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Docker/Singularity/Apptainer + OpenFOAM® + PyTorch

Overview

The Dockerfile in this repository creates an image with ESI-OpenFOAM and PyTorch support. The image is currently based on

  • Ubuntu 22.04,
  • OpenFOAM-v2206, and
  • PyTorch 1.12.1 (only CPU).

There are also convenience scripts for working with the images. The test directory contains two examples demonstrating how to compile applications using cmake and wmake

OpenFOAM is not compiled from scratch but installed via the package manager (read more). Also for PyTorch, only the pre-compiled C++ part of the library, named libtorch, is contained on the image.

How to build the images

Docker image

To build the image yourself, copy this repository and navigate into the top-level folder:

git clone https://github.com/AndreWeiner/of_pytorch_docker.git
cd of_pytorch_docker

If you want to upload the image to a Docker registry, consider the following naming convention when running the build command:

docker build -t user_name/of_pytorch:of2206-py1.12.1-cpu -f Dockerfile .

Pushing the image to Dockerhub works as follows:

docker login
docker push user_name/of_pytorch:of2206-py1.11.0-cpu

A word on Podman: due to the strong compatibility between Docker and Podman (builder), building and using the image with Podman instead of Docker should work, too, but I have not tested it yet.

Singularity/Apptainer image

For university clusters, Singularity/Apptainer is often the only supported container tool. Note that Singularity was renamed to Apptainer after joining the Linux Foundation. In contrast to the default Docker workflow, the execution of Apptainer containers does not require root-privileges (the image creation does, though). Moreover, Apptainer works out of the box with Schedulers like SLURM and was build with focus on MPI-parallel applications. The Docker image built before can be easily converted to Apptainer by running:

sudo apptainer build of2206-py1.12.1-cpu.sif docker://andreweiner/of_pytorch:of2206-py1.12.1-cpu

The image may be used similarly to the Docker image. Convenience scripts like create_openfoam_container.sh or start_openfoam.sh are not necessary because Apptainer performs similar actions by default (e.g., mapping of the user and important directories). To start an interactive shell, run:

apptainer shell of2206-py1.12.1-cpu.sif
# first thing to do inside the container
. /usr/lib/openfoam/openfoam2206/etc/bashrc
# now you are ready to run and build OpenFOAM+PyTorch applications

Usage and examples

Docker image

Copy this repository and navigate into the top-level folder:

git clone https://github.com/AndreWeiner/of_pytorch_docker.git
cd of_pytorch_docker

The script create_openfoam_container.sh creates a container with suitable settings (e.g. mapping the user into the container, mounting the current directory, setting the working directory to ./test/). The script also pulls the Docker image from Dockerhub if it cannot be found locally. The default image and container names can be changed by passing them as command line arguments.

# default settings
./create_openfoam_container.sh

# use different image, e.g., to use an older version
./create_openfoam_container.sh "andreweiner/of_pytorch:of2012-py1.7.1-cpu" "of2012-py1.7.1-cpu" 

The start_openfoam.sh script starts an interactive shell instance in the running container. If you modified the container name in the previous step, provide the modified name as command line argument.

# default
./start_openfoam.sh

# custom container name
./start_openfoam.sh "of2012-py1.7.1-cpu"

The container's entry point is set to the test directory. There you are presented with two examples:

  • tensorCreation: PyTorch tensor basics; compiled with wmake
  • simpleMLP: implementation of a simple multilayer perceptron (MLP) class; compiled with cmake

tensorCreation

To compile and run tensorCreation, execute:

# you must be inside the container for this to work
# execute ./start_openfoam.sh to launch a shell instance
cd tensorCreation
wmake
./tensorCreation

simpleMLP

To compile and run simpleMLP, execute:

# you must be inside the container for this to work
# execute ./start_openfoam.sh to launch a shell instance
cd simpleMLP
mkdir build
cd build
cmake ..
make
./simpleMLP

Singularity/Apptainer image

From the top-level folder of this repository, you can build and run the examples as follows:

apptainer shell of2206-py1.12.1-cpu.sif
# first thing to do inside the container
. /usr/lib/openfoam/openfoam2206/etc/bashrc
# go to the tensorCreation example, compile, and run
cd test/tensorCreation
wmake
./tensorCreation
# go to the simpleMLP example and execute the test script
cd ../simpleMLP
./compileAndRun.sh

To hide the additional complexity from using containers, one can also define shell functions that assemble suitable commands in the background. E.g., in this file, the function singularityRun works the same way as the frequently used runApplication but uses a Singularity/Apptainer image in the background.

Get in touch

If you would like to suggest changes or improvements regarding the

  • build process,
  • pre-installed packages,
  • examples,
  • documentation,
  • ...

please use the issue tracker.

Miscellaneous

Issue with Sourceforge

Building the Docker image sometimes fails with the error message:

E: Failed to fetch https://nav.dl.sourceforge.net/project/openfoam/repos/deb/dists/focal/main/pool/2012_1/binary-amd64/openfoam2012_1-2_amd64.deb
Could not connect to nav.dl.sourceforge.net:443 (5.154.224.27), connection timed out E: Unable to fetch some archives, maybe run apt-get update or try with --fix-missing?

The OpenFOAM Debian package is hosted on Sourceforge, and sometimes their servers are not available. Usually waiting a couple of minutes before rebuilding the image helps to solve this issue.

Older versions of the Dockerfile

There are two more Dockerfiles which were used to build previous versions of the Docker image. They remain part of the repository since they might be helpful to some users.

  • Dockerfile.abi_source: OpenFOAM is compiled from scratch; only some third-party packages are installed and, hence, some applications are missing
  • Dockerfile.no_abi: OpenFOAM is compiled from scratch with modified compiler flags to be compatible with libtorch versions prior to version 1.3

By default, the OpenFOAM library will be compiled running two jobs in parallel. If you prefer to use more jobs, set the NP build argument, e.g.:

docker build --build-args NP=8 -t user_name/of_pytorch:of1912-py1.5-cpu -f Dockerfile.abi .

I also recommend to save the Docker output in a log-file:

docker build --build-args NP=8 -t user_name/of_pytorch:of1912-py1.5-cpu -f Dockerfile.abi . &> log.docker

ABI

Since version 1.3 of PyTorch, there is a version of libtorch compiled with ABI enabled (read more). The only change in prior versions compared to a regular compilation is the additional flag

-D_GLIBCXX_USE_CXX11_ABI=0

when compiling OpenFOAM. The flag is related to backwards compatibility for standards older than C++11 (read more).

Libtorch

The PyTorch library files are located in /opt/libtorch. The environment variable TORCH_LIBRARIES can be used to indicate the location of certain header and library files to the compiler and linker. To compile PyTorch C++ code using wmake, add

EXE_INC = \
    -I$(TORCH_LIBRARIES)/include \
    -I$(TORCH_LIBRARIES)/include/torch/csrc/api/include \

to the include paths, and

EXE_LIBS = \
    -Wl,-rpath,$(TORCH_LIBRARIES)/lib $(TORCH_LIBRARIES)/lib/libtorch.so $(TORCH_LIBRARIES)/lib/libc10.so \
    -Wl,--no-as-needed,$(TORCH_LIBRARIES)/lib/libtorch_cpu.so \
    -Wl,--as-needed $(TORCH_LIBRARIES)/lib/libc10.so \
    -Wl,--no-as-needed,$(TORCH_LIBRARIES)/lib/libtorch.so

to the library paths.

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Dockerfile to create an image with OpenFOAM-plus and PyTorch support

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