cryoSPARCさまから「2.13がリリースされたよ」との連絡を頂いた。

っで早速更新してみた
まずは確認

[cryosparc@c ~]$ cryosparcm update --check
CryoSPARC current version v2.12.2
          update starting on 2020年  1月 31日 金曜日 00:45:43 JST
 
  current version v2.12.2
      new version v2.13.0
 
Update available!
[cryosparc@c ~]$

と確かにリリースされていて利用可能のようである。

では更新へ
その前にcryosparcを止める。

[cryosparc@c ~]$ cryosparcm stop
CryoSPARC is running.
Stopping cryosparc.
command_proxy: stopped
webapp: stopped
command_core: stopped
Shut down
[cryosparc@c ~]$

一見とまったように見えるが、「ps -ef |grep cryosparc」とかで要確認。
こちらではデータベース機能の「mongod」が落ちてなかったので、手動でプロセス指定で止めた。

その後で更新作業へ。

[cryosparc@c ~]$ cryosparcm update
CryoSPARC current version v2.12.2
          update starting on 2020年  1月 31日 金曜日 00:46:32 JST
 
No version specified - updating to latest version.
 
=============================
Updating to version v2.13.0.
=============================
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 --:--:--  0:00:01 --:--:--     0
100  555M  100  555M    0     0  4323k      0  0:02:11  0:02:11 --:--:-- 5709k
  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  6622k      0  0:01:36  0:01:36 --:--:-- 8028k
  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 v2.12.2 to version v2.13.0.
===================================================
 
Starting cryoSPARC System master process..
CryoSPARC is not already running.
database: started
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/cryosparc/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/(略
    "listDatabases")["databases"]]
  File "/home/cryosparc/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/(略
    with client._socket_for_reads(read_preference) as (sock_info, slave_ok):
  File "/home/cryosparc/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/(略
    return self.gen.next()
  File "/home/cryosparc/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/(略
    with self._get_socket(read_preference) as sock_info:
  File "/home/cryosparc/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/(略
    return self.gen.next()
  File "/home/cryosparc/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/(略
    server = self._get_topology().select_server(selector)
  File "/home/cryosparc/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/(略
    address))
  File "/home/cryosparc/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/(略
    self._error_message(selector))
pymongo.errors.ServerSelectionTimeoutError: localhost:39001: [Errno 111] Connection refused
[cryosparc@c  ~]$

っとエラーになってしまった。
っが原因を調べるのが面倒だったので、cryosparcアプリの再起動を試した

[cryosparc@c ~]$ cryosparcm restart
CryoSPARC is running.
Stopping cryosparc.
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://c.sybyl.local:39000
 
 
Startup can take several minutes. Point your browser to the address
and refresh until you see the cryoSPARC web interface.
[cryosparc@c ~]$

っでまぁ一応は動いてくれる。
次に、worker側の更新。こちらも従来同様に

[cryosparc@c ~]$ cp -arp  software/cryosparc/cryosparc2_master/cryosparc2_worker.tar.gz ./software/cryosparc/cryosparc2_worker/
[cryosparc@c ~]$ cd ./software/cryosparc/cryosparc2_worker/
 
[cryosparc@c cryosparc2_worker]$ bin/cryosparcw update
Updating... checking versions
Current version v2.12.2 - New version v2.13.0
=============================
Updating worker...
=============================
  Deleting old files...
  Extracting...
  Done.
  Updating dependencies...
Checking dependencies...
Dependencies for python have not changed.
Currently checking hash for ctffind
Dependencies for ctffind have not changed.
Currently checking hash for gctf
Dependencies for gctf have not changed.
Completed dependency check.
 
Successfully updated.
 
[cryosparc@c cryosparc2_worker]$ cd

最後に再度のcryosparcを再起動させてみた。

[cryosparc@c ~]$ cryosparcm start
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://c.sybyl.local:39000
 
 
Startup can take several minutes. Point your browser to the address
and refresh until you see the cryoSPARC web interface.
[cryosparc@c ~]$

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Last-modified: 2020-01-31 (金) 01:03:58 (309d)