Mili

Description

Binary Database format used by MDG codes for mesh simulations.

Table of Contents

• Developer Guide
• Developer Workflow

GitLab and LC Setup

This section includes required steps for setting up your GitLab and LC Account

GitLab Setup

1. Add an ssh key to RZ GitLab

   • Create the ssh key on the machine you will use to access gitlab, such as an RZ machine, laptop, etc.
   • Create an ssh key: ssh-keygen -t rsa -b 4096
     • Use the standard location. (~/.ssh/id_rsa and ~/.ssh/id_rsa.pub)
     • Most people press enter and don't have a password.
     • Keys should be 4096 bits or longer.
     • Use RSA
   • Add key to gitlab here: https://rzlc.llnl.gov/gitlab/-/profile/keys

2. CI Pipeline/Testing Setup

   • How CI pipelines works on GitLab
     • There is something called gitlab runners (managed by LC, not the team)
     • CI pipelines are run in the user's LC account
     • CI pipelines are run by default in your home directory in ~/.jacamar-ci/
       • Don’t do this. Your quota is small there. 24 GB.
     • CI pipelines are triggered whenever:
       • A user pushes to a branch with an open merge request
       • manually triggered through the GitLab web interface
   • Modify your home directory such that tests are run on workspace instead:
     • Make a directory in your workspace: mkdir /usr/workspace/<your-lc-username>/gitlab_testing
     • Symlink test location to this location: ln -s /usr/workspace/<your-lc-username>/gitlab_testing ~/.jacamar-ci

Local Repo Setup

Once you have complete the above steps you can clone the repository. To clone the repository into your current location run:

git clone ssh://git@rzgitlab.llnl.gov:7999/mdg/mili/mili.git

Submodules

Mili contains the following git submodules:

• mdgtest (MDG's generic testing scripts)

When checking out the repository for the first time, submodules should be updated/initialized via:

git submodule update --init --recursive

If you don't want to have to remember to update submodules when pulling, you can configure git (globally for your user on RZ, so it will effect all git repos you operate on) to automatically update submodules when you pull:

git config --global submodule.recurse true

Configuration

Mili's BLT/Cmake-based build system is largely modeled after Diablo's build system, providing a configure.py script to automate the configuration and setup of build and install directories based upon an input host-config file. A handful of example host-config files are provided for reference, consistent with the standard build options used by Mili on TOSS3 and TOSS4 machines.

Mili requires CMake version 3.18 or later. On LLNL machines, the user's local version of CMake can be updated using the module load command, e.g.:

module load cmake/3.18.0

For convenience, the module load command above may be added to the user's local .cshrc or .bashrc file to avoid having to re-load the correct CMake module after login.

Specific builds are configured via:

configure.py -hc host-configs/<host_config_file_name>.cmake -bt <build_type>

which generates corresponding build-<host_config_file_name>-<build_type> and install-<host_config_file_name>-<build_type> subdirectories, and uses CMake to generate a Makefile in the build directory.

The <build_type> can be any one of the following:

Build Type	Compiler Flags
Debug	-g
Release	-O3
RelWithDebInfo	-g -O3

The default build type is currently set to RelWithDebInfo.

Style/Formatting

Mili uses clang-format to maintain a consistant style and format throughout the code. The style rules can be found in the file clang-format.yaml in the directory griz/scripts/style/. To use clang-format you must configure using the toss3 host-config file which sets up clang-format for you. To style your code run make clangformat_style and to check if you code matches the style guide run clangformat_check.

Compilation

Once a particular build directory has been generated using the configure.py script, the code is compiled within this new directory using the standard make utility, e.g. to compile the code:

make

Testing (LLNL Specific)

The test suite for mili and xmilics reside in the directories: mili/test/mili and mili/test/xmilics. The scripts that run the tests can be found in the git submodule mdgtest in the mili/test directory.

You shouldn't run the test suite on a login node, so you will have to get access to a debug/batch node. This can be done by running the command:

sxterm 1 36 60 -p pdebug -A wbronze

You can now run the test suite as shown below:

Mili Library

mdgtest/Test.py -e mililib_env -c <path-to-code> -I <include-dir> -n1 -p1 -q -s all

Xmilics

mdgtest/Test.py -e xmilics_env -c <path-to-code> -n1 -p1 -q -s all

Licences

SPDX-License-Identifier: LGPL-2.1-or-later