Vruiz
December 12, 2022, 11:16pm
#1
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?
rbs_sci
December 13, 2022, 12:39am
#2
Does the same error happen if updating to 4.0.3?
Same problem for us on one workstation.
Vruiz
December 13, 2022, 4:56pm
#4
Hi,
I have the same error when downgrading to 4.0.3:
(base) [victor@c105627 ~]$ cryosparcm update --version=v4.0.3
CryoSPARC current version v4.1.0
update starting on Tue Dec 13 11:49:47 EST 2022
=============================
Updating to version v4.0.3.
=============================
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 792M 100 792M 0 0 21.9M 0 0:00:36 0:00:36 --:--:-- 46.2M
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 1831M 100 1831M 0 0 45.9M 0 0:00:39 0:00:39 --:--:-- 51.7M
Done.
Update will now be applied to the master installation,
followed by worker installations on other nodes.
CryoSPARC is running.
Stopping cryoSPARC
Shut down
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): ...working... done
Solving environment: ...working... 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: ...working... done
Executing transaction: ...working... 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 v4.0.3.
===================================================
Starting cryoSPARC System master process..
CryoSPARC is not already running.
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 82, 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: 6398ada174bf15b4cdac4738, topology_type: Single, servers: [<ServerDescription ('localhost', 39001) server_type: Unknown, rtt: None, error=NetworkTimeout('localhost:39001: timed out')>]>
configuring database
rbs_sci
December 14, 2022, 6:54am
#5
Can you exit the conda environment you’re in before running any cryoSPARC commands? Since cryoSPARC has its own conda environment, everything might be getting confused.
1 Like
Vruiz
December 14, 2022, 4:35pm
#6
I deactivate the conda environment by: conda deactivate then try to force update to 4.0.4:
[victor@c105627 ~]$ cryosparcm update --version=v4.0.4
CryoSPARC current version v4.1.0
update starting on Wed Dec 14 11:27:28 EST 2022
=============================
Updating to version v4.0.4.
=============================
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 731M 100 731M 0 0 34.9M 0 0:00:20 0:00:20 --:--:-- 29.5M
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 18.3M 0 0:01:39 0:01:39 --:--:-- 27.7M
Done.
Update will now be applied to the master installation,
followed by worker installations on other nodes.
CryoSPARC is not already running.
If you would like to restart, use cryosparcm restart
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): ...working... done
Solving environment: ...working... 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: ...working... done
Executing transaction: ...working... 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 v4.0.4.
===================================================
Starting cryoSPARC System master process..
CryoSPARC is not already running.
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 82, 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: 6399fa0f9235511f155d943b, topology_type: Single, servers: [<ServerDescription ('localhost', 39001) server_type: Unknown, rtt: None, error=NetworkTimeout('localhost:39001: timed out')>]>
configuring database
rbs_sci
December 15, 2022, 12:44am
#7
Since localhost:39001 is timing out, check your firewall settings?
wtempel
December 15, 2022, 2:21pm
#8
Please can you check for any “zombie” CryoSPARC-related process(es):
cryosparcm stopps xww | grep -e mongod -e cryosparc
Did you find any?cryosparcm log database
Vruiz
December 15, 2022, 5:02pm
#9
After stopping cryosparc I check for zombie processes:
[victor@c105627 ~]$ ps xww | grep -e mongod -e cryosparc
35990 pts/0 S+ 0:00 grep --color=auto -e mongod -e cryosparc
log database:
[victor@c105627 ~]$ cryosparcm log database
n: "3.11.0" }, os: { type: "Linux", name: "Linux", architecture: "x86_64", version: "3.10.0-1160.24.1.el7.x86_64" }, platform: "CPython 3.7.8.final.0" }
2022-12-13T15:14:28.406-0500 I NETWORK [listener] connection accepted from 129.112.162.193:52142 #23 (17 connections now open)
2022-12-13T15:14:30.883-0500 I NETWORK [listener] connection accepted from 129.112.162.193:52156 #24 (18 connections now open)
2022-12-13T15:14:30.884-0500 I NETWORK [conn24] received client metadata from 129.112.162.193:52156 conn24: { driver: { name: "nodejs", version: "3.3.5" }, os: { type: "Linux", name: "linux", architecture: "x64", version: "3.10.0-1160.24.1.el7.x86_64" }, platform: "Node.js v8.9.4, LE" }
2022-12-13T15:14:30.929-0500 I NETWORK [listener] connection accepted from 129.112.162.193:52158 #25 (19 connections now open)
2022-12-13T15:14:30.930-0500 I NETWORK [conn25] received client metadata from 129.112.162.193:52158 conn25: { driver: { name: "nodejs", version: "3.3.5" }, os: { type: "Linux", name: "linux", architecture: "x64", version: "3.10.0-1160.24.1.el7.x86_64" }, platform: "Node.js v8.9.4, LE" }
2022-12-13T15:14:30.950-0500 I NETWORK [listener] connection accepted from 129.112.162.193:52160 #26 (20 connections now open)
2022-12-13T15:14:30.953-0500 I NETWORK [conn26] received client metadata from 129.112.162.193:52160 conn26: { driver: { name: "nodejs", version: "3.3.5" }, os: { type: "Linux", name: "linux", architecture: "x64", version: "3.10.0-1160.24.1.el7.x86_64" }, platform: "Node.js v8.9.4, LE" }
2022-12-13T15:14:30.957-0500 I NETWORK [listener] connection accepted from 129.112.162.193:52162 #27 (21 connections now open)
2022-12-13T15:14:30.958-0500 I NETWORK [conn27] received client metadata from 129.112.162.193:52162 conn27: { driver: { name: "nodejs", version: "3.3.5" }, os: { type: "Linux", name: "linux", architecture: "x64", version: "3.10.0-1160.24.1.el7.x86_64" }, platform: "Node.js v8.9.4, LE" }
2022-12-13T15:14:40.684-0500 I NETWORK [listener] connection accepted from 129.112.162.193:52168 #28 (22 connections now open)
2022-12-13T15:14:40.687-0500 I NETWORK [listener] connection accepted from 129.112.162.193:52170 #29 (23 connections now open)
2022-12-13T15:14:40.689-0500 I NETWORK [listener] connection accepted from 129.112.162.193:52172 #30 (24 connections now open)
2022-12-13T15:15:35.332-0500 I CONTROL [signalProcessingThread] got signal 15 (Terminated), will terminate after current cmd ends
2022-12-13T15:15:35.332-0500 I NETWORK [signalProcessingThread] shutdown: going to close listening sockets...
2022-12-13T15:15:35.332-0500 I NETWORK [signalProcessingThread] removing socket file: /tmp/mongodb-39001.sock
2022-12-13T15:15:35.333-0500 I REPL [signalProcessingThread] shutting down replication subsystems
2022-12-13T15:15:35.333-0500 I REPL [signalProcessingThread] Stopping replication reporter thread
2022-12-13T15:15:35.333-0500 I REPL [signalProcessingThread] Stopping replication fetcher thread
2022-12-13T15:15:35.333-0500 I REPL [signalProcessingThread] Stopping replication applier thread
2022-12-13T15:15:35.352-0500 I NETWORK [conn16] end connection 129.112.162.193:52110 (23 connections now open)
2022-12-13T15:15:35.352-0500 I NETWORK [conn18] end connection 129.112.162.193:52114 (22 connections now open)
2022-12-13T15:15:35.352-0500 I NETWORK [conn19] end connection 129.112.162.193:52116 (21 connections now open)
2022-12-13T15:15:35.352-0500 I NETWORK [conn20] end connection 129.112.162.193:52118 (20 connections now open)
2022-12-13T15:15:35.352-0500 I NETWORK [conn12] end connection 129.112.162.193:52102 (19 connections now open)
2022-12-13T15:15:35.352-0500 I NETWORK [conn28] end connection 129.112.162.193:52168 (17 connections now open)
2022-12-13T15:15:35.352-0500 I NETWORK [conn23] end connection 129.112.162.193:52142 (15 connections now open)
2022-12-13T15:15:35.352-0500 I NETWORK [conn15] end connection 129.112.162.193:52108 (18 connections now open)
2022-12-13T15:15:35.353-0500 I NETWORK [conn27] end connection 129.112.162.193:52162 (10 connections now open)
2022-12-13T15:15:35.352-0500 I NETWORK [conn24] end connection 129.112.162.193:52156 (13 connections now open)
2022-12-13T15:15:35.352-0500 I NETWORK [conn30] end connection 129.112.162.193:52172 (14 connections now open)
2022-12-13T15:15:35.353-0500 I NETWORK [conn25] end connection 129.112.162.193:52158 (12 connections now open)
2022-12-13T15:15:35.353-0500 I NETWORK [conn26] end connection 129.112.162.193:52160 (11 connections now open)
2022-12-13T15:15:35.352-0500 I NETWORK [conn14] end connection 129.112.162.193:52106 (16 connections now open)
2022-12-13T15:15:35.353-0500 I NETWORK [conn29] end connection 129.112.162.193:52170 (9 connections now open)
2022-12-13T15:15:35.386-0500 I NETWORK [conn7] end connection 129.112.162.193:52052 (8 connections now open)
2022-12-13T15:15:35.386-0500 I NETWORK [conn9] end connection 129.112.162.193:52056 (7 connections now open)
2022-12-13T15:15:35.386-0500 I NETWORK [conn8] end connection 129.112.162.193:52054 (6 connections now open)
2022-12-13T15:15:35.394-0500 I NETWORK [conn10] end connection 129.112.162.193:52066 (5 connections now open)
2022-12-13T15:15:35.394-0500 I NETWORK [conn21] end connection 129.112.162.193:52128 (4 connections now open)
2022-12-13T15:15:35.394-0500 I NETWORK [conn22] end connection 129.112.162.193:52130 (3 connections now open)
2022-12-13T15:15:35.397-0500 I NETWORK [conn11] end connection 129.112.162.193:52100 (2 connections now open)
2022-12-13T15:15:35.414-0500 I REPL [signalProcessingThread] Stopping replication storage threads
2022-12-13T15:15:35.415-0500 I FTDC [signalProcessingThread] Shutting down full-time diagnostic data capture
2022-12-13T15:15:35.428-0500 I STORAGE [WTOplogJournalThread] oplog journal thread loop shutting down
2022-12-13T15:15:35.428-0500 I STORAGE [signalProcessingThread] WiredTigerKVEngine shutting down
2022-12-13T15:15:35.441-0500 I STORAGE [signalProcessingThread] shutdown: removing fs lock...
2022-12-13T15:15:35.442-0500 I CONTROL [signalProcessingThread] now exiting
2022-12-13T15:15:35.442-0500 I CONTROL [signalProcessingThread] shutting down with code:0
Waiting for data... (interrupt to abort)
Since proxy has been always a problem setting up our gpu under the institutional network, should I setup proxy settings again for CS v4? I have no problems downgrading to v3.4?
wtempel
December 15, 2022, 5:21pm
#10
Please can you describe your current proxy settings?
Vruiz
December 17, 2022, 12:47am
#11
My proxy settings on ~/bash_profile are:
#load proxy environments
export HTTP_PROXY="http://proxy.swmed.edu:3128"
export HTTPS_PROXY="http://proxy.swmed.edu:3128"
export ftp_proxy="proxy.swmed.edu:3128"
wtempel
December 17, 2022, 11:37pm
#12
Do you really mean ~/bash_profile or ~/.bash_profile?
wtempel
December 17, 2022, 11:44pm
#13
@Vruiz @rfronzes Please can you post the output of the commandenv | grep -i http
Vruiz
December 19, 2022, 5:52pm
#14
Sorry, I meant:
~/.bash_profile
The output of env | grep -i http is:
[victor@c105627 ~]$ env | grep -i http
HTTPS_PROXY=http://proxy.swmed.edu:3128
HTTP_PROXY=http://proxy.swmed.edu:3128
victor is the account that runs cryosparc
wtempel
December 19, 2022, 7:38pm
#15
@Vruiz Please can you confirm that
these settings were already in place when CryoSPARC v3.4.0 was running
CryoSPARC v3.4.0 functioned properly with these proxy variables defined
CryoSPARC v < 4 did not function without these proxy variables defined
wtempel
December 21, 2022, 9:26pm
#17
If CryoSPARC failed to start with a pymongo error after an update to CryoSPARC v4.1.0 or v4.1.1, you may try the following:
ensure that cryosparc_master software is at either v4.1.0 or v4.1.1
download cryosparc_master_patch.tar.gz
confirm file integrity. Output ofmd5sum cryosparc_master_patch.tar.gz8df9953103829632756b809f3c637d2f
cryosparcm stopconfirm no more CryoSPARC processes:ps xww | grep -e cryosparc -e mongod
kill, but not kill -9, any CryoSPARC-related processes that may still exist
# substitute correct paths
mv cryosparc_master_patch.tar.gz /path/to/cryosparc_master
cd /path/to/cryosparc_master
tar -xzf cryosparc_master_patch.tar.gz --overwrite --strip-components=1 --directory ./
if cryosparcm start
update worker(s)# substitute correct paths
cp /path/to/cryosparc_master/cryosparc_worker.tar.gz /path/to/cryosparc_worker/
cd /path/to/cryosparc_worker/
./bin/cryosparcw update