In order to attempt to fix the “I/O error when starting job” problem we were seeing in 2.12.4 I tried to update Cryosparc.
We have a failure updating the working, and I’m unclear on where the tar.gz download is, though I should be able to download install/configure it separately.
The good news is that I think the update to the master fixed the issue we were hoping to fix.
cryosparc_user@shiva:~$ cryosparcm status
----------------------------------------------------------------------------
CryoSPARC System master node installed at
/install/cryosparc_user/software/cryosparc/cryosparc2_master
Current cryoSPARC version: v2.12.4
----------------------------------------------------------------------------
cryosparcm process status:
app STOPPED Not started
app_dev STOPPED Not started
command_core RUNNING pid 1795, uptime 0:22:19
command_proxy RUNNING pid 1822, uptime 0:22:16
command_rtp STOPPED Not started
command_vis STARTING
database RUNNING pid 1719, uptime 0:22:21
watchdog_dev STOPPED Not started
webapp RUNNING pid 1826, uptime 0:22:14
webapp_dev STOPPED Not started
----------------------------------------------------------------------------
global config variables:
export CRYOSPARC_MASTER_HOSTNAME="shiva.wadsworth.org"
export CRYOSPARC_DB_PATH="/data"
export CRYOSPARC_BASE_PORT=39000
export CRYOSPARC_DEVELOP=false
export CRYOSPARC_INSECURE=false
cryosparc_user@shiva:~$ cryosparcm ?
Unknown command ?
cryosparc_user@shiva:~$ cryosparcm upgrade
Unknown command upgrade
cryosparc_user@shiva:~$ cryosparcm update
CryoSPARC current version v2.12.4
update starting on Mon Feb 24 11:40:42 EST 2020
No version specified - updating to latest version.
=============================
Updating to version v2.14.2.
=============================
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 555M 100 555M 0 0 14.8M 0 0:00:37 0:00:37 --:--:-- 26.2M
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 624M 100 624M 0 0 21.3M 0 0:00:29 0:00:29 --:--:-- 16.4M
Done.
Update will now be applied to the master installation,
followed by worker installations on other node.
Deleting old files...
Extracting...
Done.
Updating dependencies...
Checking dependencies...
Dependencies for python have not changed.
Currently checking hash for mongodb
Dependencies for mongodb have not changed.
Completed dependency check.
===================================================
Successfully updated master from version v2.12.4 to version v2.14.2.
===================================================
Starting cryoSPARC System master process..
CryoSPARC is not already running.
database: started
command_core: started
cryosparc command core startup complete.
command_vis: started
command_proxy: started
webapp: started
-----------------------------------------------------
CryoSPARC master started.
From this machine, access cryoSPARC at
http://localhost:39000
From other machines on the network, access cryoSPARC at
http://shiva.wadsworth.org:39000
Startup can take several minutes. Point your browser to the address
and refresh until you see the cryoSPARC web interface.
CryoSPARC is running.
Stopping cryosparc.
command_proxy: stopped
command_vis: stopped
webapp: stopped
command_core: stopped
database: stopped
Shut down
Starting cryoSPARC System master process..
CryoSPARC is not already running.
database: started
command_core: started
cryosparc command core startup complete.
command_vis: started
command_proxy: started
webapp: started
-----------------------------------------------------
CryoSPARC master started.
From this machine, access cryoSPARC at
http://localhost:39000
From other machines on the network, access cryoSPARC at
http://shiva.wadsworth.org:39000
Startup can take several minutes. Point your browser to the address
and refresh until you see the cryoSPARC web interface.
===================================================
Now updating worker nodes.
All workers:
shiva.wadsworth.org cryosparc_user@shiva.wadsworth.org
-------------------------------------------------
Updating worker shiva.wadsworth.org
Direct update
\cp -f ./cryosparc2_worker.tar.gz /home/cryosparc_user/software/cryosparc/cryosparc2_worker
cp: cannot create regular file '/home/cryosparc_user/software/cryosparc/cryosparc2_worker': No such file or directory
Failed to update shiva.wadsworth.org! Skipping...
-------------------------------------------------
---------------------------------------------------
Done updating all worker nodes.
If any nodes failed to update, you can manually update them.
Cluster worker installations must be manually updated.
To update manually, simply copy the cryosparc2_worker.tar.gz
file into the cryosparc worker installation directory, and then run
$ bin/cryosparcw update
from inside the worker installation directory.
cryosparc_user@shiva:~$ pwd
/install/cryosparc_user
cryosparc_user@shiva:~$ cd sof*
cryosparc_user@shiva:~/software$ ls
cryosparc
cryosparc_user@shiva:~/software$ cd cryo*
cryosparc_user@shiva:~/software/cryosparc$ ls -l
total 1206688
drwxrwxr-x 11 cryosparc_user syslog 4096 Feb 24 11:41 cryosparc2_master
-rw-r--r-- 1 cryosparc_user syslog 581659450 Jan 22 16:47 cryosparc2_master.tar.gz
drwxrwxr-x 8 cryosparc_user syslog 4096 Feb 21 10:36 cryosparc2_worker
-rw-r--r-- 1 cryosparc_user syslog 653965368 Jan 22 16:48 cryosparc2_worker.tar.gz
-rw-r--r-- 1 root root 344 Feb 21 10:22 install-cryo-command-howto