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* >> <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. > 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 > > <https://groups.google.com/d/msgid/dealii/0b6d6ab9-f630-4517-a2a0-7106604aa391n%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. 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.
### # # deal.II configuration: # CMAKE_BUILD_TYPE: DebugRelease # BUILD_SHARED_LIBS: ON # CMAKE_INSTALL_PREFIX: /global/project/projectdirs/m2360/packagesCPFE/dealii_trial # CMAKE_SOURCE_DIR: /global/project/projectdirs/m2360/packagesCPFE/dealii # (version 9.1.1, shortrev 777cf92a41) # CMAKE_BINARY_DIR: /global/project/projectdirs/m2360/packagesCPFE/build # CMAKE_CXX_COMPILER: Intel 19.0.0.20190206 on platform CrayLinuxEnvironment x86_64 # /opt/cray/pe/craype/2.6.2/bin/CC # CMAKE_C_COMPILER: /opt/cray/pe/craype/2.6.2/bin/cc # CMAKE_Fortran_COMPILER: /opt/cray/pe/craype/2.6.2/bin/ftn # CMAKE_GENERATOR: Unix Makefiles # # CROSSCOMPILING! # # Base configuration (prior to feature configuration): # DEAL_II_CXX_FLAGS: -fpic -ansi -w2 -diag-disable=remark -wd21 -wd68 -wd135 -wd175 -wd177 -wd191 -wd193 -wd279 -wd327 -wd383 -wd981 -wd1418 -wd1478 -wd1572 -wd2259 -wd2536 -wd2651 -wd3415 -wd15531 -wd111 -wd128 -wd185 -wd186 -wd280 -std=c++17 # DEAL_II_CXX_FLAGS_RELEASE: -O2 -no-ansi-alias -ip -funroll-loops # DEAL_II_CXX_FLAGS_DEBUG: -O0 -g -gdwarf-2 -grecord-gcc-switches # DEAL_II_LINKER_FLAGS: -Wl,--as-needed -shared-intel -rdynamic # DEAL_II_LINKER_FLAGS_RELEASE: # DEAL_II_LINKER_FLAGS_DEBUG: # DEAL_II_DEFINITIONS: # DEAL_II_DEFINITIONS_RELEASE: # DEAL_II_DEFINITIONS_DEBUG: DEBUG # DEAL_II_USER_DEFINITIONS: # DEAL_II_USER_DEFINITIONS_REL: # DEAL_II_USER_DEFINITIONS_DEB: DEBUG # DEAL_II_INCLUDE_DIRS # DEAL_II_USER_INCLUDE_DIRS: # DEAL_II_BUNDLED_INCLUDE_DIRS: # DEAL_II_LIBRARIES: # DEAL_II_LIBRARIES_RELEASE: # DEAL_II_LIBRARIES_DEBUG: # DEAL_II_COMPILER_VECTORIZATION_LEVEL: 0 # # Configured Features (DEAL_II_ALLOW_BUNDLED = ON, DEAL_II_ALLOW_AUTODETECTION = ON): # ( DEAL_II_WITH_64BIT_INDICES = OFF ) # ( DEAL_II_WITH_ADOLC = OFF ) # ( DEAL_II_WITH_ARPACK = OFF ) # ( DEAL_II_WITH_ASSIMP = OFF ) # DEAL_II_WITH_BOOST set up with bundled packages # BOOST_BUNDLED_INCLUDE_DIRS = /global/project/projectdirs/m2360/packagesCPFE/dealii/bundled/boost-1.62.0/include # BOOST_LIBRARIES = rt # DEAL_II_WITH_COMPLEX_VALUES = ON # ( DEAL_II_WITH_CUDA = OFF ) # DEAL_II_WITH_CXX14 = ON # DEAL_II_WITH_CXX17 = ON # ( DEAL_II_WITH_GINKGO = OFF ) # ( DEAL_II_WITH_GMSH = OFF ) # ( DEAL_II_WITH_GSL = OFF ) # ( DEAL_II_WITH_HDF5 = OFF ) # DEAL_II_WITH_LAPACK set up with external dependencies # LAPACK_WITH_64BIT_BLAS_INDICES = OFF # LAPACK_LINKER_FLAGS = # LAPACK_INCLUDE_DIRS = # LAPACK_USER_INCLUDE_DIRS = # LAPACK_LIBRARIES = /opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_intel_lp64.so;/opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_intel_thread.so;/opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_core.so;/opt/intel/compilers_and_libraries_2019.3.199/linux/compiler/lib/intel64/libiomp5.so;-lm;-ldl;hugetlbfs;AtpSigHandler;AtpSigHCommData;z;hdf5_hl;hdf5;hdf5hl_fortran;hdf5_fortran;mpich_intel;mpichf90_intel;ifport;ifcoremt;imf;m;ipgo;irc;pthread;svml;gcc;gcc_s;irc_s;dl;c # DEAL_II_WITH_METIS set up with external dependencies # METIS_VERSION = 5.1.0 # METIS_DIR = /global/common/sw/cray/cnl7/haswell/metis/5.1.0/intel/19.0.3.199/fpy6uzj # METIS_INCLUDE_DIRS = /global/common/sw/cray/cnl7/haswell/metis/5.1.0/intel/19.0.3.199/fpy6uzj/include # METIS_USER_INCLUDE_DIRS = /global/common/sw/cray/cnl7/haswell/metis/5.1.0/intel/19.0.3.199/fpy6uzj/include # METIS_LIBRARIES = /global/common/sw/cray/cnl7/haswell/metis/5.1.0/intel/19.0.3.199/fpy6uzj/lib/libmetis.a # DEAL_II_WITH_MPI set up with external dependencies # MPI_VERSION = 3.1 # MPI_C_COMPILER = /opt/cray/pe/craype/2.6.2/bin/cc # MPI_CXX_COMPILER = /opt/cray/pe/craype/2.6.2/bin/CC # MPI_Fortran_COMPILER = /opt/cray/pe/craype/2.6.2/bin/ftn # MPI_CXX_FLAGS = # MPI_LINKER_FLAGS = # MPI_INCLUDE_DIRS = # MPI_USER_INCLUDE_DIRS = # MPI_LIBRARIES = # DEAL_II_WITH_MUPARSER set up with bundled packages # MUPARSER_BUNDLED_INCLUDE_DIRS = /global/project/projectdirs/m2360/packagesCPFE/dealii/bundled/muparser_v2_2_4//include # ( DEAL_II_WITH_NANOFLANN = OFF ) # ( DEAL_II_WITH_NETCDF = OFF ) # ( DEAL_II_WITH_OPENCASCADE = OFF ) # DEAL_II_WITH_P4EST set up with external dependencies # P4EST_VERSION = 2.2 # P4EST_DIR = /global/project/projectdirs/m2360/packagesCPFE/p4est # P4EST_INCLUDE_DIRS = /global/project/projectdirs/m2360/packagesCPFE/p4est/include # P4EST_USER_INCLUDE_DIRS = /global/project/projectdirs/m2360/packagesCPFE/p4est/include # P4EST_LIBRARIES = /global/project/projectdirs/m2360/packagesCPFE/p4est/lib/libp4est.a;/global/project/projectdirs/m2360/packagesCPFE/p4est/lib/libsc.a;/opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_intel_lp64.so;/opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_intel_thread.so;/opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_core.so;/opt/intel/compilers_and_libraries_2019.3.199/linux/compiler/lib/intel64/libiomp5.so;-lm;-ldl;hugetlbfs;AtpSigHandler;AtpSigHCommData;z;hdf5_hl;hdf5;hdf5hl_fortran;hdf5_fortran;mpich_intel;mpichf90_intel;ifport;ifcoremt;imf;m;ipgo;irc;pthread;svml;gcc;gcc_s;irc_s;dl;c # DEAL_II_WITH_PETSC set up with external dependencies # PETSC_VERSION = 3.11.2.0 # PETSC_DIR = /global/common/sw/cray/cnl7/haswell/petsc/3.11.2/intel/19.0.3.199/hocbntp # PETSC_INCLUDE_DIRS = /global/common/sw/cray/cnl7/haswell/petsc/3.11.2/intel/19.0.3.199/hocbntp/include;/global/common/sw/cray/cnl7/haswell/hypre/2.15.1/intel/19.0.3.199/2jbygqt/include;/global/common/sw/cray/cnl7/haswell/superlu-dist/6.1.1/intel/19.0.3.199/vnkv5xn/include;/opt/cray/pe/hdf5/1.10.2.0/INTEL/16.0/include;/global/common/sw/cray/cnl7/haswell/parmetis/4.0.3/intel/19.0.3.199/koc2n7v/include;/global/common/sw/cray/cnl7/haswell/metis/5.1.0/intel/19.0.3.199/fpy6uzj/include;/global/common/sw/cray/cnl7/haswell/zlib/1.2.11/intel/19.0.3.199/si6pos6/include # PETSC_USER_INCLUDE_DIRS = /global/common/sw/cray/cnl7/haswell/petsc/3.11.2/intel/19.0.3.199/hocbntp/include;/global/common/sw/cray/cnl7/haswell/hypre/2.15.1/intel/19.0.3.199/2jbygqt/include;/global/common/sw/cray/cnl7/haswell/superlu-dist/6.1.1/intel/19.0.3.199/vnkv5xn/include;/opt/cray/pe/hdf5/1.10.2.0/INTEL/16.0/include;/global/common/sw/cray/cnl7/haswell/parmetis/4.0.3/intel/19.0.3.199/koc2n7v/include;/global/common/sw/cray/cnl7/haswell/metis/5.1.0/intel/19.0.3.199/fpy6uzj/include;/global/common/sw/cray/cnl7/haswell/zlib/1.2.11/intel/19.0.3.199/si6pos6/include # PETSC_LIBRARIES = /global/common/sw/cray/cnl7/haswell/petsc/3.11.2/intel/19.0.3.199/hocbntp/lib/libpetsc.a;/global/common/sw/cray/cnl7/haswell/hypre/2.15.1/intel/19.0.3.199/2jbygqt/lib/libHYPRE.so;/global/common/sw/cray/cnl7/haswell/superlu-dist/6.1.1/intel/19.0.3.199/vnkv5xn/lib/libsuperlu_dist.a;/opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_intel_lp64.so;/opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_sequential.so;/opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_core.so;/opt/cray/pe/hdf5/1.10.2.0/INTEL/16.0/lib/libhdf5hl_fortran.so;/opt/cray/pe/hdf5/1.10.2.0/INTEL/16.0/lib/libhdf5_fortran.so;/opt/cray/pe/hdf5/1.10.2.0/INTEL/16.0/lib/libhdf5_hl.so;/opt/cray/pe/hdf5/1.10.2.0/INTEL/16.0/lib/libhdf5.so;/global/common/sw/cray/cnl7/haswell/parmetis/4.0.3/intel/19.0.3.199/koc2n7v/lib/libparmetis.a;/global/common/sw/cray/cnl7/haswell/metis/5.1.0/intel/19.0.3.199/fpy6uzj/lib/libmetis.a;/global/common/sw/cray/cnl7/haswell/zlib/1.2.11/intel/19.0.3.199/si6pos6/lib/libz.a;dl # ( DEAL_II_WITH_SCALAPACK = OFF ) # ( DEAL_II_WITH_SLEPC = OFF ) # ( DEAL_II_WITH_SUNDIALS = OFF ) # ( DEAL_II_WITH_SYMENGINE = OFF ) # DEAL_II_WITH_THREADS set up with bundled packages # TBB_VERSION = bundled # THREADS_CXX_FLAGS = -Wno-parentheses # THREADS_DEFINITIONS_DEBUG = TBB_USE_DEBUG;TBB_DO_ASSERT=1 # THREADS_USER_DEFINITIONS_DEBUG = TBB_USE_DEBUG;TBB_DO_ASSERT=1 # THREADS_BUNDLED_INCLUDE_DIRS = /global/project/projectdirs/m2360/packagesCPFE/dealii/bundled/tbb-2018_U2/include # THREADS_LIBRARIES = dl # ( DEAL_II_WITH_TRILINOS = OFF ) # DEAL_II_WITH_UMFPACK set up with bundled packages # UMFPACK_BUNDLED_INCLUDE_DIRS = /global/project/projectdirs/m2360/packagesCPFE/dealii/bundled/umfpack/UMFPACK/Include;/global/project/projectdirs/m2360/packagesCPFE/dealii/bundled/umfpack/AMD/Include # DEAL_II_WITH_ZLIB set up with external dependencies # ZLIB_VERSION = 1.2.11 # ZLIB_INCLUDE_DIRS = /usr/include # ZLIB_LIBRARIES = /usr/lib64/libz.so # # Component configuration: # ( DEAL_II_COMPONENT_DOCUMENTATION = OFF ) # DEAL_II_COMPONENT_EXAMPLES # ( DEAL_II_COMPONENT_PACKAGE = OFF ) # ( DEAL_II_COMPONENT_PYTHON_BINDINGS = OFF ) # ###
