Myami on Ubuntu » History » Version 32
Anchi Cheng, 09/25/2012 03:33 PM
1 | 26 | Jim Pulokas | *_WARNING: This is a preliminary document. Use at your own risk!_* |
---|---|---|---|
2 | |||
3 | 1 | Jim Pulokas | h1. myami on Ubuntu |
4 | |||
5 | 24 | Jim Pulokas | This is mainly a log of various experiences installing myami on Ubuntu which will gradually evolve into a more formal document. This will attempt to demonstrate the installation of all of myami including both leginon and appion on a single Ubuntu host. This will also include running MySQL, Apache Torque, etc. on this local host without needing to connect to any other host. |
6 | 1 | Jim Pulokas | |
7 | 3 | Jim Pulokas | h2. Installing a basic Ubuntu system |
8 | 1 | Jim Pulokas | |
9 | We use Ubuntu 12.04 LTS (Precise) Desktop 64 bit. Install a basic system from an image on CD or bootable USB drive. Default selections during the install process, no 3rd party repositories, no network configuration and no updates during the installation. This makes it easier in the remainder of this document to know that we have started from a known base system. Reboot. |
||
10 | |||
11 | Following the initial reboot: |
||
12 | 4 | Jim Pulokas | * connect to the internet (click network icon in upper right) |
13 | 3 | Jim Pulokas | * update packages:<pre>sudo apt-get update |
14 | sudo apt-get upgrade</pre> |
||
15 | 1 | Jim Pulokas | * Reboot |
16 | 3 | Jim Pulokas | |
17 | You now have a basic up-to-date Ubuntu system |
||
18 | |||
19 | 18 | Jim Pulokas | h2. Installing additional packages required by myami |
20 | |||
21 | There are many additional packages to install, but we can try to condense that list to the smallest set necessary to pass to the update command which will then figure out all the other dependencies. |
||
22 | |||
23 | Here is a single command to install all the necessary packages:<pre>sudo apt-get install subversion vim python-MySQLdb python-wxgtk2.8 python-fs mysql-server php5 php5-mysql libssh2-php php5-gd</pre>During installation, you will be prompted several times to create a mysql root password. This can optionally be left blank at the expense of less security. Note: installing the vim text editor is my own preference... use an inferior text editor if you wish :) |
||
24 | |||
25 | The Scipy package is also required, but the current version 0.9.0 that comes with Ubuntu 12.04 is broken. You need to grab the more recent version of Scipy from Ubuntu Quantal (development version). To make a clean installation that will not confuse the package manager we have prepared a mini-repository that includes this new scipy. You can download and install scipy using the following set of commands copied into your terminal.<pre>sudo mkdir /usr/local/share/myami</pre>That should get your password in the sudo cache so you can copy the rest of these without entering a password:<pre>cd /usr/local/share/myami |
||
26 | sudo wget http://emg.nysbc.org/attachments/download/1488/ubuntu-scipy-0.10.1.tar.bz |
||
27 | sudo tar jxf ubuntu-scipy-0.10.1.tar.bz |
||
28 | sudo sh -c 'echo "deb file:///usr/local/share/myami/ubuntu-scipy-0.10.1 ./" > /etc/apt/sources.list.d/myami.list' |
||
29 | sudo apt-get update |
||
30 | sudo apt-get install python-scipy</pre>Make sure that last line executes (may have to hit enter). Also, you may have to confirm installing it without authentication. |
||
31 | |||
32 | 14 | Jim Pulokas | h2. Setting up MySQL databases |
33 | 12 | Jim Pulokas | |
34 | 28 | Anchi Cheng | * change bind-address in /etc/mysql/my.cnf to your mysql server address |
35 | 29 | Anchi Cheng | <pre> |
36 | 28 | Anchi Cheng | #bind-address = 127.0.0.1 |
37 | bind-address = your.fixed.ip.address |
||
38 | 29 | Anchi Cheng | </pre> |
39 | 28 | Anchi Cheng | |
40 | 12 | Jim Pulokas | * create /etc/mysql/conf.d/myami.cnf with the following contents:<pre>[mysqld] |
41 | default-storage-engine=myisam |
||
42 | query_cache_size = 100M |
||
43 | query_cache_limit = 100M</pre> |
||
44 | * restart mysql server:<pre>sudo service mysql restart</pre> |
||
45 | 14 | Jim Pulokas | * create databases:<pre>sudo mysqladmin create leginondb |
46 | 12 | Jim Pulokas | sudo mysqladmin create projectdb</pre> |
47 | 13 | Jim Pulokas | * create user and grand privileges... login to mysql as root:<pre>mysql -u root mysql</pre> |
48 | 30 | Anchi Cheng | ** once inside mysql client, grant privs:<pre>create user usr_object@'localhost'; |
49 | 12 | Jim Pulokas | grant all privileges on leginondb.* to usr_object@'localhost'; |
50 | 16 | Jim Pulokas | grant all privileges on projectdb.* to usr_object@'localhost'; |
51 | 1 | Jim Pulokas | grant alter, create, insert, select, update on `ap%`.* to usr_object@localhost;</pre> |
52 | 4 | Jim Pulokas | |
53 | 5 | Jim Pulokas | h2. Setting up Apache web server |
54 | |||
55 | create /etc/php5/conf.d/myami.ini with the following contents:<pre>error_reporting = E_ALL & ~E_NOTICE & ~E_WARNING |
||
56 | display_errors = On |
||
57 | 8 | Jim Pulokas | register_argc_argv = On |
58 | 9 | Jim Pulokas | short_open_tag = On |
59 | 7 | Jim Pulokas | max_execution_time = 300 |
60 | 10 | Jim Pulokas | max_input_time = 300 |
61 | 19 | Jim Pulokas | memory_limit = 256M</pre>restart apache:<pre>sudo service apache2 restart</pre> |
62 | 20 | Jim Pulokas | |
63 | h2. Install myami |
||
64 | |||
65 | 32 | Anchi Cheng | * check out a sandbox from the subversion repository. Note: You may use trunk which is generally unstable and untested but most up to date. Use at your own risk!:<pre>cd |
66 | svn co http://emg.nysbc.org/svn/myami/branches/myami-2.2-redux myami-2.2-redux</pre> |
||
67 | * install myami python packages:<pre>cd myami-2.2-redux |
||
68 | 20 | Jim Pulokas | sudo ./pysetup.sh install |
69 | ADD APPION PYTHON PACKAGE INSTALL HERE</pre> |
||
70 | 1 | Jim Pulokas | * create image storage directory:<pre>sudo mkdir /data |
71 | 20 | Jim Pulokas | sudo mkdir /data/leginon |
72 | 21 | Jim Pulokas | sudo chmod a+w /data/leginon</pre> |
73 | 20 | Jim Pulokas | * configure python packages:<pre>cp leginon/leginon.cfg.template ~/leginon.cfg |
74 | cp sinedon/examples/sinedon.cfg ~/sinedon.cfg |
||
75 | cp pyscope/instruments.cfg.template ~/instruments.cfg</pre>then edit and config all three of the above files. |
||
76 | * Install myamiweb:<pre>sudo cp -r myamiweb /var/www |
||
77 | sudo chmod 777 /var/www/myamiweb</pre> |
||
78 | * setup and configure redux:<pre>sudo mkdir /var/cache/myami |
||
79 | sudo mkdir /var/cache/myami/redux |
||
80 | sudo chown -R www-data.www-data /var/cache/myami |
||
81 | 31 | Jim Pulokas | sudo vim /usr/local/lib/python2.7/dist-packages/redux/pipeline.py</pre>(set cache path and size) |
82 | 22 | Jim Pulokas | * initialize databases and generate config.php using web tool: http://localhost/myamiweb/setup |
83 | 20 | Jim Pulokas | * make any manual fixes to /var/www/myamiweb/config.php, such as enable redux cache, disable regular cache... |
84 | * Other administrative setup: |
||
85 | ** http://localhost/myamiweb/admin.php |
||
86 | *** add user |
||
87 | *** import apps |
||
88 | ** http://localhost/myamiweb/project/project.php |
||
89 | *** add new project |
||
90 | 23 | Jim Pulokas | * test if leginon starts:<pre>start-leginon.py</pre> |
91 | 25 | Jim Pulokas | |
92 | h2. Optional additions |
||
93 | |||
94 | * for mounting external network shares |
||
95 | ** install nfs-common<pre>sudo apt-get install nfs-common</pre> |
||
96 | ** For automounting and similar services install NIS:<pre>sudo apt-get install nis</pre> |