Question: What does "ERROR, exit code 255 with a return code from pthread_create() is 11" mean?
Answer: Sometimes Cell Ranger will fail with the error:
ERROR; return code from pthread_create() is 11 Error detail: Resource temporarily unavailable
The type of failure is generally not reproducible in the sense that it does not tend to occur in the same stage or job chunk. This typically indicates that during the run you reached your system user limit for the set number of "max user processes".
The recommendation in this case is to increase your user limit setting for "max user processes" (
ulimit -u). Changing ulimits is tricky if not done the right way. However using your sitecheck file you can help to assess if or not there is a need. Alternatively you can throttle the resources requested by Cell Ranger via
--localcores (minimum is 8 cores) and
--localmem (minimum is 64) before starting a new pipestance run.
For more information, please see the "Resource Limits" section of the Cell Ranger systems requirements page.
Last updated: Sep 2023