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How to Update from v22 (Linux) » History » Revision 11

Revision 10 (Anchi Cheng, 02/03/2014 05:11 PM) → Revision 11/13 (Anchi Cheng, 02/03/2014 05:29 PM)

h1. How to upgrade to Leginon System version 30 from version 22 (Linux) 

 Leginon/Appion 3.0 release web image viewer will not be compatible with CentOS 5 due to prerequisites of REDUX, the new image server that is compatible with php 5.3 used in modern os.    The Leginon processing server code is still compatible with python 2.4 which came with CentOS 5 but the development from now on will assume python version 2.6 along with other default yum installed packages of CentOS 6. 

 Since this is a major change, if you have an older computer where all parts of Leginon are installed and want to keep the data in the old database, this is a good time to migrate the web server and processing server to a new computer and make the old CentOS 5 computer the dedicate database computer. 

 h1. Upgrade database server moving if want to move from CentOS 5 to CentOS 6 (non-redux version only) 

 *If Database server is separate from web server, it can stay at CentOS 5 with MySQL 5.0.    You don't need to perform the followings* 

 If Database server is NOT separated from web server, you will need the database should first be exported so that it can later be imported to export the data and import it back after OS upgrade since CentOS 6 has MySQL 5.1. newer mysql version on CentOS6.    Direct file copy of the database files will not work. 

 Repeat the following for leginondb, projectdb, and any processing database that you would like to migrate: 

 For example, for leginondb: 

 1. Use mysqldump to create an xml file of the table structure and data    each of your databases like this (This assumes that the mysql user "usr_object" has proper privileges for these): 
 <pre> 
 mysqldump -h database_host -u usr_object -p --extended-insert leginondb > leginondb.sql 
 </pre> 

 2. copy the resulting sql file to a safe place during OS upgrade. 

 3. After OS upgrade and performing database setup in [[Database_Server_Installation]] 
  
 the new machine and then import that into the empty database after the database you dump is created but not populated ("usr_object" need to have privilages to create table): 
 <pre> 
 mysql -h database_host -u usr_object -p < leginondb.sql 
 </pre> 

 Repeat this for projectdb and all appion processing database that you have created 

 h1. Upgrade web server 

 h2. Follow [[Web_Server_Installation|Complete Web Server Installation]] including os upgrade to CentOS 6 if you are upgrading from the non-redux version of myami 2.2 

 Other OS with php 5.3 and above should also work but we can't provide instruction for all individual cases. 
 # Preliminary document for Ubuntu [[Myami_on_Ubuntu]] 

 h1. Upgrade processing server 

 h2. OS upgrade to CentOS 6 upgrade is OPTIONAL for stand-alone processing server 

 h2. Download myami 3.0 source code 

 <pre> 
 svn co http://emg.nysbc.org/svn/myami/branches/myami-3.0/ 
 </pre> 

 h2. Install Appion/Leginon Packages 

 h3. Install all the myami python packages _except appion_ using the following script: 

 <pre> 
 cd /your_download_area 
 cd myami 
 sudo ./pysetup.sh install 
 </pre> 

 That will install each package, and report any failures.    To determine the cause of failure, see the generated log file "pysetup.log".    If necessary, you can enter a specific package directory and run the python setup command manually.    For example, if sinedon failed to install, you can try again like this:  

 <pre> 
 cd sinedon 
 sudo python setup.py install 
 </pre> 

 h3. Move leginon.cfg/instruments.cfg/sinedon.cfg if it was saved with the old installation. 

 Run this script to find out where it was: 
 <pre>  
 cd /your_download_area/myami/leginion/ 
 ./configcheck.py 
 </pre> 
 If the script can not find leginon.cfg, and you found a copy of leginon.cfg in $PYTHONSITEPKG/leginon/config from the last installation, move that leginon.cfg to $PYTHONSITEPKG/leginon. 

 {{include(Appion:Run Database Update Script)}} 



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 [[How_to_Update_from_v22_(Instrument_Windows_Computer)| How to Update from v2.2 (Instrument Computer) >]] 


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