GPI2.jl

GPI2.jl is a lightweight Julia wrapper for the GASPI-conforming GPI-2 library.

Installation

If you have not yet installed Julia, please follow the instructions for your operating system. GPI2.jl works with Julia v1.7. Since GPI-2 only works on Linux systems, GPI2.jl is also restricted to this platform.

GPI2.jl is a registered package. Thus to install it in your default environment, execute the following command:

julia -e 'using Pkg; Pkg.add("GPI2.jl")'

Alternatively, you can also just clone this repository and then instantiate it, i.e., installing all dependencies:

git clone https://github.com/hpsc-lab/GPI2.jl.git
julia --project=GPI2.jl -e 'using Pkg; Pkg.instantiate()'

If you decide to use the latter approach with a cloned GPI2.jl directory, in the following, you need to add --project=path/to/GPI2.jl to the julia command, e.g.,

julia --project=. -e 'using GPI2; ...'

if you are starting Julia from within the GPI2.jl folder.

Usage

Getting started

You can start running GASPI functions after executing using GPI2. All GASPI functions are prefixed by gaspi_. For example, to check the version of the currently used GPI-2 library, start the Julia REPL and paste the following snippet:

julia> using GPI2

julia> version = Ref{Cfloat}()
Base.RefValue{Float32}(0.0f0)

julia> gaspi_version(version)
GASPI_SUCCESS::gaspi_return_t = 0

julia> println("GPI-2 library version: $(version[])")
GPI-2 library version: 1.51

Parallel execution

To run a GPI-2 program in parallel, you need to start it with the helper script gaspi_run. It requires a machinefile with the names of the nodes on which a rank should be started, see also the GPI-2 docs. For a simple test, you can create a machinefile that will start three ranks on the current node by running

yes `hostname` | head -n 3 > machinefile

For convenience, GPI2.jl provides the function gaspi_run() that will start gaspi_run for you, using the GPI2_jll.jl-provided executable. GPI2.jl also provides some example files in the examples/ folder you can check out to get started.

For example, to run the hello_world.jl example in parallel, execute the following commands from the GPI2.jl directory:

julia -e 'using GPI2; gaspi_run()' -- -m machinefile $(which julia) $(pwd)/examples/hello_world.jl

You need julia twice in the command: The first one just executes the gaspi_run command, while the second one is the command that is executed in parallel. You also need the $(pwd) to ensure that gaspi_run picks the right file.

Issues when relying on the module command

If you want to start a parallel process using GPI-2's gaspi_run on a cluster where paths are set using the module command provided by, e.g., Lmod, there are some issues you need to handle in order to make a GASPI program run properly. They boil down to the fact that, as far as I can tell, GPI-2 uses SSH to set up communication between nodes and uses a non-login shell for this purpose. This means that, e.g., the module command will not work and thus you need to manually put all relevant changes to the environment variables directly in your ~/.bashrc file.

As a workaround, this repository provides two auxiliary utilities: storeenv.jl and launcher.jl. They help you to run a GPI-2-powered Julia program on a cluster with an environment modules setup by storing the entire environment and reloading it.

First, go to the folder from which you want to start your GASPI-parallelized Julia program and execute the storeenv.jl script:

julia path/to/storeenv.jl

The storeenv.jl script will record the current environment variables and store them in a file gaspi-jl-env.toml.

Then, run your Julia program in parallel with the launcher.jl script using the following command:

julia -e 'using GPI2; gaspi_run()' -- -m <machinefile> $(which julia) /abs/path/to/launcher.jl $(pwd)/gaspi-jl-env.toml path/to/julia/program.jl

The <machinefile> is the normal machinefile with all nodes on which to start a GASPI rank. The /abs/path/to/launcher.jl must be an absolute path again. The launcher script will take care of recreating the environment using the information in the TOML file $(pwd)/gaspi-jl-env.toml. Finally, you can provide the path to the Julia programm (and optional command line arguments to it) as the final part. The path to the Julia program may be relative or absolute, since the launcher knows your current directory by now.

Configuration

Using a system library

When using GPI2.jl, you can specify the path to the GASPI library you want to use. By default, GPI2.jl uses the precompiled GPI-2 library available in the GPI2_jll.jl package. This is only recommended for non-performance critical usage and/or development. To switch to a library installed on your system, execute

julia -e 'using GPI2; GPI2.use_system_library("path/to/libGPI2.so")'

where path/to/libGPI.so should be the path to your shared GPI-2 library. To switch back to using the JLL-provided library, execute

julia -e 'using GPI2; GPI2.use_jll_library()'

After switching the library, you need to restart Julia for the changes to take effect.

Generating C bindings

In case you are using a system-provided GPI-2 library with an API that is different to the one provided by the JLL-provided library, you need to re-generate the C bindings file LibGPI2.jl and tell the GPI2.jl package to use it.

To this end, enter the bindings/ directory and run the following command:

julia --project=. -e 'using Pkg; Pkg.instantiate()' # only required once
GPI_INCLUDE_DIR=path/to/GPI-2/include julia --project=. generator.jl

This will create a LibGPI2.jl file in the current working directory. To switch to the custom bindings file, execute

julia -e 'using GPI2; GPI2.use_system_bindings("path/to/LibGPI2.jl")'

where path/to/libGPI.so should be the path to your custom C bindings file. To switch back to using the JLL-compatible library, execute

julia -e 'using GPI2; GPI2.use_jll_bindings()'

After switching the C bindings, you need to restart Julia for the changes to take effect.

Authors

GPI2.jl is maintained by Michael Schlottke-Lakemper (University of Augsburg, Germany). The GPI-2 library itself is developed by the Fraunhofer Institute for Industrial Mathematics (ITWM).

License and contributing

GPI2.jl is published under the MIT license (see LICENSE.md). We are very happy to accept contributions from everyone, preferably in the form of a PR. GPI-2 itself is published under the GNU General Public license, version 3.