pramodk
commented
1 year ago @mjribeiro : I locally tried to build with NVHPC 22.11 and CUDA 11.8 but don't see obvious issue. In your logs I see:
nvc++-Fatal-/opt/nvidia/hpc_sdk/Linux_x86_64/22.11/compilers/bin/tools/cpp2 TERMINATED by signal 11
Arguments to /opt/nvidia/hpc_sdk/Linux_x86_64/22.11/compilers/bin/tools/cpp2
/opt/nvidia/hpc_sdk/Linux_x86_64/22.11/compilers/bin/tools/cpp2 /home/mafalda/nrn/src/ivoc/ivocvect.cpp ...i.e. cpp2 seems to be failing. First thing comes to my mind is if you could try with --parallel 2 or --parallel 1 in case this is memory usage related issue from the compiler itself.
My local cmake / build log is:
$ cmake .. -DNRN_ENABLE_CORENEURON=ON -DCORENRN_ENABLE_GPU=ON -DNRN_ENABLE_INTERVIEWS=OFF -DNRN_ENABLE_RX3D=OFF -DCMAKE_INSTALL_PREFIX=$HOME/install -DCMAKE_C_COMPILER=nvc -DCMAKE_CXX_COMPILER=nvc++ -DCMAKE_CUDA_COMPILER=nvcc
-- The C compiler identification is NVHPC 22.11.0
-- The CXX compiler identification is NVHPC 22.11.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /gpfs/bbp.cscs.ch/ssd/apps/bsd/pulls/1654/stage_externals/install_gcc-11.2.0-skylake/nvhpc-22.11-rx7dzj/Linux_x86_64/22.11/compilers/bin/nvc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /gpfs/bbp.cscs.ch/ssd/apps/bsd/pulls/1654/stage_externals/install_gcc-11.2.0-skylake/nvhpc-22.11-rx7dzj/Linux_x86_64/22.11/compilers/bin/nvc++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Setting build type to 'RelWithDebInfo' as none was specified.
-- 3rd party project: using Random123 from "external/Random123"
-- -DPYTHON_EXECUTABLE not specified. Looking for `python3` in the PATH exclusively...
-- Setting PYTHON_EXECUTABLE=/gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/python-3.9.7-yj5alh/bin/python3
-- Found BISON: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/bison-3.8.2-ej2cew/bin/bison (found version "3.8.2")
-- Found FLEX: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/flex-2.6.3-3mtl7j/bin/flex (found suitable version "2.6.3", minimum required is "2.6")
-- Found Readline: /usr/include
-- Found MPI_C: /usr/lib64/libpthread.so (found version "3.1")
-- Found MPI_CXX: /usr/lib64/libpthread.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1")
MPT: libxmpi.so 'HPE HMPT 2.25 10/22/21 03:19:55'
-- Found PythonInterp: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/python-3.9.7-yj5alh/bin/python3 (found suitable version "3.9.7", minimum required is "3.8")
-- Found PythonInterp: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/python-3.9.7-yj5alh/bin/python3 (found suitable version "3.9.7", minimum required is "3")
-- Found PythonLibs: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/python-3.9.7-yj5alh/lib/libpython3.9.so
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Building CoreNEURON
-- 3rd party project: using CLI11 from "external/CLI11"
-- Found Git: /usr/bin/git (found version "1.8.3.1")
-- Setting default CUDA architectures to 70;80
-- The CUDA compiler identification is NVIDIA 11.8.89
-- Detecting CUDA compiler ABI info
-- Detecting CUDA compiler ABI info - done
-- Check for working CUDA compiler: /gpfs/bbp.cscs.ch/ssd/apps/bsd/pulls/1654/stage_externals/install_gcc-11.2.0-skylake/cuda-11.8.0-wlynz6/bin/nvcc - skipped
-- Detecting CUDA compile features
-- Detecting CUDA compile features - done
-- Found CUDAToolkit: /gpfs/bbp.cscs.ch/ssd/apps/bsd/pulls/1654/stage_externals/install_gcc-11.2.0-skylake/cuda-11.8.0-wlynz6/include (found suitable version "11.8.89", minimum required is "9.0")
-- Found Perl: /usr/bin/perl (found version "5.16.3")
-- Found MOD2C: /gpfs/bbp.cscs.ch/home/kumbhar/nrn/external/mod2c
-- Using mod2c submodule from /gpfs/bbp.cscs.ch/home/kumbhar/nrn/external/mod2c
-- mod2c is used as APPLICATION_NAME
-- Found FLEX: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/flex-2.6.3-3mtl7j/bin/flex (found version "2.6.3")
--
-- CoreNEURON is enabled with following build configuration:
-- --------------------+--------------------------------------------------------
-- Build option | Status
-- --------------------+--------------------------------------------------------
-- CXX COMPILER | /gpfs/bbp.cscs.ch/ssd/apps/bsd/pulls/1654/stage_externals/install_gcc-11.2.0-skylake/nvhpc-22.11-rx7dzj/Linux_x86_64/22.11/compilers/bin/nvc++
-- COMPILE FLAGS | -mp -g -O2 --c++17 -cuda -gpu=cuda11.8,lineinfo,cc70,cc80 -acc -Mautoinline -DCORENEURON_CUDA_PROFILING -DCORENEURON_ENABLE_GPU -DCORENEURON_BUILD -DHAVE_MALLOC_H -DEIGEN_DONT_VECTORIZE=1 -DNRNMPI=1 -DMPI_NO_CPPBIND=1 -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX=1 -DLAYOUT=0 -DDISABLE_HOC_EXP -DENABLE_SPLAYTREE_QUEUING -DCORENEURON_USE_LEGACY_UNITS=0
-- Build Type | SHARED
-- MPI | ON
-- DYNAMIC | OFF
-- INC | /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/hpe-mpi-2.25.hmpt-4ukyxt/include
-- OpenMP | ON
-- Use legacy units | OFF
-- NMODL | OFF
-- MOD2CPP PATH | /gpfs/bbp.cscs.ch/home/kumbhar/nrn/build/bin/mod2c_core
-- GPU Support | ON
-- CUDA | /gpfs/bbp.cscs.ch/ssd/apps/bsd/pulls/1654/stage_externals/install_gcc-11.2.0-skylake/cuda-11.8.0-wlynz6/lib64
-- Offload | OpenACC
-- Unified Memory | OFF
-- Auto Timeout | ON
-- Wrap exp() | OFF
-- SplayTree Queue | ON
-- NetReceive Buffer | ON
-- Caliper | OFF
-- Likwid | OFF
-- Unit Tests | OFF
-- Reporting | OFF
-- --------------+--------------------------------------------------------------
--
Extracting link flags from target 'Threads::Threads', beware that this can be fragile. Got:
Extracting link flags from path '/usr/lib64/libreadline.so', beware that this can be fragile. Got: -lreadline
Extracting link flags from path '/usr/lib64/libcurses.so', beware that this can be fragile. Got: -lcurses
Extracting link flags from path '/usr/lib64/libform.so', beware that this can be fragile. Got: -lform
Generating link flags from path /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/python-3.9.7-yj5alh/lib/libpython3.9.so Got: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/python-3.9.7-yj5alh/lib/libpython3.9.so -Wl,-rpath,/gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/python-3.9.7-yj5alh/lib
Extracting link flags from path '/usr/lib64/libpthread.so', beware that this can be fragile. Got: -lpthread
Generating link flags from path /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/hpe-mpi-2.25.hmpt-4ukyxt/lib/libmpi.so Got: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/hpe-mpi-2.25.hmpt-4ukyxt/lib/libmpi.so -Wl,-rpath,/gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/hpe-mpi-2.25.hmpt-4ukyxt/lib
Generating link flags from name 'dl', beware that this can be fragile. Got: -ldl
--
-- Configured NEURON 9.0.0
--
-- You can now build NEURON using:
-- cmake --build . --parallel 8 [--target TARGET]
-- You might want to adjust the number of parallel build jobs for your system.
-- Some non-default targets you might want to build:
-- --------------+--------------------------------------------------------------
-- Target | Description
-- --------------+--------------------------------------------------------------
-- install | Will install NEURON to: /gpfs/bbp.cscs.ch/home/kumbhar/install
-- | Change the install location of NEURON using:
-- | cmake <src_path> -DCMAKE_INSTALL_PREFIX=<install_path>
-- docs | Build full docs. Calls targets: doxygen, notebooks, sphinx, notebooks-clean
-- uninstall | Removes files installed by make install (todo)
-- --------------+--------------------------------------------------------------
-- Build option | Status
-- --------------+--------------------------------------------------------------
-- C COMPILER | /gpfs/bbp.cscs.ch/ssd/apps/bsd/pulls/1654/stage_externals/install_gcc-11.2.0-skylake/nvhpc-22.11-rx7dzj/Linux_x86_64/22.11/compilers/bin/nvc
-- CXX COMPILER | /gpfs/bbp.cscs.ch/ssd/apps/bsd/pulls/1654/stage_externals/install_gcc-11.2.0-skylake/nvhpc-22.11-rx7dzj/Linux_x86_64/22.11/compilers/bin/nvc++
-- BUILD_TYPE | RelWithDebInfo (allowed: Custom;Debug;Release;RelWithDebInfo;Fast)
-- COMPILE FLAGS | -g -O2 --diag_suppress=1,47,111,128,170,174,177,180,186,301,541,550,816,941,2465
-- Shared | ON
-- Default units | modern units (2019 nist constants)
-- MPI | ON
-- DYNAMIC | OFF
-- INC | /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/hpe-mpi-2.25.hmpt-4ukyxt/include
-- LIB | /usr/lib64/libpthread.so
-- Python | ON
-- EXE | /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/python-3.9.7-yj5alh/bin/python3
-- INC | /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/python-3.9.7-yj5alh/include/python3.9
-- LIB | /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/python-3.9.7-yj5alh/lib/libpython3.9.so
-- MODULE | ON
-- DYNAMIC | OFF
-- Readline | /usr/lib64/libreadline.so
-- Curses | /usr/lib64/libcurses.so;/usr/lib64/libform.so
-- RX3D | OFF
-- Interviews | OFF
-- CoreNEURON | ON
-- PATH | /gpfs/bbp.cscs.ch/home/kumbhar/nrn/src/coreneuron
-- LINK FLAGS | -cuda -gpu=cuda11.8,lineinfo,cc70,cc80 -acc -lcorenrnmech -lcoreneuron-cuda -lpthread -Wl,-rpath,/gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/hpe-mpi-2.25.hmpt-4ukyxt/lib /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/hpe-mpi-2.25.hmpt-4ukyxt/lib/libmpi.so -ldl
-- Legacy Units| OFF
-- Tests | OFF
-- --------------+--------------------------------------------------------------
-- See documentation : https://www.neuron.yale.edu/neuron/
-- --------------+--------------------------------------------------------------
--
-- Configuring done
-- Generating done
-- Build files have been written to: /gpfs/bbp.cscs.ch/home/kumbhar/nrn/build
kumbhar@r2i3n2:~/nrn/build$ make -j12
...
nvc++-Warning-CUDA_HOME has been deprecated. Please, use NVHPC_CUDA_HOME instead.
[100%] Linking CXX executable ../../bin/nrniv
nvc++-Warning-CUDA_HOME has been deprecated. Please, use NVHPC_CUDA_HOME instead.
[100%] Built target nrniv
nvc++-Warning-CUDA_HOME has been deprecated. Please, use NVHPC_CUDA_HOME instead.
[100%] Built target hoc_module
kumbhar@r2i3n2:~/nrn/build$ make install
[ 0%] Built target CLI11
[ 3%] Built target mod2c_core
mjribeiro
Describe the issue I am currently trying to install NEURON/CoreNEURON following the instructions on the README in this repo, but the build and install step is not working. See logs and system specs below. Thank you!
To Reproduce
-DCORENRN_ENABLE_GPU=ONfor step 3/4cmake --build . --parallel 8 --target installExpected behavior The build and install step should not fail
Logs Output from
cmake --build . --parallel 8 --target install:System