cryoSPARC/update

/home/cryosparc/cryosparc_worker/bin/cryosparcw install-3dflex

[illya@s ~]$ cryosparcm update --check
CryoSPARC current version v3.3.2
          update starting on Tue Oct  4 12:04:33 JST 2022
 
  current version v3.3.2
      new version v4.0.0
 
Update available!
 
[illya@s ~]$ ps -ef |grep cryosparc
(もしプロセスがあるならkill)
 
[illya@s ~]$ ps -ef |grep mongo
(もしプロセスがあるならkill)
 
[illya@s ~]$ ls -l /tmp/cryosparc-supervisor-* /tmp/mongodb-*
(もしあるなら削除)
 
[illya@s ~]$ cryosparcm update
 :
 :
===================================================
Successfully updated master to version v4.0.0.
===================================================
 
Starting cryoSPARC System master process..
CryoSPARC is not already running.
configuring database
    detected mongo feature compatibility version mismatch
    expected: 3.6 actual: 3.4
    attempting to set mongo fcv...
    mongo fcv is 3.6
    creating cryosparc_admin
    cryosparc_admin created
    creating cryosparc_user
    cryosparc_user created
    configuration complete
database: started
    database configuration is OK.
 :
 :
 ===================================================
 Now updating worker nodes.
 ===================================================
 
All workers:
s.sybyl.local illya@s.sybyl.local
 -------------------------------------------------
Updating worker s.sybyl.local
Remote update
scp ./cryosparc_worker.tar.gz illya@s.sybyl.local:/home/illya/cryoSPARC/cryosparc_worker
ssh illya@s.sybyl.local /home/illya/cryoSPARC/cryosparc_worker/bin/cryosparcw update
Updating... checking versions
Current version v3.3.2 - New version v4.0.0
 :
 :
Successfully updated.
 
 ---------------------------------------------------
 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, copy the cryosparc_worker.tar.gz file into the
 cryosparc worker installation directory, and then run
    $ bin/cryosparcw update
 from inside the worker installation directory.
 
[illya@s ~]$

[cryosparc@c ~]$ cryosparcm update
CryoSPARC current version v2.0.27
          update starting on 2018年 11月  6日 火曜日 12:47:41 JST
 
No version specified - updating to latest version.
 
=============================
Updating to version v2.4.0.
=============================
CryoSPARC is running.
Stopping cryosparc.
command_proxy: stopped
command_vis: stopped
webapp: stopped
command_core: stopped
database: stopped
Shut down
  Downloading master update...
    :
  Downloading worker update...
    :
  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...
Legacy hash (v2.2 & older) detected. No new python dependencies need to be installed.
Currently checking hash for mongodb
Dependencies for mongodb have changed - reinstalling...
mongodb 3.4.10 installation successful.
Completed.
Completed dependency check.
 
Successfully updated master from version v2.0.27 to version v2.4.0.
 
Starting cryoSPARC System master process..
CryoSPARC is not already running.
database: started
 :
 :
[cryosparc@c ~]$

[cryosparc@c ~]$ cryosparcm patch --check
 
A cryoSPARC patch is available
 
    Current Version: v3.3.1
    Current Patch: None
    New Patch: 220315
    Released On: 2022-03-19 03:44:08
    Requires Restart: Yes
    Patch Notes:
        - Fixed: Plotting error during (legacy) local refinement
        - Added: Specify path of directory containing preprocessed micrographs for Topaz Train and Extract
        - Added: New 3D Classification advanced parameter?"Output data after every full iter"?to enable data outputs (volumes, particles, volume series) after every full iteration
        - Updated: 3D Classification volume outputs are now unmasked, fixing downstream refinements
(略
 
To install, run:
 
    cryosparcm patch
[cryosparc@c ~]$

[cryosparc@c ~]$ cryosparcm patch
 
A cryoSPARC patch is available
 
    Current Version: v3.3.1
    Current Patch: None
    New Patch: 220315
    Released On: 2022-03-19 03:44:08
    Requires Restart: Yes
    Patch Notes:
        - Fixed: Plotting error during (legacy) local refinement
        - Added: Specify path of directory containing preprocessed micrographs for Topaz Train and Extract
 
(略
Install patch? (y/n): y                        <-- patchを適用するかの最終確認
Downloading...
Downloading cryosparc_master_patch.tar.gz...
Downloading cryosparc_worker_patch.tar.gz...
Patching master...
Done.
Gathering worker info...
Patch worker s? (y/n): y                       <--- workerノードのsに適用
Patching workers...
All workers:
   s cryosparc@s
=================================================
Updating worker s: Remote update
scp cryosparc_worker_patch.tar.gz cryosparc@s:/home/cryosparc/cryoSPARC/cryosparc_worker/cryosparc_worker_patch.tar.gz
ssh cryosparc@s /home/cryosparc/cryoSPARC/cryosparc_worker/bin/cryosparcw patch
Worker patch successfully applied.
 -------------------------------------------------
=================================================
Patched 1 worker
Finishing...
Done.
Patch v3.3.1+220315 applied!
To complete installation, restart cryoSPARC with the following command:
 
    cryosparcm restart
 
[cryosparc@c ~]$ cryosparcm restart       <-- 指示に従い cryoSPARCサービスを再起動
 
(cryosparcm restartで完了なのかも知れないけど. ドキュメントでは下記も実行が要求される)
[cryosparc@c ~]$ cryosparcm cli "reload()"
[cryosparc@c ~]$ cryosparcm cli "refresh_job_types()"

[cryosparc@c cryoSPARC]$ cat cryosparc_master/patch
220315
[cryosparc@c cryoSPARC]$ cat cryosparc_master/version
v3.3.1
 
 
[cryosparc@c cryoSPARC]$ cat cryosparc_worker/patch
220315
[cryosparc@c cryoSPARC]$ cat cryosparc_worker/version
v3.3.1
[cryosparc@c cryoSPARC]$