Add a plethora of config options to a-b-c.

[thorstenhater]

Closes #1861 Closes #1783

Started to address #1861, but became much more

• arbor-build-catalogue (a-b-c) does no longer need to be in a fixed location
• nor do we statically fix the configuration for a-b-c
• instead, we rely on arbor.config to read the relevant default values
• each value can be overriden, if desired
• added many more values to the configuration
  • gpu type and arch
  • paths and prefix
  • CXX
• report default settings for better diagnosis
• implement a fallback for prefix if that does not exist; in particular for the amazing skbuild.

In endeffect to you can use a-b-c as a standalone tool, as long as you have a properly configured py-arbor.

@Helveg please test, including if it resolves #1861 for you @ all please test on your machine.

Example output after removing _skbuild

Warning: prefix '/Users/hater/src/arbor/_skbuild/macosx-11.0-x86_64-3.10/cmake-install' does not exist, falling back to '/Users/hater/src/arbor/.direnv/python-3.10.6'.
usage: arbor-build-catalogue catalogue_name mod_source_dir

Generate dynamic catalogue and build it into a shared object.

positional arguments:
  name              Catalogue name.
  modpfx            Directory name where *.mod files live.

options:
  --raw raw [raw ...]
                    Advanced: Raw mechanisms as C++ files. Per <name> the files <name>.hpp, <name>_cpu.cpp (if CPU
                    is enabled) must be present in the target directory and with GPU support also <name>_gpu.cpp and
                    <name>_gpu.cu.
  -v, --verbose     Verbose.
  -q, --quiet       Less output.
  --cpu CPU         Enable CPU support.
  --debug [path]    Don't clean up the generated temp cpp code. Can be a target path for the generated code.
  --gpu gpu         Enable GPU support
  --gpu-arch gpu_arch
                    Enable GPU support; default=-
  --cxx cxx         Use this C++ compiler; default=/usr/local/opt/llvm/bin/clang++.
  --prefix prefix   Arbor's install prefix; default=/Users/hater/src/arbor/.direnv/python-3.10.6.
  --bin bin         Look here for Arbor utils like modcc; relative to prefix, default=bin.
  --lib lib         Look here for Arbor's CMake config; relative to prefix, default=lib.
  --data data       Look here for Arbor supplementals like generate_catalogue; relative to prefix, default=lib
  -h, --help        Display this help and exit.

[brenthuisman]

@Helveg Can you confirm this solves #1861?

[Helveg]

I'm low on time, but I'll try in the near future

[brenthuisman]

@Helveg Near future has passed ;) Any update?

[Helveg]

I .. uh... LGTM? 👍 ??

[Helveg]

@thorstenhater the help text still lists --gpu gpu, is the value still required?

Edit: I also get this build error on your branch:

[ 91%] Building CXX object arborenv/CMakeFiles/arborenv.dir/gpu_uuid.cpp.o
[ 91%] Building CXX object sup/CMakeFiles/arbor-sup.dir/path.cpp.o
[ 91%] Linking CXX static library ../lib/libarborenv.a
[ 91%] Built target arborenv
[ 93%] Linking CXX static library ../lib/libarborsup.a
[ 93%] Built target arbor-sup
[ 93%] Linking CXX shared library ../../lib/dummy-catalogue.so
[ 93%] Built target dummy-catalogue
[ 93%] Linking CXX static library ../lib/libarborio.a
[ 93%] Built target arborio
[ 93%] Building CXX object lmorpho/CMakeFiles/lmorpho.dir/lmorpho.cpp.o
[ 93%] Building CXX object python/CMakeFiles/pyarb_obj.dir/cable_cell_io.cpp.o
[ 93%] Building CXX object python/CMakeFiles/pyarb_obj.dir/cable_probes.cpp.o
[ 93%] Building CXX object lmorpho/CMakeFiles/lmorpho.dir/lsys_models.cpp.o
[ 95%] Building CXX object python/CMakeFiles/pyarb_obj.dir/cells.cpp.o
[ 95%] Building CXX object python/CMakeFiles/pyarb_obj.dir/config.cpp.o
[ 95%] Building CXX object python/CMakeFiles/pyarb_obj.dir/context.cpp.o
[ 95%] Building CXX object lmorpho/CMakeFiles/lmorpho.dir/lsystem.cpp.o
/bin/sh: -c: line 0: unexpected EOF while looking for matching `"'
/bin/sh: -c: line 1: syntax error: unexpected end of file
make[2]: *** [python/CMakeFiles/pyarb_obj.dir/build.make:118: python/CMakeFiles/pyarb_obj.dir/config.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
[ 95%] Linking CXX executable ../bin/lmorpho
[ 95%] Built target lmorpho
make[1]: *** [CMakeFiles/Makefile2:2129: python/CMakeFiles/pyarb_obj.dir/all] Error 2
make: *** [Makefile:136: all] Error 2

[thorstenhater]

That's weird ... any idea where that comes from?

[Helveg]

This is my entire session on PizDaint, note that after this followed a few more rounds of rm build mkdir build blabla ...

build_adventure.txt

[thorstenhater]

No clue ... there's no trace of 'sh -c' in the whole of Arbor; at least not in this branch. This branch builds fine locally and in CI. I'll try a GPU build somewhere next week and we'll see if this is GPU specific.

[thorstenhater]

bors try

[bors[bot]]

try

Build failed:

• ci/gitlab/gitlab.com

[thorstenhater]

Confirmed ... it's due to ARB_GPU_ARCH, whomever made python/config.cpp probably should have used CMake/configure_file in the first place. But I'll switch that over here

[thorstenhater]

On second thought, though, I'd rather not expose the GPU arch used, it doesn't play a role in the interface and is thus overly restrictive.

[Helveg]

Now it builds, but I'm getting "gpu": None after building with CUDA:

(arbenv) bp000347@daint101:~/arbenv/arbor/build> CC=cc CXX=CC cmake .. \
>   -DARB_WITH_MPI=ON \
>   -DARB_WITH_PROFILING=OFF \
>   -DARB_GPU=cuda \
>   -DARB_USE_BUNDLED_LIBS=ON \
>   -DCMAKE_INSTALL_PREFIX=$HOME/arbenv \
>   -DARB_WITH_PYTHON=ON \
>   -DARB_VECTORIZE=ON
-- The C compiler identification is GNU 9.3.0
-- The CXX compiler identification is GNU 9.3.0
-- Cray Programming Environment 2.7.10 C
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /opt/cray/pe/craype/2.7.10/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Cray Programming Environment 2.7.10 CXX
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /opt/cray/pe/craype/2.7.10/bin/CC - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found CUDAToolkit: /usr/local/cuda-11.0/include (found version "11.0.194")
-- 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
-- The CUDA compiler identification is NVIDIA 11.0.194
-- Detecting CUDA compiler ABI info
-- Detecting CUDA compiler ABI info - done
-- Check for working CUDA compiler: /usr/local/cuda-11.0/bin/nvcc - skipped
-- Detecting CUDA compile features
-- Detecting CUDA compile features - done
-- Found CUDA: /usr/local/cuda-11.0 (found suitable version "11.0", minimum required is "11")
-- Using Random123 submodule: /users/bp000347/arbenv/arbor/ext>/random123
-- Found Python3: /users/bp000347/arbenv/bin/python3.9 (found suitable version "3.9.10", minimum required is "3.7.0") found components: Interpreter Development Development.Module Development.Embed
-- PYTHON_EXECUTABLE: /users/bp000347/arbenv/bin/python3.9
-- Found MPI_CXX: /opt/cray/pe/craype/2.7.10/bin/CC (found version "3.1")
-- Found MPI: TRUE (found version "3.1") found components: CXX
Catalogue name:       dummy
Catalogue mechanisms: dummy
Extra cxx files:
Catalogue sources:    /users/bp000347/arbenv/arbor/test/unit/dummy
Catalogue output:     /users/bp000347/arbenv/arbor/build/test/unit/generated/dummy
Build as standalone:  ON
Arbor cxx flags:      $<$<COMPILE_LANGUAGE:CUDA>:-Xcompiler=>-march=native;$<$<BUILD_INTERFACE:$<COMPILE_LANGUAGE:CXX>>:-fvisibility=hidden>;$<$<BUILD_INTERFACE:$<COMPILE_LANGUAGE:CUDA>>:-Xcompiler=-fvisibility=hidden>
Arbor cxx compiler:
Script prefix:        /users/bp000347/arbenv/arbor/mechanisms
Current cxx compiler: /opt/cray/pe/craype/2.7.10/bin/CC
-- Failed to locate sphinx-build executable (missing: SPHINX_EXECUTABLE)
-- Could NOT find PY_svgwrite (missing: PY_SVGWRITE)
-- pybind11 v2.10.0
-- Performing Test HAS_FLTO
-- Performing Test HAS_FLTO - Success
-- Found PY_mpi4py: /users/bp000347/arbenv/lib/python3.9/site-packages/mpi4py
-- Python module installation path: /users/bp000347/arbenv/lib/python3.9/site-packages
-- Configuring done
-- Generating done
-- Build files have been written to: /users/bp000347/arbenv/arbor/build
(arbenv) bp000347@daint101:~/arbenv/arbor/build> make install -j 8
[  0%] Generating _always_rebuild
[  0%] Building catalogue dummy
[  0%] Building catalogue bbp
[  2%] Building catalogue default
[  2%] Building catalogue allen
[  4%] Generating version.hpp-test
[  4%] Built target bbp_catalogue_cpp_target
[  4%] Built target default_catalogue_cpp_target
[  4%] Built target dummy_catalogue_cpp_target
[  4%] Built target allen_catalogue_cpp_target
[  4%] Generating arbor/version.hpp
[  4%] Built target generate_version_hpp
[  4%] Building CXX object modcc/CMakeFiles/libmodcc.dir/astmanip.cpp.o
[  4%] Building CXX object modcc/CMakeFiles/libmodcc.dir/blocks.cpp.o
[  4%] Building CXX object modcc/CMakeFiles/libmodcc.dir/errorvisitor.cpp.o
[  4%] Building CXX object modcc/CMakeFiles/libmodcc.dir/functioninliner.cpp.o
[  6%] Building CXX object modcc/CMakeFiles/libmodcc.dir/functionexpander.cpp.o
[  6%] Building CXX object modcc/CMakeFiles/libmodcc.dir/lexer.cpp.o
[  6%] Building CXX object modcc/CMakeFiles/libmodcc.dir/kineticrewriter.cpp.o
[  6%] Building CXX object modcc/CMakeFiles/libmodcc.dir/expression.cpp.o
[  6%] Building CXX object modcc/CMakeFiles/libmodcc.dir/linearrewriter.cpp.o
[  6%] Building CXX object modcc/CMakeFiles/libmodcc.dir/module.cpp.o
[  6%] Building CXX object modcc/CMakeFiles/libmodcc.dir/parser.cpp.o
[  6%] Building CXX object modcc/CMakeFiles/libmodcc.dir/solvers.cpp.o
[  6%] Building CXX object modcc/CMakeFiles/libmodcc.dir/symdiff.cpp.o
[  8%] Building CXX object modcc/CMakeFiles/libmodcc.dir/symge.cpp.o
[  8%] Building CXX object modcc/CMakeFiles/libmodcc.dir/token.cpp.o
[  8%] Building CXX object modcc/CMakeFiles/libmodcc.dir/io/prefixbuf.cpp.o
[  8%] Building CXX object modcc/CMakeFiles/libmodcc.dir/printer/cexpr_emit.cpp.o
[  8%] Building CXX object modcc/CMakeFiles/libmodcc.dir/printer/cprinter.cpp.o
[  8%] Building CXX object modcc/CMakeFiles/libmodcc.dir/printer/marks.cpp.o
[  8%] Building CXX object modcc/CMakeFiles/libmodcc.dir/printer/gpuprinter.cpp.o
[ 10%] Building CXX object modcc/CMakeFiles/libmodcc.dir/printer/infoprinter.cpp.o
[ 10%] Building CXX object modcc/CMakeFiles/libmodcc.dir/printer/printerutil.cpp.o
[ 10%] Linking CXX static library ../lib/libmodcc.a
[ 10%] Built target libmodcc
[ 10%] Building CXX object modcc/CMakeFiles/modcc.dir/modcc.cpp.o
[ 10%] Linking CXX executable ../bin/modcc
[ 10%] Built target modcc
[ 10%] modcc generating: /users/bp000347/arbenv/arbor/build/test/unit/generated/dummy/dummy.hpp;/users/bp000347/arbenv/arbor/build/test/unit/generated/dummy/dummy_cpu.cpp;/users/bp000347/arbenv/arbor/build/test/unit/generated/dummy/dummy_gpu.cpp;/users/bp000347/arbenv/arbor/build/test/unit/generated/dummy/dummy_gpu.cu
[ 10%] modcc generating: /users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/CaDynamics_E2.hpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/CaDynamics_E2_cpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/CaDynamics_E2_gpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/CaDynamics_E2_gpu.cu
[ 10%] modcc generating: /users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/Ca_HVA.hpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/Ca_HVA_cpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/Ca_HVA_gpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/Ca_HVA_gpu.cu
[ 10%] modcc generating: /users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/Ca_LVAst.hpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/Ca_LVAst_cpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/Ca_LVAst_gpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/Ca_LVAst_gpu.cu
[ 12%] modcc generating: /users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/CaDynamics.hpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/CaDynamics_cpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/CaDynamics_gpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/CaDynamics_gpu.cu
[ 12%] modcc generating: /users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/Ih.hpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/Ih_cpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/Ih_gpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/Ih_gpu.cu[ 12%] modcc generating: /users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/Ca_HVA.hpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/Ca_HVA_cpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/Ca_HVA_gpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/Ca_HVA_gpu.cu
[ 12%] modcc generating: /users/bp000347/arbenv/arbor/build/mechanisms/generated/default/exp2syn.hpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/default/exp2syn_cpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/default/exp2syn_gpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/default/exp2syn_gpu.cu
[ 12%] modcc generating: /users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/Ca_LVA.hpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/Ca_LVA_cpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/Ca_LVA_gpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/Ca_LVA_gpu.cu
[ 12%] modcc generating: /users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/Im.hpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/Im_cpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/Im_gpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/Im_gpu.cu[ 12%] modcc generating: /users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/Ih.hpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/Ih_cpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/Ih_gpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/Ih_gpu.cu
[ 14%] modcc generating: /users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/K_Pst.hpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/K_Pst_cpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/K_Pst_gpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/K_Pst_gpu.cu
[ 14%] modcc generating: /users/bp000347/arbenv/arbor/build/mechanisms/generated/default/expsyn.hpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/default/expsyn_cpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/default/expsyn_gpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/default/expsyn_gpu.cu
[ 14%] modcc generating: /users/bp000347/arbenv/arbor/build/mechanisms/generated/default/expsyn_curr.hpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/default/expsyn_curr_cpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/default/expsyn_curr_gpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/default/expsyn_curr_gpu.cu
[ 14%] modcc generating: /users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/Im.hpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/Im_cpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/Im_gpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/Im_gpu.cu
[ 14%] Built target build_catalogue_dummy_mods
[ 14%] modcc generating: /users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/Im_v2.hpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/Im_v2_cpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/Im_v2_gpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/Im_v2_gpu.cu
[ 14%] modcc generating: /users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/K_Tst.hpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/K_Tst_cpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/K_Tst_gpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/K_Tst_gpu.cu
[ 14%] modcc generating: /users/bp000347/arbenv/arbor/build/mechanisms/generated/default/expsyn_stdp.hpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/default/expsyn_stdp_cpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/default/expsyn_stdp_gpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/default/expsyn_stdp_gpu.cu
[ 14%] modcc generating: /users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/Nap_Et2.hpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/Nap_Et2_cpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/Nap_Et2_gpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/Nap_Et2_gpu.cu
[ 14%] modcc generating: /users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/NaTa_t.hpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/NaTa_t_cpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/NaTa_t_gpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/NaTa_t_gpu.cu
[ 14%] modcc generating: /users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/SK_E2.hpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/SK_E2_cpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/SK_E2_gpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/SK_E2_gpu.cu
[ 14%] modcc generating: /users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/NaTs2_t.hpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/NaTs2_t_cpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/NaTs2_t_gpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/NaTs2_t_gpu.cu
[ 14%] modcc generating: /users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/K_P.hpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/K_P_cpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/K_P_gpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/K_P_gpu.cu
[ 17%] modcc generating: /users/bp000347/arbenv/arbor/build/mechanisms/generated/default/kamt.hpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/default/kamt_cpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/default/kamt_gpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/default/kamt_gpu.cu
[ 17%] modcc generating: /users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/SKv3_1.hpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/SKv3_1_cpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/SKv3_1_gpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/bbp/SKv3_1_gpu.cu
[ 19%] modcc generating: /users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/K_T.hpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/K_T_cpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/K_T_gpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/K_T_gpu.cu
[ 19%] modcc generating: /users/bp000347/arbenv/arbor/build/mechanisms/generated/default/hh.hpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/default/hh_cpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/default/hh_gpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/default/hh_gpu.cu
[ 19%] modcc generating: /users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/Kd.hpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/Kd_cpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/Kd_gpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/Kd_gpu.cu
[ 19%] modcc generating: /users/bp000347/arbenv/arbor/build/mechanisms/generated/default/kdrmt.hpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/default/kdrmt_cpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/default/kdrmt_gpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/default/kdrmt_gpu.cu
[ 19%] modcc generating: /users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/Kv2like.hpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/Kv2like_cpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/Kv2like_gpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/Kv2like_gpu.cu
[ 19%] modcc generating: /users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/Kv3_1.hpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/Kv3_1_cpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/Kv3_1_gpu.cpp;/users/bp000347/arbenv/arbor/build/mechanisms/generated/allen/Kv3_1_gpu.cu
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/users/bp000347/arbenv/arbor/arbor/morph/segment_tree.cpp: In function 'std::map<unsigned int, std::vector<unsigned int> > arb::tree_to_children(const arb::segment_tree&)':
/users/bp000347/arbenv/arbor/arbor/morph/segment_tree.cpp:29:26: warning: comparison of integer expressions of different signedness: 'int' and 'arb::msize_t' {aka 'unsigned int'} [-Wsign-compare]
   29 |     for (auto ix = 0; ix < tree.size(); ++ix) result[parents[ix]].push_back(ix);
      |                       ~~~^~~~~~~~~~~~~
/users/bp000347/arbenv/arbor/arbor/morph/segment_tree.cpp: In function 'bool arb::equivalent(const arb::segment_tree&, const arb::segment_tree&)':
/users/bp000347/arbenv/arbor/arbor/morph/segment_tree.cpp:108:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<arb::msegment>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  108 |         for (auto ix = 0; ix < as.size(); ++ix) {
      |                           ~~~^~~~~~~~~~~
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[ 82%] Building CUDA object arbor/CMakeFiles/arbor.dir/__/mechanisms/generated/default/decay_gpu.cu.o
[ 82%] Building CXX object arbor/CMakeFiles/arbor.dir/__/mechanisms/generated/default/inject_cpu.cpp.o
[ 85%] Building CXX object arbor/CMakeFiles/arbor.dir/__/mechanisms/generated/default/inject_gpu.cpp.o
[ 85%] Building CUDA object arbor/CMakeFiles/arbor.dir/__/mechanisms/generated/default/inject_gpu.cu.o
[ 85%] Linking CUDA device code CMakeFiles/arbor.dir/cmake_device_link.o
[ 85%] Linking CXX static library ../lib/libarbor.a
[ 85%] Built target arbor
[ 85%] Building CXX object sup/CMakeFiles/arbor-sup.dir/ioutil.cpp.o
[ 85%] Building CXX object sup/CMakeFiles/arbor-sup.dir/path.cpp.o
[ 85%] Building CXX object arborenv/CMakeFiles/arborenv.dir/arbenvexcept.cpp.o
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[ 85%] Building CXX object arborio/CMakeFiles/arborio.dir/asc_lexer.cpp.o
[ 85%] Building CXX object test/unit/CMakeFiles/dummy-catalogue.dir/dummy_catalogue.cpp.o
In file included from /users/bp000347/arbenv/arbor/build/test/unit/generated/dummy/dummy.hpp:4,
                 from /users/bp000347/arbenv/arbor/build/test/unit/dummy_catalogue.cpp:6:
/users/bp000347/arbenv/arbor/build/arbor/include/arbor/version.hpp:27: warning: "ARB_GPU_ENABLED" redefined
   27 | #define ARB_GPU_ENABLED
      |
<command-line>: note: this is the location of the previous definition
[ 85%] Building CXX object test/unit/CMakeFiles/dummy-catalogue.dir/generated/dummy/dummy_cpu.cpp.o
[ 85%] Building CXX object arborenv/CMakeFiles/arborenv.dir/default_env.cpp.o
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[ 89%] Building CXX object arborenv/CMakeFiles/arborenv.dir/gpu_uuid.cpp.o
[ 89%] Building CXX object arborio/CMakeFiles/arborio.dir/neurolucida.cpp.o
[ 89%] Building CXX object arborio/CMakeFiles/arborio.dir/swcio.cpp.o
[ 89%] Building CXX object arborio/CMakeFiles/arborio.dir/cableio.cpp.o
[ 89%] Building CXX object arborio/CMakeFiles/arborio.dir/cv_policy_parse.cpp.o
[ 91%] Building CXX object arborio/CMakeFiles/arborio.dir/label_parse.cpp.o
[ 91%] Linking CXX static library ../lib/libarborenv.a
[ 91%] Built target arborenv
[ 93%] Linking CXX static library ../lib/libarborsup.a
[ 93%] Built target arbor-sup
[ 93%] Linking CXX shared library ../../lib/dummy-catalogue.so
[ 93%] Built target dummy-catalogue
[ 93%] Linking CXX static library ../lib/libarborio.a
[ 93%] Built target arborio
[ 93%] Building CXX object python/CMakeFiles/pyarb_obj.dir/cable_cell_io.cpp.o
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[ 95%] Building CXX object lmorpho/CMakeFiles/lmorpho.dir/lsys_models.cpp.o
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[ 95%] Linking CXX executable ../bin/lmorpho
[ 95%] Built target lmorpho
[ 95%] Building CXX object python/CMakeFiles/pyarb_obj.dir/event_generator.cpp.o
[ 95%] Building CXX object python/CMakeFiles/pyarb_obj.dir/identifiers.cpp.o
[ 97%] Building CXX object python/CMakeFiles/pyarb_obj.dir/mechanism.cpp.o
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[ 97%] Building CXX object python/CMakeFiles/pyarb_obj.dir/mpi.cpp.o
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[ 97%] Building CXX object python/CMakeFiles/pyarb_obj.dir/pyarb.cpp.o
[ 97%] Building CXX object python/CMakeFiles/pyarb_obj.dir/recipe.cpp.o
[ 97%] Building CXX object python/CMakeFiles/pyarb_obj.dir/schedule.cpp.o
[100%] Building CXX object python/CMakeFiles/pyarb_obj.dir/simulation.cpp.o
[100%] Building CXX object python/CMakeFiles/pyarb_obj.dir/single_cell_model.cpp.o
[100%] Building CXX object python/CMakeFiles/pyarb_obj.dir/env.cpp.o
[100%] Built target pyarb_obj
[100%] Linking CXX shared module arbor/_arbor.cpython-39-x86_64-linux-gnu.so
[100%] Linking CXX static library ../../../lib/libpy_unit_lib.a
[100%] Built target py_unit_lib
[100%] Built target pyarb
Install the project...
-- Install configuration: "release"
-- Installing: /users/bp000347/arbenv/bin/arbor-build-catalogue
-- Installing: /users/bp000347/arbenv/share/arbor/BuildModules.cmake
-- Installing: /users/bp000347/arbenv/share/arbor/generate_catalogue
-- Up-to-date: /users/bp000347/arbenv/include/arbor
-- Up-to-date: /users/bp000347/arbenv/include/arbor/util
-- Installing: /users/bp000347/arbenv/include/arbor/util/any_ptr.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/util/extra_traits.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/util/uninitialized.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/util/expected.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/util/compat.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/util/hash_def.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/util/typed_map.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/util/visibility.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/util/unique_any.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/util/scope_exit.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/util/pp_util.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/util/lexcmp_def.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/util/any_cast.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/util/handle_set.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/util/any_visitor.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/morph
-- Installing: /users/bp000347/arbenv/include/arbor/morph/isometry.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/morph/region.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/morph/segment_tree.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/morph/morphology.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/morph/label_dict.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/morph/primitives.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/morph/locset.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/morph/place_pwlin.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/morph/morphexcept.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/morph/stitch.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/morph/cv_data.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/morph/embed_pwlin.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/morph/mprovider.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/morph/mcable_map.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/benchmark_cell.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/arb_types.h
-- Up-to-date: /users/bp000347/arbenv/include/arbor/spike_event.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/mechinfo.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/cable_cell_param.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/spike_source_cell.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/cable_cell.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/mechanism.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/s_expr.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/arb_types.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/arbexcept.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/lif_cell.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/common_types.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/mechcat.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/generic_event.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/constants.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/simple_sampler.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/context.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/schedule.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/fvm_types.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/cv_policy.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/arb_types.inc
-- Up-to-date: /users/bp000347/arbenv/include/arbor/simd
-- Up-to-date: /users/bp000347/arbenv/include/arbor/simd/native.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/simd/avx.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/simd/simd.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/simd/generic.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/simd/avx512.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/simd/neon.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/simd/approx.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/simd/implbase.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/simd/sve.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/simd/simd_io.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/event_generator.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/simulation.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/symmetric_recipe.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/iexpr.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/domdecexcept.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/load_balance.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/domain_decomposition.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/gpu
-- Up-to-date: /users/bp000347/arbenv/include/arbor/gpu/gpu_common.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/gpu/math_cu.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/gpu/reduce_by_key.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/gpu/gpu_api.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/gpu/cuda_api.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/gpu/hip_api.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/recipe.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/assert.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/sampling.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/mechanism_abi.h
-- Up-to-date: /users/bp000347/arbenv/include/arbor/communication
-- Up-to-date: /users/bp000347/arbenv/include/arbor/communication/mpi_error.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/math.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/spike.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/profile
-- Installing: /users/bp000347/arbenv/include/arbor/profile/meter_manager.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/profile/timer.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/profile/profiler.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/profile/meter.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor/profile/clock.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arbor
-- Installing: /users/bp000347/arbenv/include/arbor/assert_macro.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/version.hpp
-- Installing: /users/bp000347/arbenv/include/arbor/export.hpp
-- Installing: /users/bp000347/arbenv/bin/modcc
-- Up-to-date: /users/bp000347/arbenv/include/arbor/export.hpp
-- Installing: /users/bp000347/arbenv/lib64/libarbor.a
-- Installing: /users/bp000347/arbenv/include/arborenv/export.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arborenv
-- Up-to-date: /users/bp000347/arbenv/include/arborenv/arbenvexcept.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arborenv/with_mpi.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arborenv/gpu_env.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arborenv/concurrency.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arborenv/default_env.hpp
-- Installing: /users/bp000347/arbenv/lib64/libarborenv.a
-- Installing: /users/bp000347/arbenv/include/arborio/export.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arborio
-- Installing: /users/bp000347/arbenv/include/arborio/swcio.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arborio/cv_policy_parse.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arborio/xml.hpp
-- Up-to-date: /users/bp000347/arbenv/include/arborio/cableio.hpp
-- Installing: /users/bp000347/arbenv/include/arborio/neuroml.hpp
-- Installing: /users/bp000347/arbenv/include/arborio/neurolucida.hpp
-- Installing: /users/bp000347/arbenv/include/arborio/label_parse.hpp
-- Installing: /users/bp000347/arbenv/lib64/libarborio.a
-- Up-to-date: /users/bp000347/arbenv/lib/python3.9/site-packages/arbor
-- Installing: /users/bp000347/arbenv/lib/python3.9/site-packages/arbor/VERSION
-- Installing: /users/bp000347/arbenv/lib/python3.9/site-packages/arbor/_arbor.cpython-39-x86_64-linux-gnu.so
-- Installing: /users/bp000347/arbenv/lib/python3.9/site-packages/arbor/__init__.py
-- Old export file "/users/bp000347/arbenv/lib64/cmake/arbor/arbor-targets.cmake" will be replaced.  Removing files [/users/bp000347/arbenv/lib64/cmake/arbor/arbor-targets-release.cmake].
-- Installing: /users/bp000347/arbenv/lib64/cmake/arbor/arbor-targets.cmake
-- Installing: /users/bp000347/arbenv/lib64/cmake/arbor/arbor-targets-release.cmake
-- Installing: /users/bp000347/arbenv/lib64/cmake/arbor/arbor-config.cmake
-- Installing: /users/bp000347/arbenv/lib64/cmake/arbor/arbor-config-version.cmake
-- Installing: /users/bp000347/arbenv/bin/lmorpho
(arbenv) bp000347@daint101:~/arbenv/arbor/build> cd $HOME
(arbenv) bp000347@daint101:~> make install -j8
make: *** No rule to make target 'install'.  Stop.
(arbenv) bp000347@daint101:~> python
Python 3.9.10 (main, Mar 25 2022, 16:10:13)
[GCC 9.3.0 20200312 (Cray Inc.)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import arbor
>>> arbor.config()
{'mpi': True, 'mpi4py': True, 'gpu': None, 'vectorize': True, 'profiling': False, 'neuroml': False, 'bundled': True, 'version': '0.7.1-dev', 'source': '2022-09-20T11:41:40+02:00 a66cb8e5ea7319d8cfe8d56a14822af0569747f1', 'arch': 'native', 'prefix': '/users/bp000347/arbenv', 'binary_path': 'bin', 'lib_path': 'lib64', 'data_path': 'share', 'CXX': '/opt/cray/pe/craype/2.7.10/bin/CC'}
>>> arbor.__path__
['/users/bp000347/arbenv/lib/python3.9/site-packages/arbor']

[thorstenhater]

@Helveg now give it a spin.

[Helveg]

New build error after pulling:

[ 36%] Building CXX object arbor/CMakeFiles/arbor.dir/communication/mpi_context.cpp.o
[ 36%] Building CXX object arbor/CMakeFiles/arbor.dir/__/mechanisms/generated/bbp/bbp_catalogue.cpp.o
make[2]: *** No rule to make target 'mechanisms/generated/bbp/CaDynamics_E2_gpu.cpp', needed by 'arbor/CMakeFiles/arbor.dir/__/mechanisms/generated/bbp/CaDynamics_E2_gpu.cpp.o'.  Stop.
make[2]: *** Waiting for unfinished jobs....
[ 36%] Building CXX object arbor/CMakeFiles/arbor.dir/__/mechanisms/generated/bbp/CaDynamics_E2_cpu.cpp.o
make[1]: *** [CMakeFiles/Makefile2:811: arbor/CMakeFiles/arbor.dir/all] Error 2
make: *** [Makefile:136: all] Error 2

[Helveg]

arbor.txt

[thorstenhater]

@Helveg I cannot reproduce this, neither locally nor on a GPU cluster. I merged master to be up to date. Potentiall that's a machine-specific issue (one I don't have access to).

[brenthuisman]

@Helveg Did the commit merging master help you out?

[brenthuisman]

@Helveg we're releasing this week. If you can give it, you confirmation that your issue was resolved would be nice to have.

[Helveg]

Still errors out building on PizDaint with GPU. I'll attach the log on Monday. But is your bors build passing now?

[thorstenhater]

Monday is after our release window, I would appreciate resolving this before v0.8. As I said, I cannot reproduce your error on our machines and bors keeps failing for other reasons. We'll have some more eyes on this soon.

[thorstenhater]

bors try

[boeschf]

@thorstenhater I've just tried building this branch on Piz Daint (GPU partition) - i didn't find any problems (apart from a missing file when compiling the ubenches target, which I'll fix when I get around to it). @Helveg: I posted my setup below, maybe you'll find a discrepancy

module load daint-gpu/21.09
module load craype-accel-nvidia60
module switch cudatoolkit cudatoolkit/21.5_11.3
module rm PrgEnv-cray
module load PrgEnv-gnu
module switch gcc gcc/9.3.0
module load cray-python/3.9.4.1
# I load my own cmake here
module use /project/csstaff/boeschf/modules
module load cmake/3.20
export CRAYPE_LINK_TYPE=dynamic

CC=cc CXX=CC ccmake \
    -DMPI_CXX_SKIP_MPICXX=ON \
    -DARB_GPU=cuda \
    -DCMAKE_CUDA_ARCHITECTURES=60 \
    -DCMAKE_CUDA_RUNTIME_LIBRARY=Shared \
    -DCUDA_USE_STATIC_CUDA_RUNTIME=OFF \
    -DCMAKE_CUDA_FLAGS="-ccbin /opt/cray/pe/craype/2.7.10/bin/CC" \
    ..

[Helveg]

Yours is a bit more extensive than mine, but mine used to work. Could you give it a go with this setup to confirm something is afoot?

module load daint-gpu cudatoolkit CMake gcc/9.3.0
module switch PrgEnv-cray PrgEnv-gnu
CC=cc CXX=CC cmake .. \
  -DARB_WITH_MPI=ON \
  -DARB_WITH_PROFILING=OFF \
  -DARB_GPU=cuda \
  -DARB_USE_BUNDLED_LIBS=ON \
  -DARB_WITH_PYTHON=ON \
  -DARB_VECTORIZE=ON
make install -j 8

@brenthuisman you once mentioned providing official build notes for supported platforms?

[bors[bot]]

try

Timed out.