I installed the latest patch on an AWS pcluster installation so I could import an existing project, using the following:
cryosparcm patch --download
cryosparcm patch --install
mv cryosparc_master/cryosparc_worker_patch.tar.gz cryosparc_worker/
However, my project tree view is now completely broken with all the links wiped out. How do I restore the tree view? Restart and reboot failed to fix.
Does this mean you see all the job cards, but they’re not connected to each other?
Can you try connecting an existing job to a new job and see what happens?
Also, are you able to send us screenshots of what you’re seeing?
Correct, I see all the jobs but the connections are gone. I tried connecting a new job and the link to the old one looks fine. I refreshed the tree-view page and it shows the single new link. All other jobs appear at the top in order of creation, unlinked.
I didn’t take a screenshot, sorry. Since I was completely stuck I continued to look for solutions. In the end I tore down the cluster and EC2 instance and recreated it with our AWS deploy script, re-imported from S3 via FSxL and the tree view was restored.
I am still unable to continue work on the restored project.
Failures depend on the jobs type: 2D class selection and sharpening work fine. Ab-initio stalls at “Loading a ParticleStack with x items…” I get no error from the GUI, can’t see anything in the job logs and nothing in the /var/log either, squeue and scontrol say the job is running. But the job just sits there.
To rule out RAM issues, I tested loading small subsets of particles. Still ab-initio gets stuck at "Loading a ParticleStack…”.
I’ve now installed 3.3.1 from scratch, no patching. Project now imports great. Still can’t continue processing. Ab-initio stalls at "Loading a ParticleStack…”.
I cloned an Ab initio job that previously completed and tried running it, using the same GPU lane. The cloned job stalls at "Loading a ParticleStack…”.
Grateful for any suggestions as I am again completely stuck.
@iphan Please can you provide the stdout for this job (see
cryosparcm joblog ...), after obfuscating any confidential information.