Hi,
I upgraded CS from 3.3.4 to v4.1.0 and I got this error:
(base) [victor@c105627 ~]$ cryosparcm update --version=v4.1.0
CryoSPARC current version v3.4.0
update starting on Mon Dec 12 18:11:10 EST 2022
=============================
Updating to version v4.1.0.
=============================
CryoSPARC is running.
Stopping cryoSPARC
app: stopped
command_core: stopped
command_rtp: stopped
webapp: stopped
command_vis: stopped
database: stopped
Shut down
Removing previous downloads...
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 842M 100 842M 0 0 60.8M 0 0:00:13 0:00:13 --:--:-- 62.2M
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 1876M 100 1876M 0 0 60.4M 0 0:00:31 0:00:31 --:--:-- 65.7M
Done.
Update will now be applied to the master installation,
followed by worker installations on other nodes.
Deleting old files...
Extracting...
Done.
===================================================
Installing latest master dependencies.
===================================================
Checking dependencies...
Dependencies for python have changed - reinstalling...
------------------------------------------------------------------------
Installing anaconda python...
------------------------------------------------------------------------
PREFIX=/home/victor/cryosparc/cryosparc_master/deps/anaconda
Unpacking payload ...
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /home/victor/cryosparc/cryosparc_master/deps/anaconda
added / updated specs:
- _libgcc_mutex==0.1=main
- _openmp_mutex==4.5=1_gnu
- brotlipy==0.7.0=py37h27cfd23_1003
- ca-certificates==2022.3.29=h06a4308_1
- certifi==2021.10.8=py37h06a4308_2
- cffi==1.15.0=py37hd667e15_1
- charset-normalizer==2.0.4=pyhd3eb1b0_0
- colorama==0.4.4=pyhd3eb1b0_0
- conda-content-trust==0.1.1=pyhd3eb1b0_0
- conda-package-handling==1.8.1=py37h7f8727e_0
- conda==4.12.0=py37h06a4308_0
- cryptography==36.0.0=py37h9ce1e76_0
- idna==3.3=pyhd3eb1b0_0
- ld_impl_linux-64==2.35.1=h7274673_9
- libffi==3.3=he6710b0_2
- libgcc-ng==9.3.0=h5101ec6_17
- libgomp==9.3.0=h5101ec6_17
- libstdcxx-ng==9.3.0=hd4cf53a_17
- ncurses==6.3=h7f8727e_2
- openssl==1.1.1n=h7f8727e_0
- pip==21.2.2=py37h06a4308_0
- pycosat==0.6.3=py37h27cfd23_0
- pycparser==2.21=pyhd3eb1b0_0
- pyopenssl==22.0.0=pyhd3eb1b0_0
- pysocks==1.7.1=py37_1
- python==3.7.13=h12debd9_0
- readline==8.1.2=h7f8727e_1
- requests==2.27.1=pyhd3eb1b0_0
- ruamel_yaml==0.15.100=py37h27cfd23_0
- setuptools==61.2.0=py37h06a4308_0
- six==1.16.0=pyhd3eb1b0_1
- sqlite==3.38.2=hc218d9a_0
- tk==8.6.11=h1ccaba5_0
- tqdm==4.63.0=pyhd3eb1b0_0
- urllib3==1.26.8=pyhd3eb1b0_0
- wheel==0.37.1=pyhd3eb1b0_0
- xz==5.2.5=h7b6447c_0
- yaml==0.2.5=h7b6447c_0
- zlib==1.2.12=h7f8727e_1
The following NEW packages will be INSTALLED:
_libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main
_openmp_mutex pkgs/main/linux-64::_openmp_mutex-4.5-1_gnu
brotlipy pkgs/main/linux-64::brotlipy-0.7.0-py37h27cfd23_1003
ca-certificates pkgs/main/linux-64::ca-certificates-2022.3.29-h06a4308_1
certifi pkgs/main/linux-64::certifi-2021.10.8-py37h06a4308_2
cffi pkgs/main/linux-64::cffi-1.15.0-py37hd667e15_1
charset-normalizer pkgs/main/noarch::charset-normalizer-2.0.4-pyhd3eb1b0_0
colorama pkgs/main/noarch::colorama-0.4.4-pyhd3eb1b0_0
conda pkgs/main/linux-64::conda-4.12.0-py37h06a4308_0
conda-content-tru~ pkgs/main/noarch::conda-content-trust-0.1.1-pyhd3eb1b0_0
conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.8.1-py37h7f8727e_0
cryptography pkgs/main/linux-64::cryptography-36.0.0-py37h9ce1e76_0
idna pkgs/main/noarch::idna-3.3-pyhd3eb1b0_0
ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.35.1-h7274673_9
libffi pkgs/main/linux-64::libffi-3.3-he6710b0_2
libgcc-ng pkgs/main/linux-64::libgcc-ng-9.3.0-h5101ec6_17
libgomp pkgs/main/linux-64::libgomp-9.3.0-h5101ec6_17
libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-9.3.0-hd4cf53a_17
ncurses pkgs/main/linux-64::ncurses-6.3-h7f8727e_2
openssl pkgs/main/linux-64::openssl-1.1.1n-h7f8727e_0
pip pkgs/main/linux-64::pip-21.2.2-py37h06a4308_0
pycosat pkgs/main/linux-64::pycosat-0.6.3-py37h27cfd23_0
pycparser pkgs/main/noarch::pycparser-2.21-pyhd3eb1b0_0
pyopenssl pkgs/main/noarch::pyopenssl-22.0.0-pyhd3eb1b0_0
pysocks pkgs/main/linux-64::pysocks-1.7.1-py37_1
python pkgs/main/linux-64::python-3.7.13-h12debd9_0
readline pkgs/main/linux-64::readline-8.1.2-h7f8727e_1
requests pkgs/main/noarch::requests-2.27.1-pyhd3eb1b0_0
ruamel_yaml pkgs/main/linux-64::ruamel_yaml-0.15.100-py37h27cfd23_0
setuptools pkgs/main/linux-64::setuptools-61.2.0-py37h06a4308_0
six pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_1
sqlite pkgs/main/linux-64::sqlite-3.38.2-hc218d9a_0
tk pkgs/main/linux-64::tk-8.6.11-h1ccaba5_0
tqdm pkgs/main/noarch::tqdm-4.63.0-pyhd3eb1b0_0
urllib3 pkgs/main/noarch::urllib3-1.26.8-pyhd3eb1b0_0
wheel pkgs/main/noarch::wheel-0.37.1-pyhd3eb1b0_0
xz pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
yaml pkgs/main/linux-64::yaml-0.2.5-h7b6447c_0
zlib pkgs/main/linux-64::zlib-1.2.12-h7f8727e_1
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 not changed.
Completed dependency check.
Generating '/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/libtiff/tiff_h_4_4_0.py' from '/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/../include/tiff.h'
===================================================
Successfully updated master to version v4.1.0.
===================================================
Starting cryoSPARC System master process..
CryoSPARC is not already running.
configuring database
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/home/victor/cryosparc/cryosparc_master/cryosparc_compute/database_management.py", line 41, in configure_mongo
initializeReplicaSet()
File "/home/victor/cryosparc/cryosparc_master/cryosparc_compute/database_management.py", line 83, in initializeReplicaSet
admin_db.command(({'serverStatus': 1}))
File "/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/database.py", line 758, in command
read_preference, session) as (sock_info, secondary_ok):
File "/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/contextlib.py", line 112, in __enter__
return next(self.gen)
File "/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/mongo_client.py", line 1387, in _socket_for_reads
server = self._select_server(read_preference, session)
File "/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/mongo_client.py", line 1346, in _select_server
server = topology.select_server(server_selector)
File "/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/topology.py", line 246, in select_server
address))
File "/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/topology.py", line 203, in select_servers
selector, server_timeout, address)
File "/home/victor/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/topology.py", line 220, in _select_servers_loop
(self._error_message(selector), timeout, self.description))
pymongo.errors.ServerSelectionTimeoutError: localhost:39001: timed out, Timeout: 20.0s, Topology Description: <TopologyDescription id: 6397b569e1aba78fbdbbd388, topology_type: Single, servers: [<ServerDescription ('localhost', 39001) server_type: Unknown, rtt: None, error=NetworkTimeout('localhost:39001: timed out')>]>
Downgrading back to 3.4.0 bring CS back again and everything work well.
Any advice?