まず確認

[cryosparc@c ~]$ cryosparcm update --check
CryoSPARC current version v2.15.0
          update starting on Fri Dec 11 03:01:27 JST 2020
 
  current version v2.15.0
      new version v3.0.0
 
Update available!
[cryosparc@c ~]$

と最新は確かにv3.0.0みたい。
っで、cryosparcを停止する
ここでは systemctl で cryosparc を自動起動させるようにしたので root で操作します
参照: cryoSPARC#w9335327

[root@c ~]# systemctl stop cryosparc.service
 
[root@c ~]# ps -ef |grep cryosparc             <-- プロセスが本当にないのかを確認します

っで更新
ユーザ cryosparc で行います。

[cryosparc@c ~]$ cryosparcm update
CryoSPARC current version v2.15.0
          update starting on Fri Dec 11 03:05:55 JST 2020
 
No version specified - updating to latest version.
 
=============================
Updating to version v3.0.0.
=============================
CryoSPARC is not already running.
If you would like to restart, use cryosparcm restart
  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  769M  100  769M    0     0  5001k      0  0:02:37  0:02:37 --:--:-- 16.8M
  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 2903M  100 2903M    0     0  12.6M      0  0:03:50  0:03:50 --:--:-- 17.3M
  Done.
 
 Update will now be applied to the master installation,
 followed by worker installations on other nodes.
 
  Deleting old files...
  Extracting...
  Done.
  Updating dependencies...
Could not find conda environment: cryosparc_master_env
You can list all discoverable environments with `conda info --envs`.
 
Warning: Could not activate conda environment; this indicates that a cryoSPARC installation is either incomplete or in progress
===================================================
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=/home/cryosparc/software/cryosparc/cryosparc2_master/deps/anaconda
Unpacking payload ...
Collecting package metadata (current_repodata.json): done
Solving environment: done
 
## Package Plan ##
 
  environment location: /home/cryosparc/software/cryosparc/cryosparc2_master/deps/anaconda
 
  added / updated specs:
(略
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 3.4.10 installation successful.
  ------------------------------------------------------------------------
  Completed.
  Completed dependency check.
 
===================================================
Successfully updated master to version v3.0.0.
===================================================
 
Starting cryoSPARC System master process..
CryoSPARC is not already running.
database: started
command_core: started
  cryosparc command core startup complete.
command_vis: started
command_rtp: started
  cryosparc live startup complete.
webapp: started
app: started
liveapp: started
-----------------------------------------------------
 
CryoSPARC master started.
 From this machine, access cryoSPARC at
    http://localhost:39000
 and access cryoSPARC Live at
    http://localhost:39006
 please note the legacy croSPARC Live application is running at
    http://localhost:39007
 
 From other machines on the network, access cryoSPARC at
    http://c.sybyl.local:39000
 and access cryoSPARC Live at
    http://c.sybyl.local:39006
 
 
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
app: stopped
command_core: stopped
command_rtp: stopped
command_vis: stopped
liveapp: stopped
webapp: 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_rtp: started
  cryosparc live startup complete.
webapp: started
app: started
liveapp: started
-----------------------------------------------------
 
CryoSPARC master started.
 From this machine, access cryoSPARC at
    http://localhost:39000
 and access cryoSPARC Live at
    http://localhost:39006
 please note the legacy croSPARC Live application is running at
    http://localhost:39007
 
 From other machines on the network, access cryoSPARC at
    http://c.sybyl.local:39000
 and access cryoSPARC Live at
    http://c.sybyl.local:39006
 
 
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:
 ---------------------------------------------------
 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 cryosparc2_worker.tar.gz file into the
 cryosparc worker installation directory, and then run
    $ bin/cryosparcw update
 from inside the worker installation directory.
 
[cryosparc@c ~]$

次に worker 側もupdateします。

[cryosparc@c ~]$ cd /home/cryosparc/software/cryosparc/cryosparc2_worker
[cryosparc@c cryosparc2_worker]$
 
[cryosparc@c cryosparc2_worker]$ cp -arp  ../cryosparc2_master/cryosparc2_worker.tar.gz .
[cryosparc@c cryosparc2_worker]$ bin/cryosparcw update
Updating... checking versions
Current version v2.15.0 - New version v3.0.0
=============================
Updating worker...
=============================
  Deleting old files...
  Extracting...
  Done.
  Updating dependencies...
Checking dependencies...
Dependencies for python have changed - reinstalling...
  ------------------------------------------------------------------------
  Installing anaconda python...
  ------------------------------------------------------------------------
PREFIX=/home/cryosparc/software/cryosparc/cryosparc2_worker/deps/anaconda
Unpacking payload ...
Collecting package metadata (current_repodata.json): done
Solving environment: done
 
## Package Plan ##
 
  environment location: /home/cryosparc/software/cryosparc/cryosparc2_worker/deps/anaconda
 
  added / updated specs:
(略
installation finished.
  ------------------------------------------------------------------------
    Done.
    anaconda python installation successful.
  ------------------------------------------------------------------------
  Extracting all conda packages...
  ------------------------------------------------------------------------
 
  ------------------------------------------------------------------------
    Done.
    conda packages installation successful.
  ------------------------------------------------------------------------
  Preparing to install all pip packages...
  ------------------------------------------------------------------------
Processing ./deps_bundle/python/python_packages/pip_packages/pycuda-2020.1.tar.gz
Processing ./deps_bundle/python/python_packages/pip_packages/scikit_cuda-0.5.3-py2.py3-none-any.whl
Skipping wheel build for pycuda, due to binaries being disabled for it.
Installing collected packages: scikit-cuda, pycuda
    Running setup.py install for pycuda ... done
Successfully installed pycuda-2020.1 scikit-cuda-0.5.3
  ------------------------------------------------------------------------
    Done.
    pip packages installation successful.
  ------------------------------------------------------------------------
  Main dependency installation completed. Continuing...
  ------------------------------------------------------------------------
Completed.
Currently checking hash for ctffind
Dependencies for ctffind have changed - reinstalling...
  ------------------------------------------------------------------------
  ctffind 4.1.10 installation successful.
  ------------------------------------------------------------------------
Completed.
Currently checking hash for gctf
Dependencies for gctf have changed - reinstalling...
  ------------------------------------------------------------------------
  Gctf v1.06 installation successful.
  ------------------------------------------------------------------------
Completed.
Completed dependency check.
 
Successfully updated.
 
[cryosparc@c cryosparc2_worker]$

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Last-modified: 2020-12-11 (金) 03:37:26 (77d)