Hello there, I'm currently building dealii via candi on a brand new cluster and I am facing a few issues.
First, this is what I am compiling with 1) nixpkgs/.16.09 3) gcccore/.5.4.0 5) openmpi/2.1.1 2) StdEnv/2016.4 4) gcc/5.4.0 6) imkl/11.3.4.258 GNU bash, version 4.3.48(1)-release (x86_64-unknown-linux-gnu) The first issue was related to bash, where a workaround was provided here: https://groups.google.com/forum/#!topic/dealii/0qa82g629OQ unset -f module unset -f ml Then, I ran into this issue "CMake stuck at Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG with -Wl,--as-needed and ld.bfd" https://github.com/dealii/dealii/issues/3686 where I applied the workaround of deleting the offending lines in cmake/setup_finalize.cmake However, now dealii compiles but fails all tests with these issues: /cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: error: undefined reference to .... /cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_intel_lp64.so: error: undefined reference to 'strrchr' /cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_intel_lp64.so: error: undefined reference to 'getcwd' etc ../../lib/libdeal_II.g.so.8.5.0: error: undefined reference to 'pthread_mutexattr_init' ../../lib/libdeal_II.g.so.8.5.0: error: undefined reference to 'pthread_mutexattr_settype' ../../lib/libdeal_II.g.so.8.5.0: error: undefined reference to 'pthread_mutexattr_destroy' ../../lib/libdeal_II.g.so.8.5.0: error: undefined reference to 'pthread_mutex_trylock' etc I'm guessing there are some issues with linker flags - where shall I implement these in the candi build? I feel like this is a MKL problem perhaps, similar to: https://software.intel.com/en-us/forums/intel-math-kernel-library/topic/295086 https://software.intel.com/en-us/articles/symbol-lookup-error-when-linking-intel-mkl-with-gcc-on-ubuntu I'm building with dealii 8.5.0. Thanks in advance for your help! Phil -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
