# Singularity workshop FAQ - 2023.03.10 https://pmitev.github.io/UPPMAX-Singularity-workshop - Q: Please discuss the concepts of docker vs containers. - A: Answer ... - Q: Please discuss the difference between apptainer vs enroot containers. - A: Answer ... - Q: Singularity hub vs docker hub - A: Answer ... - Q: What is recipe? What is the extension of recipe file? Is it just a sequence of codes where we build a container and install stuffs inside that? - A: Answer ... - Q: Containers versus build environments provided by HPC centres. What are the differences? - A: Answer ... - Q: How can one use MPI from inside a singularity container? - A: There are different ways to use MPI with Singularity/Apptainer containers. One of them is by using the host and container MPI installed libraries (both versions should match). This is a recommended way. Another way is by using the MPI directly from the container by using an "agent", thus no host MPI installation is required but this way is tricky. The last way I know to use MPI is by binding the MPI installation on the host, here the MPI in the container is not needed. (See for further information: https://apptainer.org/docs/user/1.0/mpi.html, https://docs.sylabs.io/guides/3.3/user-guide/mpi.html) - Q: How to convert docker image to singularity so we can run doker image in UPPMAX - A: https://pmitev.github.io/UPPMAX-Singularity-workshop/docker2singularity/ - Q: What are the differences between Apptainer and Singularity? - A: At the moment there are not noticeable differences they would diverge in the future. - Q: How to run R with packages from Bioconductor and Posit in a Singularity container? - A: Here is a recent R setup with Packages installation and https://github.com/pmitev/UPPMAX-Singularity/blob/main/ArchR/ArchR-20.04.def - Q: Is it possible to bind Windows or MacOS paths when building a Singularity image? (bind means using -B argument) - A: In principle yes `singularity build -h` - Q: How to run a singularity container on nodes? When I submit job with a singularity part, it usually appears in my home directory, which does not work for lagre calculations. - A: - Q: - A: - Q: - A: - Q: - A: - Q: - A: - Q: - A: - Q: - A: - Q: - A: - Q: - A: - Q: - A: - Q: - A: - Q: - A: - Q: - A: - Q: - A: - Q: - A: