JDK 11 available from the commandline. To verify:
javac -version
Should return with something like (only the first 11 is important):
javac 11.0.10
To access dvc you need to use VPN or have a whitelisted IP.
Since dvc configuration contains secret keys to a dedicated S3 bucket and - for security reasons - the required credentials are not stored in this repository, they need to be acquired in some other way (email, SMS) from admin.
The credentials consist of the key id and the secret key. Once they are known, they need to be configured in the local config (so that they don't get commited by accident):
dvc remote modify --local icm_s3 access_key_id 'KEY_ID_GOES_HERE'
dvc remote modify --local icm_s3 secret_access_key 'SECRET_ACCESS_KEY_GOES_HERE'
Checkout the large files from DVC:
dvc pull
Gradle is the build system used by the project. It should not be installed on the machine, it is bundled with pdyn2-stack so that building only requires Java.
It will, however, take some liberties with your home directory
(namely, a dir called .gradle containing cache and some binaries will appear)
and it will consume some resources (a daemon process called gradle will linger on,
to speed up future builds. It can be safely killed.)
To run gradle, use the script gradlew (there's a gradlew.bat version which works on Windows as well`).
To clean:
./gradlew clean
To build:
./gradlew build
The simplest way to run selected classes project is with GUI.
From shell - it's easy to run main pandemic using gradle (on windows we can use gradlew.bat instead)
./gradlew run
However, the project has a convenient way to create a complete runnable distribution of pdyn2 (which will run across various linux / unix / windows / macos environments) by executing
./gradle installDist
A whole distribution (including the dependencies) will be created
in the pdyn2/build/install/pdyn2 directory, consisting of two directories: libs
(containing the compiled Java code) and bin, containing the scripts: pdyn2 and pdyn2.bat (separately for windows and unix).
The scripts can be run from anywhere, but they will require input and output dirs under the current workdir.
Assuming we are on a HPC cluster, have the whole project checked out and Java 11 in path, we could run it by executing:
./gradle installDist
./build/install/rename_me/rename_me
(caveat: input and output directories must be present, large files dvc'ed, social structure created).