On Sat, 2 Aug 2014 09:24:58 +0100 "Garth N. Wells" <[email protected]> wrote:
> I’ve just had this problem. Try adding -DDOLFIN_ENABLE_OPENMP=off > > By default, DOLFIN will enable OpenMP and add the flag -openmp, and > with this flag Intel MPI will link to the threaded MPI libraries. If > PETSc was not built with threaded MPI, I then I get the the reported > error when linking DOLFIN. Disabling OpenMP in DOLFIN fixes this > issue for me. Note that current PETSc stable 3.5.1 does not allow any of these PETSc configuring flags --with-openmp --with-pthreadclasses --with-threadcomm. Build system suggests using dev version for using these. Jan > > Garth > > On 30 Jul 2014, at 23:46, Chang, Christopher > <[email protected]> wrote: > > > Thanks Jan, I'll try a simpler build first. > > > > -----Original Message----- > > From: Jan Blechta [mailto:[email protected]] > > Sent: Monday, July 28, 2014 3:36 PM > > To: Chang, Christopher > > Cc: [email protected] > > Subject: Re: [FEniCS-support] Installation--PETSc test failing > > > > [Please, post CMakeError.log again to > > [email protected] and keep it in CC] > > > > There is problem in linking > > --------------------------------------------------------------- > > ld: MPIR_Thread: TLS definition > > in /nopt/nrel/apps/impi/4.1.1.036/intel64/lib/libmpi_dbg_mt.so > > section .tbss mismatches non-TLS definition > > in /nopt/nrel/apps/impi/4.1.1.036/intel64/lib/libmpi.so > > section .bss /nopt/nrel/apps/impi/4.1.1.036/intel64/lib/libmpi_dbg_mt.so: > > could not read symbols: Bad value > > --------------------------------------------------------------- > > which guides us to some discussions, e.g. > > https://software.intel.com/en-us/forums/topic/392483. You could try > > disabling threads and/or OpenMP in PETSc. > > > > Jan > > > > > > On Mon, 28 Jul 2014 14:57:15 -0600 > > "Chang, Christopher" <[email protected]> wrote: > > > >> Jan, > >> > >> Thanks! Attached. > >> > >> -----Original Message----- > >> From: Jan Blechta [mailto:[email protected]] > >> Sent: Monday, July 28, 2014 2:20 PM > >> To: Chang, Christopher > >> Cc: [email protected] > >> Subject: Re: [FEniCS-support] Installation--PETSc test failing > >> > >> Ok. Attach, please, CMakeError.log. > >> > >> Jan > >> > >> > >> On Mon, 28 Jul 2014 13:47:11 -0600 > >> "Chang, Christopher" <[email protected]> wrote: > >> > >>> Hi Jan, > >>> > >>> Thanks. I realized I left out some other useful information in > >>> addition to the version. I should have said, I'm trying to build > >>> Dolfin. UFL, FFC, Fiat, and instant went in OK. I am building > >>> Dolfin from the Git repo, > >>> https://bitbucket.org/fenics-project/dolfin.git . The last > >>> timestamp in the log was on July 22, 2014. Unfortunately, > >>> petsc4py wouldn't build against PETSc < 3.5. I guess I could keep > >>> multiple PETSc installation handy, but I was hoping to avoid it. > >>> > >>> Thanks, > >>> > >>> Chris > >>> > >>> -----Original Message----- > >>> From: Jan Blechta [mailto:[email protected]] > >>> Sent: Monday, July 28, 2014 1:39 PM > >>> To: Chang, Christopher > >>> Cc: [email protected] > >>> Subject: Re: [FEniCS-support] Installation--PETSc test failing > >>> > >>> Which version of FEniCS are trying to build? Only current FEniCS > >>> dev works with PETSc 3.5. Pick PETSc 3.4 for building FEniCS 1.4 > >>> release. > >>> > >>> Jan > >>> > >>> > >>> On Mon, 28 Jul 2014 13:31:32 -0600 > >>> "Chang, Christopher" <[email protected]> wrote: > >>> > >>>> Hi, > >>>> > >>>> I am trying to install FEniCS from source, building with the > >>>> Intel tools. I have succeeded in building and installing PETSc > >>>> 3.5.1 and petsc4py, and have pointed CMake to the relevant > >>>> locations. However, during the "cmake ." stage of the build, I > >>>> get > >>>> > >>>> -- Checking for package 'PETSc' > >>>> -- PETSC_DIR is /home/cchang/petsc-3.5.1 > >>>> -- PETSC_ARCH is impi-intel > >>>> -- Found petscconf.h > >>>> -- Performing test PETSC_TEST_RUNS - Failed > >>>> -- Performing test PETSC_TEST_3RD_PARTY_LIBS_RUNS - Failed > >>>> -- PETSc configured without Cusp support > >>>> -- PETSc could not be found. Be sure to set PETSC_DIR and > >>>> PETSC_ARCH. (missing: PETSC_TEST_RUNS) > >>>> > >>>> I can't troubleshoot further, because I don't know where the > >>>> output of whatever tests are being done is. Can anyone tell what > >>>> is going wrong with the build from output above? > >>>> > >>>> Thanks, > >>>> > >>>> Chris > >>>> > >>>> -- > >>>> Christopher H. Chang, Ph.D. > >>>> Computational Scientist IV > >>>> National Renewable Energy Laboratory > >>>> 15013 Denver West Parkway, MS ESIF301 Golden, CO 80401 Phone > >>>> (303) 275-3751 Fax (303) 275-4007 > >>>> > >>> > >>> _______________________________________________ > >>> fenics-support mailing list > >>> [email protected] > >>> http://fenicsproject.org/mailman/listinfo/fenics-support > >> > > > > _______________________________________________ > > fenics-support mailing list > > [email protected] > > http://fenicsproject.org/mailman/listinfo/fenics-support > > _______________________________________________ > fenics-support mailing list > [email protected] > http://fenicsproject.org/mailman/listinfo/fenics-support _______________________________________________ fenics-support mailing list [email protected] http://fenicsproject.org/mailman/listinfo/fenics-support
