Preliminary build instructions

Please note this project is in very early stages. It is expected these build instructions will change and become more robust as the project evolves. The current build instructions are for early adapters to test and give us feedback. Where things need improvement we've added notes and are very happy to get feedback.

pre-requisites

Install a c++ compiler

For windows look at the CLIc_prototype windows build guide and install Microsoft Build tools (or Visual Studio Community edition) as explained here. Hint: during installation, activate Windows C++ development.

Install OpenCL

Note. As we create builds for different operating systems these instructions may change.

Currently we have only built on Windows using the Nvidia distribution of OpenCL version 11.2

The OpenCL include and lib folders are defined here

Add the folder where "cl.exe" lives to the PATH, e.g. this one:

C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.29.30133\bin\Hostx64\x64

Follow the instructions to build CLIc. Make sure when setting up CMAKE, that it is built into this directory as explained here.

../CLIc_prototype/build/

Java Development Kit

Download and install a Java-Development-Kit (JDK), preferably version 11, e.g. from azul.

Set the environment variable JAVA_HOME to a valid SDK, e.g.:

setx JAVA_HOME C:\Users\rober\.jdks\azul-11.0.14.1\
echo %JAVA_HOME%

Maven

Download apache-maven, unzip it and make it part of PATH:

C:\programs\apache-maven-3.8.4-bin\apache-maven-3.8.4\bin

git

Install git-scm and add it to the PATH so that bash can be called from any command line.

cmake

Download and install cmake.

CLIc_prototype

Get CLIc_prototype and put code in the same directory as clesperantoj_prototype.

Build and install using CLIc_prototype/build as the folder to place the build files generated by cmake and CLIc_prototype/bin as the installation folder where the binaries will be placed.
It is important to use this code and installation folder as clesperantoj_protyotype uses them as include and link paths.

If using the cmake windows GUI and Visual Studio GUI

1. Project Build files are specified by changing the 'Where to build the binaries' option on the CMake GUI.
2. The installation folder is specified by the CMAKE_INSTALL_PREFIX option in the options table. This should be for example:

C:/structure/code/CLIc_prototype/bin

If using cmake from command line you need to use a bash prompt embedded in the x64 Native Tools command prompt.

Open the x64 Native Tools Command Prompt for VS 2019 (64 bit!), then run 'C:\Program Files\Git\bin\sh.exe' (optionally add 'C:\Program Files\Git\bin' to windows path and then just type sh), then navigate to the root directory of this project and run

cmake -S . -B ./build -D CMAKE_INSTALL_PREFIX=/path/to/installation/folder
cmake --build ./build --parallel 10 --target install

You can modify installation location using -D CMAKE_INSTALL_PREFIX=/path/to/installation/folder

Build clesperantoj_prototype

Open the x64 Native Tools Command Prompt for VS 2019 (64 bit!), navigate to the root directory of this project and run

mvn

Running the prototype

After the build succeeded, you can run the main functions in this package and play with clesperantoj. This is recommended to do from an IDE such as IntellIJ by clicking on the green triangle next to the main function:

Trouble shooting

• Take a look at the javacpp section of the poml.xml and make sure the includePath and linkPath locations exist on your machine.

• Sometimes we had to make a trivial change to [clesperantoj][https://github.com/clEsperanto/clesperantoj_prototype/blob/javacpp/src/main/java/net/clesperanto/clicwrapper/clesperantoj.java], like adding a space, to activate the parser that generated the java wrapper.)

• In some cases, the build fails when executed the first time. You find a potential workaround explained here.

• You may need to add the src/gen/java path to the java build path in your IDE.

  • For Eclipse follow below instructions

1. Go to Project -> Properties -> Java Build Path -> Source (tab). Then add src/main as a source folder.
2. Right-clicking your project, then click Properties .
3. In the left pane, click Java Build Path . In the right pane, select the Source tab .
4. Here you can add/edit/remove source folders.

Acknowledgements

This project was supported by the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy – EXC2068 - Cluster of Excellence "Physics of Life" of TU Dresden. This project has been made possible in part by grant number 2021-237734 (GPU-accelerating Fiji and friends using distributed CLIJ, NEUBIAS-style, EOSS4) from the Chan Zuckerberg Initiative DAF, an advised fund of the Silicon Valley Community Foundation.