cryoSPARC/update

cryoSPARCさまから「2.14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 v2.13.2
          update starting on 2020年  2月 23日 日曜日 16:32:52 JST
 
  current version v2.13.2
      new version v2.14.2
 
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
command_vis: stopped
webapp: stopped
command_core: stopped
database: 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。
*もしデータベース機能の「mongod」が落ちてないなら手動でそのプロセスを殺す。そして確認のため「cryosparcm start」「cryosparcm stop」を行ってコマンドで落ちることを確認

その後で更新作業へ。

[cryosparc@c ~]$ cryosparcm update
CryoSPARC current version v2.13.2
          update starting on 2020年  2月 23日 日曜日 16:40:35 JST
 
No version specified - updating to latest version.
 
=============================
Updating to version v2.14.2.
=============================
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  1841k      0  0:05:08  0:05:08 --:--:-- 11.4M
  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  10.3M      0  0:01:00  0:01:00 --:--:-- 16.6M
  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 v2.13.2 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://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 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
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
  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
  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アプリを手動で再起動を試した

[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 ~]$

まぁいいみたい。どうもworker部分で引っかかったのかと思っている。
っで再度停止させて

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

今度はworkerをupdateします

[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 v2.13.2 - New version v2.14.2
=============================
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]$

これで更新は完了。っでcryoSPARCを起動します

[cryosparc@c cryosparc2_worker]$ cd
[cryosparc@c ~]$
[cryosparc@c ~]$ cryosparcm status
----------------------------------------------------------------------------
CryoSPARC System master node installed at
/home/cryosparc/software/cryosparc/cryosparc2_master
Current cryoSPARC version: v2.14.2
----------------------------------------------------------------------------
 
cryosparcm is not running.
 
----------------------------------------------------------------------------
 
global config variables:
 
export CRYOSPARC_LICENSE_ID="xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx"
export CRYOSPARC_MASTER_HOSTNAME="c.sybyl.local"
export CRYOSPARC_DB_PATH="/home/cryosparc/cryosparc_database"
export CRYOSPARC_BASE_PORT=39000
export CRYOSPARC_DEVELOP=false
export CRYOSPARC_INSECURE=false
 
[cryosparc@c ~]$
[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: 2020-02-23 (日) 17:27:11 (96d)