The NEURON build system now uses cmake as of version 7.8 circa Nov 2019. The previous autotools (./configure) build system is still supported for the time being but any features that use submodules would need to build those separately.
git clone https://github.com/neuronsimulator/nrn nrn cd nrn mkdir build cd build cmake .. # default install to /usr/local make -j sudo make -j install
-j option to make invokes a parallel make using all available cores.
This is often very much faster than a single process make. One can add a number
make -j 6) to specify the maximum number of processes
to use. This can be useful if there is the possibility of running out of memory.
Sadly, there is no equivalent in cmake to the autotool’s
to list all the options. The closest is
cmake .. -LH
cmake .. as above and lists the cache variables along with help
strings which are not marked as INTERNAL or ADVANCED. Alternatively,
allows one to interactively inspect cached variables.
In the build folder,
cmake -LH (missing <path-to-source) will not
run cmake, but if there is a
CMakeCache.txt file, the cache variables
will be listed.
The above default
cmake .. specifies a default installation location
and build type, and includes (or leaves out) the following major
cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local \ -DCMAKE_BUILD_TYPE=RelWithDebInfo \ -DNRN_ENABLE_INTERVIEWS=ON \ -DNRN_ENABLE_MPI=ON \ -DNRN_ENABLE_PYTHON=ON \ -DNRN_ENABLE_CORENEURON=OFF
Cmake option values persist with subsequent invocations of cmake unless explicitly changed by specifying arguments to cmake (or by modifying them with ccmake). It is intended that all build dependencies are taken into account so that it is not necessary to start fresh with an empty build folder when modifying cmake arguments. However, there may be unknown exceptions to this (bugs) so in case of problems it is generally sufficient to delete all contents of the build folder and start again with the desired cmake arguments.
First arg is always
<path-to-source> which is the path (absolute or relative)
to the top level nrn folder (e.g. cloned from github). It is very common
to create a folder named
build in the top level nrn folder and run cmake
in that. e.g.
cd nrn mkdir build cd build cmake .. <more args>
Install path prefix, prepended onto install directories. This can be a full path or relative. Default is /usr/local . A common install folder is ‘install’ in the build folder. e.g.-DCMAKE_INSTALL_PREFIX=install
so that the installation folder is
.../nrn/build/install. In this case the user should prepend
.../nrn/build/install/binto PATH and it may be useful toexport PYTHONPATH=.../nrn/build/install/lib/python
where in each case
...is the full path prefix to nrn.
Empty or one of Custom;Debug;Release;RelWithDebInfo;Fast.
- RelWithDebInfo means to compile using -O2 -g options.
- Debug means to compile with just -g (and optimization level -O0) This is very useful for debugging with gdb as, otherwise, local variables may be optimized away that are useful to inspect.
- Release means to compile with -O2 -DNDEBUG. The latter eliminates assert statements.
- Custom requires that you specify flags with CMAKE_C_FLAGS and CMAKE_CXX_FLAGS
- Fast requires that you specify flags as indicated in nrn/cmake/ReleaseDebugAutoFlags.cmake
Custom and Fast depend on specific compilers and (super)computers and are tailored to those machines. See
Enable GUI with INTERVIEWS
Unless you specify IV_DIR, InterViews will be automatically cloned as a subproject, built, and installed in CMAKE_INSTALL_PREFIX.
The directory containing a CMake configuration file for iv.
IV_DIR is the install location of iv and the directory actually containing the cmake configuration files is
IV_DIR/lib/cmake. This is useful when you have many clones of nrn for different development purposes and wish to use a single independent InterViews installation for many/all of them. E.g. I generally invoke
dlopen X11 after launch
This is most useful for building Mac distributions where XQuartz (X11) may not be installed on the user’s machine and the user does not require InterViews graphics. If XQuartz is subsequently installed, InterViews graphics will suddenly be available.
Enable MPI support
Requires an MPI installation, e.g. openmpi or mpich. Note that the Python mpi4py module generally uses openmpi which cannot be mixed with mpich.
Enable dynamic MPI library support
This is mostly useful for binary distibutions where MPI may or may not exist on the target machine.
semicolon (;) separated list of MPI include directories to build against. Default to first found mpi)
Cmake knows about openmpi, mpich, mpt, and msmpi. The dynamic loader for linux tries to load libmpi.so and if that fails, libmpich.so (the latter is good for cray mpi). The system then checks to see if a specific symbol exists in the libmpi… and determines whether to load the libnrnmp_xxx.so for openmpi, mpich, or mpt. To make binary installers good for openmpi and mpich, I use
-DNRN_MPI_DYNAMIC="/usr/local/include/;/home/hines/soft/mpich/include" This option is ignored unless NRN_ENABLE_MPI_DYNAMIC=ON
Enable Python interpreter support (default python, fallback to python3, but see PYTHON_EXECUTABLE below)
Enable dynamic Python version support
This is mostly useful for binary distributions where it is unknown which version, if any, of python exists on the target machine.
semicolon (;) separated list of python executables to create interfaces. (default python3)
If the string is empty use the python specified by PYTHON_EXECUTABLE or else the default python. Binary distributions often specify a list of python versions so that if any one of them is available on the target machine, NEURON + Python will be fully functional. Eg. the mac package build script on my machine, nrn/bldnrnmacpkgcmake.sh uses-DNRN_PYTHON_DYNAMIC="python2.7;python3.6;python3.7;python3.8"
This option is ignored unless NRN_ENABLE_PYTHON_DYNAMIC=ON
Use provided python binary instead of the one found by CMake. This must be a full path. We generally use-DPYTHON_EXECUTABLE=`which python3.7`
Enable installation of NEURON Python module.
By default, the neuron module is installed in CMAKE_INSTALL_PREFIX/lib/python.
setup.py options, everything after setup.py install
To install in site-packages use an empty string-DNRN_MODULE_INSTALL_OPTIONS=""
This option is (or should be) ignored unless NRN_ENABLE_MODULE_INSTALL=ON.
Enable rx3d support
No longer any reason to turn this off as build time is not significantly increased due to compiling cython generated files with -O0 by default.
Optimization level for Cython generated files (non-zero may compile slowly)
It is not clear to me if -O0 has significantly less performance than -O2. Binary distributions are (or should be) built with-DNRN_RX3D_OPT_LEVEL=2
Enable CoreNEURON support
If ON and no argument pointing to an external installation, CoreNEURON will be cloned as a submodule along with all its NMODL submodule dependencies.
Enable CoreNEURON compatibility for MOD files
CoreNEURON does not allow the common NEURON THREADSAFE promotion of GLOBAL variables that appear on the right hand side of assignment statements to become thread specific variables. This option is automatically turned on if NRN_ENABLE_CORENEURON=ON.
There are a large number of cmake arguments specific to a CoreNEURON build that are explained in ???.
Occasionally useful advanced options:¶
See all the options with
ccmake ..in the build folder. They are also in the CMakeCache.txt file. Following is a definitely incomplete list.
On the mac, prior to knowing about
export SDK_ROOT=$(xcrun -sdk macosx --show-sdk-path)I got into the habit of-DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++
to avoid the problem of gcc not being able to find stdio.h when python was compiling inithoc.cpp
C plus plus compiler
Compiler flag to build tools like nocmodl, modlunit.
In cluster environment with different architecture of login node and compute node, we need to compile tools like nocmodl and modlunit with different compiler options to run them on login/build nodes. This option appends provided flags to CMAKE_CXX_FLAGS.
For example, with intel compiler compiling NEURON for KNL but building on a Skylake node: .. code-block:-DCMAKE_BUILD_TYPE=Custom -DCMAKE_CXX_FLAGS="-xMIC-AVX512" -DNRN_NMODL_CXX_FLAGS="-XHost"
Path to a file.
If cmake can’t find readline and you don’t want the nrn internal version, you
can give this hint as to where it is.
Enable unit tests
Clones the submodule catch2 from https://github.com/catchorg/Catch2.git and after a build using
makecan run the tests with
make test. May also need to
pip install pytest.
make testis quite terse. To get the same verbose output that is seen with the CI tests, use
ctest -VV(executed in the build folder). One can also run individual test files with
python3 -m pytest <testfile.py>or all the test files in that folder with
python3 -m pytest. Note: It is helpful to
make testfirst to ensure any mod files needed are available to the tests. If running a test outside the folder where the test is located, it may be necessary to add the folder to PYTHONPATH. Note: The last python mentioned in the
-DNRN_PYTHON_DYNAMIC=...(if the semicolon separated list is non-empty and
-DNRN_ENABLE_PYTHON_DYNAMIC=ON) is the one used for
ctest -VV. Otherwise the value specified by
Examplemkdir build cmake .. -DNRN_ENABLE_TESTS=ON ... make -j make test ctest -VV cd ../test/pynrn python3 -m pytest python3 -m pytest test_currents.py
Enable code coverage
sudo apt install lcov).
Provides two make targets to simplify the repeated “run tests, examine coverage” workflow.
make cover_beginerases all previous coverage data (
*.gcdafiles), and creates a baseline report. (Note all files and folders are created in the
CMAKE_BINARY_DIRwhere you ran cmake.)
make cover_htmlcreates a coverage report for the sum of all the software runs since the last
cover_beginand prints a file url that you can paste into your browser to review the coverage.
When using an iterative workflow to examine test coverage of a single or a few files, the above targets run much faster when this option is combined with NRN_COVERAGE_FILES:STRING=
Code coverage without the use of this option is explained in Developer Builds: Code Coverage
Coverage limited to semicolon (;) separated list of file paths relative to
` -DNRN_COVERAGE_FILES="src/nrniv/partrans.cpp;src/nmodl/parsact.cpp;src/nrnpython/nrnpy_hoc.cpp" `
Enable CMake code formatting
Clones the submodule coding-conventions from https://github.com/BlueBrain/hpc-coding-conventions.git. Also need to
pip install cmake-format=0.6.0 --user. After a build using
makecan reformat cmake files with
make cmake-formatSee nrn/CONTRIBUTING.md for further details. How does one reformat a specific cmake file?
Miscellaneous Rarely used options specific to NEURON:¶
Enable Observer to be a subclass of DiscreteEvent Can save space but a lot of component destruction may not notify other components that are watching it to no longer use that component. Useful only if one builds a model without needing to eliminate pieces of the model.
Default is to use modern faraday, R, etc. from 2019 nist constants. When Off or ON, and in the absence of the
NRNUNIT_USE_LEGACY=0or1environment variable, the default dynamic value of
h.nrnunit_use_legacy()will be 0 or 1 respectively.
At launch time (or import neuron), use of legacy or modern units can be specified with the
NRNUNIT_USE_LEGACY=0or1environment variable. The use of legacy or modern units can be dynamically specified after launch with the
h.nrnunit_use_legacy(0or1)function (with no args, returns the current use flag).
Dynamically load nrnmech shared library
Enable use of memacs
Microemacs is a tiny emacs like editor I have been using since the mid-eighties. I might be the only one in the world who uses it now.
Allow use of Pthreads
Turned on when creating python wheels.
Build binary special
nrnivmodl by default creates shell script called ‘special’ which runs nrniv and specifies the argument
-dll /path/to/libnrnmech.soor whatever the name is of the shared library created by nrnivmodl. This option forces nrnivmodl to create a binary version of special that can be run, for example, with gdb or valgrind.
It is not often needed as nrniv has a
-dll <path/to/libnrnmech.so>option. Also by default, if the current working directory on launch has a folder named
x86_64(or whatever the CPU happens to be), the nrnmech library in that folder will be automatically loaded.
Use internal Readline library shipped with NEURON
Forces use of the readline code distributed with NEURON even if there is a system supplied readline.