Project

General

Profile

Appion Home » History » Revision 29

Revision 28 (Amber Herold, 04/01/2010 11:04 AM) → Revision 29/101 (Amber Herold, 04/01/2010 11:06 AM)

 
 h1. Complete Installation 




 h2. Four Parts of Leginon System 


 !http://emg.nysbc.org/software/leginon/images/images/Leg_Proj_parts.png! 

 Leginon as a system that we distribute can be divided into three parts: 



 h2. Processing Server (Python-side) 


 Python (and some c) scripts that handle instrument control, data acquisition, and 
 processing. 





 h2. Database Server (MySQL-side) 


 a MySQL server that handles the database 





 h2. Web Server (PHP-side) 


 This includes php and Java scripts at a webserver that we will create to retrieve image 
 and metadata from the database and file-storage system. 





 h2. File Server 


 This is up to you to set up to store lots of data coming out of Leginon system. 







 h2. What is in this chapter 



 Leginon runs under both the Linux and Microsoft Windows Operating systems. However, the 
 current php-mrctool can not be installed on Windows which means mrc images can not be viewed 
 on the web. See the section on Possible Computer Set-up Configurations for details. 


 The many components for the Leginon system are divided into packages and need to be 
 installed separately. It has been integrated with several third party software packages that 
 are necessary for its operation. The installation documentation will describe how to set-up 
 Leginon and give hints as to how to install and set-up the necessary third-party software. 
 This documentation is not intended to support the additional, but necessary third-party 
 software. 


 There has been interest in installing Leginon under Mac OS X. While this is possible in 
 theory, we have not been successful in installing a fully functional system. The two main 
 problems are (1) compilation of php-mrctool from the pre-installed php and (2) wxPython on Mac 
 is unable to hide bitmap objects which makes Leginon graphical user interface difficult to 
 use. 


 See <link linkend="InstT_install">Installation Troubleshooting</link> and "Leginon <ulink 
 url="http://emg.nysbc.org/bb/viewforum.php?f=2">Leginon Bulletin Board":http://emg.nysbc.org/bb/viewforum.php?f=2 Board</ulink> searching 
 for "install" if you run into problems. 





 h2.    Possible Computer Set-up Configurations 



 Computer(s) used for the whole Leginon system need to support five functions: 
 *    TEM/Camera control and data output (by python-side packages of Leginon 
 system) 


 *The computer attached to the microscope/camera is used for this function. 
 Therefore, it is on a Windows computer. 


 *    General Leginon operation such as target selection and image processing (processing 
 server of Leginon system) 


 *    Image data storage. 


 *    Other meta-data storage through MySQL database (by database server of Leginon 
 system) 


 *    Web server (using PHP-side of Leginon system). 


 *Important* The MRC module that is used to load mrc formatted files to the web 
 pages is not compiled on Windows. Therefore, this function must be on a linux box unless 
 you don't need to see the images*** 





 The five functions can be distributed to five different computers on a network or all on 
 one single computer. However, since the latter minimal setup requires the use of the computer 
 attached to the microscope for all functions, it is not advisable. 


 Processing server of Leginion is a multi-platform software, meaning it can run on both 
 Microsoft Windows and Linux. It is also inherently designed to utilize distributed systems on 
 a network. MySQL used in the database server is also supported by multiple platforms. This is 
 not true for the Web server because the custom MRC module used in the web viewer only compiles 
 on linux machines. Therefore, one of the computer not part of the microscope must be a linux. 
 The following examples show several arrangements that take advantage of distributed system. 
 Other combinations are possible, but will basically be variations on one of the following 
 themes. 



 h2.    A: 1 Windows computer (attached to the Microscope) &amp; 1 Linux computer (for all 
 other functions, separate from the Microscope) (Good for single user and small-scale 
 acquisition) 





 *    Install the latest processing server side of Leginon release (and supporting 
 packages) on the Windows computer controlling the microscope and on the Linux computer 
 which is to run Leginon image acquisition and processing. 


 *    Install the additional modules needed for CCD camera and film interaction on the 
 Windows computer controlling the microscope. 


 *    Install MySQL, PHP, the Apache Web Server, and dbem tools only on the Linux 
 computer that will perform these functions, (i.e. NOT the computer controlling the 
 microscope). 









 h2.    B: 1 Windows computer (attached to the Microscope) &amp; 4 Linux computers (one for 
 each function) (Good for multiple microsopes, users and large-scale acquisition) 



 This is the set-up at NRAMM. It has the processing server side of Leginon installed on 
 the Windows computer attached to the microscope and on the Linux computer that is used for 
 running Leginon. A second Linux machine is dedicated to the database while the web-based 
 viewer is hosted by another server. 




 *    Install the python-side Leginon (and supporting packages) on the Windows computer 
 controlling the microscope and on the Linux computer that is to run Leginon. You can 
 make the latter installation accessable to any numbers of linux computers on your 
 network. 


 *    Install MySQL, PHP, the Apache Web Server, and dbem tools on the second Linux 
 computer that will serve as the database/web server/PHP host. 


 *    The computer hosting the data storage should be accessable by all linux 
 boxes. 









 h2.    C: 1 Windows computer (attached to the Microscope), 1 Windows computer running python- 
 and MySQL-side functions and 1 Linux computer as web server (Has been applied 
 successfully) 



 The data storage may be on one of these computers that is accessable by other 
 computers. 







 h2.    Ports that Leginon system uses: 



 This information is useful if you want to open specific ports between computers with a 
 firewall in between. 




 * MySQL normally uses port 3306 (but configurable in /etc/my.cnf) 


 * Leginon Client running on TEM host: port 55555 


 * Leginon main program on the processing server: dynamically assigned ports between 
 49152 and 65535 


 There is no strict port assignment since we could potentially have more than one 
 Leginon process running on the same linux host talking to different TEM hosts. It is 
 probably good enough if you only worry about opening up the first few of those ports in 
 your firewall (maybe 49152 through 49160, or something like that). 


 See more discussion at Leginon bulletin board thread on ""network "<ulink 
 url="http://emg.nysbc.org/bb/viewtopic.php?t=7">network problem, Leginon not seeing 
 tecnai host":http://emg.nysbc.org/bb/viewtopic.php?t=7 " host</ulink>" 









 h2. Where to Register and download Leginon system 



 "http://www.leginon.org/":http://www.leginon.org is the home. Please 
 register if you want to recieve support from Leginon team. 


 *    python-side Leginon packages 


 direct link: "http://emg.nysbc.org/software/leginon/":http://emg.nysbc.org/software/leginon/ <ulink url="http://emg.nysbc.org/software/leginon/" 
 >http://emg.nysbc.org/software/leginon/</ulink> 


 *    mrctools: including the tools for reading mrc images on the web 


 direct link: "http://emg.nysbc.org/software/mrctools/":http://emg.nysbc.org/software/mrctools/ <ulink url="http://emg.nysbc.org/software/mrctools/" 
 >http://emg.nysbc.org/software/mrctools/</ulink> 


 *    dbemtools: including the tools for administration and webviewing 


 direct link: "http://emg.nysbc.org/software/dbemtools/":http://emg.nysbc.org/software/dbemtools/ <ulink url="http://emg.nysbc.org/software/dbemtools/" 
 >http://emg.nysbc.org/software/dbemtools/</ulink> 


 *    project tools (optional): For administration and webviewing of projects 


 direct link: "http://emg.nysbc.org/software/dbemtools/":http://emg.nysbc.org/software/dbemtools/ <ulink url="http://emg.nysbc.org/software/dbemtools/" 
 >http://emg.nysbc.org/software/dbemtools/</ulink> 







 h2.    Processing server-side Leginon Installation 



 For the lack of better name, processing server-side Leginon refers to packages that 
 performs the general functions of image acquisition and processing. The instructions here are 
 for Linux. Refer to Windows Installation for Windows specific instructions. 



 h2. Download svn checkout script from Leginon website 



 "http://www.leginon.org/":http://www.leginon.org/ Download 
 svnget-1.6.sh to a convenient location such as your home directory. 





 h2. Check out SVN Source Files from the depository 



 run svnget-1.6.sh. It does the 
 following:<pre>mkdir Leginon-1.6-ALL 
 cd Leginon-1.6-ALL 
 svn co http://emg.nysbc.org/svn/leginon/branches/1.6 Leginon 
 svn co http://emg.nysbc.org/svn/pyami/branches/leg1.6 pyami 
 svn co http://emg.nysbc.org/svn/pyScope/branches/leg1.6 pyScope 
 svn co http://emg.nysbc.org/svn/sinedon/branches/leg1.6 sinedon 
 svn co http://emg.nysbc.org/svn/numextension/branches/leg1.6 numextension 
 svn co http://emg.nysbc.org/svn/libcv/branches/leg1.6 libcv 
 svn co http://emg.nysbc.org/svn/ImageViewer/branches/leg1.6 ImageViewer</pre> 


 If the process fails, you probably do not have svn client installed. Skip to "Install 
 the supporting packages first if missing:", then try this again. 





 h2.    Perform system check: 



 In addition to the downloads from our svn depository, there are several other 
 requirements that you will get either from your OS installation source, or from its 
 respective website. The system check in the Leginon package checks your system to see if you 
 already have these requirements 



 <pre>cd your_download_area/Leginon-1.6-ALL/Leginon 
 python syscheck.py</pre> 



 If python is not installed, this, of course will not run. If you see any lines like "*** 
 Failed...", then you have something missing. Otherwise, everything should result in 
 "OK". 





 h2.    Install the supporting packages first if missing: 



 Follow the instruction for your specific Linux distribution. 


 For example, SUSE users can use YaST to install them; RedHat and CentOS users can use 
 yum. 


 *SciPy may not build properly on some versions of SuSE due to an incompatible LAPACK 
 package that comes with SuSE. You can get scipy as well as a compatible LAPACK etc. from 
 http://repos.opensuse.org/science (need to specify your SuSE version and machine 
 etc.) 





 h2.    Required supporting packages: 




 |_.Name:|_.Download site:|_.yum package name|_.SuSE rpm name| 
 |Python 2.4 or newer|"http://www.python.org":http://www.python.org|python|python-devel| 
 |wxPython 2.5.2.8 or newer|"http://www.wxpython.org":http://www.wxpython.org|wxPython|python-wxGTK| 
 |MySQL Python client 1.2 or newer|"http://sourceforge.net/projects/mysql-python":http://sourceforge.net/projects/mysql-python|MySQL-python|python-mysql| newer|<ulink url="http://sourceforge.net/projects/mysql-python" 
 >http://sourceforge.net/projects/mysql-python</ulink>|MySQL-python|python-mysql| 
 |Python Imaging Library (PIL) 1.1.4 or newer|"http://www.pythonware.com/products/pil/":http://www.pythonware.com/products/pil/|python-imaging|python-imaging| newer|<ulink url="http://www.pythonware.com/products/pil/" 
 >http://www.pythonware.com/products/pil/</ulink>|python-imaging|python-imaging| 
 |Python XML module 0.8.3 or newer|"http://pyxml.sourceforge.net":http://pyxml.sourceforge.net|PyXML|python-xml| 
 |NumPy 1.0.1 or newer|"http://www.scipy.org":http://www.scipy.org|numpy|numpy| 
 |SciPy 0.5.1 (tested, others may work)*|"http://www.scipy.org":http://www.scipy.org , "http://repos.opensuse.org/science":http://repos.opensuse.org/science *|scipy|python-scipy| <ulink 
 url="http://repos.opensuse.org/science" 
 >http://repos.opensuse.org/science</ulink>*|scipy|python-scipy| 




 *SciPy may not build properly on some versions of SuSE due to an incompatible LAPACK 
 package that comes with SuSE. You can get scipy as well as a compatible LAPACK etc. from 
 http://repos.opensuse.org/science (need to specify your SuSE version and machine 
 etc.) 





 h2.    Optional supporting packages: 





 *    For using Matlab to explore holefinding algorithm (Matlab HoleFinder) 


 pymat: "http://sourceforge.net/projects/pymat":http://sourceforge.net/projects/pymat <ulink url="http://sourceforge.net/projects/pymat" 
 >http://sourceforge.net/projects/pymat</ulink> 









 h2. Install the packages you downloaded from svn depository 



 Here are the packages you need to install with python installer inside the 
 Leginon-1.6-ALL folder. 



 |_.Name:|_.Purpose:| 
 | Leginon|modular TEM image acquisition| 
 | pyami|general functions| 
 | pyScope|microscope control and monitoring| 
 | sinedon|Leginon/database interaction| 
 | numExtension|c extension for numerical processing| 
 | libCV|small c library of algorithm from computer vision field| 
 | ImageViewer|image viewing for tomography| 






 *    run syscheck.py again to make sure you have everything. 


 *    Install the package in _each folder_ with commands 
 like 
 these<pre>cd /your_download_area/Leginon-1.6-ALL/Leginon 
 python setup.py install 

 cd ../pyami 
 python setup.py install 
 cd ../pyScope 
 python setup.py install 
 cd ../sinedon 
 python setup.py install 
 cd ../numextension 
 python setup.py install 
 cd ../libcv 
 python setup.py install 
 cd ../ImageViewer 
 python setup.py install</pre> 









 h2.    python-site-package-path: where the installed python 
 packages went: 


 Python installer put the packages you installed to its site-packages directory. This 
 enable all users on the same computer to access them. The easiest way to find where your 
 installed package is called by python is to load a module from the package using interactive 
 python command lines like this: 




 *    Start python command line from shell 



 <pre>> python</pre> 



 *    Import a module from the package. Let's try sinedon here. All packages installed 
 through the above setup.py script should go to the same place. 



 <pre>python> import sinedon</pre> 



 *    If the module is loaded successfully, call the module attribute __path__ (two 
 underscrolls before "path" and two underscrolls after) will return the location of the 
 module it is loaded from 



 <pre>python> sinedon.__path__ 

 RETURNS, For example, 
 python> <module 'sinedon' from '/usr/lib/python2.5/site-packages/sinedon/__init__.pyc'> </pre> 


 In this case, /usr/lib/python2.5/site-packages/ is your python-site-package-path. 
 If you go to that directory, you will find all the packages you just installed. 









 h2.    Configure leginon.cfg: 


 Leginon can be configured at three levels: 




 *    A skeleton (default) configuration file is available: 



 <pre> _<link linkend="package_path">[python-site-package-path]</link>_/Leginon/config/default.cfg</pre> 



 *    Configurations for all users 



 <pre> _<link linkend="package_path">[python-site-package-path]</link>_/Leginon/config/leginon.cfg</pre> 



 Example of the configuration that you should set: (Here we assume your leginon 
 database is named "dbemdata", and Leginon log into the database as a user named 
 "usr_object" with no password 
 set).<pre>[Images] 
 path: _your_storage_disk_path_/leginon 
 </pre> 


 *    Configurations for individual users that overrides the all-user configuration if 
 exists 



 <pre> ~/leginon.cfg</pre> 



 This configuration should include all the minimal configuration above and 
 additional configuration for individual user for 
 convenience<pre>[User] 
 Fullname: _your_name_    #The name you entered in the leginon administration web page. Note that it is case sensitive</pre> 









 h2.    Names used in the example installation 


 From this point on, you will need to enter database user names for different 
 configuration files and settings. These are NOT Leginon user names but what is required by 
 MySQL database interaction. Consistent names are essential. In the example shown here, the 
 leginon database is called "dbemdata", the project database is called "projectdata". The 
 MySQL user name are the same, "usr_object", and in this case without a password. 





 h2.    Configure sinedon.cfg: 


 Sinedon is designed to be able to interact with multiple databases. It can be 
 configured at global or user level. 




 *    An example configuration file is available at: 



 <pre>/your_download_area/Leginon-1.6-ALL/sinedon/examples/sinedon.cfg</pre> 



 *    Configurations for all users should be placed at the following path 



 <pre>    _<link linkend="package_path">[python-site-package-path]</link>_/sinedon/sinedon.cfg</pre> 



 *    Modify host,db,user,passwd to what is used. Note that the user here is MySQL user 
 Leginon uses to communicate with the database for all Leginon users. For Leginon that 
 uses Project database, set the following: 



 <pre>[global] 
 host: _your_database_host_ 
 user: usr_object 
 passwd: 

 [projectdata] 
 db: projectdata 

 [leginondata] 
 db: dbemdata 
 </pre> 



 *    Add database configuration if you intend to use grid-inserting robot. The Robot2 
 module uses the database to communicate to the robot. Applications that carries the 
 name "Robot" requires this to be set. In general, using the same database as the 
 general leginon database is fine. 



 <pre>[robot2] 
 db: dbemdata</pre> 












 h2. Database Server-side Installation 



 The following is for the computer that hosts the databases. This involves installing MySQL 
 server and creation/configuration of the leginon and project databases. 





 |_.Name:|_.Download site:| 
 |MySQL-Server 5.0 or higher|"http://www.mysql.com":http://www.mysql.com| 
 |MySQL-Client 5.0 or higher|"http://www.mysql.com":http://www.mysql.com| 





 h2.    MySQL 





 *    Install MySQL-Server 




 *    Use your package installer (yum, zypper, YaST) if available. 


 OR 


 *    Download the latest MySQL-server RPM for Linux from "www.mysql.com":http://www.mysql.com *    Install the MySQL-server rpm: 


 <pre> rpm -Uvh MySQL-server-5.0.xx-y.i386.rpm</pre> 
 (substitute correct version numbers) 






 *    Install MySQL-Client 




 *    Use your package installer (yum, zypper, YaST) if available. 


 OR 


 *    Download the latest MySQL-client RPM for Linux from "www.mysql.com":http://www.mysql.com *    Install the MySQL-client rpm: 


 <pre> rpm -Uvh MySQL-client-5.0.xx-y.i386.rpm</pre> 
 (substitute correct version numbers) 






 *    MySQL configuration file is usually located in /usr/share/mysql. There are 
 several examples there: 



 <pre>> ls /usr/share/mysql/my* 
 /usr/share/mysql/my-huge.cnf 
 /usr/share/mysql/my-innodb-heavy-4G.cnf 
 /usr/share/mysql/my-large.cnf 
 /usr/share/mysql/my-medium.cnf 
 /usr/share/mysql/my-small.cnf 
 > </pre> 



 *    Configure my.cnf in /etc using my-huge.cnf as the template 




 * <pre>> cp /usr/share/mysql/my-huge.cnf /etc/my.cnf</pre> 



 *    Edit /etc/my.cnf to add or change query cache variables like these: 

 <pre>query_cache_type= 1 
 query_cache_size = 100M 
 query_cache_limit= 100M</pre> 







 *    start MySQL Server 

 <pre> >/etc/init.d/mysqld start</pre> 

 on some installation, 

 <pre> >/etc/init.d/mysql start</pre> 

 For future reference: start | stop | restart MySQL Server with similar 
 commands: 

 <pre> >/etc/init.d/mysqld start 
 >/etc/init.d/mysqld stop 
 >/etc/init.d/mysqld restart</pre> 

 If you want to start MySQL automatically at boot on SuSE 

 <pre> SuSE >chkconfig mysql on 
 </pre> 

 *    For future reference, the database location will be: 



 <pre>> cd /var/lib/mysql 
 Directory: /var/lib/mysql 
 > ls 
 yourdbserver.pid 
 ib_logfile0 
 mysql 
 mysql.sock 
 test 
 > </pre> 



 *    Create leginon database, here we call <link linkend="db_example_names" 
 >dbemdata</link> 

 <pre> >mysqladmin create dbemdata</pre> 



 *    Create project database, here we call <link linkend="db_example_names" 
 >projectdata</link> (optional) 

 <pre> >mysqladmin create projectdata</pre> 



 *    Connect to mysql db 

 <pre>>mysql mysql 

 mysql> select user, password, host from user; 
 +------+----------+-----------+ 
 | user | password | host        | 
 +------+----------+-----------+ 
 | root |            | localhost | 
 | root |            | host1       | 
 |        |            | host1       | 
 |        |            | localhost | 
 +------+----------+-----------+ 
 4 rows in set (0.00 sec)</pre> 



 *    Create and grant privileges to a user called <link linkend="db_example_names" 
 >usr_object</link> for the databases on both the localhost and other hosts involved. 
 For example, use wild card '%' for all hosts. You may also set specific privilege to 
 the user. See MySQL Reference Manual for details 

 <pre>mysql> create user usr_object@'localhost'; 
 mysql> grant all privileges on dbemdata.* to usr_object@'localhost'; 
 mysql> grant all privileges on projectdata.* to usr_object@'localhost';</pre> 

 Similarly, 

 <pre>mysql> create usr_object@'%'; 
 mysql> grant all privileges on dbemdata.* to usr_object@'%'; 
 mysql> grant all privileges on projectdata.* to usr_object@'%'; 
 </pre> 

 *    Change Root passworld 

 <pre>mysql> update user set password=password('_a passwd_') where user="root"; 
 Query OK, 2 rows affected (0.01 sec) 
 Rows matched: 2    Changed: 2    Warnings: 0 

 mysql>^D or exit;</pre> 
 From now on, you will need to specify the password to connect to the database as 
 root user like this: 

 <pre>>mysql -u root -p mysql</pre> 

 _***If your password change does not take effect in your next 
 database connection, you will need to flush the mysql pivileges cache as mysql root 
 and connecting with you old password (or no password in the above 
 case):_ 

 <pre>>mysql -u root mysql</pre> 
 <pre>mysql> flush privileges; 
 mysql>^D or exit;</pre> 

 *    Check MySQL variables 

 <pre>>mysql -u usr_object dbemdata 

 mysql> SHOW VARIABLES LIKE 'query%'; 
 +------------------------------+-----------+ 
 | Variable_name                  | Value       | 
 +------------------------------+-----------+ 
 | ft_query_expansion_limit       | 20          | 
 | have_query_cache               | YES         | 
 | long_query_time                | 10          | 
 | query_alloc_block_size         | 8192        | 
 | query_cache_limit              | 104857600 | <<---This should correspond to your change 
 | query_cache_min_res_unit       | 4096        | 
 | query_cache_size               | 104857600 | <<---This should correspond to your change 
 | query_cache_type               | ON          | <<---This should correspond to your change 
 | query_cache_wlock_invalidate | OFF         | 
 | query_prealloc_size            | 8192        | 
 +------------------------------+-----------+ 
 10 rows in set (0.00 sec) 

 mysql> exit;</pre> 



 *    Make sure MySQL is running 

 <pre>prompt:~> mysqlshow 
 +--------------+ 
 | Databases      | 
 +--------------+ 
 | mysql          | 
 | dbemdata       | 
 | projectdata    | 
 +--------------+</pre> 



 *    Or check with the following php script (if already installed) 

 <pre><? 
 mysql_connect('your_host.your_institute.edu', 'usr_object', '','dbemdata'); 
 echo mysql_stat(); 
 ?> </pre> 


 Output 

 <pre> Uptime: 1452562 Threads: 1 Questions: 618 Slow queries: 0 Opens: 117 Flush tables: 1 Open tables: 106 Queries per second avg: 0.000</pre> 










 h2.    Web server set up and Installation 



 The following applies to the computer that will host the web-accessable image viewers ( a 
 part of dbem tools) and project manager (a part of project tools). 



 h2. Differences between Linux flavors 



 Different Linux flavors often put web server and mysql-related files in different 
 locations. This can be confusing. From experience, we found the equivalent on CentOS vs 
 SuSE. Here we list them for reference. If your system use a different naming and you are 
 willing to share your experience, please send us the list. We will add it here: 



 |_.File or Command Head|_.CentOS|_.SuSE| 
 | php.ini|/etc/| /etc/php5/apache2/| 
 | httpd.conf|/etc/httpd/conf/|/etc/php5/apache2/| 
 | default document_root|/var/www/html/|/srv/www/htdocs/| 
 | apache start/stop/restart command head|/etc/init.d/httpd|/etc/init.d/apache2| 
 | mysql start/stop/restart command head|/etc/init.d/mysqld|/etc/init.d/mysql| 







 h2. Prerequisites for dbemtools, projecttools, and mrctools extension 



 The dbemtools are mostly php scripts that run at the web server. The followings are 
 required before installation of dbemtools and the mrc extension that handles mrc files to be 
 displayed. Some of these packages may be found on the SuSE Linux DVD or included in common 
 package repository. MySQL and the Apache Web Server can be downloaded from their respective 
 websites. 



 |_.Name:|_.Download site:|_.yum package name|_.SuSE rpm name| 
 | Apache|"www.apache.org":http://www.apache.org| httpd| apache2| 
 | php|"www.php.net":http://www.php.net| php| php| 
 | php-devel*|"rpmfind.net/linux/RPM/Development_Languages_PHP.html":http://rpmfind.net/linux/RPM/Development_Languages_PHP.html| php-devel*|<ulink url="http://rpmfind.net/linux/RPM/Development_Languages_PHP.html" 
 >rpmfind.net/linux/RPM/Development_Languages_PHP.html</ulink>| php-devel| php-devel| 
 | php-gd (including GD library, its development libraries and header *)|"www.php.ned/gd":http://www.libgd.org (Use gd2)| php-gd, gd-devel| php-gd,gd-devel| 
 | fftw3 library (including development libraries and header *)|"www.fftw.org":http://www.fftw.org (Use fftw3.x)| fftw3-devel| fftw3-devel| 




 * mrctools are compiled and added to php extension with php-devel package. Mrctools use 
 GD and FFTW3 that need to be compiled from their development libraries while the extension 
 is compiled. If GD and FFTW3 sources were downloaded and compiled directly on your computer, 
 these development files are included. If (as in most cases) GD and FFTW3 are installed from 
 rpm, they are not included. An error message will appear when you attempt to compile 
 mrctools. In this case, you will need separate download and installation of GD-devel and 
 FFTW3-devel. Search "http://rpmfind.net/linux/rpm2html/":http://rpmfind.ned/linux/rpm2html/ <ulink url="http://rpmfind.ned/linux/rpm2html/" 
 >http://rpmfind.net/linux/rpm2html/</ulink> for GD-devel and FFTW3-devel for the rpm 
 distribution needed for your system. 





 h2. Installation tools 



 Use the installation tools available for your linux distribution. 




 *    For example, Use yum utility to install. 


 *    For example, Use the SuSE Linux YaST2 utility or zypper (openSuSE 10.2 and above) 
 to install. 


 * "A <ulink url="http://emg.nysbc.org/bb/viewtopic.php?t=238">A list of required CENTOS 
 rpms and instruction":http://emg.nysbc.org/bb/viewtopic.php?t=238 instruction</ulink> can be found at dbemtools bulletin board at 
 leginon.org. 









 h2.    PHP, PHP-devel, gd, and fftw3 


 Install the packages using your installation tools if available. For example, to 
 install gd as php extension you may use 



 <pre>CentOS> yum install php-gd 
 SuSE10.2 and above> zypper install php-gd</pre> 






 h2.    Configure php.ini 



 Edit the following two sections in php.ini (found as /etc/php.ini on CentOS and 
 /etc/php5/apache2/php.ini on SuSE) so that they look like the following: 



 <pre>register_argc_argv = On</pre> 




 <pre>short_open_tag = On</pre> 




 <pre>max_execution_time = 300       ; Maximum execution time of each script, in seconds 
 max_input_time = 300       ; Maximum amount of time each script may spend parsing request data 
 memory_limit = 256M        ; Maximum amount of memory a script may consume (8MB)</pre> 



 You may want to increase max_input_time and memory_limit if the server is heavily used. 
 At NRAMM, max_input_time=600 and memory_limit=4000M. 





 h2.    Apache Web Server 





 *    Install the Apache Web Server with the YaST or yum utility. 


 *    Find "httpd.conf". 


 This is /etc/httpd/conf/httpd.conf on CentOS and /etc/php5/apache2/httpd.conf on 
 SuSE 


 *    Edit the "httpd.conf" configuration file to look like the following: 



 <pre><IfModule mod_dir.c> 
 DirectoryIndex index.htm index.shtm index.html index.shtml index.php 
 </IfModule></pre> 


 (Note: It may be possible to edit httpd.conf in YaST2 as well.) 


 *    Restart the web server. 



 <pre>apachectl restart 
 or 
 /etc/init.d/httpd restart       (ON CentOS) 
 or 
 /etc/init.d/apache2 restart     (ON SuSE)</pre> 



 If you want to start the web server automatically at boot on SuSE 

 <pre> SuSE >chkconfig apache2 on 
 </pre> 








 h2. Check php information 


 Create the following info.php in your web server document root directory (/var/www/html 
 on CentOS. /srv/www/htdocs on SuSE. You can find its location in httpd.conf mentioned above 
 under the line starting 
 DocumentRoot).<pre><?php 
 phpinfo(); 
 ?></pre> 


 Visit this page at http://yourhost/info.php 


 You will see comprehensive tables of php and apache information, including the location 
 of the addition .ini files, extension, include path, and what extension is enabled. 


 Here is an example screen shot of the part of the info.php page that tells you where 
 php.ini and other configuration files are. 



 !http://emg.nysbc.org/software/leginon/images/images/phpini.png! 






 h2.    mrctools Installation 



 mrctools are installed as php extension and are required for displaying mrc files live 
 on the web browser. 



 h2.    Install php-devel packages on the web server if missing: 


 You can check whether php-devel is installed by 
 typing<pre> >phpize</pre> 


 Follow the instruction for your specific Linux distribution. 


 For example, SUSE users can use YaST or zypper to install them 





 h2.    php-GD/FFTW3-devel 



 Follow instructions from the download site. These may be included already. If not, 
 mrctools installation will fail. 





 h2.    mrctools Installation 



 mrctools are installed from php devel directory. This is usually /usr/include/php/ext 
 where you will find other php extension source such as gd. After the installation, mrc.so 
 should be placed in php's extension directory (Look for "extension_dir" in 
 http://your_host/<link linkend="install_infophp">info.php</link> 




 *    Download dbem tools from "http://emg.nysbc.org/software/mrctools":http://emg.nysbc.org/software/mrctools . <ulink url="http://emg.nysbc.org/software/mrctools" 
 >http://emg.nysbc.org/software/mrctools</ulink>. 


 *    Follow the instruction at "http://emg.nysbc.org/software/mrctools/mrc_so.php":http://emg.nysbc.org/software/mrctools/mrc_so.php <ulink 
 url="http://emg.nysbc.org/software/mrctools/mrc_so.php" 
 >http://emg.nysbc.org/software/mrctools/mrc_so.php</ulink> for installation and 
 testing. The next session about checking php information can also help debugging the 
 installation 









 h2.    Check php information 



 Visit or refresh http://yourhost/info.php <link linkend="install_infophp">which you 
 created earlier</link>. It should have a section looking like this (The version should 
 correspond to what you've just installed): 



 !http://emg.nysbc.org/software/leginon/images/images/phpmrc.png! 



 If mrc is not listed, the extension did not get added at the right order. 





 h2.    Alternative approach if mrc module does not show up in info.php output 



 * find in the <link linkend="install_infophp">info.php web page</link> the location 
 of "additional .ini files parsed" in the first table (such as 
 /etc/php.d/conf.d/*). 


 *    Go to the directory and make a copy of any ini file to use as a template for 
 mrc.ini 



 <pre>>cd [additional_ini_directory] 
 >cp gd.ini mrc.ini</pre> 



 *    Edit mrc.ini to the following 



 <pre>; comment out next line to disable mrc extension in php 
 extension=mrc.so</pre> 



 *    Comment out mrc extension from php.ini (found in /etc/php.ini/ on a typical PHP 
 installation) 



 <pre>;extension=mrc.so</pre> 



 *    restart your webserver 



 <pre>> /etc/init.d/httpd restart</pre> 










 h2.    Web Viewing Tools (dbemtools) Linux 
 Installation 



 php and java scripts for viewing images and Leginon information through the web 
 server. 




 *    Download dbem tools from "http://emg.nysbc.org/software/dbemtools":http://emg.nysbc.org/software/dbemtools . <ulink url="http://emg.nysbc.org/software/dbemtools" 
 >http://emg.nysbc.org/software/dbemtools</ulink>. 


 *    Unpack the package in your [webdirectory] 



 <pre>>cd [webdirectory] 			 #/var/www/html in this example 
 [webdirectory>tar zxvf dbem_1_5_1.tgz</pre> 



 *    Copy config.php.template to config.php and edit the latter by adding these MySQL 
 parameters: 

 "config.php" should be located in /var/www/html/dbem_1_5_1/ on CentOS and 
 /srv/www/htdocs/dbem_1_5_1/ on SuSE. 



 <pre><? 
 // ---define dbem web tools base ---// 
 define('BASE_URL',"/dbem_1_5_1/"; 
 // --- Leginon Viewer Configuration --- // 

 // --- Set your leginon MySQL database server parameters 

 $DB_HOST      = "[your database host]"; 
 $DB_USER      = "<link linkend="db_example_names">usr_object</link>"; 
 $DB_PASS      = ""; 
 $DB          = "<link linkend="db_example_names">dbemdata</link>"; 

 // --- XML test dataset 
 $XML_DATA = "test/viewerdata.xml"; 

 // --- Project database config 

 $PROJECT_URL = "/project_1_2"; 
 $PROJECT_DB_HOST = "[your database host]"; 
 $PROJECT_DB_USER = "<link linkend="db_example_names">usr_object</link>"; 
 $PROJECT_DB_PASS = ""; 
 $PROJECT_DB = "<link linkend="db_example_names">projectdata</link>"; 
 </pre> 



 *    Test the set-up by visiting http://yourhost/dbem_1_5_1 









 h2.    Project management tools Linux Installation 



 Leginon sessions can be catagorized into different projects. The projects are created 
 and viewed trhough a set of web tools. To access them, install the tools on the web server. 
 The same project management tools are also used to create and track appion processing 
 databases. If you want to use our processing pipeline, Appion, in the future, you must 
 install this. 



 h2. Prerequisites for project tools 



 installed dbemtools and its prerequisites 





 h2. project tools 


 Current release: project 1.2. 




 *    Download project tools from "http://emg.nysbc.org/software/dbemtools":http://emg.nysbc.org/software/dbemtools . <ulink 
 url="http://emg.nysbc.org/software/dbemtools" 
 >http://emg.nysbc.org/software/dbemtools</ulink>. 


 *    Unpack the package in your [webdirectory] 



 <pre>>cd [webdirectory] 			 #/var/www/html in this example 
 [webdirectory]>tar zxvf project_1_2.tgz</pre> 



 *    Go to the uncompressed directory 
 project_1_2.<pre>> cd project_1_2</pre> 


 * Copy config.php.template to _config.php_ 



 <pre>> cp config.php.template to config.php</pre> 



 * Edit _config.php_: You need to insert these MySQL 
 parameters in project tool's config.php 



 <pre>// --- Project Configuration --- // 

 // --- Leginon database config 
 $DBEM_PATH="../dbem_1_5_1/"; 

 $DB_HOST    = "[your database host]"; 
 $DB_USER    = "usr_object"; 
 $DB_PASS    = ""; 
 $DB     = "<link linkend="db_example_names">dbemdata</link>"; 

 // --- Project database config 
 $PROJECT_DB_HOST = "[your database host]"; 
 $PROJECT_DB_USER = "<link linkend="db_example_names">usr_object</link>"; 
 $PROJECT_DB_PASS = ""; 
 $PROJECT_DB = "<link linkend="db_example_names">projectdata</link>"; 
 </pre> 



 *    Test the set-up by visiting http://yourhost/project_1_2 











 h2.    Other Tools 


 This section includes tools that may help with Leginon development. 



 h2.    phpMyAdmin 





 *    Download phpMyAdmin from Yast2 or "www.phpmyadmin.net":http://www.phpmyadmin.net <ulink url="http://www.phpmyadmin.net" 
 >www.phpmyadmin.net</ulink> 




 *    Download phpMyAdmin into the directory where the web server has been 
 installed. 






 *    Check phpMyAdmin installation: 



 <pre>>rpm -qa |grep -i phpmyadmin </pre> 



 *    Install from tarball: 



 <pre>> cd [webdirectory] 
 [webdirectory]>tar zxvf phpMyAdmin-2.x.tar.gz</pre> 



 or Install with yum if availabe: 



 <pre>> yum install phpMyAdmin</pre> 



 *    Create phpMyAdmin configuration file called config.inc.php from a 
 sample. 



 <pre>[webdirectory]>cd phpMyAdmin 
 (if you install with yum, the program directory is /usr/share/phpMyAdmin) 

 > cp config.sample.inc.php config.inc.php 
 </pre> 



 *    Make sure these are set correctly in _config.inc.php_. Note that these are for MySQL which we set earlier. 
 You can set specific user, but it is safer just leave it blank. 



 <pre> 
 $cfg['Servers'][$i]['host']              = '[your host]'; 
 $cfg['Servers'][$i]['port']              = ''; 
 $cfg['Servers'][$i]['socket']            = ''; 
 $cfg['Servers'][$i]['connect_type']      = 'tcp'; 
 $cfg['Servers'][$i]['extension']         = 'mysql'; 
 $cfg['Servers'][$i]['compress']          = FALSE; 
 $cfg['Servers'][$i]['controluser']       = ''; 
 $cfg['Servers'][$i]['auth_type']       = 'http'; 
 $cfg['Servers'][$i]['user']            = ''; 
 $cfg['Servers'][$i]['password']        = ''; 
 </pre> 



 *    For additional security, you may restrict mysql root access 



 <pre> 
 $cfg['Servers'][$i]['AllowRoot']       = FALSE; 
 </pre> 



 *    If you want to access phpMyAdmin from another computer, you can add it to its 
 web access configuration file found as /etc/httpd/conf.d/phpMyAdmin.conf in a 
 typical installation 



 <pre> 
 <Directory /usr/share/phpMyAdmin/> 
 order deny,allow 
 deny from all 
 allow from 127.0.0.1 
 allow from YOUR_IP_ADDRESS 
 </Directory> 
 </pre> 














 h2.    Windows installation 




 h2.    Processing-side Leginon Windows Installation 




 h2.    Install Python and Support Packages (Note that python 2.5 must be used): 



 This list does not include pyton XML module because it is included in the python 
 package for window. 



 |_.Name:|_.Download site:| 
 |Python 2.5*|"http://www.python.org":http://www.python.org| 
 |Python for Windows extension (pywin32)|"http://sourceforge.net/projects/pywin32/":http://sourceforge.net/projects/pywin32/| (pywin32)|<ulink url="http://sourceforge.net/projects/pywin32/" 
 >http://sourceforge.net/projects/pywin32/</ulink>| 
 |wxPython 2.5.2.8 or newer|"http://www.wxpython.org":http://www.wxpython.org| 
 |MySQL Python client 1.2 or newer|"http://sourceforge.net/projects/mysql-python":http://sourceforge.net/projects/mysql-python| newer|<ulink url="http://sourceforge.net/projects/mysql-python" 
 >http://sourceforge.net/projects/mysql-python</ulink>| 
 |Python Imaging Library (PIL) 1.1.4 or newer|"http://www.pythonware.com/products/pil/":http://www.pythonware.com/products/pil/| newer|<ulink url="http://www.pythonware.com/products/pil/" 
 >http://www.pythonware.com/products/pil/</ulink>| 
 |NumPy 1.0b5 (tested, others may work)|"http://www.scipy.org":http://www.scipy.org| 
 |SciPy 0.5.1 or newer|"http://www.scipy.org":http://www.scipy.org| 
 |Tortoise SVN client|"http://tortoisesvn.tigris.org":http://tortoisesvn.tigris.org| client|<ulink url="http://tortoisesvn.tigris.org" 
 >http://tortoisesvn.tigris.org</ulink>| 




 *Python 2.5 is the only python version that we have compiled numExtension. libCV and 
 comarray in. Therefore no other python version works for now. 


 Execute the installer file and follow the directions. 





 h2. Packages required from NRAMM 



 Here are the packages you need to install with python installer 



 |_.Name:|_.Purpose:| 
 | Leginon|modular TEM image acquisition| 
 | pyami|general functions| 
 | sinedon|Leginon/database interaction| 
 | pyScope|microscope control and monitoring| 
 | ImageViewer|image viewing for tomography| 




 Because numextension and libCV requires extra compilers, we have created window 
 installer for them for python 2.5 and made them available through "http://www.leginon.org/":http://www.leginon.org/ 

 |_.Downloadfile Name|_.Installed Python Package File|_.Purpose:| 
 |NumExtension-1.2.0.win32-py2.5.exe|numextension.pyd|c extension for numerical processing| 
 |libCV-0.2.win32-py2.5.exe|libCV.pyd|small c library of algorithm from computer vision field| 







 h2. Check out SVN Source Files from the depository 



 Use your mouse to do the following 
 * Create Leginon-1.6-ALL directory somewhere at your convenience 


 * Change directory into Leginon-1.6-ALL 


 * Right-click the mouse botton in this directory window and select Tortoise svn 
 Checkout in the menu:!http://emg.nysbc.org/software/leginon/images/images/svnmenu.png! 


 * Set up svn checkout window like this for <link linkend="windows_packages">EACH 
 of the leginon packages</link>.!http://emg.nysbc.org/software/leginon/images/images/svnco.png! 








 h2. Install the packages you downloaded from NRAMM svn depository 





 * Start a command line Window from Start Menu 


 * Install the package in each folder with commands such as 
 <pre>cd Your_Download_Place\Leginon-1.6-ALL\leginon 
 c:\\python25\python.exe setup.py install</pre> 









 h2. Download the two Window Installer Files from Leginon website 



 "http://www.leginon.org/":http://www.leginon.org/ h2. Install individual packages 



 Excute the installer files and follow the instruction. 





 h2.    Mapping Drives: 



 If you plan to run Leginon directly on the Windows machine, such as in <link 
 linkend="config_C">configuration C</link>, and your data files are served through a 
 Samba server on a Linux machine, you will need to map the network drive. For example, if 
 your Samba server has a hostname your_smbserver, and you have set up a share called 
 [your_share_point] which points to /your_data_path/ and leginon data will be saved under a 
 folder in /your_data_path/leginon/ 




 *    Start, My Computer 


 *    Tools menu, Map network drive 


 *    Use an unmapped drive such as Z: 

 Enter shared path in Windows format 
 as<pre>\\your_smbserver\your_share_point</pre> 


 *    Add the drive and the Linux path to leginon.cfg on the Windows machine 
 as<pre>[Drive Mapping] 
 Z:/your_data_path</pre> 


 *    Add image path to leginon.cfg on the Windows machine in Linux format 
 as<pre>[Images] 
 path:/your_data_path/leginon</pre> 









 h2.    Configure leginon.cfg: 


 Follow instruction in "<link linkend="leginon_cfg">Configure leginon.cfg</link>" in 
 the section for Linux installation but note the location of the configuration files 
 follows. In addition, if the storage disk is mapped onto the Windows PC as drive Z, this 
 mapping should be included in leginon.cfg. See above. 




 *    Configurations for all users 



 <pre> <Python directory>\Lib\site-packages\Leginon\config\leginon.cfg</pre> 


 Example: 
 <pre> C:\Python25\Lib\site-packages\Leginon\config\leginon.cfg</pre> 


 *    Configurations for individual users 



 <pre> <Home directory>\leginon.cfg</pre> 


 Example: 
 <pre> C:\Documents and Settings\Leginon User\leginon.cfg </pre> 


 *    A skeleton (default) configuration file is available: 



 <pre> C:\Python25\Lib\site-packages\Leginon\config\default.cfg</pre> 










 h2.    Configure sinedon.cfg: 


 Sinedon is designed to be able to interact with multiple databases. 

 Follow instruction in "<link linkend="sinedon_cfg">Configure sinedon.cfg</link>" in 
 the section for Linux installation but note the location of the configuration files 
 follows. 




 * For all users, put sinedon.cfg with the installed package 
 as<pre>C:\Python25\Lib\site-packages\sinedon\sinedon.cfg</pre> 


 *    Your home directory on 
 Windows:<pre>C:\Documents and Settings\your_name></pre> 


 * the skeleton sinedon configuration file 
 is<pre>C:\Python25\Lib\site-packages\sinedon\examples\sinedon.cfg</pre> 









 h2.    Create Leginon and Leginon Client shortcut in Start menu menu under Leginon 



 This instruction refers to Windows XP 




 * Go to C:\Documents and Settings\All Users\Start Menu\Programs\ and create a new 
 folder named Leginon. 


 * In another window, go 
 to<pre>C:\Python25\Lib\site-packages\Leginon</pre> 


 * Create a shortcut from start-leginon.py as Leginon and a shortcut from 
 launcher.py as Leginon Client. 


 * Move the two shortcuts into 
 <pre>C:\Documents and Settings\All Users\Start Menu\Programs\Leginon</pre> 









 h2.    Additional Software (Optional): 


 TightVNC (http://www.tightvnc.com) 









 h2. Database server Windows Installation 




 h2. We do not do this at NRAMM. Please follow the instruction in Linux installation and 
 modify it for Windows at your own risk. 



 For a good Windows specific instruction for general PHP configuration with MySQL for 
 Apache 2 in Windows, try http://www.artfulsoftware.com/php_mysql_win.html. 









 h2.    Additional installation on the microscope computer: 



 The full leginon and its supporting packages need to be installed on the Windows computer 
 controlling the microscope. Additional programs are required for communication with the CCD 
 and extra functions for Tecnai scripting not supported as default by FEI Tecnai 
 microscopes 



 h2.    Required supporting programs for the CCD camera from camera makers 



 Install and register the following programs for CCD cameras from the two makes: 



 |_.Camera Make:|_.File:| 
 | Gatan|TecnaiCCD.dll| 
 | Tietz|CAMC4.exe*| 




 * We have experienced slowness of the CAMC4.exe comes with later version Tecnai TUI/TIA. 
 Replacing it with an earlier version of CAMC4.exe resolved the problem. 





 h2. Additional Package required from NRAMM for Gatan camera or camera that uses TIA 



 For Gatan Camera or FEI Eagle Camera that uses TIA, comarray package need to be install 
 with python 



 |_.SVN Package Name|_.Installed Python Package Name|_.Reason for update:| 
 |comarray|comarray|com module output conversion to array| 






 * <link linkend="window_svn">Check out the comarray package</link> from svn 
 depository with your SVN client 

 <pre>cd Leginon-1.6-ALL 
 svn co http://emg.nysbc.org/svn/comarray/branches/leg1.6 comarray</pre> 

 * Start a command line Window from Start Menu 


 * Install the package with commands such as 
 <pre>cd Your_Download_Place\Leginon-1.6-ALL\comarray 
 c:\\python25\python.exe setup.py install</pre> 









 h2.    Supporting programs for film exposure 



 Install the following if you need film exposure on FEI Tecnai TEM through Leginon, 
 available through FEI. Please contact Max Otten: <email>mto@feico.com</email> and request 
 for adaexp.exe that works with your version of Tecnai user interface program. 



 |_.Name:|_.File:| 
 | exposure adaptor|adaexp.exe| 







 h2.    Register adaexep.exe 



 *    From the command prompt: 

 <pre>adaexp.exe /regserver</pre> 

 *    From the program start menu under pyScope or 
 C:\Python25\Lib\site-packages\pyScope\ 

 <pre>updatecom.py</pre> 








 h2. Modify instruments.cfg: 



 Sinedon now have full control of database interaction, therefore, the database 
 configuration in leginon.cfg is no longer needed. 




 * Modify the file instruments.cfg in the installed pyScope directory to that for 
 your microscope and camera. For example, if your microscope uses Tecnai Scripting 
 Interface and you have a Gatan camera that you interface through 
 DigitalMicrograph: 



 <pre>[tem] 
 class: tecnai.Tecnai 
 [camera] 
 class: gatan.Gatan</pre> 



 The file contains other examples of microscope and camera drivers that we 
 distribute from NRAMM. 









 h2. Run updatecom.py 



 From a command line window: 



 <pre>cd C:\python25\Lib\Site-Packages\pyScope 
 C:\python25\python.exe updatecom.py</pre> 



 This should generate a few files, including tecnaicom.py, gatancom.py and tietzcom.py, 
 in the same directory. 





 h2. Additional setup on Tietz PXL camera (optional) 



 The actual Tietz PXL camera dimension is slightly larger than 2048 x 2048. If you'd like 
 to take the images using the maximum of 2048 x 2048 pixels, you may modify the function that 
 get camera dimension in tietz.py of pyScope package. 


 *    Go to C:\Python25\Lib\site-packages\pyScope\ 


 *    Edit tietz.py with a plain text editor 


 *    Find the lines: 



 <pre> def getCameraSize(self): 
 # {'type': dict, 'values': {'x': {'type': int}, 'y': {'type': int}}}} 
 x = self._getParameterValue('cpTotalDimensionX') 
 y = self._getParameterValue('cpTotalDimensionY') 
 return {'x': x, 'y': y} 
 </pre> 



 *    Change the last line to: 



 <pre>      return {'x': 2048, 'y': 2048}</pre> 








 h2.    Additional Software (Optional): 


 TightVNC (http://www.tightvnc.com) if you get tired of going into the microscope room 
 just to open the column valves. 









 h2.    What is next 




 h2.    Perform Administration Setup 


 See Next chapter on <link linkend="addusers">Leginon Administration Tools</link>. 






 h2.    Create a test project 


 See the chapter on <link linkend="project">Project Management Tools</link>. 





 h2.    Perform Microscope Setup and Test run 


 See the chapter on <link linkend="runleg_chapter">Start Leginon</link>. 







 h2.    Backup Practices 




 h2.    Ideal setup: 




 h2.    Regular computer backup 



 To protect your program installation. 





 h2.    Full backup of the databases every night 



 The database is the metadata generated by Leginon named "dbemdata" in the installation 
 example. 





 h2. Full/Incremental/differential backup of the images 



 The image files located in [your storage disk] should be backup in full at least once 
 a month, and nightly in differential or incremental mode. 







 h2.    Current NRAMM setup: 



 Because our tape backup system is not on-site and the data have to transfer over slow 
 network to perform the task, we have not been able to backup in the ideal setting. Here is 
 what we currently do: 



 h2.    Regular computer backup 



 TSRI Research Computing provides regular back up service that does full backup of the 
 computers every four weeks and incremental backup every night. The full backup expires in 
 4 months and the incremental backup one month. We do this for the computers running 
 Leginon main program, the database server, as well as the web server. 





 h2.    Regular backup &amp; tar of the databases every night 



 On top of the TSRI backup, we also tar the database everynight and store it on the 
 institutional tape library. 





 h2.    rsync to a tape library of the image storage disk 



 As our image storage disks total 15T byte, we currently use rsync function to update a 
 copy on our institutional tape library. It creates new files, updates old files, but does 
 not remove old files on the tape if it is removed on the storage disk. We do not think 
 this is the best solution since it is not possible to retrieve old files that have been 
 modified on a later time.