Hi Jean-Paul, Thank you for your suggestion. I shall try the installation process with fewer processors(perhaps 4) and if even that doesn't work, then I will try it in serial.
Best, Aaditya On Friday, August 21, 2020 at 1:07:54 PM UTC-4 Jean-Paul Pelteret wrote: > Hi Aaditaya, > > I don’t think that I’ve ever seen anyone have this problem before. We > build the expand_instantiations binary, and its supposed to be used when > expanding files in which we define various combinations of template > parameters to instantiate templates within the library. If you’re > interested, you can read more about this here > https://dealii.org/current/doxygen/deal.II/CodingConventions.html > under the "Instantiation of templated functions" section. > > I’m not at all sure what’s gone wrong, but what might be happening is that > by building in parallel with so many processes you somehow manage to get to > an object that requires some template parameter expansions before this > expand_instantiations binary has finished building. Perhaps you can try > building in serial (or with fewer process) for a little bit, and then > cancel once you see that you’re definitely at a point where the main > library object modules are being compiled. > > Perhaps there’s something more that we can do from our side if this is > indeed the cause of the problem, but that would be a question for Matthias > (who manages our CMake configuration) to answer. I’m not sure if we can > somehow delay all other tasks until expand_instantiations binary has been > built. > > I hope that this helps you to resolve the issue. > > Best, > Jean-Paul > > > On 20 Aug 2020, at 16:16, Aaditya Lakshmanan <aadit...@gmail.com> wrote: > > Hi Everyone, > > I have been trying to install deal.ii on NERSC Cori > cluster for use on the KNL compute nodes using the following procedure : > > > Clone and setup : > > *git clone --single-branch --branch dealii-9.1 * > *https://github.com/dealii/dealii.git* > <https://github.com/dealii/dealii.git> > > *mkdir build* > > *mkdir dealii_trial* > > *cd build * > > > Build and install on an interactive node : > > *cmake -DCMAKE_SYSTEM_NAME=CrayLinuxEnvironment -DCMAKE_C_COMPILER=cc > -DCMAKE_CXX_COMPILER=CC -DCMAKE_Fortran_COMPILER=ftn -DDEAL_II_WITH_MPI=ON > -DDEAL_II_WITH_PETSC=ON -DDEAL_II_WITH_P4EST=ON > -DDEAL_II_WITH_LAPACK=ON > -DCMAKE_INSTALL_PREFIX=/global/project/projectdirs/m2360/packagesCPFE/dealii_trial/ > > ../dealii* > > which completes without any issues after which > > > *make -j 32 install* > > eventually yields the following error : > > -------------------------------------------------------------------------- > > [ 27%] Building CXX object > bundled/umfpack/AMD/Source/CMakeFiles/obj_amd_long_debug.dir/amd_defaults.cc.o > > /bin/sh: expand_instantiations: command not found > > make[2]: *** > [source/numerics/CMakeFiles/obj_numerics_inst.dir/build.make:91: > source/numerics/data_out_dof_data.inst] Error 127 > > make[2]: *** Waiting for unfinished jobs.... > > --------------------------------------------------------------------------- > > Details on procedure before cloning deal.ii are included below : > > (i) I first loaded the necessary modules so that *module list* displayed > > Currently Loaded Modulefiles: > > 1) modules/3.2.11.4 16) > rca/2.2.20-7.0.1.1_4.46__g8e3fb5b.ari > > 2) > altd/2.0 > 17) > atp/2.1.3 > > 3) > darshan/3.1.7 18) > PrgEnv-intel/6.0.5 > > 4) intel/19.0.3.199 > 19) > craype-mic-knl > > 5) craype-network-aries 20) > cray-mpich/7.7.14 > > 6) > craype/2.6.2 21) > craype-hugepages2M > > 7) udreg/2.3.2-7.0.1.1_3.31__g8175d3d.ari 22) valgrind/3.15.0 > > 8) ugni/6.0.14.0-7.0.1.1_7.33__ge78e5b0.ari 23) zlib/1.2.11 > > 9) > pmi/5.0.14 > 24) > metis/5.1.0 > > 10) dmapp/7.1.1-7.0.1.1_4.48__g38cf134.ari 25) parmetis/4.0.3 > > 11) gni-headers/5.0.12.0-7.0.1.1_6.28__g3b1768f.ari 26) > superlu-dist/6.1.1 > > 12) xpmem/2.2.20-7.0.1.1_4.10__g0475745.ari 27) hypre/2.15.1 > > 13) job/2.2.4-7.0.1.1_3.36__g36b56f4.ari 28) > cmake/3.14.4 > > 14) dvs/2.12_2.2.156-7.0.1.1_8.9__g5aab709e 29) cray-hdf5/ > 1.10.2.0 > > 15) alps/6.6.58-7.0.1.1_6.4__g437d88db.ari 30) > petsc-real-64/3.11.2 > > > (ii) Set environment variables for dynamic linking > > *export XTPE_LINK_TYPE=dynamic* > > *export CRAYPE_LINK_TYPE=dynamic* > > > (iii) p4est installation > > *./configure --prefix=/global/project/projectdirs/m2360/packagesCPFE/p4est > --host=x86_64 --enable-vtk-zlib=yes --enable-mpi=yes F77=ftn FC=ftn CC=cc > CXX=CC* > > *make -j 32* > > *make -j 32 install * > > *export P4EST_DIR=/global/project/projectdirs/m2360/packagesCPFE/p4est* > > I did initially submit a ticket on NERSC support for assistance with the > installation process and after a few iterations, the person( > https://github.com/JBlaschke) helping me out asked me to contact the > developers. I would really appreciate your help on this. > > Thank you. > > > > -- > 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+un...@googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/dealii/aaff8931-185f-46d0-8f2c-eb535ae9428en%40googlegroups.com > > <https://groups.google.com/d/msgid/dealii/aaff8931-185f-46d0-8f2c-eb535ae9428en%40googlegroups.com?utm_medium=email&utm_source=footer> > . > > > -- 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. 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