Hi,
One system updated smoothly to 3.0 from 2.16beta, but the second (which I was updating from 2.15) failed with the attached error log. Any ideas?
Cheers
Oli
PS I tried force updating the dependencies for the worker, which seemed to work, but now when I launch a job it just hangs at launching…
CryoSPARC current version v2.15.1-live_privatebeta
update starting on Thu Dec 10 10:51:09 PST 2020
No version specified - updating to latest version.
=============================
Updating to version v3.0.0.
=============================
CryoSPARC is running.
Stopping cryosparc
command_rtp: stopped
app: stopped
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 769M 100 769M 0 0 47.4M 0 0:00:16 0:00:16 --:--:-- 49.9M
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 2903M 100 2903M 0 0 60.5M 0 0:00:47 0:00:47 --:--:-- 52.3M
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=/home/user/cryosparc2_master/deps/anaconda
Unpacking payload ...
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /home/user/cryosparc2_master/deps/anaconda
added / updated specs:
- _libgcc_mutex==0.1=main
- ca-certificates==2020.1.1=0
- certifi==2020.4.5.1=py37_0
- cffi==1.14.0=py37he30daa8_1
- chardet==3.0.4=py37_1003
- conda-package-handling==1.6.1=py37h7b6447c_0
- conda==4.8.3=py37_0
- cryptography==2.9.2=py37h1ba5d50_0
- idna==2.9=py_1
- ld_impl_linux-64==2.33.1=h53a641e_7
- libedit==3.1.20181209=hc058e9b_0
- libffi==3.3=he6710b0_1
- libgcc-ng==9.1.0=hdf63c60_0
- libstdcxx-ng==9.1.0=hdf63c60_0
- ncurses==6.2=he6710b0_1
- openssl==1.1.1g=h7b6447c_0
- pip==20.0.2=py37_3
- pycosat==0.6.3=py37h7b6447c_0
- pycparser==2.20=py_0
- pyopenssl==19.1.0=py37_0
- pysocks==1.7.1=py37_0
- python==3.7.7=hcff3b4d_5
- readline==8.0=h7b6447c_0
- requests==2.23.0=py37_0
- ruamel_yaml==0.15.87=py37h7b6447c_0
- setuptools==46.4.0=py37_0
- six==1.14.0=py37_0
- sqlite==3.31.1=h62c20be_1
- tk==8.6.8=hbc83047_0
- tqdm==4.46.0=py_0
- urllib3==1.25.8=py37_0
- wheel==0.34.2=py37_0
- xz==5.2.5=h7b6447c_0
- yaml==0.1.7=had09818_2
- zlib==1.2.11=h7b6447c_3
The following NEW packages will be INSTALLED:
_libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main
ca-certificates pkgs/main/linux-64::ca-certificates-2020.1.1-0
certifi pkgs/main/linux-64::certifi-2020.4.5.1-py37_0
cffi pkgs/main/linux-64::cffi-1.14.0-py37he30daa8_1
chardet pkgs/main/linux-64::chardet-3.0.4-py37_1003
conda pkgs/main/linux-64::conda-4.8.3-py37_0
conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.6.1-py37h7b6447c_0
cryptography pkgs/main/linux-64::cryptography-2.9.2-py37h1ba5d50_0
idna pkgs/main/noarch::idna-2.9-py_1
ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7
libedit pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0
libffi pkgs/main/linux-64::libffi-3.3-he6710b0_1
libgcc-ng pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
ncurses pkgs/main/linux-64::ncurses-6.2-he6710b0_1
openssl pkgs/main/linux-64::openssl-1.1.1g-h7b6447c_0
pip pkgs/main/linux-64::pip-20.0.2-py37_3
pycosat pkgs/main/linux-64::pycosat-0.6.3-py37h7b6447c_0
pycparser pkgs/main/noarch::pycparser-2.20-py_0
pyopenssl pkgs/main/linux-64::pyopenssl-19.1.0-py37_0
pysocks pkgs/main/linux-64::pysocks-1.7.1-py37_0
python pkgs/main/linux-64::python-3.7.7-hcff3b4d_5
readline pkgs/main/linux-64::readline-8.0-h7b6447c_0
requests pkgs/main/linux-64::requests-2.23.0-py37_0
ruamel_yaml pkgs/main/linux-64::ruamel_yaml-0.15.87-py37h7b6447c_0
setuptools pkgs/main/linux-64::setuptools-46.4.0-py37_0
six pkgs/main/linux-64::six-1.14.0-py37_0
sqlite pkgs/main/linux-64::sqlite-3.31.1-h62c20be_1
tk pkgs/main/linux-64::tk-8.6.8-hbc83047_0
tqdm pkgs/main/noarch::tqdm-4.46.0-py_0
urllib3 pkgs/main/linux-64::urllib3-1.25.8-py37_0
wheel pkgs/main/linux-64::wheel-0.34.2-py37_0
xz pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
yaml pkgs/main/linux-64::yaml-0.1.7-had09818_2
zlib pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3
Preparing transaction: done
Executing transaction: done
installation finished.
------------------------------------------------------------------------
Done.
anaconda python installation successful.
------------------------------------------------------------------------
Extracting all conda packages...
------------------------------------------------------------------------
..........................................................................
------------------------------------------------------------------------
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.
===================================================
Successfully updated master to version v3.0.0.
===================================================
Starting cryoSPARC System master process..
Traceback (most recent call last):
File "/home/user/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisorctl", line 10, in <module>
from importlib.metadata import distribution
ModuleNotFoundError: No module named 'importlib.metadata'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/user/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisorctl", line 13, in <module>
from importlib_metadata import distribution
ModuleNotFoundError: No module named 'importlib_metadata'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/user/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisorctl", line 15, in <module>
from pkg_resources import load_entry_point
File "/home/user/cryosparc2_master/deps/anaconda/lib/python3.7/site-packages/pkg_resources/__init__.py", line 3252, in <module>
@_call_aside
File "/home/user/cryosparc2_master/deps/anaconda/lib/python3.7/site-packages/pkg_resources/__init__.py", line 3236, in _call_aside
f(*args, **kwargs)
File "/home/user/cryosparc2_master/deps/anaconda/lib/python3.7/site-packages/pkg_resources/__init__.py", line 3265, in _initialize_master_working_set
working_set = WorkingSet._build_master()
File "/home/user/cryosparc2_master/deps/anaconda/lib/python3.7/site-packages/pkg_resources/__init__.py", line 584, in _build_master
ws.require(__requires__)
File "/home/user/cryosparc2_master/deps/anaconda/lib/python3.7/site-packages/pkg_resources/__init__.py", line 901, in require
needed = self.resolve(parse_requirements(requirements))
File "/home/user/cryosparc2_master/deps/anaconda/lib/python3.7/site-packages/pkg_resources/__init__.py", line 787, in resolve
raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'supervisor==4.2.1' distribution was not found and is required by the application
CryoSPARC is already running.
If you would like to restart, use cryosparcm restart
Traceback (most recent call last):
File "/home/user/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisorctl", line 10, in <module>
from importlib.metadata import distribution
ModuleNotFoundError: No module named 'importlib.metadata'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/user/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisorctl", line 13, in <module>
from importlib_metadata import distribution
ModuleNotFoundError: No module named 'importlib_metadata'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/user/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisorctl", line 15, in <module>
from pkg_resources import load_entry_point
File "/home/user/cryosparc2_master/deps/anaconda/lib/python3.7/site-packages/pkg_resources/__init__.py", line 3252, in <module>
@_call_aside
File "/home/user/cryosparc2_master/deps/anaconda/lib/python3.7/site-packages/pkg_resources/__init__.py", line 3236, in _call_aside
f(*args, **kwargs)
File "/home/user/cryosparc2_master/deps/anaconda/lib/python3.7/site-packages/pkg_resources/__init__.py", line 3265, in _initialize_master_working_set
working_set = WorkingSet._build_master()
File "/home/user/cryosparc2_master/deps/anaconda/lib/python3.7/site-packages/pkg_resources/__init__.py", line 584, in _build_master
ws.require(__requires__)
File "/home/user/cryosparc2_master/deps/anaconda/lib/python3.7/site-packages/pkg_resources/__init__.py", line 901, in require
needed = self.resolve(parse_requirements(requirements))
File "/home/user/cryosparc2_master/deps/anaconda/lib/python3.7/site-packages/pkg_resources/__init__.py", line 787, in resolve
raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'supervisor==4.2.1' distribution was not found and is required by the application
CryoSPARC is running.
Stopping cryosparc
Traceback (most recent call last):
File "/home/user/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisorctl", line 10, in <module>
from importlib.metadata import distribution
ModuleNotFoundError: No module named 'importlib.metadata'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/user/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisorctl", line 13, in <module>
from importlib_metadata import distribution
ModuleNotFoundError: No module named 'importlib_metadata'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/user/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisorctl", line 15, in <module>
from pkg_resources import load_entry_point
File "/home/user/cryosparc2_master/deps/anaconda/lib/python3.7/site-packages/pkg_resources/__init__.py", line 3252, in <module>
@_call_aside
File "/home/user/cryosparc2_master/deps/anaconda/lib/python3.7/site-packages/pkg_resources/__init__.py", line 3236, in _call_aside
f(*args, **kwargs)
File "/home/user/cryosparc2_master/deps/anaconda/lib/python3.7/site-packages/pkg_resources/__init__.py", line 3265, in _initialize_master_working_set
working_set = WorkingSet._build_master()
File "/home/user/cryosparc2_master/deps/anaconda/lib/python3.7/site-packages/pkg_resources/__init__.py", line 584, in _build_master
ws.require(__requires__)
File "/home/user/cryosparc2_master/deps/anaconda/lib/python3.7/site-packages/pkg_resources/__init__.py", line 901, in require
needed = self.resolve(parse_requirements(requirements))
File "/home/user/cryosparc2_master/deps/anaconda/lib/python3.7/site-packages/pkg_resources/__init__.py", line 787, in resolve
raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'supervisor==4.2.1' distribution was not found and is required by the application```