Handling the `pthread_create()` Error in R

Problem

Recently, while working on normalizing an RGSet object using the preprocessQuantile function in R, I encountered the following error:

mSetSq <- preprocessQuantile(rgSet)
Error in normalize.quantiles(mat[Index2, ]) : 
  ERROR; return code from pthread_create() is 22

This error indicates a problem with creating a new thread during the normalization process, specifically related to the pthread_create() function. The error code 22 corresponds to an invalid argument passed to pthread_create.

Possible Causes

This error can occur due to several reasons:

1. Resource Limits:
   • Thread Limits: The system may have hit its limit on the number of allowable threads. If the number of threads exceeds what’s allowed by the operating system, new threads cannot be created.
   • Stack Size: If the stack size for threads is too small, pthread_create might fail to create new threads.
2. Memory Constraints:
   • When working with large datasets, you might run out of memory, leading to issues with thread creation. This is especially common in high-performance computing tasks that involve large matrices or high parallelism.
3. Excessive Parallelism:
   • The underlying R package might attempt to create too many threads simultaneously, overwhelming the system’s resources, particularly on machines with many cores.
4. Threading Library Issues:
   • There could be compatibility or configuration issues with the threading libraries used by R, particularly in non-standard environments or containers.
5. Package-Specific Bugs:
   • The preprocessCore package, or any dependent package, might have bugs or incompatibilities when threading is enabled, leading to this issue.

Solution Using renv

To address this issue, we can disable threading in the preprocessCore package, which is responsible for the normalize.quantiles function. Disabling threading will force the package to run in single-threaded mode, which can avoid the pthread_create() errors.

Here’s how you can solve the issue using renv, a dependency management tool for R:

# Step 1: Set the configuration arguments to disable threading for preprocessCore
configure.args <- c(preprocessCore = "--disable-threading")
options(configure.args = configure.args)

# Step 2: Reinstall the preprocessCore package from source with threading disabled
renv::install("bioc::preprocessCore", rebuild = TRUE, force = TRUE, update = TRUE, type = "source")

# Step 3: Restart R to apply the changes

Explanation

• configure.args = c(preprocessCore = "--disable-threading"): This line sets the configuration argument to disable threading specifically for the preprocessCore package. This tells the package to avoid creating multiple threads, which is the root cause of the error.

• renv::install(...): This command reinstalls the preprocessCore package from source with the new configuration, ensuring that threading is disabled.

• Restart R: After reinstalling the package, you need to restart your R session for the changes to take effect.

Conclusion

This solution effectively resolves the pthread_create() error by limiting the package to single-threaded operations. While this may reduce the performance slightly in multi-core environments, it ensures stability and avoids the threading issues that lead to the error.

By following the steps outlined above, you can continue with your analysis without interruptions from this threading issue.

Remember, when dealing with parallel processing and threading in R, it’s crucial to balance performance with system limitations to avoid such errors.