Hi,
I am trying to update cryosparc from v2.15.0 to V4.0.1 on single work station. However the is error message and the update is not complete.
How to fix the error and finish the update? here is the details for the error. Thank you very much!
----------------------------------------------------
cryoSPARC current version v2.15.0
No version specified - updating to latest version.
=============================
Updating to version v4.0.1.
=============================
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 --:--:-- 0:00:02 --:--:-- 0
100 792M 100 792M 0 0 12.0M 0 0:01:05 0:01:05 --:--:-- 6594k
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 1831M 100 1831M 0 0 14.1M 0 0:02:09 0:02:09 --:--:-- 11.5M
Done.
Update will now be applied to the master installation,
followed by worker installations on other nodes.
Deleting old files...
Extracting...
Done.
Updating dependencies...
===================================================
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=/usr/local/cryosparc/cryosparc2_master/deps/anaconda
Unpacking payload ...
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /usr/local/cryosparc/cryosparc2_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 changed - reinstalling...
------------------------------------------------------------------------
mongodb 3.6.23 installation successful.
------------------------------------------------------------------------
Completed.
Completed dependency check.
Generating '/usr/local/cryosparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/libtiff/tiff_h_4_4_0.py' from '/usr/local/cryosparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/lib/../include/tiff.h'
===================================================
Successfully updated master to version v4.0.1.
===================================================
Starting cryoSPARC System master process..
CryoSPARC is not already running.
configuring database
Traceback (most recent call last):
File "/usr/local/cryosparc/cryosparc2_master/cryosparc_compute/database_management.py", line 41, in configure_mongo
initializeReplicaSet()
File "/usr/local/cryosparc/cryosparc2_master/cryosparc_compute/database_management.py", line 82, in initializeReplicaSet
admin_db.command(({'serverStatus': 1}))
File "/usr/local/cryosparc/cryosparc2_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 "/usr/local/cryosparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/contextlib.py", line 112, in __enter__
return next(self.gen)
File "/usr/local/cryosparc/cryosparc2_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 "/usr/local/cryosparc/cryosparc2_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 "/usr/local/cryosparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/site-packages/pymongo/topology.py", line 246, in select_server
address))
File "/usr/local/cryosparc/cryosparc2_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 "/usr/local/cryosparc/cryosparc2_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: [Errno 111] Connection refused, Timeout: 20.0s, Topology Description: <TopologyDescription id: 6346944a79322821597f9e45, topology_type: Single, servers: [<ServerDescription ('localhost', 39001) server_type: Unknown, rtt: None, error=AutoReconnect('localhost:39001: [Errno 111] Connection refused')>]>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/usr/local/cryosparc/cryosparc2_master/cryosparc_compute/database_management.py", line 68, in configure_mongo
mongod.wait(5)
File "/usr/local/cryosparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/subprocess.py", line 1019, in wait
return self._wait(timeout=timeout)
File "/usr/local/cryosparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/subprocess.py", line 1645, in _wait
raise TimeoutExpired(self.args, timeout)
subprocess.TimeoutExpired: Command '['mongod', '--dbpath', '/usr/local/cryosparc/cryosparc2_database', '--port', '39001', '--oplogSize', '64', '--replSet', 'meteor', '--nojournal']' timed out after 5 seconds