Problems updating from 3.0 to 3.2

Troubleshooting
1

I am unable to complete the update to v3.2.
I ran cryosparcm update --version=v3.2.0
which exited saying that the update process completed for both master and worker. However when I try cryosparcm start I get:

`Warning: conda environment not found; this indicates that a cryoSPARC installation is either incomplete or in progress
Starting cryoSPARC System master process…
Fatal Python error: _PyMainInterpreterConfig_Read: memory allocation failed
ValueError: character U+6900632d is not in range [U+0000; U+10ffff]

Current thread 0x00002b417cebeb80 (most recent call first):
`

I noticed there were errors in the dependency update step. I fix this I have tried cryosparcm forcedeps, which reproduces the same errors:

`Warning: conda environment not found; this indicates that a cryoSPARC installation is either incomplete or in progress
Checking dependencies…
Forcing dependencies to be reinstalled…

rm: cannot remove ‘/home/cryoem-group1/cryosparc03sa/software/cryosparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/lib/.nfs00000022887b080d0000808e’: Device or resource busy
Installing anaconda python…

ERROR: File or directory already exists: ‘/home/cryoem-group1/cryosparc03sa/software/cryosparc/cryosparc2_master/deps/anaconda’
If you want to update an existing installation, use the -u option.

Done.
anaconda python installation successful.

Extracting all conda packages…

…/home/cryoem-group1/cryosparc03sa/software/cryosparc/cryosparc2_master/deps_bundle_hashes/python/install_python.sh: line 18: /home/cryoem-group1/cryosparc03sa/software/cryosparc/cryosparc2_master/deps/anaconda/etc/profile.d/conda.sh: No such file or directory
/home/cryoem-group1/cryosparc03sa/software/cryosparc/cryosparc2_master/deps_bundle_hashes/python/install_python.sh: line 19: conda: command not found
/home/cryoem-group1/cryosparc03sa/software/cryosparc/cryosparc2_master/deps_bundle_hashes/python/install_python.sh: line 20: conda: command not found
/home/cryoem-group1/cryosparc03sa/software/cryosparc/cryosparc2_master/deps_bundle_hashes/python/install_python.sh: line 21: conda: command not found

Done.
conda packages installation successful.

Main dependency installation completed. Continuing…

Completed.
Currently checking hash for mongodb
Forcing reinstall for dependency mongodb…

mongodb 3.4.10 installation successful.

Completed.
Completed dependency check.
`
Any suggestions to fix this?

Thanks

2

I was able to fix the dependency issues by running lsof +D /[path-to-deps] which indicated some PIDs of python that were using the .nfs file.

After killing those I was able to finish the install process. However, now when I run jobs, I see this error in cryosparcm joblog:

Traceback (most recent call last): File "<string>", line 1, in <module> ModuleNotFoundError: No module named 'cryosparc_compute.run'

This may be related to my attempts at following the steps listed in this post

3

Running bin/cryosparcw update again solved all issues. It seems like restarting the physical server prior to attempting the update would have saved me a lot of headache.

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