Hi Aaditya, it looks like you are cross compiling due to the cray system you are on? I don't have first-hand experience, but I know some users have had success with it in the past.
The error message stems from the fact that we build a small tool "expand_instantiations" during the build process. If you are cross compiling, this executable obviously won't work, so the rest of the build fails. Take a look at https://dealii.org/9.2.0/developers/porting.html (search for expand_instantiations) and let us know if that helps. Best, Timo On Fri, Aug 21, 2020 at 2:52 PM Aaditya Lakshmanan <aaditya8...@gmail.com> wrote: > > Hi Jean-Paul, > I cleaned the previous installation, deleted all the files generated in > the build directory and attempted a fresh build process as follows : > > 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 ran successfully after which I tried installing deal.ii via > > make -j 4 install > > which exited with the following error(just as before) : > > [ 40%] Building CXX object > bundled/muparser_v2_2_4/CMakeFiles/obj_muparser_release.dir/src/muParserTest.cpp.o > [ 40%] Generating data_out_dof_data.inst > /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[1]: *** [CMakeFiles/Makefile2:3074: > source/numerics/CMakeFiles/obj_numerics_inst.dir/all] Error 2 > make[1]: *** Waiting for unfinished jobs.... > [ 41%] Built target obj_muparser_debug > [ 41%] Generating fe_abf.inst > > In the build/bin directory there is a file expand_instantiations of the > following type : > > expand_instantiations: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), > dynamically linked, interpreter /lib64/l, > BuildID[sha1]=3ee25c761ad827a88f618b972735b201bc6a2bbe, for GNU/Linux 3.2.0, > with debug_info, not stripped > > Is that the file you were referring to earlier? I have attached the > detailed.log file generated in the build directory. Let me know if you need > any more information from me. Thank you for your help. > > Best, > Aaditya > > On Friday, August 21, 2020 at 2:03:59 PM UTC-4 Jean-Paul Pelteret wrote: >> >> Hi Aaditya, >> >> Great, let us know if that works for you. You should see the >> expand_instantiations binary appear in the “bin” sub-directory with your >> build folder. If it still doesn’t appear there, then perhaps you could >> create a new build directory and then post the configuration and full build >> logs that come from a fresh build. It could also be that this utility >> program is failing to build. >> >> Best, >> Jean-Paul >> >> On 21 Aug 2020, at 19:37, Aaditya Lakshmanan <aadit...@gmail.com> wrote: >> >> 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 >>> >>> 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. >>> >>> >> >> -- >> 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/0b6d6ab9-f630-4517-a2a0-7106604aa391n%40googlegroups.com. >> >> > -- > 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. > To view this discussion on the web visit > https://groups.google.com/d/msgid/dealii/a2e65ec8-9691-4fbc-9722-182304e229d8n%40googlegroups.com. -- Timo Heister http://www.math.clemson.edu/~heister/ -- 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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