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Kevin" Seung Whan Chung edited this page Jun 15, 2023 · 18 revisions

Quick Start (on your local machine)

Docker container librom_env provides a containerized environment with all the prerequisites for libROM. In order to compile and use libROM in the Docker container, follow these steps:

docker pull ghcr.io/llnl/librom/librom_env:latest
  • Clone libROM repository
git clone https://github.com/LLNL/libROM.git
  • Launch the Docker container with the cloned repository
docker run -it --volume ./libROM:/home/test/libROM ghcr.io/llnl/librom/librom_env:latest
  • This will lead to a terminal with the cloned repository mounted at ~/libROM. Compile libROM with the pre-set environment variables
mkdir build
cd build
cmake ~/libROM -DCMAKE_TOOLCHAIN_FILE=${TOOLCHAIN_FILE} -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DUSE_MFEM=${USE_MFEM} -DMFEM_USE_GSLIB=${MFEM_USE_GSLIB}
make -j 4

Some notes about using the Docker container:

  • Any change within the container will not be saved, except those happening in the mounted directory ./libROM.
  • Any change in /home/test/libROM in the container is instantaneously reflected into the actual directory ./libROM, and vice versa.

Quartz/Singularity

Quartz has singularity available in the default path (no module required). If you want to run a Docker container built elsewhere, you will need to convert it to a Singularity format first. Before starting, we strongly recommend to work in a directory where you have a enough disk quota (lustre1, lustre2, etc). If in the login node, the container might exceed your disk quota and will not work properly.

Here is an example pulling from GitHub Container Registry.

  • Login with your github username/personal access token for SingularityCE.
singularity remote login --username your-github-username docker://ghcr.io
  • Build the container image file from GitHub Containter Registry. NOTE: make sure to build it at a directory with enough disk quota.
singularity build librom_env docker://ghcr.io/llnl/librom/librom_env:latest
  • Clone libROM repository. NOTE: do this also at the same directory with enough disk quota.
git clone https://github.com/LLNL/libROM.git
  • Run container shell with the built container file, with the cloned repository mounted at /home/test/libROM 
singularity shell --cleanenv --contain -B ./libROM:/home/test/libROM librom_env

You can also mount multiple directories as your working directory, for example, for a dir1 and dir2 on LC machine,

singularity shell --cleanenv --contain -B ./libROM:/home/test/libROM,dir1:/home/test/dir1,dir2:/home/test/dir2 librom_env
  • On LC machine, there are some differences when you entered into the container terminal.
    • Unlike your local laptop/desktop, the home directory will be your login node by default, not /home/test.
    • Unlike your local laptop/desktop, you will have write permission only in the mounted directories. In the example above, you have write permission only on /home/test/libROM, /home/test/dir1, /home/test/dir2 (NOT on /home/test itself).

Move to the working directory to start compiling:

cd /home/test/libROM
mkdir build
cmake .. -DCMAKE_TOOLCHAIN_FILE=${TOOLCHAIN_FILE} -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DUSE_MFEM=${USE_MFEM} -DMFEM_USE_GSLIB=${MFEM_USE_GSLIB}
make -j 4

Some details

  • Machine architecture: Linux-x86_64
  • From: ubuntu:22.04
  • Dependencies:
    • cmake-3.22.1
    • hypre-2.20.0
    • parmetis-4.0.3
    • gslib-1.0.7
    • mfem: latest verified commit on May 02, 2023
    • googletest-v1.12.1: the last release that supports c++11
  • Environmental variables preset for libROM cmake:
    • TOOLCHAIN_FILE=/env/dependencies/librom_env.cmake
    • BUILD_TYPE=Optimized
    • USE_MFEM=On
    • MFEM_USE_GSLIB=On
  • Miscellaneous packages
    • Debugging tools: valgrind, lldb, gdb
    • Python packages: numpy, scipy, argparse, tables, PyYAML, h5py, pybind11, pytest, mpi4py
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