-
Notifications
You must be signed in to change notification settings - Fork 16
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
resume/continue job #182
Comments
Hey Xabier Firstly thank you for your interest in GraftM! The step that uses the most memory in GraftM is pplacer. The more sequences within a GraftM package, the more memory is required. In the publication for pplacer they demonstrate that the memory requirements are linear with respect to the number of taxa in the tree (Fig. 3). We're working now on estimating the memory usage you can expect for each of the 16S rRNA GraftM packages - we will get back to you on this. May I ask what specific GraftM package you were using for this run? Unfortunately there is currently no way of picking up a failed GraftM run. Hopefully in most instances the time to re-run graftM graft isn't too much. To overwrite the previous run you can use the Thanks again Xabier, you'll hear from us soon. Joel |
Hi Joe, PS: I think you have the wrong pplacer indicated in the README |
Hey Xabier, So we've traced this down to an issue in the way memory usage is reported for pplacer. In the short term a work around could be found by specifying less threads overall the get past the memory cap. In the longer term we will raise an issue with pplacer and look at implementing a separate Apologies for the delayed reply on this one, Joel |
Hi Joel, |
Hi,
I've just installed GraftM in our cluster. I got GraftM (
graft
) to run but it crashed for not allocating enough RAM.I realised that there is no indication for resuming or continuing a crashed job. I tried to run the same command but it stops to avoid overwriting in the directory. This is the message:
Is there any way to resume or at least a way to estimate the memory to be used?
Thank you in advance,
Xabier
The text was updated successfully, but these errors were encountered: