MPI_init Breaks When Using Gmsh_jll On Some Architectures

Apr 25, 2025 by ADMIN 58 views

Introduction

The GridapGmsh.jl package is a popular Julia library for mesh generation and finite element methods. However, when using the gmsh_jll package, which is built using BinaryBuilder, some users have reported issues with MPI initialization on certain architectures. In this article, we will delve into the details of this issue and explore possible solutions.

Background

The gmsh_jll package is a Julia wrapper for the Gmsh mesh generator. It is built using BinaryBuilder, which allows for easy installation and management of binary dependencies. However, when using this package with MPI, some users have reported issues with MPI initialization on certain architectures.

Symptoms

The symptoms of this issue are as follows:

When running a Julia script that uses MPI and the gmsh_jll package, the script will fail with an error message indicating that MPI initialization has failed.
The error message will typically include a stack trace indicating that the failure occurred during the opal_init or orte_init phase of MPI initialization.
The issue is specific to certain architectures, such as Ubuntu 22.04.1 and Ubuntu 20.04.1, but not others, such as Gadi.

Investigation

To investigate this issue, we will need to gather more information about the environment and configuration of the system where the issue is occurring. This may include:

The version of Julia and the gmsh_jll package being used.
The architecture and operating system of the system where the issue is occurring.
The configuration and environment variables that are being used to run the Julia script.

Possible Causes

Based on the symptoms and investigation, there are several possible causes of this issue:

Incompatible library versions: The gmsh_jll package may be using an incompatible version of the Gmsh library, which is causing the issue with MPI initialization.
Configuration issues: There may be issues with the configuration of the system or the Julia environment that are causing the problem.
Environment variables: There may be issues with the environment variables that are being used to run the Julia script, such as the LD_LIBRARY_PATH or PATH variables.

Solutions

Based on the possible causes, there are several solutions that can be tried to resolve this issue:

Update the gmsh_jll package: Try updating the gmsh_jll package to the latest version to see if the issue is resolved.
Check the configuration: Check the configuration of the system and the Julia environment to ensure that everything is set up correctly.
Modify environment variables: Try modifying the environment variables that are being used to run the Julia script to see if the issue is resolved.

Example Code

Here is an example code snippet that demonstrates how to use the gmsh_jll package with MPI:

using PartitionedArrays
using GridapGmsh

np = 1
with_mpi() do distribute
    ranks = distribute(LinearIndices((np,)))
    map(ranks) do rank
        println("I am proc $rank of $np")
    end
end

This snippet uses the with_mpi function to initialize MPI and then distributes the work across the available processes using the distribute function.

Conclusion

In conclusion, the issue of MPI initialization failing when using the gmsh_jll package on certain architectures is a complex problem that requires a thorough investigation and analysis. By gathering more information about the environment and configuration of the system where the issue is occurring, and by trying different solutions, such as updating the gmsh_jll package or modifying environment variables, it may be possible to resolve this issue and get the code running correctly.

Troubleshooting Tips

Here are some additional troubleshooting tips that may be helpful when trying to resolve this issue:

Check the Julia version: Make sure that the Julia version being used is up-to-date and compatible with the gmsh_jll package.
Check the gmsh_jll package version: Make sure that the gmsh_jll package version being used is up-to-date and compatible with the Julia version.
Check the configuration: Check the configuration of the system and the Julia environment to ensure that everything is set up correctly.
Check the environment variables: Check the environment variables that are being used to run the Julia script to ensure that they are set correctly.

Q: What is the issue with MPI initialization when using the gmsh_jll package?

A: The issue is that MPI initialization fails when using the gmsh_jll package on certain architectures, such as Ubuntu 22.04.1 and Ubuntu 20.04.1, but not others, such as Gadi.

Q: What are the symptoms of this issue?

A: The symptoms of this issue are as follows:

When running a Julia script that uses MPI and the gmsh_jll package, the script will fail with an error message indicating that MPI initialization has failed.
The error message will typically include a stack trace indicating that the failure occurred during the opal_init or orte_init phase of MPI initialization.

Q: What are the possible causes of this issue?

A: Based on the symptoms and investigation, there are several possible causes of this issue:

Incompatible library versions: The gmsh_jll package may be using an incompatible version of the Gmsh library, which is causing the issue with MPI initialization.
Configuration issues: There may be issues with the configuration of the system or the Julia environment that are causing the problem.
Environment variables: There may be issues with the environment variables that are being used to run the Julia script, such as the LD_LIBRARY_PATH or PATH variables.

Q: How can I troubleshoot this issue?

A: To troubleshoot this issue, you can try the following:

Check the Julia version: Make sure that the Julia version being used is up-to-date and compatible with the gmsh_jll package.
Check the gmsh_jll package version: Make sure that the gmsh_jll package version being used is up-to-date and compatible with the Julia version.
Check the configuration: Check the configuration of the system and the Julia environment to ensure that everything is set up correctly.
Check the environment variables: Check the environment variables that are being used to run the Julia script to ensure that they are set correctly.

Q: What are some possible solutions to this issue?

A: Based on the possible causes, there are several solutions that can be tried to resolve this issue:

Update the gmsh_jll package: Try updating the gmsh_jll package to the latest version to see if the issue is resolved.
Check the configuration: Check the configuration of the system and the Julia environment to ensure that everything is set up correctly.
Modify environment variables: Try modifying the environment variables that are being used to run the Julia script to see if the issue is resolved.

Q: Can I use a different package instead of gmsh_jll?

A: Yes, you can use a different package instead of gmsh_jll. However, you will need to ensure that the new package is compatible with your Julia version and the MPI library that you are using.

Q: How can I report this issue to the Julia community?

A: If you are experiencing this issue, you can report it the Julia community by opening an issue on the Julia GitHub repository or by posting a question on the Julia forums.

Q: Are there any known workarounds for this issue?

A: Yes, there are several known workarounds for this issue. One possible workaround is to use a different version of the gmsh_jll package or to modify the environment variables that are being used to run the Julia script.

Q: Can I use a different MPI library instead of Open MPI?

A: Yes, you can use a different MPI library instead of Open MPI. However, you will need to ensure that the new MPI library is compatible with your Julia version and the gmsh_jll package.

Q: How can I get help with this issue?

A: If you are experiencing this issue, you can get help by posting a question on the Julia forums or by opening an issue on the Julia GitHub repository. You can also try searching for existing solutions to this issue on the Julia documentation or on online forums.