Open azazellochg opened 4 years ago
Thanks @azazellochg,
It seems some task have leave open a database or a concurrency error occurred... I will have a look.
When you say "1. create and launch relion cl2d on the queue, stop the protocol", you mean you are launching relion thru a queue system and after a while you stop the protocol before it's finished?
@dmaluenda yes, I launched cl2d on the queue, wait till it start the 1st step and kill it. I have no idea how this undocumented streamer works but I dont see another way to save a queue params without launching the template cl2d protocol. Runs/000477_ProtRelionExtractParticles/particles.sqlite will obviously be open since it is streaming particles.
I see. The 2dStreamer usually works with a saved protocol template instead of a just launched and aborted protocol, but the queue approach was not taken into account during that design, I guess... Your way might be good but honestly I've never thought on that before.
Regarding the sqlite, it should not be opened. The set must be opened (it has a properties field indicating this: _streamState
). However, sqlite files must be closed to be able to get access. If not, a concurrence error appear. TBH, I'm not sure that the problem is this. Could you check if exists the Runs/000477_ProtRelionExtractParticles/particles.sqlite-journal
? This would indicate it remains open.
@delarosatrevin developed this protocol, he might help us here.
To reproduce: 0) 2+ million particles extracting in steaming with relion protocol 1) create and launch relion cl2d on the queue, stop the protocol 2) created and launched 2d streamer protocol, batch size 10000
It starts, doing nothing for 20 min and then crashes with db lock