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quinoacomputing / quinoa

Adaptive computational fluid dynamics
https://quinoacomputing.github.io
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Compilation Error (Inciter Build). Charm build failed #569

Closed pkgudla closed 1 year ago

pkgudla commented 1 year ago

Hi,

I was trying to compile inciter executables on a linux cluster. Below are the installation that were executed:

git clone --branch=develop https://github.com/quinoacomputing/quinoa.git && cd quinoa git submodule init && git submodule update && cd external git -c submodule."src/pugixml".update=none -c submodule."src/rngsse2".update=none -c submodule."src/testu01".update=none -c submodule."src/tut".update=none -c submodule."src/backward-cpp".update=none -c submodule."src/omega_h".update=none -c submodule."src/doxygen".update=none -c submodule."src/m.css".update=none -c submodule."src/root".update=none -c submodule."src/aec".update=none submodule update --init --recursive

cd quinoa && mkdir external/build && cd external/build cmake -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_C_COMPILER=mpicc -DCMAKE_Fortran_COMPILER=mpif90 -DINCITER_ONLY=true .. make -sj$(grep -c processor /proc/cpuinfo)

Here the error messages

[ 32%] Built target numdiff [ 52%] Built target pegtl [ 64%] Built target hdf5 [ 64%] Performing build step for 'charm' [ 68%] Built target highwayhash CMake Error at /users/PYS0404/com0720/Projects/quinoa/external/build/charm/src/charm-stamp/charm-build-RELEASE.cmake:49 (message): Command failed: No such file or directory

'/users/PYS0404/com0720/Projects/quinoa/external/install/intel-x86_64/charm/buildold' 'charm++' 'mpi-linux-x86_64' '--build-shared' '--with-production' '-j28' '-O3' '-DNDEBUG'

See also

/users/PYS0404/com0720/Projects/quinoa/external/build/charm/src/charm-stamp/charm-build-*.log

make[2]: [charm/src/charm-stamp/charm-build] Error 1 make[1]: [CMakeFiles/charm.dir/all] Error 2 make[1]: *** Waiting for unfinished jobs.... [ 80%] Built target netcdf

For some reason....charm build failed. I checked the charm-build-*.log files, both of them are empty.

Can you point to what I might be doing wrong here. Please note that, I was cloning the "develop" branch

Thx

jbakosi commented 1 year ago

Hello @pkgudla,

it looks like charm's install step failed for you. Can you go into external/install/intel-x86_64/charm/ and rerun their build script buildold and see its screen output to see what is missing?

You can see how quinoa's cmake attempted to run buildold in external/build/charm/src/charm-stamp/charm-build-RELEASE.cmake.

Cheers, J

adityakpandare commented 1 year ago

Hello @pkgudla, is this issue resolved?

pkgudla commented 1 year ago

Thank you for you comments. I finally got time to re-ran the compilation instructions and give it another go. I was able to reproduce the same error. When I check it further, "buildold" is itself missing. Infact quinoa/external/install/intel-x86_64/charm/ folder seems completely empty. I also noted following comment at the end of cloning the repo

Unable to checkout '327dc62b5f54a55393074410e6846a78c564fe45' in submodule path 'src/charm'`

The issue seems to be failure to clone charm, resulting in a charm build failure. I have pasted as much info as I can just incase I overlooked something here. Please advise how this can be addressed.

Thanks again in advance for your comments.

Here is the command used to clone the repo and tpl specific to "Inciter" tool.

git clone --branch=develop https://github.com/quinoacomputing/quinoa.git && cd quinoa git submodule init && git submodule update && cd external git -c submodule."src/pugixml".update=none -c submodule."src/rngsse2".update=none -c submodule."src/testu01".update=none -c submodule."src/tut".update=none -c submodule."src/backward-cpp".update=none -c submodule."src/omega_h".update=none -c submodule."src/doxygen".update=none -c submodule."src/m.css".update=none -c submodule."src/root".update=none -c submodule."src/aec".update=none -c submodule."src/sol2".update=none submodule update --init --recursive

Here is the complete output after executing the above command (please note the last line)

-bash-4.2$ git -c submodule."src/pugixml".update=none -c submodule."src/rngsse2".update=none -c submodule."src/testu01".update=none -c submodule."src/tut".update=none -c submodule."src/backward-cpp".update=none -c submodule."src/omega_h".update=none -c submodule."src/doxygen".update=none -c submodule."src/m.css".update=none -c submodule."src/root".update=none -c submodule."src/aec".update=none -c submodule."src/sol2".update=none submodule update --init --recursive Submodule 'cmake' (https://github.com/quinoacomputing/cmake-modules.git) registered for path 'cmake' Submodule 'src/backward-cpp' (https://github.com/bombela/backward-cpp.git) registered for path 'src/backward-cpp' Submodule 'src/boost' (https://github.com/quinoacomputing/Boost.git) registered for path 'src/boost' Submodule 'src/brigand' (https://github.com/edouarda/brigand.git) registered for path 'src/brigand' Submodule 'src/charm' (https://github.com/UIUC-PPL/charm.git) registered for path 'src/charm' Submodule 'src/doxygen' (https://github.com/doxygen/doxygen) registered for path 'src/doxygen' Submodule 'src/exam2m' (https://github.com/Charmworks/ExaM2M.git) registered for path 'src/exam2m' Submodule 'src/hdf5' (https://github.com/HDFGroup/hdf5.git) registered for path 'src/hdf5' Submodule 'src/hdf5-ampi' (https://github.com/UIUC-PPL/hdf5-ampi.git) registered for path 'src/hdf5-ampi' Submodule 'src/highwayhash' (https://github.com/google/highwayhash.git) registered for path 'src/highwayhash' Submodule 'src/lapack' (https://github.com/Reference-LAPACK/lapack.git) registered for path 'src/lapack' Submodule 'src/m.css' (https://github.com/mosra/m.css) registered for path 'src/m.css' Submodule 'src/netcdf' (https://github.com/Unidata/netcdf-c.git) registered for path 'src/netcdf' Submodule 'src/numdiff' (https://github.com/quinoacomputing/ndiff.git) registered for path 'src/numdiff' Submodule 'src/pegtl' (https://github.com/taocpp/PEGTL.git) registered for path 'src/pegtl' Submodule 'src/pugixml' (https://github.com/zeux/pugixml.git) registered for path 'src/pugixml' Submodule 'src/sol2' (https://github.com/ThePhD/sol2.git) registered for path 'src/sol2' Submodule 'src/trilinos' (https://github.com/trilinos/Trilinos.git) registered for path 'src/trilinos' Submodule 'src/tut' (https://github.com/mrzechonek/tut-framework.git) registered for path 'src/tut' Cloning into 'cmake'... remote: Enumerating objects: 2955, done. remote: Counting objects: 100% (149/149), done. remote: Compressing objects: 100% (110/110), done. remote: Total 2955 (delta 75), reused 91 (delta 39), pack-reused 2806 Receiving objects: 100% (2955/2955), 733.26 KiB | 0 bytes/s, done. Resolving deltas: 100% (1879/1879), done. Submodule path 'cmake': checked out 'eeeaeabd6ec0e0e44253b96be9cbab3f2a6b33be' Skipping submodule 'src/backward-cpp' Cloning into 'src/boost'... remote: Enumerating objects: 106423, done. remote: Total 106423 (delta 0), reused 0 (delta 0), pack-reused 106423 Receiving objects: 100% (106423/106423), 138.84 MiB | 37.76 MiB/s, done. Resolving deltas: 100% (65254/65254), done.

Submodule path 'src/boost': checked out '9be6dd96c6d100b586acc5a4e36d30aedaad8667' Cloning into 'src/brigand'... remote: Enumerating objects: 3928, done. remote: Counting objects: 100% (107/107), done. remote: Compressing objects: 100% (72/72), done. remote: Total 3928 (delta 44), reused 46 (delta 23), pack-reused 3821 Receiving objects: 100% (3928/3928), 1.10 MiB | 0 bytes/s, done. Resolving deltas: 100% (2854/2854), done. Submodule path 'src/brigand': checked out '523ee302474447c808b688607b7353ffd3e5d4bd' Cloning into 'src/charm'... remote: Enumerating objects: 217218, done. remote: Counting objects: 100% (1328/1328), done. remote: Compressing objects: 100% (523/523), done. remote: Total 217218 (delta 827), reused 1187 (delta 779), pack-reused 215890 Receiving objects: 100% (217218/217218), 135.79 MiB | 39.94 MiB/s, done. Resolving deltas: 100% (161304/161304), done. fatal: reference is not a tree: 327dc62b5f54a55393074410e6846a78c564fe45 Skipping submodule 'src/doxygen' Cloning into 'src/exam2m'... remote: Enumerating objects: 1403, done. remote: Counting objects: 100% (348/348), done. remote: Compressing objects: 100% (127/127), done. remote: Total 1403 (delta 232), reused 321 (delta 220), pack-reused 1055 Receiving objects: 100% (1403/1403), 3.80 MiB | 0 bytes/s, done. Resolving deltas: 100% (958/958), done. Submodule path 'src/exam2m': checked out 'd016297220933cdbdd982528c0ce781065693931' Submodule 'external/src/brigand' (https://github.com/edouarda/brigand.git) registered for path 'external/src/brigand' Submodule 'external/src/charm' (https://github.com/UIUC-PPL/charm.git) registered for path 'external/src/charm' Submodule 'external/src/hdf5' (https://github.com/HDFGroup/hdf5.git) registered for path 'external/src/hdf5' Submodule 'external/src/hdf5-ampi' (https://github.com/UIUC-PPL/hdf5-ampi.git) registered for path 'external/src/hdf5-ampi' Submodule 'external/src/highwayhash' (https://github.com/google/highwayhash.git) registered for path 'external/src/highwayhash' Submodule 'external/src/lapack' (https://github.com/Reference-LAPACK/lapack.git) registered for path 'external/src/lapack' Submodule 'external/src/netcdf' (https://github.com/Unidata/netcdf-c.git) registered for path 'external/src/netcdf' Submodule 'external/src/trilinos' (https://github.com/trilinos/Trilinos.git) registered for path 'external/src/trilinos' Cloning into 'external/src/brigand'... remote: Enumerating objects: 3928, done. remote: Counting objects: 100% (107/107), done. remote: Compressing objects: 100% (72/72), done. remote: Total 3928 (delta 44), reused 46 (delta 23), pack-reused 3821 Receiving objects: 100% (3928/3928), 1.10 MiB | 0 bytes/s, done. Resolving deltas: 100% (2854/2854), done. Submodule path 'src/exam2m/external/src/brigand': checked out '523ee302474447c808b688607b7353ffd3e5d4bd' Cloning into 'external/src/charm'... remote: Enumerating objects: 217218, done. remote: Counting objects: 100% (1328/1328), done. remote: Compressing objects: 100% (523/523), done. remote: Total 217218 (delta 827), reused 1187 (delta 779), pack-reused 215890 Receiving objects: 100% (217218/217218), 135.79 MiB | 38.54 MiB/s, done. Resolving deltas: 100% (161304/161304), done. Submodule path 'src/exam2m/external/src/charm': checked out '4bf158d1b773580b32f7c424efdcec86b98ae610' Cloning into 'external/src/hdf5'... remote: Enumerating objects: 368379, done. remote: Counting objects: 100% (7/7), done. remote: Compressing objects: 100% (7/7), done. remote: Total 368379 (delta 1), reused 0 (delta 0), pack-reused 368372 Receiving objects: 100% (368379/368379), 240.07 MiB | 43.34 MiB/s, done. Resolving deltas: 100% (305759/305759), done. Submodule path 'src/exam2m/external/src/hdf5': checked out '646fc294078f560fc9bef784cb1c4e27cdc51f5b' Cloning into 'external/src/hdf5-ampi'... remote: Enumerating objects: 4728, done. remote: Total 4728 (delta 0), reused 0 (delta 0), pack-reused 4728 Receiving objects: 100% (4728/4728), 14.41 MiB | 18.05 MiB/s, done. Resolving deltas: 100% (2654/2654), done. Submodule path 'src/exam2m/external/src/hdf5-ampi': checked out '70077883c5509e57f75a0aecbcb0a043e28ffb98' Cloning into 'external/src/highwayhash'... remote: Enumerating objects: 1037, done. remote: Counting objects: 100% (279/279), done. remote: Compressing objects: 100% (62/62), done. remote: Total 1037 (delta 234), reused 224 (delta 217), pack-reused 758 Receiving objects: 100% (1037/1037), 583.76 KiB | 0 bytes/s, done. Resolving deltas: 100% (725/725), done. Submodule path 'src/exam2m/external/src/highwayhash': checked out '0aaf66bb8a1634ceee4b778df51a652bdf4e1f17' Cloning into 'external/src/lapack'... remote: Enumerating objects: 75189, done. remote: Counting objects: 100% (1191/1191), done. remote: Compressing objects: 100% (417/417), done. remote: Total 75189 (delta 855), reused 1015 (delta 773), pack-reused 73998 Receiving objects: 100% (75189/75189), 23.39 MiB | 30.46 MiB/s, done. Resolving deltas: 100% (70760/70760), done. Submodule path 'src/exam2m/external/src/lapack': checked out 'aefe75153596de43210057558301efbebcb3793c' Cloning into 'external/src/netcdf'... remote: Enumerating objects: 60710, done. remote: Counting objects: 100% (43/43), done. remote: Compressing objects: 100% (26/26), done. remote: Total 60710 (delta 17), reused 33 (delta 17), pack-reused 60667 Receiving objects: 100% (60710/60710), 53.72 MiB | 32.26 MiB/s, done. Resolving deltas: 100% (46227/46227), done. Submodule path 'src/exam2m/external/src/netcdf': checked out 'c35e47e4f95aeacc8e7e1d2f531a153f8d7923c8' Cloning into 'external/src/trilinos'... remote: Enumerating objects: 1238666, done. remote: Counting objects: 100% (288/288), done. remote: Compressing objects: 100% (125/125), done. remote: Total 1238666 (delta 193), reused 235 (delta 162), pack-reused 1238378 Receiving objects: 100% (1238666/1238666), 766.13 MiB | 32.72 MiB/s, done. Resolving deltas: 100% (938567/938567), done. Submodule path 'src/exam2m/external/src/trilinos': checked out 'e3c83e3d5caca8f59432f6f5d2e33ae142a16eff' Cloning into 'src/hdf5'... remote: Enumerating objects: 368379, done. remote: Counting objects: 100% (7/7), done. remote: Compressing objects: 100% (7/7), done. remote: Total 368379 (delta 1), reused 0 (delta 0), pack-reused 368372 Receiving objects: 100% (368379/368379), 239.89 MiB | 47.43 MiB/s, done. Resolving deltas: 100% (305748/305748), done. Submodule path 'src/hdf5': checked out 'a8ee85971b4251a3383d82fdd68bf150e0acad39' Cloning into 'src/hdf5-ampi'... remote: Enumerating objects: 4728, done. remote: Total 4728 (delta 0), reused 0 (delta 0), pack-reused 4728 Receiving objects: 100% (4728/4728), 14.41 MiB | 25.72 MiB/s, done. Resolving deltas: 100% (2654/2654), done. Submodule path 'src/hdf5-ampi': checked out '207fb893e3c9abfa80f12a47ca1e14c814a36f30' Cloning into 'src/highwayhash'... remote: Enumerating objects: 1037, done. remote: Counting objects: 100% (279/279), done. remote: Compressing objects: 100% (62/62), done. remote: Total 1037 (delta 234), reused 224 (delta 217), pack-reused 758 Receiving objects: 100% (1037/1037), 583.76 KiB | 0 bytes/s, done. Resolving deltas: 100% (725/725), done. Submodule path 'src/highwayhash': checked out '14dedecd1de87cb662f7a882ea1578d2384feb2f' Cloning into 'src/lapack'... remote: Enumerating objects: 75189, done. remote: Counting objects: 100% (1194/1194), done. remote: Compressing objects: 100% (422/422), done. remote: Total 75189 (delta 858), reused 1008 (delta 771), pack-reused 73995 Receiving objects: 100% (75189/75189), 24.82 MiB | 34.28 MiB/s, done. Resolving deltas: 100% (69915/69915), done. Submodule path 'src/lapack': checked out 'aefe75153596de43210057558301efbebcb3793c' Skipping submodule 'src/m.css' Cloning into 'src/netcdf'... remote: Enumerating objects: 60710, done. remote: Counting objects: 100% (43/43), done. remote: Compressing objects: 100% (26/26), done. remote: Total 60710 (delta 17), reused 33 (delta 17), pack-reused 60667 Receiving objects: 100% (60710/60710), 53.72 MiB | 31.01 MiB/s, done. Resolving deltas: 100% (46227/46227), done. Submodule path 'src/netcdf': checked out 'c35e47e4f95aeacc8e7e1d2f531a153f8d7923c8' Cloning into 'src/numdiff'... remote: Enumerating objects: 912, done. remote: Total 912 (delta 0), reused 0 (delta 0), pack-reused 912 Receiving objects: 100% (912/912), 1014.04 KiB | 0 bytes/s, done. Resolving deltas: 100% (727/727), done. Submodule path 'src/numdiff': checked out 'a2be3a91e9f541a7b357f672c21b2e6fa491d794' Cloning into 'src/pegtl'... remote: Enumerating objects: 30256, done. remote: Counting objects: 100% (4240/4240), done. remote: Compressing objects: 100% (909/909), done. remote: Total 30256 (delta 3096), reused 4151 (delta 3031), pack-reused 26016 Receiving objects: 100% (30256/30256), 5.53 MiB | 0 bytes/s, done. Resolving deltas: 100% (21598/21598), done. Submodule path 'src/pegtl': checked out '26df6aa2d6e582d098b85478a34d4487de8c82c5' Skipping submodule 'src/pugixml' Skipping submodule 'src/sol2' Cloning into 'src/trilinos'... remote: Enumerating objects: 1238666, done. remote: Counting objects: 100% (288/288), done. remote: Compressing objects: 100% (125/125), done. remote: Total 1238666 (delta 193), reused 235 (delta 162), pack-reused 1238378 Receiving objects: 100% (1238666/1238666), 766.13 MiB | 35.18 MiB/s, done. Resolving deltas: 100% (938567/938567), done. Submodule path 'src/trilinos': checked out 'e3c83e3d5caca8f59432f6f5d2e33ae142a16eff' Skipping submodule 'src/tut' Unable to checkout '327dc62b5f54a55393074410e6846a78c564fe45' in submodule path 'src/charm'

Configuring tpl build with the following options went well and its output is also pasted below

-bash-4.2$ cmake -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_C_COMPILER=mpicc -DCMAKE_Fortran_COMPILER=mpif90 -DINCITER_ONLY=true -DCHARM_EXTRA_ARGS="--enable-error-checking;--with-prio-type=int;--enable-randomized-msgq;--suffix;randq-debug" -DCHARM_EXTRA_ARGS="smp" -DCHARM_EXTRA_ARGS="--enable-tracing;--enable-commthread-tracing" .. -- The C compiler identification is Intel 19.0.5.20190815 -- The CXX compiler identification is Intel 19.0.5.20190815 -- The Fortran compiler identification is Intel 19.0.5.20190815 -- Check for working C compiler: /apps/openmpi/intel/19.0/4.0.3-hpcx/bin/mpicc -- Check for working C compiler: /apps/openmpi/intel/19.0/4.0.3-hpcx/bin/mpicc - works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /apps/openmpi/intel/19.0/4.0.3-hpcx/bin/mpicxx -- Check for working CXX compiler: /apps/openmpi/intel/19.0/4.0.3-hpcx/bin/mpicxx - works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working Fortran compiler: /apps/openmpi/intel/19.0/4.0.3-hpcx/bin/mpif90 -- Check for working Fortran compiler: /apps/openmpi/intel/19.0/4.0.3-hpcx/bin/mpif90 - works -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Checking whether /apps/openmpi/intel/19.0/4.0.3-hpcx/bin/mpif90 supports Fortran 90 -- Checking whether /apps/openmpi/intel/19.0/4.0.3-hpcx/bin/mpif90 supports Fortran 90 - yes -- CMAKE_BUILD_TYPE not specified, setting to 'Release' -- Detected OS: "rhel" -- BUILD_SHARED_LIBS not specified, setting to 'ON' -- BUILD_SHARED_LIBS: ON -- Detected target architecture: x86_64 -- CMAKE_INSTALL_PREFIX not specified, setting to '/users/PYS0404/com0720/Projects/quinoa/external/install/intel-x86_64' -- Found 1 PEs -- Could NOT find Charm (missing: CHARM_COMPILER CHARM_INCLUDE_DIRS CHARM_RUN) -- Charm++ architecture/version: mpi-linux-x86_64 -- Found MPI_C: /apps/openmpi/intel/19.0/4.0.3-hpcx/bin/mpicc (found version "3.1") -- Found MPI_CXX: /apps/openmpi/intel/19.0/4.0.3-hpcx/bin/mpicxx (found version "3.1") -- Found MPI_Fortran: /apps/openmpi/intel/19.0/4.0.3-hpcx/bin/mpif90 (found version "3.1") -- Found MPI: TRUE (found version "3.1")
-- MPI C wrapper: /apps/openmpi/intel/19.0/4.0.3-hpcx/bin/mpicc -- MPI C++ wrapper: /apps/openmpi/intel/19.0/4.0.3-hpcx/bin/mpicxx -- MPI Fortran wrapper: /apps/openmpi/intel/19.0/4.0.3-hpcx/bin/mpif90 -- MPI C compiler: /apps/openmpi/intel/19.0/4.0.3-hpcx/bin/mpicc -- MPI C++ compiler: /apps/openmpi/intel/19.0/4.0.3-hpcx/bin/mpicxx -- MPI Fortran compiler: /apps/openmpi/intel/19.0/4.0.3-hpcx/bin/mpif90 -- Underlying C compiler: /opt/intel/19.0.5/compilers_and_libraries_2019/linux/bin/intel64/icc -- Underlying C++ compiler: /opt/intel/19.0.5/compilers_and_libraries_2019/linux/bin/intel64/icpc -- Underlying Fortran compiler: /opt/intel/19.0.5/compilers_and_libraries_2019/linux/bin/intel64/ifort -- Charmrun: /users/PYS0404/com0720/Projects/quinoa/external/install/intel-x86_64/charm/bin/charmrun -- Charm build target: charm++ -- Charm++ extra build args (CHARM_EXTRA_ARGS): --enable-tracing;--enable-commthread-tracing -- Could NOT find LIBCXX (missing: LIBCXX_LIBRARIES LIBCXXABI_LIBRARIES LIBCXX_INCLUDE_DIRS) -- HDF5: Using hdf5 compiler wrapper to determine C configuration -- Found HDF5: /usr/lib64/libhdf5.so (found version "1.8.12") found components: C HL -- HDF5 either not found, not parallel, disabled, or AMPI is enabled: will build -- Could NOT find NetCDF (missing: NETCDF_INCLUDES) -- NetCDF either not found or AMPI is enabled: will build -- Could NOT find Boost: Found unsuitable version "1.53.0", but required is at least "1.56.0" (found /usr/include) -- Could NOT find PEGTL: Found unsuitable version "0.0.0", but required is at least "2.0.0" (found ) -- Found MKL: /opt/intel/19.0.5/compilers_and_libraries_2019/linux/mkl/lib/intel64/libmkl_intel_ilp64.so;/opt/intel/19.0.5/compilers_and_libraries_2019/linux/mkl/lib/intel64/libmkl_sequential.so;/opt/intel/19.0.5/compilers_and_libraries_2019/linux/mkl/lib/intel64/libmkl_core.so
-- Zoltan2, SEACASExodus, and Exodiff either not found or AMPI is enabled: will build -- Could NOT find NumDiff (missing: NUMDIFF_EXECUTABLE) -- Could NOT find HighwayHash (missing: HIGHWAYHASH_INCLUDE_DIRS) -- Could NOT find Brigand (missing: BRIGAND_INCLUDE_DIRS) -- C compiler flags: '-O3 -DNDEBUG' -- C++ compiler flags: '-O3 -DNDEBUG' -- Fortran compiler flags: '-O3' -- Will build the following 9 TPLs for executable(s) inciter: boost;brigand;charm;hdf5;highwayhash;netcdf;numdiff;pegtl;trilinos -- Configuring done -- Generating done -- Build files have been written to: /users/PYS0404/com0720/Projects/quinoa/external/build

Building tpl failed with charm

[ 44%] Performing configure step for 'highwayhash' [ 44%] Performing configure step for 'boost' [ 44%] No configure step for 'charm' [ 48%] Performing build step for 'charm' CMake Error at /users/PYS0404/com0720/Projects/quinoa/external/build/charm/src/charm-stamp/charm-build-RELEASE.cmake:49 (message): Command failed: No such file or directory

'/users/PYS0404/com0720/Projects/quinoa/external/install/intel-x86_64/charm/buildold' 'charm++' 'mpi-linux-x86_64' '--enable-tracing' '--enable-commthread-tracing' '--build-shared' '--with-production' '-j1' '-O3' '-DNDEBUG'

See also

/users/PYS0404/com0720/Projects/quinoa/external/build/charm/src/charm-stamp/charm-build-*.log

make[2]: [charm/src/charm-stamp/charm-build] Error 1 make[1]: [CMakeFiles/charm.dir/all] Error 2 make[1]: ** Waiting for unfinished jobs.... -- highwayhash configure command succeeded. See also /users/PYS0404/com0720/Projects/quinoa/external/build/highwayhash/src/highwayhash-stamp/highwayhash-configure-.log [ 52%] No build step for 'highwayhash' [ 56%] No install step for 'highwayhash' [ 56%] Completed 'highwayhash' [ 56%] Built target highwayhash [ 56%] No build step for 'brigand'

jbakosi commented 1 year ago

I'm not sure why charm, after a successful clone, cannot check out commit 327dc62b5 for you, since it works fine for me. Can you please try the following?

git clone --branch=develop https://github.com/quinoacomputing/quinoa.git
cd quinoa
git submodule init && git submodule update
cd external/src/charm
git checkout 327dc62b5f54a55393074410e6846a78c564fe45

See if the above runs without error. This is what cmake is doing. If this runs for you fine, you should be able to continue by building the third-party libraries:

cd quinoa
mkdir external/build; cd external/build; cmake -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_C_COMPILER=mpicc -DCMAKE_Fortran_COMPILER=mpif90 .. && make

and continue with https://quinoacomputing.github.io/archive/index.html#mainpage_build.

pkgudla commented 1 year ago

git clone --branch=develop https://github.com/quinoacomputing/quinoa.git cd quinoa git submodule init && git submodule update cd external/src/charm git checkout 327dc62b5f54a55393074410e6846a78c564fe45

Tried the above instrction set: After the last instruction here is the error

-bash-4.2$ git checkout 327dc62b5f54a55393074410e6846a78c564fe45 fatal: reference is not a tree: 327dc62b5f54a55393074410e6846a78c564fe45

I checked online...couldn't make sense. I'm using following git --version, if that is anyway relevant

-bash-4.2$ git --version git version 1.8.3.1

adityakpandare commented 1 year ago

Please update your git, and retry the clone from a fresh directory. 1.8.3 is quite dated, and issues might arise due to this.

pkgudla commented 1 year ago

Did that.... -bash-4.2$ git --version git version 2.27.1 -bash-4.2$ git checkout 327dc62b5f54a55393074410e6846a78c564fe45 fatal: reference is not a tree: 327dc62b5f54a55393074410e6846a78c564fe45

adityakpandare commented 1 year ago

Just to confirm: did you try completely removing your local quinoa directory and starting afresh?

pkgudla commented 1 year ago

yes i did

gitsh-4.2$ git clone --branch=develop https://github.com/quinoacomputing/quinoa. Cloning into 'quinoa'... remote: Enumerating objects: 92672, done. remote: Counting objects: 100% (2607/2607), done. remote: Compressing objects: 100% (576/576), done. remote: Total 92672 (delta 2054), reused 2555 (delta 2026), pack-reused 90065 Receiving objects: 100% (92672/92672), 217.64 MiB | 27.65 MiB/s, done. Resolving deltas: 100% (74055/74055), done. Updating files: 100% (2440/2440), done. -bash-4.2$ cd quinoa/ -bash-4.2$ git--version -bash: git--version: command not found -bash-4.2$ git --version git version 2.27.1 -bash-4.2$ git submodule init Submodule 'external' (https://github.com/quinoacomputing/quinoa-tpl) registered for path 'external' -bash-4.2$ git submodule update Cloning into '/users/PYS0404/com0720/Projects/quinoa/external'... Submodule path 'external': checked out '773f67f525bb33497b3798add7dbc957b0419ee9' -bash-4.2$ cd external/src/charm/ -bash-4.2$ git checkout 327dc62b5f54a55393074410e6846a78c564fe45 fatal: reference is not a tree: 327dc62b5f54a55393074410e6846a78c564fe45 -bash-4.2$

adityakpandare commented 1 year ago

Thanks for confirming. Could you check if git clone --recurse-submodules https://github.com/quinoacomputing/quinoa.git can create a recursive clone without similar errors? I suspect something amiss with using the recursive clone and excluding submodules in conjunction.

jbakosi commented 1 year ago

This is strange and I cannot locally reproduce it. Here is another idea:

git clone --recurse-submodules https://github.com/quinoacomputing/quinoa-tpl.git

Then copy the whole charm directory from /src/charm to quinoa/external/src/.

This avoids the git checkout on charm, which is the step that breaks.

pkgudla commented 1 year ago

Thank you Joszef and Aditya for your prompt help so far...was very helpful. The issue seems to be with the single core login instance I was using to compile the code. When I instead started using full node (28 core) for running these instructions....everything went well. Didn't have any issue anymore. I might get back to you as I explore the code further. Before that, I have a quick question regarding the time discretization or ODE solvers that are already implemented. Besides TVD RK scheme, are any local time stepping schemes have been explored ?

adityakpandare commented 1 year ago

I'm glad your compilation issue was fixed. Feel free to create github/issues if you have further questions. We have the following time discretization schemes implemented in the code:

  1. TVDRK3 from Gottlieb and Shu (https://doi.org/10.1090/S0025-5718-98-00913-2) with the Discontinuous Galerkin discretization;
  2. TVDRK3 from Waltz et al. (https://doi.org/10.1016/j.compfluid.2013.12.021) with the edge-based finite element discretization (called ALECG);
  3. A local time stepping scheme implemented by @jbakosi in the edge-based finite element method.

Most of these details can be found on our inciter doc page https://quinoacomputing.github.io/inciter_main.html.