.1 > linux-vdso.so.1 => (0x7fff9115e000) > libmpi.so.1 => /usr/lib/libmpi.so.1 (0x7faf95f87000) > libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x7faf95c81000) > libmetis.so.3.1 => /usr/lib/libmetis.so.3.1 (0x7faf95a34000) > libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x7faf9566b000) > libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x7faf95468000) > libhwloc.so.5 => /usr/lib/x86_64-linux-gnu/libhwloc.so.5 > (0x7faf95228000) > libltdl.so.7 => /usr/lib/x86_64-linux-gnu/libltdl.so.7 > (0x7faf9501e000) > libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 > (0x7faf94e0) > /lib64/ld-linux-x86-64.so.2 (0x7faf9654e000) > libnuma.so.1 => > /soft/com/packages/pgi/19.3/linux86-64/19.3/lib/libnuma.so.1 > (0x7faf94bf5000) > libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x7faf949f1000) > > You have something in /usr/lib referring to something in > /soft/com/packages/pgi/ ?? Must be due to LD_LIBRARY_PATH. Checking back the original issue: LD_LIBRARY_PATH=/home/lailai/nonroot/mpi/mpich/3.3-intel19/lib:/opt/intel/lib/intel64:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib: Ok - all this stuff in LD_LIBRARY_PATH is the trigger of the original issue. Satish
Re: [petsc-users] errors when using elemental with petsc3.10.5
> On Aug 22, 2019, at 6:48 PM, Balay, Satish 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 => (0x7fff9115e000) libmpi.so.1 => /usr/lib/libmpi.so.1 (0x7faf95f87000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x7faf95c81000) libmetis.so.3.1 => /usr/lib/libmetis.so.3.1 (0x7faf95a34000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x7faf9566b000) libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x7faf95468000) libhwloc.so.5 => /usr/lib/x86_64-linux-gnu/libhwloc.so.5 (0x7faf95228000) libltdl.so.7 => /usr/lib/x86_64-linux-gnu/libltdl.so.7 (0x7faf9501e000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x7faf94e0) /lib64/ld-linux-x86-64.so.2 (0x7faf9654e000) libnuma.so.1 => /soft/com/packages/pgi/19.3/linux86-64/19.3/lib/libnuma.so.1 (0x7faf94bf5000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x7faf949f1000) 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 >>> 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
Re: [petsc-users] errors when using elemental with petsc3.10.5
Compilers are supposed to prefer libraries in specified -L path before system stuff. >> 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^~ $ 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 > > 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
Re: [petsc-users] errors when using elemental with petsc3.10.5
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 > 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,
Re: [petsc-users] errors when using elemental with petsc3.10.5
> ./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
Re: [petsc-users] errors when using elemental with petsc3.10.5
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 > > >> > >
Re: [petsc-users] errors when using elemental with petsc3.10.5
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 > >> > >
Re: [petsc-users] errors when using elemental with petsc3.10.5
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 >
