> 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 >>>>>>>>>> >>>> >>>> >>>> >> >
Re: [petsc-users] errors when using elemental with petsc3.10.5
Smith, Barry F. via petsc-users Thu, 22 Aug 2019 17:04:24 -0700
- Re: [petsc-users] errors when using elemen... Balay, Satish via petsc-users
- Re: [petsc-users] errors when using e... Balay, Satish via petsc-users
- Re: [petsc-users] errors when usi... Balay, Satish via petsc-users
- Re: [petsc-users] errors when... Balay, Satish via petsc-users
- Re: [petsc-users] errors ... Smith, Barry F. via petsc-users
- Re: [petsc-users] er... Balay, Satish via petsc-users
- Re: [petsc-users... Smith, Barry F. via petsc-users
- Re: [petsc-u... Balay, Satish via petsc-users
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