gkyl install

There are two options for installing gkyl. One can install directly from the source code, or via the Conda package. Installing directly from the source is the preferred option, as this method gives users more control over the installation process. For many users who will wish to run gkyl on a cluster, which will have cluster-built versions of the Message Passing Interface (MPI) for parallel simulations, and potentially other gkyl depedencies, the source build will allow users to set the appropriate paths to the cluster installations of these dependencies.

Installing from source (preferred)

To install gkyl from source, first clone the GitHub repository using:

git clone https://github.com/ammarhakim/gkyl

Navigate into the gkyl directory to begin.

In many cases, an installation of gkyl will involve building most of gkyl’s dependencies only require a modern C/C++ compiler and Python 3. The full list of dependencies is:

  • C/C++ compiler with C++17 support (But NOT Clang >= 12.0 provided by Xcode 12)
  • Python 3 >=3.6
  • MPI compiler with MPI3 support (>=openmpi 3.0 or >=mpich 3.0)
  • LuaJIT 2.1.0
  • ADIOS 1.13.1 (But NOT >=ADIOS 2.0)
  • Eigen 3.3.7
  • CUDA Toolkit >=10.2 (if building with GPU support)

The following instructions assume that at minimum the user has both a C/C++ compiler with C++17 support and Python 3.

Installing from source manually

If machine files are not available, the dependencies, configuration, and build can be done manually.

The first step is to build the dependencies. Depending on your system, building dependencies can be complicated. On a Mac or Linux machine you can simply run the mkdeps.sh script in the install-deps directory. To build dependencies cd to:

cd gkyl/install-deps

First, please check details by running:

./mkdeps.sh -h

On most supercomputers you will likely need to use the system recommended compilers and MPI libraries. In this case, you should pass the appropriate compilers to mkdeps.sh as follows:

./mkdeps.sh CC=cc CXX=cxx MPICC=mpicc MPICXX=mpicxx ....

You should only build libraries not provided by the system. In practice, this likely means LuaJIT, ADIOS and, perhaps Eigen. (Many supercomputer centers at DOE already offer ADIOS builds and should be preferred instead of your own builds). A typical command will be:

./mkdeps.sh --build-adios=yes --build-luajit=yes --build-eigen=yes

(in addition, you may need to specify compilers also).

By default, the mkdeps.sh script will install dependencies in $HOME/gkylsoft directory. If you install it elsewhere, you will need to modify the instructions below accordingly.

Once you have all dependencies installed, you can build gkyl itself by cd-ing to the top-directory in the source:

cd gkyl

gkyl uses the Waf build system. You do NOT need to install waf as it is included with the distribution. However, waf depends on Python (included on most systems). Waf takes a number of options. To get a list do

./waf --help

There are two build scenarios: first, all dependencies are installed in $HOME/gkylsoft directory, and second, you are using some libraries supplied by your system.

If you have installed all dependencies in the gkylsoft directory you can simply run:

./waf configure CC=mpicc CXX=mpicxx

where CC and CXX are names of the MPI compilers to use. Note that in some cases the full path to the compiler may need to be specified. If the compilers are already in your path, then you can omit all flags.

If you need to use system supplied builds, you need to specify more complex set of paths. Although you can do this by passing options to the waf build script, it is easiest to follow these steps:

  • Copy the configure-par.sh-in script to configure-par.sh
  • Modify this script to reflect the locations of various libraries on your machine. In particular, if you are using pre-built libraries you will likely need to change the information about MPI and ADIOS.
  • Run the configure-par.sh script

Once the configuration is complete, run the following command to build and install (note: if you are working on a cluster and using environment modules, you may need to load them at this point):

./waf build install

The builds are created in the ‘build’ directory and the executable is installed in $HOME/gkylsoft/gkyl/bin, unless you specified a different install prefix. The executable can only be run from the install directory [1].

If you need to clean up a build do:

./waf clean

If you need to uninstall do:

./waf uninstall

LuaJIT builds easily on most machines with standard GCC compiler. Often, you may run into problems on older gcc as they do not include the log2 and exp2 functions unless c99 standard is enabled. To get around this, modify the src/Makefile in LuaJIT. To do this, change the line:

CC= $(DEFAULT_CC)

to:

CC= $(DEFAULT_CC) -std=gnu99

To build on Mac OS X Mojave and beyond you must set the following env flag:

export MACOSX_DEPLOYMENT_TARGET=10.YY

where YY is the version number of the OSX operating system. For example, to build on OS X Mojave the env flag is:

export MACOSX_DEPLOYMENT_TARGET=10.14

and to build on OS X Catalina the env flag is:

export MACOSX_DEPLOYMENT_TARGET=10.15

Installing with Conda

The gkyl package is also available to be installed via Conda, although this gives less flexibility for keeping the code up-to-date as gkyl development continues. Once Conda is installed and added to the PATH, gkyl can be obtained with:

conda install -c gkyl gkeyll

Note, that this will also install all dependencies into the Conda install directory. Often this may lead to some conflicts, particularly for the MPI installation, specially if there is another version of MPI already located in the system. gkyl should be run using the MPI provided by Conda.

In general, having Conda and source-built gkyl on the same machine can cause confusion. In that case please use explicit paths to the mpiexec and gkyl executable you wish to use when running simulations.

Troubleshooting

Having trouble building? We will try to compile a list of suggestions and common error messages in this troubleshooting site.

Footnotes

[1]The reason for this is that gkyl is in reality a LuaJIT compiler extended with MPI. Hence, for the compiler to find Lua modules (i.e. gkyl specific code) certain paths need to be set which is done relative to the install location.