Project

General

Profile

Edit History

Start with existing CentOS installation » History » Version 69

Amber Herold, 04/06/2010 01:24 PM

1 25 Amber Herold 
h1. Start with existing CentOS 5.3 64-bit installation
2 5 Amber Herold 





    3
    
    
    
{{>toc}}





    4
    1
    Amber Herold
    





    5
    69
    Amber Herold
    
h2. 1 Download additional software 





    6
    2
    Amber Herold
    





    7
    56
    Amber Herold
    
[[Download additional Software]]





    8
    1
    Amber Herold
    





    9
    24
    Amber Herold
    
----





    10
    1
    Amber Herold
    





    11
    69
    Amber Herold
    
h2. 2 Database Server Installation





    12
    
    
    
 





    13
    55
    Amber Herold
    





    14
    
    
    
[[Setup MySQL database]]





    15
    
    
    





    16
    1
    Amber Herold
    
----





    17
    55
    Amber Herold
    





    18
    69
    Amber Herold
    
h2. 3 Processing Server Installation 





    19
    55
    Amber Herold
    





    20
    47
    Amber Herold
    





    21
    49
    Amber Herold
    
[[Setup Appion programs]]





    22
    
    
    





    23
    57
    Amber Herold
    
----





    24
    41
    Amber Herold
    





    25
    69
    Amber Herold
    
h2. 4 Web Server Installation





    26
    13
    Amber Herold
    





    27
    58
    Amber Herold
    





    28
    60
    Amber Herold
    
Refer to [[Web Server Installation]]





    29
    
    
    





    30
    59
    Amber Herold
    





    31
    
    
    
*TODO:* The next steps have already been completed, grab any extra info from here and move to other location.





    32
    2
    Amber Herold
    





    33
    15
    Amber Herold
    





    34
    2
    Amber Herold
    
h3. Install DBEM and project php source 





    35
    
    
    





    36
    
    
    
Please consult the other [[Start_with_existing_ANY_Linux_flavor_OS#3-Web-server-side-installation|Install guide]]





    37
    
    
    





    38
    
    
    
h3. Configuration 





    39
    13
    Amber Herold
    





    40
    2
    Amber Herold
    
h4. configure apache 





    41
    
    
    





    42
    
    
    
* allow REMOTE_HOST lookups in apache





    43
    
    
    





    44
    
    
    
<pre>





    45
    13
    Amber Herold
    
$ sudo nano /etc/httpd/conf/httpd.conf





    46
    2
    Amber Herold
    
</pre>





    47
    
    
    





    48
    
    
    
* turn _HostnameLookups_ to On





    49
    
    
    





    50
    
    
    
<pre>





    51
    13
    Amber Herold
    
HostnameLookups On





    52
    2
    Amber Herold
    
</pre>





    53
    
    
    





    54
    
    
    
* restart the webserver





    55
    
    
    





    56
    
    
    
<pre>





    57
    
    
    
$ sudo /sbin/service httpd restart





    58
    1
    Amber Herold
    
</pre>





    59
    15
    Amber Herold
    





    60
    2
    Amber Herold
    
h4. configure project_1_2, dbem_1_5_1, and dbem_1_5_1/processing 





    61
    
    
    





    62
    
    
    
Please consult the other [[Start_with_existing_ANY_Linux_flavor_OS#3-Web-server-side-installation|Install guide]]





    63
    16
    Amber Herold
    





    64
    2
    Amber Herold
    
h3. Initialize database tables from the web tools 





    65
    
    
    





    66
    
    
    
Please consult [[Start_with_existing_ANY_Linux_flavor_OS#4-Create-a-test-project-and-processing-database|Create a test project and processing database]]





    67
    
    
    





    68
    
    
    
h3. Potential problems 





    69
    
    
    





    70
    
    
    
h4. Firewall settings 





    71
    
    
    





    72
    
    
    
You may need to configure your firewall to allow incoming HTTP (port 80) and MySQL (port 3306) traffic:





    73
    
    
    





    74
    
    
    
<pre>





    75
    
    
    
$ system-config-securitylevel





    76
    
    
    
</pre>





    77
    
    
    





    78
    
    
    
h4. Security-enhanced linux 





    79
    
    
    





    80
    1
    Amber Herold
    
"Security-enhanced linux (SELinux)":http://en.wikipedia.org/wiki/Security-Enhanced_Linux  may be preventing your files from loading. To fix this run the following command:





    81
    2
    Amber Herold
    





    82
    
    
    
<pre>





    83
    
    
    
$ sudo /usr/bin/chcon -R -t httpd_sys_content_t /var/www/html/





    84
    
    
    
</pre>





    85
    
    
    





    86
    
    
    
see "this website":http://docs.fedoraproject.org/selinux-apache-fc3/sn-simple-setup.html  for more details on SELinux





    87
    13
    Amber Herold
    





    88
    
    
    
----





    89
    1
    Amber Herold
    





    90
    69
    Amber Herold
    
h2. 5 Install external packages 





    91
    2
    Amber Herold
    





    92
    
    
    
*Please follow individual package installation instruction provided with them*





    93
    
    
    





    94
    1
    Amber Herold
    
h3. Compile Xmipp for OpenMPI 





    95
    13
    Amber Herold
    





    96
    
    
    
[[Install Xmipp]]





    97
    2
    Amber Herold
    





    98
    
    
    
----





    99
    56
    Amber Herold
    





    100
    69
    Amber Herold
    
h2. 6 Install a PBS job submission system





    101
    51
    Amber Herold
    





    102
    2
    Amber Herold
    
[[Install PBS]]





    103
    56
    Amber Herold
    





    104
    
    
    
----





    105
    61
    Amber Herold
    





    106
    69
    Amber Herold
    
h2. 7 Do testing (Start at 4 of any flavor)





    107
    61
    Amber Herold
    





    108
    64
    Amber Herold
    
[[Start_with_existing_ANY_Linux_flavor_OS#4-Create-a-test-project-and-processing-database|Get started with a project]]





    109
    65
    Amber Herold
    
This has some repeated information.





    110
    
    
    
Basically need to do the following:





    111
    
    
    





    112
    
    
    
# Add a group





    113
    
    
    
# Add a user





    114
    
    
    
# Add instruments





    115
    
    
    
# Create a project





    116
    
    
    
# Create the project database





    117
    
    
    
# Upload images to a new session





    118
    
    
    
# View the images





    119
    61
    Amber Herold
    
----