Neko  0.8.0-rc2
A portable framework for high-order spectral element flow simulations
Installing Neko

Neko can be installed in various ways, either building directly from source, manually compiling all dependencies and Neko or via Spack. Pre-built Docker images are also provided for each release of Neko.

Building from source

To build Neko, you will need a Fortran compiler supporting the Fortran-08 standard, autotools, pkg-config, a working MPI installation supporting the Fortran 2008 bindings (mpi_f08), BLAS/LAPACK and JSON-Fortran. Optional dependencies are PFunit, gslib and ParMETIS.

Follow the steps below to install the less common dependencies (e.g. JSON-Fortran).

Dependencies

Building JSON Fortran

Download and compile, at least version 0.7.1 of JSON Fortran from the main repository.

Note
Neko requires JSON Fortran to be configured with USE_GNU_INSTALL_CONVENTION.
git clone --depth=1 https://github.com/jacobwilliams/json-fortran.git
cd json-fortran && mkdir b && cd b
cmake -DCMAKE_INSTALL_PREFIX=/path/to/installation -DUSE_GNU_INSTALL_CONVENTION=ON ..
make install

Now ad the installation path to PKG_CONFIG_PATH (and if needed LD_LIBRARY_PATH).

Note
On certain systems lib should be substituted with lib64
export PKG_CONFIG_PATH=/path/to/installation/lib/pkgconfig:$PKG_CONFIG_PATH
export LD_LIBRARY_PATH=/path/to/installation/lib:$LD_LIBRARY_PATH

Building gslib (optional)

If you have a Nek5000 installation, use:

export GSLIB=/path/to/Nek5000/3rd_party/gslib/gslib/src

If not, you should download and compile gslib. In a folder outside of Neko:

git clone https://github.com/Nek5000/gslib.git
cd gslib
make

Check that libgs.a has been created:

$ ls build/lib
libgs.a

Now add the path to gslib to an environment variable GSLIB

export GSLIB=$(pwd)/build

Later, when configuring Neko, add the following option to enable gslib

--with-gslib=${GSLIB}

Make sure you see the following message during the configuration:

checking for fgslib_gs_setup in -lgs... yes

Building ParMETIS (optional)

The following steps is an example on how to build and install ParMETIS

$ wget http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/parmetis-4.0.3.tar.gz
$ tar xzf parmetis-4.0.3.tar.gz && cd parmetis-4.0.3 && make config prefix=/parmetis_install_path
$ make -j$(nproc) && make install
Note
ParMETIS might not install metis.h, check if it is found in /parmetis_install_path/include. If this is not the case, repeat the same make config prefix=/parmetis_install_path and make install commands from the metis subfolder.

Bulding PFunit (optional)

To build the PFunit testing framework, please refers to the Testing page

Building Neko

Neko uses autotools as its build system. The first step is to run the configure script, located in the top directory.

<path-to-neko>/configure FC=<Fortran compiler> CC=<C compiler> \
MPIFC=<MPI Fortran compiler> MPICC=<MPI C ompiler> \
FCFLAGS=<Fortran compiler flags> CFLAGS=<C compiler flags> \
--prefix=<installation path> [options]

In the above command, [options] refers to either optional features or packages.

Features are enabled and disabled by passing either --enable-FEATURE[=arg] or --disable-FEATURE to configure. A list of currently supported features are given in the table below.

Name Description
--enable-real=Xp Specify working precision of REAL types:
spREAL(kind=4)
dpREAL(kind=8) (default)
qpREAL(kind=16)
--enable-contrib Compile various tools
--enable-device-mpi Enable device aware MPI

Optional packages are controlled by passing either --with-PACKAGE[=ARG] or --without-PACKAGE to configure. A list of all supported optional packages are given in the table below.

Name Description
--with-blas=<lib> Use BLAS library <lib>
--with-lapack=<lib> Use LAPACK library <lib>
--with-metis=DIR Directory for metis
--with-metis-libdir=LIBDIR Directory for metis library (if different)
--with-parmetis=DIR Compile with support for parmetis library
--with-parmetis-libdir=LIBDIR Directory for parmetis library (if different)
--with-adios2=DIR Compile with support for ADIOS2
--with-gslib=DIR Compile with support for gslib
--with-libxsmm Compile with support for libxsmm
--with-hip=DIR Compile with HIP backend
--with-cuda=DIR Compile with CUDA backend
--with-opencl=DIR Compile with OpenCL backend
--with-nvtx=DIR Compile with support for NVTX
--with-roctx=DIR Compile with support for ROCTX
--with-pfunit=DIR Directory for pFUnit (see Testing)
Note
Accelerators backends are not enabled as a feature in Neko, but rather via optional packages.

Once configured, to compile and install Neko issue make followed by make install

Compiling Neko for CPU or SX-Aurora

For a standard CPU or SX-Aurora build of Neko, simply run the configure script as given above, using appropriate compilers and compiler flags, e.g:

$ ./configure FC=gfortran FCFLAGS="-O2 -pedantic -std=f2008" --prefix=/opt/pkg/neko
$ make && make install

Compiling Neko for NVIDIA GPUs

To compile Neko for NVIDIA GPUs

  • Make sure you have the CUDA Toolkit installed (e.g. nvidia-cuda-toolkit)
  • Configure Neko to use CUDA using the --with-cuda=/path/to/cuda argument to configure, e.g.:
    $ ./configure --with-cuda=/usr/local/cuda
  • CUDA compiler flags and options can be passed using CUDA_CFLAGS, CUDA_ARCH and NVCC respectively, e.g:
    $ ./configure --with-cuda=/usr/local/cuda CUDA_CFLAGS=-O3 CUDA_ARCH=-arch=sm_80 NVCC=/usr/local/cuda/bin/nvcc
  • Build using make && make install

Compiling Neko for AMD GPUs

To compile Neko for AMD GPUs

  • Make sure you have the ROCm Toolkit installed
  • Configure Neko to use HIP using the --with-hip=/path/to/hip argument to configure, e.g.:
    $ ./configure --with-hip=/opt/rocm/hip
  • HIP compiler flags and options can be passed using HIP_HIPCC_FLAGS and HIPCC, respectively, e.g.:
    $ ./configure --with-hip=/opt/rocm/hip HIP_HIPCC_FLAGS=-O3 HIPCC=/opt/rocm/hip/bin/hipcc
Note
More examples, and instructions for specific machines can be found on Neko's user discussions pages.

Installing via Spack

Neko is distributed as part of the package manager Spack as neko. The package can install releases of Neko as well as the latest commit to the develop branch, for most of Neko's supported backends. For a list of all supported variants, see spack info neko

Quick start guide with Spack

To install a CPU build of Neko using Spack, follow the steps below:

$ git clone https://github.com/spack/spack.git
$ cd spack
$ . share/spack/setup-env.sh
$ spack install neko

For a GPU build using e.g. CUDA, change the last line to :

$ spack install neko+cuda

For a more detailed guide on getting started with Spack, please refer to the offical documentation: https://spack.readthedocs.io/en/latest/getting_started.html

Using a Docker container

Perhaps the easiest way to quickly give Neko a try is using a Docker container. Below we assume that you have Docker up and running on your system. The released container images can be found here: https://gitlab.com/ExtremeFLOW/neko/container_registry. Select the image with the release you want to use. Here we will use version 0.6.1, but in most cases you will want to simply pick up the latest version available. To the left of every image there is a button with three dots. Click on it to get the full path to the image in the correct format for Docker. For our release this is registry.gitlab.com/extremeflow/neko/release-0.6.1-ubunut20.04-x86_64-gcc-12.3. To get the image on you machine use docker pull:

docker pull registry.gitlab.com/extremeflow/neko/release-0.6.1-ubunut20.04-x86_64-gcc-12.3

Now, let's verify that the image has been added using docker image ls. There should be a row of the following kind in the output.

registry.gitlab.com/extremeflow/neko/release-0.6.1-ubunut20.04-x86_64-gcc-12.3 latest 6a9febfaa645 3 months ago 2.71GB

The third column contains the ID of the image. We will need that to run Neko in the container. The typical scenario is that you want to run a case stored on your computer inside the container. For that we will need to mount the directory with the case to the container file system. This is done using the the -v flag to the docker run command. For example, we will consider that the case resides in /home/user/case and we will mount it to /case inside the container. The full command to execute is the following:

docker run --rm -v /home/user/case:/case 6a9febfaa645 bin/bash -c "cd /case && mpirun -n 2 neko case_file.case"

The --rm flag tells Docker to remove the container after the run is finished. Note that we use the image ID from before as the third argument. As the run command we simply use bash, followed by a sequence of commands to actually execute the case. The commands are chained using &&, so one can easily add additional steps, for example, running makeneko.