Skip to content

[WIP] Enabling a complex query retry if memory on the cluster is insufficient #46

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.

Sign up for GitHub

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

Open
mwang87 wants to merge 4 commits into
base: master
Choose a base branch
from
Open

[WIP] Enabling a complex query retry if memory on the cluster is insufficient #46

Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
99608b5
testing complex retry
mwang87 Jul 19, 2021
ab59e25
updating retry condition
mwang87 Jul 19, 2021
fa64060
adding note
mwang87 Jul 19, 2021
158f105
making the memory more complex
mwang87 Jul 19, 2021
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
11 changes: 7 additions & 4 deletions workflow/workflow.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,11 +17,14 @@ params.PYTHONRUNTIME = "python" // this is a hack because CCMS cluster does not

if(params.parallel_files == "YES"){
process queryData {
errorStrategy 'ignore'
//errorStrategy 'ignore'
time '2h'
//maxRetries 3
//memory { 6.GB * task.attempt }
memory { 8.GB }

// This enable multiple retries with increasing ram, and if this all fails, lets retire it
// https://github.com/nextflow-io/nextflow/issues/563
maxRetries 3
errorStrategy { (task.exitStatus in 137..140 && task.attempt <= maxRetries) ? 'retry' : 'ignore' }
memory { 8.GB + 12.G * task.attempt }

publishDir "$params.publishdir/msql", mode: 'copy'

Expand Down