I ran into an issue while installing a cluster worker (v2.5) according to the instructions. When logged into a gpu node, (through SLURM
sinteractive), the installer was unable to download the pip package
... Retrying (Retry(total=0, connect=None, read=None, redirect=None)) after connection broken by 'NewConnectionError('<pip._vendor.requests.packages.urllib3.connection.VerifiedHTTPSConnection object at 0x7eff69c16210>: Failed to establish a new connection: [Errno 101] Network is unreachable',)': /simple/pluggy/ Could not find a version that satisfies the requirement pluggy<0.7,>=0.5 (from pytest>=2->pycuda==2018.1.1) (from versions: ) No matching distribution found for pluggy<0.7,>=0.5 (from pytest>=2->pycuda==2018.1.1)
It appears that this dependancy is not bundled with the installer, and I’m running into our cluster firewall.
Although cryosparcm does run without
pluggy, the T20S tutorial fails at the motion correction step. I was able to work around this issue by running the following from a login node, from the
eval $(./bin/cryosparcw env) pip install deps_bundle/python/python_packages/pip_packages/*.tar.gz --no-binary :all:
(at least the motion correction job appears to be running now, I see graphs of drift for each movie)