Dear cryoSPARC team,
I tried upgrading to the newest version of cryosparc on a gpu machine where former version 2.15.0 ran without issues. Below is the output of the update command. Since then, nothing seems to work, using cryosparcm always result in the error “Warning: conda environment not found; this indicates that a cryoSPARC installation is either incomplete or in progress”
Here full error :
cryosparcm update
CryoSPARC current version v2.15.0
update starting on mar. 09 févr. 2021 19:17:02 CET
No version specified - updating to latest version.
=============================
Updating to version v3.1.0.
=============================
CryoSPARC is running.
Stopping cryosparc
command_proxy: stopped
command_vis: stopped
webapp: stopped
command_core: stopped
database: stopped
Shut down
Downloading master update...
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 779M 100 779M 0 0 12.1M 0 0:01:03 0:01:03 --:--:-- 9995k
Downloading worker update...
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 2914M 100 2914M 0 0 11.2M 0 0:04:18 0:04:18 --:--:-- 13.5M
Done.
Update will now be applied to the master installation,
followed by worker installations on other nodes.
Deleting old files...
Extracting...
Done.
Updating dependencies...
Could not find conda environment: cryosparc_master_env
You can list all discoverable environments with `conda info --envs`.
Warning: Could not activate conda environment; this indicates that a cryoSPARC installation is either incomplete or in progress
===================================================
Warning: cryoSPARC v2 dependencies and cryosparc2_worker.tar.gz detected.
Performing full v3 worker update in 10 seconds (to cancel, press Ctrl + C)
...
===================================================
Installing latest master dependencies.
===================================================
Checking dependencies...
Dependencies for python have changed - reinstalling...
------------------------------------------------------------------------
Installing anaconda python...
------------------------------------------------------------------------
PREFIX=/data/4TB/cryosparc/CryoSPARC/software/cryosparc/cryosparc2_master/deps/anaconda
Unpacking payload ...
Traceback (most recent call last):
File "entry_point.py", line 59, in <module>
File "concurrent/futures/process.py", line 555, in __init__
File "concurrent/futures/process.py", line 165, in __init__
File "multiprocessing/queues.py", line 42, in __init__
File "multiprocessing/context.py", line 68, in Lock
File "multiprocessing/synchronize.py", line 162, in __init__
File "multiprocessing/synchronize.py", line 57, in __init__
PermissionError: [Errno 13] Permission denied
[890968] Failed to execute script entry_point
------------------------------------------------------------------------
Done.
anaconda python installation successful.
------------------------------------------------------------------------
Extracting all conda packages...
------------------------------------------------------------------------
........................................................................../data/4TB/cryosparc/CryoSPARC/software/cryosparc/cryosparc2_master/deps_bundle_hashes/python/install_python.sh: line 18: /data/4TB/cryosparc/CryoSPARC/software/cryosparc/cryosparc2_master/deps/anaconda/etc/profile.d/conda.sh: No such file or directory
/data/4TB/cryosparc/CryoSPARC/software/cryosparc/cryosparc2_master/deps_bundle_hashes/python/install_python.sh: line 19: conda: command not found
/data/4TB/cryosparc/CryoSPARC/software/cryosparc/cryosparc2_master/deps_bundle_hashes/python/install_python.sh: line 20: conda: command not found
/data/4TB/cryosparc/CryoSPARC/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
Dependencies for mongodb have changed - reinstalling...
------------------------------------------------------------------------
mongodb 3.4.10 installation successful.
------------------------------------------------------------------------
Completed.
Completed dependency check.
Warning: conda environment not found; this indicates that a cryoSPARC installation is either incomplete or in progress
===================================================
Successfully updated master to version v3.1.0.
===================================================
Warning: conda environment not found; this indicates that a cryoSPARC installation is either incomplete or in progress
Starting cryoSPARC System master process..
/data/4TB/cryosparc/CryoSPARC/software/cryosparc/cryosparc2_master/bin/cryosparcm: line 662: supervisorctl: command not found
CryoSPARC is already running.
If you would like to restart, use cryosparcm restart
Warning: conda environment not found; this indicates that a cryoSPARC installation is either incomplete or in progress
/data/4TB/cryosparc/CryoSPARC/software/cryosparc/cryosparc2_master/bin/cryosparcm: line 153: supervisorctl: command not found
CryoSPARC is running.
Stopping cryoSPARC
/data/4TB/cryosparc/CryoSPARC/software/cryosparc/cryosparc2_master/bin/cryosparcm: line 786: supervisorctl: command not found
Thanks in advance for help
Ambroise