Closed xLinkKnight closed 3 months ago
Yes- WATCHDOG is editable in config, and this is something that may need to be done for large searches. See https://github.com/Rappsilber-Laboratory/xisearch?tab=readme-ov-file#search-settings . Simply add WATCHDOG:10000 in your config file to increase the timer to 10,000 seconds. I should improve clarity on what that means.
Perfect! I missed it by only reviewing the BasicConfig file and looking for any commented out setting.
Can the hardcoded parameters dictating the thread/search closure be user editable?
Specifically in
main/java/rappsilber/applications/SimpleXiProcess.java
Code snippet:
We're running into the issue where xiSEARCH will close because the 30 min watchdog timer expires. Our search scenario consists of 200-2000 protein entries. We aren't resource limited as we've inspected our thread and RAM utilization. We're not approaching our memory limits as we've used the -Xmx flag to fully make use of system memory.
We've only noticed that the search would progress and the CPU utilization would plummet after some arbitrary time. For example, invoking a search with 128 threads out of our our 256 thread system will correctly tax the system to ~50%. After about a day, the utilization would drop to 1-5% with no indication as to what changed in the log. No threads were closed. We're using version 1.7.6.7.
We see the following:
I've attempted to play around with the BufferInput and BufferOutput parameters to help with the issue. Not sure if this was correct to do.