Frequently Asked Questions#

  1. How do I limit the number of cores that are used to build the project in VS Code?

The CMake Tools extension supports a number of parameters to configure the build. Those can be set in the file .vscode/settings.json. To limit the number of cores use the parameter cmake.parallelJobs.

  1. How do I configure SSH on Windows?

The SSH configuration file on Windows 10 is located at C:\Users\<username>\.ssh\config. Note that the contents of this file also have an impact on how Docker connects to a remote container. For instance, the file could look like this (replace (...) by suitable settings); see also the Euler documentation:

Host (...)
    User (...)
    HostName (...)
    IdentityFile (...)

In case VS Code asks for the key passphrase too often, consider setting up the SSH agent; see the VS Code documentation for more information.

  1. I cannot attach to containers via SSH with VS Code.

First check that attaching to the workstation via VS Code and SSH works, and that the containers can be started via the docker-compose.yml file in the repository. If this is the case, make sure that the rootless Docker context is activated on the workstation. For this purpose run docker context use rootless on the workstation. If the problem persists, try uninstalling and installing rootless Docker on the workstation (following the instructions here), and then activating the rootless context.

  1. VS Code reports a “Bad CMake executable”.

If VS Code shows the error Bad CMake executable "". Is it installed or settings contain the correct path (cmake.cmakePath)?, then the most likely reason for the error is that the VS Code windows is not yet attached to a container. If you are using a custom container, then make sure that CMake is installed in the container.

  1. VS Code asks for a password even though I have created an SSH key.

Please make sure that you have provided the public key in the workstation’s authorized_keys file; see e.g. scicomp.ethz.ch.

  1. When interacting with git I am asked for a password even though I’ve added a public key.

git may not be aware of the key to use for the remote repository. To solve the problem, add an entry to .ssh/config (or similar), specifying the private key to use (replace (...) by a suitable path):

Host gitlab.ethz.ch
    HostName gitlab.ethz.ch
    IdentityFile (...)

  1. Attaching to the container with VS Code fails with the error message Cannot connect to the Docker daemon at unix:///run/user//docker.sock. Is the docker daemon running? (note the missing user ID between /user/ and /docker.sock).

This error was caused by an incompatibility of the Remote-Containers plugin with the Leibniz configuration. The error should no longer occur with the latest version of the plugin.

  1. How can I link against a version of PETSc that is compiled with enabled debug checks?

Install the Ubuntu package libpetsc-real3.12-dbg (if you are using a real scalar type). Then, before running CMake, set the environment variable PKG_CONFIG_PATH to /usr/lib/petscdir/petsc3.12/x86_64-linux-gnu-real-debug/lib/pkgconfig (remember to clear CMake's cache if it does exist already). If you are using VS Code, this can also be accomplished by adding the following to settings.json:

"cmake.configureEnvironment": {
  "PKG_CONFIG_PATH": "/usr/lib/petscdir/petsc3.12/x86_64-linux-gnu-real-debug/lib/pkgconfig"
}

  1. Why do I see the error Read -1, expected ..., errno =1 when running an executable in parallel in the Docker container?

This is a known issue, see the corresponding issue on GitHub. Setting the following environment variable works:

export OMPI_MCA_btl_vader_single_copy_mechanism=none

  1. How can I add a new developer user to the project?

Please ask the new developer to login to gitlab.ethz.ch once. Then send an email to manuel.weberndorfer@id.ethz.ch with the username of the new developer.

  1. The solver does not converge for my scenario. What can I do?

Jed Brown (one of the PETSc developers) offers advice for both nonlinear systems and linear systems.

  1. How can I use distributed SuperLU with PETSc?

According to the PETSc documentation, this is possible with the flags -pc_type lu -pc_factor_mat_solver_type superlu_dist.

  1. When I submit my job on Euler via bsub, the error message is “Permission denied”. How can I fix this?

Very often, the reason for this error is that the file that bsub tries to execute is not executable (e.g. a text file). In this case Linux refuses to execute the file. You can confirm that this is the issue by attempting to execute the file on the login node (i.e. without bsub); this should yield the same error. Frequently, the problem is that a different executable was intended to be used. Otherwise it is possible to mark a file as executable via chmod +x followed by the path to the file.

  1. Docker Desktop fails to start on Windows.

To use Docker Desktop on Windows, make sure to install Ubuntu 22.04 from the Microsoft store, and activate “Use the WSL 2 based engine” in the Docker settings (“General”).