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CONTAINER-README.md

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Using the FigureGen Containers

Contact: Georgia Stuart, georgia.stuart@austin.utexas.edu
7 February 2021

Input File Setup

For both Singularity and Docker container use, the path option for ghostscript and gmt must be left blank. See autotest/docker-test/BathyFilledCPT.inp for example.

Singularity Containers

Singularity is a container platform designed for use with HPC systems. We provide three Singularity definition files:

  • figuregen.def provides MPI-enabled FigureGen for use on local Linux/Unix machines.
  • figuregen-serial.def provides serial (not MPI-enabled) FigureGen for use on local Linux/Unix machines.
  • figuregen-tacc.def is compatible with TACC or TACC-like HPC systems.

In addition, we maintain a FigureGen folder at the Singularity Container Library.

Using pre-built Singularity containers from the library

Running singularity containers assumes your current working directory is where your ADCIRC datafiles are. By default, singularity mounts your current working directory and $HOME so we have direct file access.

To download the image from the cloud library (e.g., to the root FigureGen folder of this repository, or to some other convenient location for singularity images), run the command:

singularity pull figuregen.sif library://georgiastuart/figuregen/figuregen

This command will pull down the latest figuregen image located at the cloud library and save it locally to figuregen.sif. Similarly, replace figuregen with figuregen-serial or figuregen-tacc to run the serial or TACC versions of figuregen, respectively.

NOTE

To run on TACC machines (excluding Lonestar 5), you must load the module:

module load tacc-singularity

Do not run Singularity on a TACC login node. Request an idev node or include in a slurm script.

To use an idev node on Stampede2, run

idev -A <account number> -N 1 -n <processes (at least 2)>

At least two processes must be specified to run the TACC-compatible singularity container. It cannot run serially.

singularity pull figuregen-serial.sif library://georgiastuart/figuregen/figuregen-serial
singularity pull figuregen-tacc.sif library://georgiastuart/figuregen/figuregen-tacc

To run the tests in this repository, cd to autotest/TestFiles and run the following command (for example):

MPI Example
singularity exec <path to figuregen.sif> mpirun -np <num processes> figuregen -I ../Tests/BathyFilledCPT.inp
Serial Example
singularity exec <path to figuregen-serial.sif> figuregen -I ../Tests/BathyFilledCPT.inp
TACC/HPC Example (e.g. on Stampede2. DO NOT RUN ON LOGIN NODE.)
ibrun singularity exec <path to figuregen-tacc.sif> figuregen -I ../Tests/BathyFilledCPT.inp

Note: The TACC container gives some harmless errors that can be safely ignored.

Building Singularity Containers

To build a Singularity container yourself, from the root FigureGen directory of this repository, use this command on a machine where you have sudo privileges:

sudo singularity build figuregen.sif container-files/singularity-def-files/figuregen.def

Replace figuregen.def with figuregen-serial.def or figuregen-tacc.def as appropriate.

Docker Containers

For use on MacOS and Windows, we also provide Docker containers. All docker container instructions rely on your data files and input files being in the same directory (e.g., the autotest/docker-test directory in this repository).

We maintain two Docker images for use on local machines (not HPC clusters. Use Singularity for HPC).

georgiastuart/figuregen
georgiastuart/figuregen-serial

Install Docker

Mac instructions: https://docs.docker.com/docker-for-mac/install/
Windows instructions: https://docs.docker.com/docker-for-windows/install/

Run FigureGen Containers

Running FigureGen in a Docker container requires four steps:

  1. Pull the desired Docker container (listed above)
  2. Launch the container and bind the directory with your data and input files to /data
  3. Execute the figuregen executable and set working directory to /data
  4. Shut the docker container down

Pull the Docker Image

First, pull the Docker image with the following command:

docker pull georgiastuart/figuregen

Similarly, georgiastuart/figuregen-serial.

Launch the Docker Container

We need to launch the docker container while binding your desired data directory to /data in the container. Use the following command (assuming your current working directory is where your data and input files are):

Mac/Linux
docker run -d -it --name figuregen --mount type=bind,source="$(pwd)",target=/data georgiastuart/figuregen
Windows (Command Prompt)
docker run -d -it --name figuregen --mount type=bind,source="%cd%",target=/data georgiastuart/figuregen
Windows (Power Shell)
docker run -d -it --name figuregen --mount type=bind,source="${PWD}",target=/data georgiastuart/figuregen

Similarly for georgiastuart/figuregen-serial.

Run the FigureGen Program

Next, we will run the FigureGen program and set the working directory to /data:

docker exec -it -w /data figuregen mpirun -np <num processes> figuregen -I <input file name>

Shut Down the Container

Finally, after your plots are satisfactory, we shut down the Docker container. A new container must be launched each time you want to plot in a new directory.

docker stop figuregen

Tests Completed:

  1. Tested figuregen.sif / figuregen-serial.sif on Ubuntu 20.10 Host Machine (7 Feb 2021)
  2. Tested figuregen-tacc.sif on TACC's Stampede2 on idev node (7 Feb 2021)
  3. Tested georgiastuart/figuregen / georgiastuart/figuregen-serial Docker container on MacOS 10.15.7 (7 Feb 2021)
  4. Tested georgiastuart/figuregen Docker container on Windows 10 (7 Feb 2021)