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.
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
