search

neuronsimulator / nrn

NEURON Simulator
http://nrn.readthedocs.io
Other
403 stars 118 forks source link

Build on Ubuntu 21.10 (wsl1 or wsl2 on win 10) broken #1770

Closed cstricker closed 2 years ago

cstricker commented 2 years ago

Context

Even after a fresh git pull, I run into a problem towards the very end of the build of nrniv. It is in the code section on Tests - and complains about an error in a cmake file.

Overview of the issue

As a consequence, the build is aborted...

Expected result/behavior

This only happens on Ubuntu - the same build on macOS (12.3.1) is fine.

NEURON setup

Minimal working example - MWE

Create a new install location and build from source. Important to include tests.

Logs (output of the relevant section)

[ 96%] Building CXX object test/CMakeFiles/testneuron.dir/unit_tests/unit_test.cpp.o
Syntax error: "(" unexpected/bin/sh: 1: /bin/sh: 1: [ 96%] Building CXX object src/nrniv/CMakeFiles/nrniv.dir/__/ivoc/nrnmain.cpp.o

[ 96%] Building CXX object src/nrniv/CMakeFiles/nrniv.dir/__/oc/ockludge.cpp.o
Syntax error: "(" unexpectedSyntax error: "(" unexpected[ 97%] Building CXX object src/nrniv/CMakeFiles/nrniv.dir/__/oc/modlreg.cpp.o
[ 97%] Building special[-core] for test pynrn_tests::basic_tests
make[2]: *** [test/CMakeFiles/NRN_TEST_nrnivmodl_85f65074ccf5b78091d712a908f4bce80fc8c3391faee99cc2e0a5396441738f.dir/build.make:81: test/nrnivmodl/85f65074ccf5b78091d712a908f4bce80fc8c3391faee99cc2e0a5396441738f/x86_64/special] Error 2

make[1]: *** [CMakeFiles/Makefile2:2249: test/CMakeFiles/NRN_TEST_nrnivmodl_85f65074ccf5b78091d712a908f4bce80fc8c3391faee99cc2e0a5396441738f.dir/all] Error 2
/bin/sh: 1: make[2]: *** [test/external/reduced_dentate/CMakeFiles/NRN_TEST_nrnivmodl_a206ed622f59aee520dad866043bc6fa986b37e4757ca60cc079a832492cb0a5.dir/build.make:108: test/nrnivmodl/a206ed622f59aee520dad866043bc6fa986b37e4757ca60cc079a832492cb0a5/x86_64/special] Error 2
make[1]: *** Waiting for unfinished jobs....
make[2]: *** [test/external/testcorenrn/CMakeFiles/NRN_TEST_nrnivmodl_ce2ac938a8522792dca306f6a0a64f31253023aac268369b00c24ac5466e99dd.dir/build.make:86: test/nrnivmodl/ce2ac938a8522792dca306f6a0a64f31253023aac268369b00c24ac5466e99dd/x86_64/special] Error 2
Syntax error: "(" unexpectedmake[1]: *** [CMakeFiles/Makefile2:2330: test/external/reduced_dentate/CMakeFiles/NRN_TEST_nrnivmodl_a206ed622f59aee520dad866043bc6fa986b37e4757ca60cc079a832492cb0a5.dir/all] Error 2

make[1]: *** [CMakeFiles/Makefile2:2438: test/external/testcorenrn/CMakeFiles/NRN_TEST_nrnivmodl_ce2ac938a8522792dca306f6a0a64f31253023aac268369b00c24ac5466e99dd.dir/all] Error 2
make[2]: *** [test/CMakeFiles/NRN_TEST_nrnivmodl_ffaa542179ffd173f541057357044fa76c1a848fac1421d71f92610e4d24f3cc.dir/build.make:82: test/nrnivmodl/ffaa542179ffd173f541057357044fa76c1a848fac1421d71f92610e4d24f3cc/x86_64/special] Error 2
make[1]: *** [CMakeFiles/Makefile2:2168: test/CMakeFiles/NRN_TEST_nrnivmodl_ffaa542179ffd173f541057357044fa76c1a848fac1421d71f92610e4d24f3cc.dir/all] Error 2
[
pramodk commented 2 years ago

Dear @cstricker,

Thank you for posting the issue.

I tried to reproduce the issue on vanilla Ubuntu 21.10 docker image but couldn't do so. I don't have WSL access at the moment but something we can check bit later this week (@alexsavulescu @nrnhines).

It would be great if you could provide the cmake configure command with all options and output of the same command. For example, in my case its:

Note: -DNRN_ENABLE_TESTS=ON is optional, and you can also disable GUI & RXD components if you are not interested: -DNRN_ENABLE_RX3D=OFF -DNRN_ENABLE_INTERVIEWS=OFF


root@65181a658935:/nrn/build# cmake .. -DCMAKE_INSTALL_PREFIX=`pwd`/install -DNRN_ENABLE_TESTS=ON -DNRN_ENABLE_CORENEURON=ON
-- Sub-project : using iv from from /nrn/external/iv
-- Checking for include files
-- Checking for functions
-- Checking for include directories
-- Checking for types
--
-- Configured INTERVIEWS 0.1
--
-- Some things you can do now:
-- --------------+--------------------------------------------------------------
-- Command       |   Description
-- --------------+--------------------------------------------------------------
-- make install  | Will install INTERVIEWS to: /nrn/build/install
--               | Change the install location of NEURON using:
--               |     cmake <src_path> -DCMAKE_INSTALL_PREFIX=<install_path>
-- --------------+--------------------------------------------------------------
-- Build option  | Status
-- --------------+--------------------------------------------------------------
-- BUILD_TYPE    | RelWithDebInfo (allowed: Debug;Release;RelWithDebInfo)
-- SHARED        | OFF
-- X11_DYNAMIC   | OFF
-- --------------+--------------------------------------------------------------
--  See more : https://github.com/neuronsimulator/iv
-- --------------+--------------------------------------------------------------
--
-- Found PythonInterp: /usr/bin/python3 (found suitable version "3.9.7", minimum required is "3.7")
-- Found PythonInterp: /usr/bin/python3 (found suitable version "3.9.7", minimum required is "3")
-- Building CoreNEURON from submodule
-- Sub-project : using coreneuron from from /nrn/external/coreneuron
-- CORENRN_FORMATTING: OFF
-- CORENRN_FORMATTING_ON: all
-- CORENRN_FORMATTING_CPP_CHANGES_ONLY: OFF
-- CORENRN_TEST_FORMATTING: OFF
-- CORENRN_FORMATTING_NO_SUBMODULES: ON
-- CORENRN_CLANG_FORMAT: OFF
-- CORENRN_CMAKE_FORMAT: OFF
-- CORENRN_GIT_HOOKS: OFF
-- CORENRN_GIT_COMMIT_HOOKS:
-- CORENRN_GIT_PUSH_HOOKS: courtesy-msg
-- CORENRN_STATIC_ANALYSIS: OFF
-- CORENRN_TEST_STATIC_ANALYSIS: OFF
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
-- Doxygen not found, building docs has been disabled
-- Found PythonInterp: /usr/bin/python3 (found version "3.9.7")
-- Using mod2c submodule from /nrn/external/coreneuron/external/mod2c
-- mod2c is used as APPLICATION_NAME
-- Boost not found, unit tests disabled
--
-- Configured CoreNEURON 1.0
--
-- You can now build CoreNEURON 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 CoreNEURON to: /nrn/build/install
-- docs                | Build full docs. Calls targets: doxygen, sphinx
-- --------------------+--------------------------------------------------------
--  Build option       | Status
-- --------------------+--------------------------------------------------------
-- CXX COMPILER        | /usr/bin/c++
-- COMPILE FLAGS       |  -fopenmp  -Wno-unknown-pragmas -g  -O2 -Wno-write-strings -std=c++14
-- Build Type          | SHARED
-- MPI                 | ON
--   DYNAMIC           | OFF
--   INC               | /usr/include/x86_64-linux-gnu/mpich
-- OpenMP              | ON
-- Use legacy units    | OFF
-- NMODL               | OFF
-- MOD2CPP PATH        | /nrn/build/bin/mod2c_core
-- GPU Support         | OFF
-- Auto Timeout        | ON
-- Wrap exp()          | OFF
-- SplayTree Queue     | ON
-- NetReceive Buffer   | ON
-- Caliper             | OFF
-- Likwid              | OFF
-- Unit Tests          | ON
-- Reporting           | OFF
-- --------------+--------------------------------------------------------------
--  See documentation : https://github.com/BlueBrain/CoreNeuron/
-- --------------+--------------------------------------------------------------
--
Extracting link flags from target 'Threads::Threads', beware that this can be fragile. Got:
Generating link flags from path /usr/lib/x86_64-linux-gnu/libreadline.so Got: /usr/lib/x86_64-linux-gnu/libreadline.so -Wl,-rpath,/usr/lib/x86_64-linux-gnu
Generating link flags from path /usr/lib/x86_64-linux-gnu/libcurses.so Got: /usr/lib/x86_64-linux-gnu/libcurses.so -Wl,-rpath,/usr/lib/x86_64-linux-gnu
Generating link flags from path /usr/lib/x86_64-linux-gnu/libform.so Got: /usr/lib/x86_64-linux-gnu/libform.so -Wl,-rpath,/usr/lib/x86_64-linux-gnu
Generating link flags from path /usr/lib/x86_64-linux-gnu/libpython3.9.so Got: /usr/lib/x86_64-linux-gnu/libpython3.9.so -Wl,-rpath,/usr/lib/x86_64-linux-gnu
Generating link flags from path /usr/lib/x86_64-linux-gnu/libmpich.so Got: /usr/lib/x86_64-linux-gnu/libmpich.so -Wl,-rpath,/usr/lib/x86_64-linux-gnu
Generating link flags from path /usr/lib/x86_64-linux-gnu/libX11.so Got: /usr/lib/x86_64-linux-gnu/libX11.so -Wl,-rpath,/usr/lib/x86_64-linux-gnu
Generating link flags from path /usr/lib/x86_64-linux-gnu/libXext.so Got: /usr/lib/x86_64-linux-gnu/libXext.so -Wl,-rpath,/usr/lib/x86_64-linux-gnu
-- Sub-project : using catch2 from from /nrn/external/catch2
-- 3rd party project: using rxd/testdata from "test/rxd/testdata"
-- mpiexec does not support --oversubscribe
-- Could NOT find mpi4py (missing: MPI4PY_LOCATION _MPI4PY_VERSION_MATCH)
-- Could NOT find mpi4py (missing: MPI4PY_LOCATION _MPI4PY_VERSION_MATCH)
-- Disabling coreneuron_modtests::fornetcon_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::direct_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::direct_hoc_gpu: gpu not enabled
-- Disabling coreneuron_modtests::spikes_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::spikes_file_mode_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::fast_imem_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::datareturn_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::test_units_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::test_netmove_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::test_pointer_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::test_watchrange_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::test_psolve_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::test_ba_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::test_natrans_py_gpu: gpu not enabled
-- Could NOT find mpi4py (missing: MPI4PY_LOCATION _MPI4PY_VERSION_MATCH)
-- Disabling coreneuron_modtests::spikes_mpi_file_mode_py_gpu: gpu not enabled
-- Disabling coreneuron_modtests::inputpresyn_py_gpu: gpu not enabled
-- Disabling reduced_dentate::coreneuron_gpu: gpu not enabled
-- Disabling external_ringtest::coreneuron_gpu_mpi_offline_saverestore: gpu not enabled
-- Disabling external_ringtest::coreneuron_gpu_mpi: gpu not enabled
-- Disabling external_ringtest::coreneuron_gpu_mpi_offline: gpu not enabled
-- Disabling external_ringtest::coreneuron_gpu_mpi_threads: gpu not enabled
-- Disabling testcorenrn_bbcore::coreneuron_gpu_online: gpu not enabled
-- Disabling testcorenrn_bbcore::coreneuron_gpu_online_psolve_alternate: gpu not enabled
-- Disabling testcorenrn_bbcore::coreneuron_gpu_offline: gpu not enabled
-- Disabling testcorenrn_conc::coreneuron_gpu_online: gpu not enabled
-- Disabling testcorenrn_conc::coreneuron_gpu_online_psolve_alternate: gpu not enabled
-- Disabling testcorenrn_conc::coreneuron_gpu_offline: gpu not enabled
-- Disabling testcorenrn_deriv::coreneuron_gpu_online: gpu not enabled
-- Disabling testcorenrn_deriv::coreneuron_gpu_online_psolve_alternate: gpu not enabled
-- Disabling testcorenrn_deriv::coreneuron_gpu_offline: gpu not enabled
-- Disabling testcorenrn_gf::coreneuron_gpu_online: gpu not enabled
-- Disabling testcorenrn_gf::coreneuron_gpu_online_psolve_alternate: gpu not enabled
-- Disabling testcorenrn_gf::coreneuron_gpu_offline: gpu not enabled
-- Disabling testcorenrn_kin::coreneuron_gpu_online: gpu not enabled
-- Disabling testcorenrn_kin::coreneuron_gpu_online_psolve_alternate: gpu not enabled
-- Disabling testcorenrn_kin::coreneuron_gpu_offline: gpu not enabled
-- Disabling testcorenrn_patstim::coreneuron_gpu_offline_saverestore: gpu not enabled
-- Disabling testcorenrn_patstim::coreneuron_gpu_offline: gpu not enabled
-- Disabling testcorenrn_vecplay::coreneuron_gpu_online: gpu not enabled
-- Disabling testcorenrn_vecplay::coreneuron_gpu_online_psolve_alternate: gpu not enabled
-- Disabling testcorenrn_vecplay::coreneuron_gpu_offline: gpu not enabled
-- Disabling testcorenrn_vecevent::coreneuron_gpu_online: gpu not enabled
-- Disabling testcorenrn_vecevent::coreneuron_gpu_online_psolve_alternate: gpu not enabled
-- Disabling testcorenrn_vecevent::coreneuron_gpu_offline: gpu not enabled
-- Disabling testcorenrn_watch::coreneuron_gpu_online: gpu not enabled
-- Disabling testcorenrn_watch::coreneuron_gpu_online_psolve_alternate: gpu not enabled
-- Disabling testcorenrn_watch::coreneuron_gpu_offline: gpu not enabled
--
-- Configured NEURON 8.0
--
-- 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: /nrn/build/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    | /usr/bin/cc
-- CXX COMPILER  | /usr/bin/c++
-- BUILD_TYPE    | RelWithDebInfo (allowed: Custom;Debug;Release;RelWithDebInfo;Fast)
-- COMPILE FLAGS | -g  -O2 -Wno-write-strings
-- Shared        | ON
-- Default units | modern units (2019 nist constants)
-- MPI           | ON
--   DYNAMIC     | OFF
--   INC         | /usr/include/x86_64-linux-gnu/mpich
--   LIB         | /usr/lib/x86_64-linux-gnu/libmpichcxx.so
-- Python        | ON
--   EXE         | /usr/bin/python3
--   INC         | /usr/include/python3.9
--   LIB         | /usr/lib/x86_64-linux-gnu/libpython3.9.so
--   MODULE      | ON
--   DYNAMIC     | OFF
-- Readline      | /usr/lib/x86_64-linux-gnu/libreadline.so
-- Curses        | /usr/lib/x86_64-linux-gnu/libcurses.so;/usr/lib/x86_64-linux-gnu/libform.so
-- RX3D          | ON
--   OptLevel    | 0
-- Interviews    | ON
--   PATH        | /nrn/external/iv
--   INC         | /nrn/external/iv/src/include
--   X11 (INC)   | /usr/include
--       (LIBDIR)| /usr/lib/x86_64-linux-gnu
-- CoreNEURON    | ON
--   PATH        | /nrn/external/coreneuron
--   LINK FLAGS  | -Lx86_64 -lcorenrnmech
--   Legacy Units| OFF
-- Tests         | ON
-- --------------+--------------------------------------------------------------
--  See documentation : https://www.neuron.yale.edu/neuron/
-- --------------+--------------------------------------------------------------
--
-- Configuring done
-- Generating done
-- Build files have been written to: /nrn/build
cstricker commented 2 years ago

G’day Pramod

thanks for looking into this. Below is the output after a fresh pull this morning. I hope this helps and cheers

Christian.

+/home/stricker/.local/src/neuron/buildnrn:82> cmake .. '-DNRN_ENABLE_INTERVIEWS=ON' '-DNRN_ENABLE_PYTHON=ON' '-DNRN_ENABLE_MPI=ON' '-DNRN_ENABLE_RX3D=ON' '-DNRN_ENABLE_CORENEURON=OFF' '-DNRN_ENABLE_TESTS=ON' '-DNRN_ENABLE_BINARY_SPECIAL=ON' '-DPYTHON_EXECUTABLE=/usr/bin/python3' '-DCMAKE_INSTALL_PREFIX=/usr/local/bin/neuron' -- The C compiler identification is GNU 11.2.0 -- The CXX compiler identification is GNU 11.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - 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: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Setting build type to 'RelWithDebInfo' as none was specified. -- Found BISON: /usr/bin/bison (found version "3.7.6") -- Found FLEX: /usr/bin/flex (found version "2.6.4") -- Found Readline: /usr/include -- Found PythonInterp: /usr/bin/python3 (found version "3.9.7") -- Found Cython: /home/stricker/.local/bin/cython (found version "0.29.28") -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- Detected OpenMPI 4.1.0 -- Sub-module : missing /home/stricker/.local/src/neuron/nrn/external/iv : running git submodule update --init Submodule 'modules/iv' (https://github.com/neuronsimulator/iv.git) registered for path 'external/iv' Cloning into '/home/stricker/.local/src/neuron/nrn/external/iv'... Submodule path 'external/iv': checked out 'ea2b4b474ec516c952e44c3b60e1c80fd3b9d666' -- Found X11: /usr/include -- Checking for include files -- Checking for functions -- Checking for include directories -- Checking for types

-- Configured INTERVIEWS 0.1

-- Some things you can do now: -- --------------+-------------------------------------------------------------- -- Command | Description -- --------------+-------------------------------------------------------------- -- make install | Will install INTERVIEWS to: /usr/local/bin/neuron -- | Change the install location of NEURON using: -- | cmake -DCMAKE_INSTALL_PREFIX= -- --------------+-------------------------------------------------------------- -- Build option | Status -- --------------+-------------------------------------------------------------- -- BUILD_TYPE | RelWithDebInfo (allowed: Debug;Release;RelWithDebInfo) -- SHARED | OFF -- X11_DYNAMIC | OFF -- --------------+-------------------------------------------------------------- -- See more : https://github.com/neuronsimulator/iv -- --------------+--------------------------------------------------------------

-- Found PythonInterp: /usr/bin/python3 (found suitable version "3.9.7", minimum required is "3.7") -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.9.7", minimum required is "3") -- Found PythonLibs: /usr/lib/x86_64-linux-gnu/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 Extracting link flags from target 'Threads::Threads', beware that this can be fragile. Got: Generating link flags from path /usr/lib/x86_64-linux-gnu/libreadline.so Got: /usr/lib/x86_64-linux-gnu/libreadline.so -Wl,-rpath,/usr/lib/x86_64-linux-gnu Generating link flags from path /usr/lib/x86_64-linux-gnu/libcurses.so Got: /usr/lib/x86_64-linux-gnu/libcurses.so -Wl,-rpath,/usr/lib/x86_64-linux-gnu Generating link flags from path /usr/lib/x86_64-linux-gnu/libform.so Got: /usr/lib/x86_64-linux-gnu/libform.so -Wl,-rpath,/usr/lib/x86_64-linux-gnu Generating link flags from path /usr/lib/x86_64-linux-gnu/libpython3.9.so Got: /usr/lib/x86_64-linux-gnu/libpython3.9.so -Wl,-rpath,/usr/lib/x86_64-linux-gnu Generating link flags from path /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so Got: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so -Wl,-rpath,/usr/lib/x86_64-linux-gnu/openmpi/lib Generating link flags from path /usr/lib/x86_64-linux-gnu/libSM.so Got: /usr/lib/x86_64-linux-gnu/libSM.so -Wl,-rpath,/usr/lib/x86_64-linux-gnu Generating link flags from path /usr/lib/x86_64-linux-gnu/libICE.so Got: /usr/lib/x86_64-linux-gnu/libICE.so -Wl,-rpath,/usr/lib/x86_64-linux-gnu Generating link flags from path /usr/lib/x86_64-linux-gnu/libX11.so Got: /usr/lib/x86_64-linux-gnu/libX11.so -Wl,-rpath,/usr/lib/x86_64-linux-gnu Generating link flags from path /usr/lib/x86_64-linux-gnu/libXext.so Got: /usr/lib/x86_64-linux-gnu/libXext.so -Wl,-rpath,/usr/lib/x86_64-linux-gnu -- Sub-module : missing external/coding-conventions : running git submodule update --init Submodule 'external/coding-conventions' (https://github.com/BlueBrain/hpc-coding-conventions.git) registered for path 'external/coding-conventions' Cloning into '/home/stricker/.local/src/neuron/nrn/external/coding-conventions'... Submodule path 'external/coding-conventions': checked out '7eaad9d932f1fdcd7421d943cbf7bc5fcd6c5165' -- Sub-module : missing /home/stricker/.local/src/neuron/nrn/external/catch2 : running git submodule update --init Submodule 'external/catch2' (https://github.com/catchorg/Catch2.git) registered for path 'external/catch2' Cloning into '/home/stricker/.local/src/neuron/nrn/external/catch2'... Submodule path 'external/catch2': checked out 'c4e3767e265808590986d5db6ca1b5532a7f3d13' -- Found pytest: /home/stricker/.local/lib/python3.9/site-packages/pytest (found version "7.1.1") -- Found pytest_cov: /home/stricker/.local/lib/python3.9/site-packages/pytest_cov (found version "3.0.0") -- Fetching git submodule test/rxd/testdata: running git submodule update --init;--recursive;--depth;1 -- test/rxd/testdata Submodule 'test/rxd/testdata' (https://github.com/neuronsimulator/rxdtestdata) registered for path 'test/rxd/testdata' Cloning into '/home/stricker/.local/src/neuron/nrn/test/rxd/testdata'... From https://github.com/neuronsimulator/rxdtestdata

-- Disabling coreneuron_modtests::fornetcon_py_cpu: coreneuron not enabled -- Disabling coreneuron_modtests::direct_py_cpu: coreneuron not enabled -- Disabling coreneuron_modtests::direct_hoc_cpu: coreneuron not enabled -- Disabling coreneuron_modtests::spikes_py_cpu: coreneuron not enabled -- Disabling coreneuron_modtests::spikes_file_mode_py_cpu: coreneuron not enabled -- Disabling coreneuron_modtests::fast_imem_py_cpu: coreneuron not enabled -- Disabling coreneuron_modtests::datareturn_py_cpu: coreneuron not enabled -- Disabling coreneuron_modtests::test_units_py_cpu: coreneuron not enabled -- Disabling coreneuron_modtests::test_netmove_py_cpu: coreneuron not enabled -- Disabling coreneuron_modtests::test_pointer_py_cpu: coreneuron not enabled -- Disabling coreneuron_modtests::test_watchrange_py_cpu: coreneuron not enabled -- Disabling coreneuron_modtests::test_psolve_py_cpu: coreneuron not enabled -- Disabling coreneuron_modtests::test_ba_py_cpu: coreneuron not enabled -- Disabling coreneuron_modtests::test_natrans_py_cpu: coreneuron not enabled -- Disabling coreneuron_modtests::spikes_mpi_py_cpu: coreneuron not enabled -- Disabling coreneuron_modtests::spikes_mpi_file_mode_py_cpu: coreneuron not enabled -- Disabling coreneuron_modtests::inputpresyn_py_cpu: coreneuron not enabled -- Disabling coreneuron_modtests::fornetcon_py_gpu: coreneuron not enabled -- Disabling coreneuron_modtests::direct_py_gpu: coreneuron not enabled -- Disabling coreneuron_modtests::direct_hoc_gpu: coreneuron not enabled -- Disabling coreneuron_modtests::spikes_py_gpu: coreneuron not enabled -- Disabling coreneuron_modtests::spikes_file_mode_py_gpu: coreneuron not enabled -- Disabling coreneuron_modtests::fast_imem_py_gpu: coreneuron not enabled -- Disabling coreneuron_modtests::datareturn_py_gpu: coreneuron not enabled -- Disabling coreneuron_modtests::test_units_py_gpu: coreneuron not enabled -- Disabling coreneuron_modtests::test_netmove_py_gpu: coreneuron not enabled -- Disabling coreneuron_modtests::test_pointer_py_gpu: coreneuron not enabled -- Disabling coreneuron_modtests::test_watchrange_py_gpu: coreneuron not enabled -- Disabling coreneuron_modtests::test_psolve_py_gpu: coreneuron not enabled -- Disabling coreneuron_modtests::test_ba_py_gpu: coreneuron not enabled -- Disabling coreneuron_modtests::test_natrans_py_gpu: coreneuron not enabled -- Disabling coreneuron_modtests::spikes_mpi_py_gpu: coreneuron not enabled -- Disabling coreneuron_modtests::spikes_mpi_file_mode_py_gpu: coreneuron not enabled -- Disabling coreneuron_modtests::inputpresyn_py_gpu: coreneuron not enabled CMake Warning at cmake/NeuronTestHelper.cmake:205 (message): nrn_add_test_group couldn't find the names of the builtin CoreNEURON modfiles that nrnivmodl-core implicitly depends on and CoreNEURON is being built internally Call Stack (most recent call first): test/external/reduced_dentate/CMakeLists.txt:2 (nrn_add_test_group)

-- Disabling reduced_dentate::coreneuron_cpu: coreneuron not enabled -- Disabling reduced_dentate::coreneuron_gpu: coreneuron not enabled CMake Warning at cmake/NeuronTestHelper.cmake:205 (message): nrn_add_test_group couldn't find the names of the builtin CoreNEURON modfiles that nrnivmodl-core implicitly depends on and CoreNEURON is being built internally Call Stack (most recent call first): test/external/ringtest/CMakeLists.txt:4 (nrn_add_test_group)

-- Disabling external_ringtest::neuron: mod_compatibility not enabled -- Disabling external_ringtest::neuron_mpi: mod_compatibility not enabled -- Disabling external_ringtest::coreneuron_cpu_mpi_offline_saverestore: coreneuron not enabled -- Disabling external_ringtest::coreneuron_cpu_mpi: coreneuron not enabled -- Disabling external_ringtest::coreneuron_cpu_mpi_offline: coreneuron not enabled -- Disabling external_ringtest::coreneuron_cpu_mpi_threads: coreneuron not enabled -- Disabling external_ringtest::coreneuron_gpu_mpi_offline_saverestore: coreneuron not enabled -- Disabling external_ringtest::coreneuron_gpu_mpi: coreneuron not enabled -- Disabling external_ringtest::coreneuron_gpu_mpi_offline: coreneuron not enabled -- Disabling external_ringtest::coreneuron_gpu_mpi_threads: coreneuron not enabled -- Skipping comparison job for group external_ringtest because no tests were enabled. CMake Warning at cmake/NeuronTestHelper.cmake:205 (message): nrn_add_test_group couldn't find the names of the builtin CoreNEURON modfiles that nrnivmodl-core implicitly depends on and CoreNEURON is being built internally Call Stack (most recent call first): test/external/testcorenrn/CMakeLists.txt:62 (nrn_add_test_group)

-- Disabling testcorenrn_bbcore::coreneuron_gpu_online: coreneuron not enabled -- Disabling testcorenrn_bbcore::coreneuron_gpu_online_psolve_alternate: coreneuron not enabled -- Disabling testcorenrn_bbcore::coreneuron_gpu_offline: coreneuron not enabled -- Disabling testcorenrn_bbcore::coreneuron_cpu_online: coreneuron not enabled -- Disabling testcorenrn_bbcore::coreneuron_cpu_online_psolve_alternate: coreneuron not enabled -- Disabling testcorenrn_bbcore::coreneuron_cpu_offline: coreneuron not enabled -- Disabling testcorenrn_conc::coreneuron_gpu_online: coreneuron not enabled -- Disabling testcorenrn_conc::coreneuron_gpu_online_psolve_alternate: coreneuron not enabled -- Disabling testcorenrn_conc::coreneuron_gpu_offline: coreneuron not enabled -- Disabling testcorenrn_conc::coreneuron_cpu_online: coreneuron not enabled -- Disabling testcorenrn_conc::coreneuron_cpu_online_psolve_alternate: coreneuron not enabled -- Disabling testcorenrn_conc::coreneuron_cpu_offline: coreneuron not enabled -- Disabling testcorenrn_deriv::coreneuron_gpu_online: coreneuron not enabled -- Disabling testcorenrn_deriv::coreneuron_gpu_online_psolve_alternate: coreneuron not enabled -- Disabling testcorenrn_deriv::coreneuron_gpu_offline: coreneuron not enabled -- Disabling testcorenrn_deriv::coreneuron_cpu_online: coreneuron not enabled -- Disabling testcorenrn_deriv::coreneuron_cpu_online_psolve_alternate: coreneuron not enabled -- Disabling testcorenrn_deriv::coreneuron_cpu_offline: coreneuron not enabled -- Disabling testcorenrn_gf::neuron: mod_compatibility not enabled -- Disabling testcorenrn_gf::coreneuron_gpu_online: coreneuron not enabled -- Disabling testcorenrn_gf::coreneuron_gpu_online_psolve_alternate: coreneuron not enabled -- Disabling testcorenrn_gf::coreneuron_gpu_offline: coreneuron not enabled -- Disabling testcorenrn_gf::coreneuron_cpu_online: coreneuron not enabled -- Disabling testcorenrn_gf::coreneuron_cpu_online_psolve_alternate: coreneuron not enabled -- Disabling testcorenrn_gf::coreneuron_cpu_offline: coreneuron not enabled -- Skipping comparison job for group testcorenrn_gf because no tests were enabled. -- Disabling testcorenrn_kin::coreneuron_gpu_online: coreneuron not enabled -- Disabling testcorenrn_kin::coreneuron_gpu_online_psolve_alternate: coreneuron not enabled -- Disabling testcorenrn_kin::coreneuron_gpu_offline: coreneuron not enabled -- Disabling testcorenrn_kin::coreneuron_cpu_online: coreneuron not enabled -- Disabling testcorenrn_kin::coreneuron_cpu_online_psolve_alternate: coreneuron not enabled -- Disabling testcorenrn_kin::coreneuron_cpu_offline: coreneuron not enabled -- Disabling testcorenrn_patstim::neuron: mod_compatibility not enabled -- Disabling testcorenrn_patstim::coreneuron_gpu_offline_saverestore: coreneuron not enabled -- Disabling testcorenrn_patstim::coreneuron_gpu_offline: coreneuron not enabled -- Disabling testcorenrn_patstim::coreneuron_cpu_offline_saverestore: coreneuron not enabled -- Disabling testcorenrn_patstim::coreneuron_cpu_offline: coreneuron not enabled -- Skipping comparison job for group testcorenrn_patstim because no tests were enabled. -- Disabling testcorenrn_vecplay::neuron: mod_compatibility not enabled -- Disabling testcorenrn_vecplay::coreneuron_gpu_online: coreneuron not enabled -- Disabling testcorenrn_vecplay::coreneuron_gpu_online_psolve_alternate: coreneuron not enabled -- Disabling testcorenrn_vecplay::coreneuron_gpu_offline: coreneuron not enabled -- Disabling testcorenrn_vecplay::coreneuron_cpu_online: coreneuron not enabled -- Disabling testcorenrn_vecplay::coreneuron_cpu_online_psolve_alternate: coreneuron not enabled -- Disabling testcorenrn_vecplay::coreneuron_cpu_offline: coreneuron not enabled -- Skipping comparison job for group testcorenrn_vecplay because no tests were enabled. -- Disabling testcorenrn_vecevent::coreneuron_gpu_online: coreneuron not enabled -- Disabling testcorenrn_vecevent::coreneuron_gpu_online_psolve_alternate: coreneuron not enabled -- Disabling testcorenrn_vecevent::coreneuron_gpu_offline: coreneuron not enabled -- Disabling testcorenrn_vecevent::coreneuron_cpu_online: coreneuron not enabled -- Disabling testcorenrn_vecevent::coreneuron_cpu_online_psolve_alternate: coreneuron not enabled -- Disabling testcorenrn_vecevent::coreneuron_cpu_offline: coreneuron not enabled -- Disabling testcorenrn_watch::coreneuron_gpu_online: coreneuron not enabled -- Disabling testcorenrn_watch::coreneuron_gpu_online_psolve_alternate: coreneuron not enabled -- Disabling testcorenrn_watch::coreneuron_gpu_offline: coreneuron not enabled -- Disabling testcorenrn_watch::coreneuron_cpu_online: coreneuron not enabled -- Disabling testcorenrn_watch::coreneuron_cpu_online_psolve_alternate: coreneuron not enabled -- Disabling testcorenrn_watch::coreneuron_cpu_offline: coreneuron not enabled -- Disabling testcorenrn_netstimdirect::direct_netstimdirect: coreneuron not enabled -- Disabling testcorenrn_netstimdirect::direct_netstimdirect_psolve_alternate: coreneuron not enabled -- Skipping comparison job for group testcorenrn_netstimdirect because no tests were enabled. -- Found OpenSSL: /usr/lib/x86_64-linux-gnu/libcrypto.so (found version "1.1.1l") CMake Warning at cmake/NeuronTestHelper.cmake:205 (message): nrn_add_test_group couldn't find the names of the builtin CoreNEURON modfiles that nrnivmodl-core implicitly depends on and CoreNEURON is being built internally Call Stack (most recent call first): test/external/tqperf/CMakeLists.txt:2 (nrn_add_test_group)

-- Disabling tqperf::coreneuron: coreneuron not enabled

-- Configured NEURON 8.0

-- 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: /usr/local/bin/neuron -- | Change the install location of NEURON using: -- | cmake -DCMAKE_INSTALL_PREFIX= -- docs | Build full docs. Calls targets: doxygen, notebooks, sphinx, notebooks-clean -- uninstall | Removes files installed by make install (todo) -- --------------+-------------------------------------------------------------- -- Build option | Status -- --------------+-------------------------------------------------------------- -- C COMPILER | /usr/bin/cc -- CXX COMPILER | /usr/bin/c++ -- BUILD_TYPE | RelWithDebInfo (allowed: Custom;Debug;Release;RelWithDebInfo;Fast) -- COMPILE FLAGS | -g -O2 -Wno-write-strings -- Shared | ON -- Default units | modern units (2019 nist constants) -- MPI | ON -- DYNAMIC | OFF -- INC | /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi;/usr/lib/x86_64-linux-gnu/openmpi/include -- LIB | /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so -- Python | ON -- EXE | /usr/bin/python3 -- INC | /usr/include/python3.9 -- LIB | /usr/lib/x86_64-linux-gnu/libpython3.9.so -- MODULE | ON -- DYNAMIC | OFF -- Readline | /usr/lib/x86_64-linux-gnu/libreadline.so -- Curses | /usr/lib/x86_64-linux-gnu/libcurses.so;/usr/lib/x86_64-linux-gnu/libform.so -- RX3D | ON -- OptLevel | 0 -- Interviews | ON -- PATH | /home/stricker/.local/src/neuron/nrn/external/iv -- INC | /home/stricker/.local/src/neuron/nrn/external/iv/src/include -- X11 (INC) | /usr/include -- (LIBDIR)| /usr/lib/x86_64-linux-gnu -- CoreNEURON | OFF -- Tests | ON -- --------------+-------------------------------------------------------------- -- See documentation : https://www.neuron.yale.edu/neuron/ -- --------------+--------------------------------------------------------------

-- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project:

NRN_ENABLE_BINARY_SPECIAL

-- Build files have been written to: /home/stricker/.local/src/neuron/nrn/build

On 8 Apr 2022, at 06:30, Pramod Kumbhar @.**@.>> wrote:

Dear @cstrickerhttps://aus01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fcstricker&data=04%7C01%7Cchristian.stricker%40anu.edu.au%7Cf8ba23a266f4466a6abd08da18d57506%7Ce37d725cab5c46249ae5f0533e486437%7C0%7C0%7C637849603995660494%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=6SDZBxy5OW4JnGg%2Bet0O23ugqR6GdYKsCdksdZ8FK8M%3D&reserved=0,

Thank you for posting the issue.

I tried to reproduce the issue on vanilla Ubuntu 21.10 docker image but couldn't do so. I don't have WSL access at the moment but something we can check bit later this week @.***https://aus01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Falexsavulescu&data=04%7C01%7Cchristian.stricker%40anu.edu.au%7Cf8ba23a266f4466a6abd08da18d57506%7Ce37d725cab5c46249ae5f0533e486437%7C0%7C0%7C637849603995660494%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=HXfEHPagb2Rx4%2FbGOdbrz%2B9GR%2F4OZCAQLTNqsrFL6Xg%3D&reserved=0 @nrnhineshttps://aus01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnrnhines&data=04%7C01%7Cchristian.stricker%40anu.edu.au%7Cf8ba23a266f4466a6abd08da18d57506%7Ce37d725cab5c46249ae5f0533e486437%7C0%7C0%7C637849603995660494%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=u0iQFPwrT3Zv6erxAVAkpeiiy32XRmmGcPkJ6m3yJFU%3D&reserved=0).

It would be great if you could provide the cmake configure command with all options and output of the same command. For example, in my case its:

Note: -DNRN_ENABLE_TESTS=ON is optional, and you can also disable GUI & RXD components if you are not interested: -DNRN_ENABLE_RX3D=OFF -DNRN_ENABLE_INTERVIEWS=OFF

@.***:/nrn/build# cmake .. -DCMAKE_INSTALL_PREFIX=pwd/install -DNRN_ENABLE_TESTS=ON -DNRN_ENABLE_CORENEURON=ON -- Sub-project : using iv from from /nrn/external/iv -- Checking for include files -- Checking for functions -- Checking for include directories -- Checking for types

-- Configured INTERVIEWS 0.1

-- Some things you can do now: -- --------------+-------------------------------------------------------------- -- Command | Description -- --------------+-------------------------------------------------------------- -- make install | Will install INTERVIEWS to: /nrn/build/install -- | Change the install location of NEURON using: -- | cmake -DCMAKE_INSTALL_PREFIX= -- --------------+-------------------------------------------------------------- -- Build option | Status -- --------------+-------------------------------------------------------------- -- BUILD_TYPE | RelWithDebInfo (allowed: Debug;Release;RelWithDebInfo) -- SHARED | OFF -- X11_DYNAMIC | OFF -- --------------+-------------------------------------------------------------- -- See more : https://github.com/neuronsimulator/iv -- --------------+--------------------------------------------------------------

-- Found PythonInterp: /usr/bin/python3 (found suitable version "3.9.7", minimum required is "3.7") -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.9.7", minimum required is "3") -- Building CoreNEURON from submodule -- Sub-project : using coreneuron from from /nrn/external/coreneuron -- CORENRN_FORMATTING: OFF -- CORENRN_FORMATTING_ON: all -- CORENRN_FORMATTING_CPP_CHANGES_ONLY: OFF -- CORENRN_TEST_FORMATTING: OFF -- CORENRN_FORMATTING_NO_SUBMODULES: ON -- CORENRN_CLANG_FORMAT: OFF -- CORENRN_CMAKE_FORMAT: OFF -- CORENRN_GIT_HOOKS: OFF -- CORENRN_GIT_COMMIT_HOOKS: -- CORENRN_GIT_PUSH_HOOKS: courtesy-msg -- CORENRN_STATIC_ANALYSIS: OFF -- CORENRN_TEST_STATIC_ANALYSIS: OFF -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Doxygen not found, building docs has been disabled -- Found PythonInterp: /usr/bin/python3 (found version "3.9.7") -- Using mod2c submodule from /nrn/external/coreneuron/external/mod2c -- mod2c is used as APPLICATION_NAME -- Boost not found, unit tests disabled

-- Configured CoreNEURON 1.0

-- You can now build CoreNEURON 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 CoreNEURON to: /nrn/build/install -- docs | Build full docs. Calls targets: doxygen, sphinx -- --------------------+-------------------------------------------------------- -- Build option | Status -- --------------------+-------------------------------------------------------- -- CXX COMPILER | /usr/bin/c++ -- COMPILE FLAGS | -fopenmp -Wno-unknown-pragmas -g -O2 -Wno-write-strings -std=c++14 -- Build Type | SHARED -- MPI | ON -- DYNAMIC | OFF -- INC | /usr/include/x86_64-linux-gnu/mpich -- OpenMP | ON -- Use legacy units | OFF -- NMODL | OFF -- MOD2CPP PATH | /nrn/build/bin/mod2c_core -- GPU Support | OFF -- Auto Timeout | ON -- Wrap exp() | OFF -- SplayTree Queue | ON -- NetReceive Buffer | ON -- Caliper | OFF -- Likwid | OFF -- Unit Tests | ON -- Reporting | OFF -- --------------+-------------------------------------------------------------- -- See documentation : https://github.com/BlueBrain/CoreNeuron/ -- --------------+--------------------------------------------------------------

Extracting link flags from target 'Threads::Threads', beware that this can be fragile. Got: Generating link flags from path /usr/lib/x86_64-linux-gnu/libreadline.so Got: /usr/lib/x86_64-linux-gnu/libreadline.so -Wl,-rpath,/usr/lib/x86_64-linux-gnu Generating link flags from path /usr/lib/x86_64-linux-gnu/libcurses.so Got: /usr/lib/x86_64-linux-gnu/libcurses.so -Wl,-rpath,/usr/lib/x86_64-linux-gnu Generating link flags from path /usr/lib/x86_64-linux-gnu/libform.so Got: /usr/lib/x86_64-linux-gnu/libform.so -Wl,-rpath,/usr/lib/x86_64-linux-gnu Generating link flags from path /usr/lib/x86_64-linux-gnu/libpython3.9.so Got: /usr/lib/x86_64-linux-gnu/libpython3.9.so -Wl,-rpath,/usr/lib/x86_64-linux-gnu Generating link flags from path /usr/lib/x86_64-linux-gnu/libmpich.so Got: /usr/lib/x86_64-linux-gnu/libmpich.so -Wl,-rpath,/usr/lib/x86_64-linux-gnu Generating link flags from path /usr/lib/x86_64-linux-gnu/libX11.so Got: /usr/lib/x86_64-linux-gnu/libX11.so -Wl,-rpath,/usr/lib/x86_64-linux-gnu Generating link flags from path /usr/lib/x86_64-linux-gnu/libXext.so Got: /usr/lib/x86_64-linux-gnu/libXext.so -Wl,-rpath,/usr/lib/x86_64-linux-gnu -- Sub-project : using catch2 from from /nrn/external/catch2 -- 3rd party project: using rxd/testdata from "test/rxd/testdata" -- mpiexec does not support --oversubscribe -- Could NOT find mpi4py (missing: MPI4PY_LOCATION _MPI4PY_VERSION_MATCH) -- Could NOT find mpi4py (missing: MPI4PY_LOCATION _MPI4PY_VERSION_MATCH) -- Disabling coreneuron_modtests::fornetcon_py_gpu: gpu not enabled -- Disabling coreneuron_modtests::direct_py_gpu: gpu not enabled -- Disabling coreneuron_modtests::direct_hoc_gpu: gpu not enabled -- Disabling coreneuron_modtests::spikes_py_gpu: gpu not enabled -- Disabling coreneuron_modtests::spikes_file_mode_py_gpu: gpu not enabled -- Disabling coreneuron_modtests::fast_imem_py_gpu: gpu not enabled -- Disabling coreneuron_modtests::datareturn_py_gpu: gpu not enabled -- Disabling coreneuron_modtests::test_units_py_gpu: gpu not enabled -- Disabling coreneuron_modtests::test_netmove_py_gpu: gpu not enabled -- Disabling coreneuron_modtests::test_pointer_py_gpu: gpu not enabled -- Disabling coreneuron_modtests::test_watchrange_py_gpu: gpu not enabled -- Disabling coreneuron_modtests::test_psolve_py_gpu: gpu not enabled -- Disabling coreneuron_modtests::test_ba_py_gpu: gpu not enabled -- Disabling coreneuron_modtests::test_natrans_py_gpu: gpu not enabled -- Could NOT find mpi4py (missing: MPI4PY_LOCATION _MPI4PY_VERSION_MATCH) -- Disabling coreneuron_modtests::spikes_mpi_file_mode_py_gpu: gpu not enabled -- Disabling coreneuron_modtests::inputpresyn_py_gpu: gpu not enabled -- Disabling reduced_dentate::coreneuron_gpu: gpu not enabled -- Disabling external_ringtest::coreneuron_gpu_mpi_offline_saverestore: gpu not enabled -- Disabling external_ringtest::coreneuron_gpu_mpi: gpu not enabled -- Disabling external_ringtest::coreneuron_gpu_mpi_offline: gpu not enabled -- Disabling external_ringtest::coreneuron_gpu_mpi_threads: gpu not enabled -- Disabling testcorenrn_bbcore::coreneuron_gpu_online: gpu not enabled -- Disabling testcorenrn_bbcore::coreneuron_gpu_online_psolve_alternate: gpu not enabled -- Disabling testcorenrn_bbcore::coreneuron_gpu_offline: gpu not enabled -- Disabling testcorenrn_conc::coreneuron_gpu_online: gpu not enabled -- Disabling testcorenrn_conc::coreneuron_gpu_online_psolve_alternate: gpu not enabled -- Disabling testcorenrn_conc::coreneuron_gpu_offline: gpu not enabled -- Disabling testcorenrn_deriv::coreneuron_gpu_online: gpu not enabled -- Disabling testcorenrn_deriv::coreneuron_gpu_online_psolve_alternate: gpu not enabled -- Disabling testcorenrn_deriv::coreneuron_gpu_offline: gpu not enabled -- Disabling testcorenrn_gf::coreneuron_gpu_online: gpu not enabled -- Disabling testcorenrn_gf::coreneuron_gpu_online_psolve_alternate: gpu not enabled -- Disabling testcorenrn_gf::coreneuron_gpu_offline: gpu not enabled -- Disabling testcorenrn_kin::coreneuron_gpu_online: gpu not enabled -- Disabling testcorenrn_kin::coreneuron_gpu_online_psolve_alternate: gpu not enabled -- Disabling testcorenrn_kin::coreneuron_gpu_offline: gpu not enabled -- Disabling testcorenrn_patstim::coreneuron_gpu_offline_saverestore: gpu not enabled -- Disabling testcorenrn_patstim::coreneuron_gpu_offline: gpu not enabled -- Disabling testcorenrn_vecplay::coreneuron_gpu_online: gpu not enabled -- Disabling testcorenrn_vecplay::coreneuron_gpu_online_psolve_alternate: gpu not enabled -- Disabling testcorenrn_vecplay::coreneuron_gpu_offline: gpu not enabled -- Disabling testcorenrn_vecevent::coreneuron_gpu_online: gpu not enabled -- Disabling testcorenrn_vecevent::coreneuron_gpu_online_psolve_alternate: gpu not enabled -- Disabling testcorenrn_vecevent::coreneuron_gpu_offline: gpu not enabled -- Disabling testcorenrn_watch::coreneuron_gpu_online: gpu not enabled -- Disabling testcorenrn_watch::coreneuron_gpu_online_psolve_alternate: gpu not enabled -- Disabling testcorenrn_watch::coreneuron_gpu_offline: gpu not enabled

-- Configured NEURON 8.0

-- 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: /nrn/build/install -- | Change the install location of NEURON using: -- | cmake -DCMAKE_INSTALL_PREFIX= -- docs | Build full docs. Calls targets: doxygen, notebooks, sphinx, notebooks-clean -- uninstall | Removes files installed by make install (todo) -- --------------+-------------------------------------------------------------- -- Build option | Status -- --------------+-------------------------------------------------------------- -- C COMPILER | /usr/bin/cc -- CXX COMPILER | /usr/bin/c++ -- BUILD_TYPE | RelWithDebInfo (allowed: Custom;Debug;Release;RelWithDebInfo;Fast) -- COMPILE FLAGS | -g -O2 -Wno-write-strings -- Shared | ON -- Default units | modern units (2019 nist constants) -- MPI | ON -- DYNAMIC | OFF -- INC | /usr/include/x86_64-linux-gnu/mpich -- LIB | /usr/lib/x86_64-linux-gnu/libmpichcxx.so -- Python | ON -- EXE | /usr/bin/python3 -- INC | /usr/include/python3.9 -- LIB | /usr/lib/x86_64-linux-gnu/libpython3.9.so -- MODULE | ON -- DYNAMIC | OFF -- Readline | /usr/lib/x86_64-linux-gnu/libreadline.so -- Curses | /usr/lib/x86_64-linux-gnu/libcurses.so;/usr/lib/x86_64-linux-gnu/libform.so -- RX3D | ON -- OptLevel | 0 -- Interviews | ON -- PATH | /nrn/external/iv -- INC | /nrn/external/iv/src/include -- X11 (INC) | /usr/include -- (LIBDIR)| /usr/lib/x86_64-linux-gnu -- CoreNEURON | ON -- PATH | /nrn/external/coreneuron -- LINK FLAGS | -Lx86_64 -lcorenrnmech -- Legacy Units| OFF -- Tests | ON -- --------------+-------------------------------------------------------------- -- See documentation : https://www.neuron.yale.edu/neuron/ -- --------------+--------------------------------------------------------------

-- Configuring done -- Generating done -- Build files have been written to: /nrn/build

— Reply to this email directly, view it on GitHubhttps://aus01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fneuronsimulator%2Fnrn%2Fissues%2F1770%23issuecomment-1092172782&data=04%7C01%7Cchristian.stricker%40anu.edu.au%7Cf8ba23a266f4466a6abd08da18d57506%7Ce37d725cab5c46249ae5f0533e486437%7C0%7C0%7C637849603995660494%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=yWD%2BRW4usglrq%2BDjDiQqzTgGUqQidxl0gl7qZ%2FLOMo4%3D&reserved=0, or unsubscribehttps://aus01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAD5QLAGIHNHCYS2AXW63T63VD5AWHANCNFSM5SYKBR5A&data=04%7C01%7Cchristian.stricker%40anu.edu.au%7Cf8ba23a266f4466a6abd08da18d57506%7Ce37d725cab5c46249ae5f0533e486437%7C0%7C0%7C637849603995815992%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=0KsKRperUrjjjpDCixV15VANB4a209%2FNghPCVR8J5hY%3D&reserved=0. You are receiving this because you were mentioned.Message ID: @.***>

pramodk commented 2 years ago

Thanks for the details. With the provided cmake configure command I am not able to reproduce the issue inside docker with Ubuntu 21.10. So looks like something specific to WSL setup. We will take a look.

By the way, it seems like error appears while building tests. In the meantime you can temporarily disable tests and see if rest of the installation finishes and if it's usable.

cstricker commented 2 years ago

G’day Pramod

thanks - just to confirm that if I turn off the test, I can build nrniv - no issues. And the build binary is “normal”. I hope this helps and cheers

Christian.

On 8 Apr 2022, at 15:43, Pramod Kumbhar @.**@.>> wrote:

Thanks for the details. With the provided cmake configure command I am not able to reproduce the issue inside docker with Ubuntu 21.10. So looks like something specific to WSL setup. We will take a look.

By the way, it seems like error appears while building tests. In the meantime you can temporarily disable tests and see if rest of the installation finishes and if it's usable.

— Reply to this email directly, view it on GitHubhttps://aus01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fneuronsimulator%2Fnrn%2Fissues%2F1770%23issuecomment-1092462273&data=04%7C01%7Cchristian.stricker%40anu.edu.au%7C6cbb11f472d147b5598308da1922c4ce%7Ce37d725cab5c46249ae5f0533e486437%7C0%7C0%7C637849934361731497%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=HcgRDLM9bAkoidb6ewWlr0GeWJwzG8ERAmyBICksTWY%3D&reserved=0, or unsubscribehttps://aus01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAD5QLAFGDEXSZXWPQGE7HGTVD7BRRANCNFSM5SYKBR5A&data=04%7C01%7Cchristian.stricker%40anu.edu.au%7C6cbb11f472d147b5598308da1922c4ce%7Ce37d725cab5c46249ae5f0533e486437%7C0%7C0%7C637849934361731497%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=Ppmi20LDkBl9ezxTuKbVPhoeYMenLrRarDHxhzAIIIg%3D&reserved=0. You are receiving this because you were mentioned.Message ID: @.***>

pramodk commented 2 years ago

We have reproduced the issue, thanks to @jorblancoa! Should be able to PR a fix soon!

alexsavulescu commented 2 years ago

@cstricker would you mind trying now?

cstricker commented 2 years ago

Thanks Alex - rebuilt and tried - and it works now. Thanks for doing that. Cheers Christian.