2
$\begingroup$

Using the sample data in the 2,700 PBMC clustering tutorial, the session crashes at the ScaleData() step. The progress bar remains at 0% and hangs, followed by an R crash. I've tried reducing the size for number of genes to scale at in a single computation with the argument block.size with no change. The Seurat S4 object is only ~70mb so I can't imagine I'm exceeding the RStudio Cloud 1gb RAM limitations.

If you'd like to check out the cloud instance I can add you to the workspace temporarily. There is a limit on members allowed in a workspace.

I've been trying to run this tutorial on another remote cluster in RStudio inside of a container (Singularity here vs. Docker in RStudio Cloud) and am hitting the same snag.

I get receive no errors from RStudio Cloud, but in the other evirnment I get this error:

ERROR session hadabend; LOGGED FROM: rstudio::core::Error {anonymous}::rInit(const rstudio::r::session::RInitInfo&) /home/ubuntu/rstudio/src/cpp/session/SessionMain.cpp:563.

On this issue thread someone mentions it they receive this error message when hitting their RAM limits.

The source for ScaleData() can be found in the Github repo.

$\endgroup$
  • 1
    $\begingroup$ Are you following the tutorial exactly? I don't see ScaleData in the tutorial. $\endgroup$ – Devon Ryan Nov 12 '18 at 14:49
  • 1
    $\begingroup$ RegressOut() is a deprecated function, regression now happens in the data scaling step. vars.to.regress is now passed as an argument to ScaleData(). Somehow you've got an old version of the tutorial, see this tutorial compiled 22 March, 2018. $\endgroup$ – Kohl Kinning Nov 12 '18 at 16:05
2
$\begingroup$

It seems RStudio server doesn't know it's limitations. Currently, Projects are limited to 1GB of RAM. Using the R package ulimit which mirrors the function of ulimit and allows implementation of memory limits in linux I was able to set my own limitations within the R session. After setting the limit to 1GB I see the ulimit limitation being tripped when invoking ScaleData(). Looks like a case of exceeding available system resources.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.