cryosparc_master
installation have access to cryosparcm
, cryoSPARC's built-in command-line utility for all administrative, management and advanced usage tasks.bash
) and enter any of the commands described below.cryosparcm
to the $PATH
environment variable via ~/.bashrc
for the <cryosparcuser>
UNIX user account (see Prerequisites & System Requirements for details).cryosparc_master
installation directory and run ./bin/cryosparcm
instead of cryosparcm
cryosparcm update
cryosparcm patch
--help
flag to see full usagecryosparcm patch
: Automatically installs the latest patches on workstations or master node and connected workers. Not recommended for clusters: Use the --download
and --install
flags instead.cryosparcm patch --force
: Reinstalls the latest patches in case something went wrong with a previous attemptcryosparcm patch --check
: Shows information about the latest patches without installingcryosparcm patch --download
: Downloads the latest patches without installing them. Follow the resulting instructions to install the master and worker patchescryosparcm patch --install
: Run this command immediately after a --download
to install the patch on the master node.cryosparcm patch
, when prompted restart with cryosparcm restart
.cryosparcm cluster
cryosparcm cluster example <cluster_type>
cluster_info.json
and cluster_script.sh
respectively.cryosparcm cluster dump <name>
cryosparcm cluster connect
cluster_info.json
and cluster_script.sh
from the current directory. Connects a new or updates an existing cluster configuration using the name from cluster_info.json
.cryosparcm cluster remove <name>
<cryosparcuser>
(the user that installed cryoSPARC), and can only be executed on the master node. If these conditions are not met, you may see the following error:CRYOSPARC_FORCE_HOSTNAME
variable just before calling the command:CRYOSPARC_HOSTNAME_CHECK
to cryosparc_master/config.sh
. You can also set CRYOSPARC_FORCE_HOSTNAME
in this file to permanently suppress this error.cryosparcm status
database
, webapp
, command_core
, etc). Also prints out configuration environment variables.cryosparcm start
start
.cryosparcm stop
cryosparcm restart
cryosparcm stop && cryosparcm start
cryosparcm jobstatus
cryosparcm backup
mongodump
. By default, the function creates a folder named backup
inside the database path specified by the CRYOSPARC_DB_PATH
environment variable in cryosparc_master/config.sh
(e.g., /u/cryosparcuser/cryosparc_db/backup
) and saves the backup as an .archive
file with the current date and time in its path (e.g., cryosparc_backup_2021_06_14_11h27.archive
) inside this folder.--dir
flag. To change the name of the backup file, specify the --file
flag.cron
job to execute the cryosparcm backup
command on a schedule, ensuring you always have a recent copy of the database that you can restore in case anything goes wrong.--file=database_backup_$(date +"%A").archive
will simulate a rolling-window backup, as a backup file will be created with the day of the week in the file path (e.g., database_backup_Friday.archive
). This allows you to keep a one-week buffer for the backup while limiting how much space the backups take, since future backups will overwrite a file if they are made on the same day.cryosparcm restore
cryosparcm changeport <port>
--yes
or -y
flag to proceed without confirmation.cryosparcm checkdb
cryosparcm fixdbport
cryosparcm licensestatus
cryosparcm log <process>
<process>
which can be one of the following:command_core
command_rtp
command_vis
database
webapp
app
control C
on your keyboard, and then q
.cryosparcm log
usage, run cryosparcm log -h
:command_core
, command_rtp
and command_vis
support the following arguments with the exception of database
, which also supports the date filter.--days|-d N
--date|-D YYYY-MM-DD
--name|-n NAME
cryosparcm log command_core -n COMMAND.SCHEDULER
--func|-f FUNCTION
cryosparcm log command_core -f get_gpu_info_run
--level|-l LEVEL
cryosparcm log command_core -l ERROR
tail
. For example, to see the last 1000 lines of the log:cryosparcm joblog PX JXX
JXX
in project PX
. Includes the standard input and error from the python process for the job.joblog
shows the full stdout
for the job, which is more comprehensive than the job log in the web interface and is more helpful for debugging.cryosparcm log
​cryosparcm listusers
cryosparcm createuser
cryosparcm resetpassword
<password>
provided. Full use:cryosparcm updateuser
--name
and --admin
flags are optional.cryosparcm env
eval
to define the variables output by the env
command.cryosparcm cli
cryosparcm icli
cryosparcm rtpcli
cryosparcm downloadtest
cryosparcm help
cryosparcm mongo
cryosparcm call <command>
eval $(cryosparc env)
followed by another shell command.