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Start with existing CentOS installation » History » Version 57

Amber Herold, 03/17/2010 02:47 PM

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h1. Start with existing CentOS 5.3 64-bit installation
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{{>toc}}





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h2. 3 Download additional software 





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[[Download additional Software]]





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h2. 4 MRC PHP Extension Installation and Testing





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[[MRC PHP Extension Installation and Testing]]





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h2. 5 Setup MySQL (appiondata) databases 





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[[Setup MySQL database]]





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h2. 6 Compile and setup Appion python programs 





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[[Setup Appion programs]]





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h2. 7 Install webpages (myamiweb)





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Refer to [[Start_with_existing_ANY_Linux_flavor_OS#3-Web-server-side-installation|Web server side installation]]





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h3. Install MRC Tools 





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h4. Compile MRC tools 





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* Go to your php devel directory and untar the archive





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* If unsure where it is, use info.php to find it under *extension_dir*





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<pre>





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$ cd /usr/include/php/ext/





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$ sudo mkdir mrc





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$ sudo chmod 777 mrc





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$ sudo chown $USER mrc





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</pre>





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* Unpackage MRC Tools from http://emg.nysbc.org/software/mrctools/





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<pre>





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$ tar zxvf ~/php_mrc.tgz





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$ cd mrc/





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* Compile and install the MRC module





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<pre>





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$ phpize





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$ ./configure 





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$ make





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$ sudo make install





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h4. Configure PHP for MRC Tools 





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* Edit your php configuration file php.ini to add "mrc.so" extension.





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<pre>





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$ sudo nano /etc/php.d/mrc.ini





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</pre>





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* add mrc.so to extensions





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<pre>





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; Enable mrc extension module





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extension=mrc.so





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</pre>





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* To test MRC tools, go to this website:





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http://emg.nysbc.org/software/mrctools/mrc_so.php





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h3. Configure PHP 





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* increase the memory limit, EM images are big 64MB:





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<pre>





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memory_limit = 256M; Maximum amount of memory





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</pre>





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* Turn error display on:





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<pre>





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display_errors = On





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</pre>





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<pre>





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error_reporting = E_ALL & ~E_NOTICE





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</pre>





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* restart the webserver





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<pre>





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$ sudo /sbin/service httpd restart





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</pre>





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h3. Install DBEM and project php source 





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





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h3. Configuration 





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h4. configure apache 





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* allow REMOTE_HOST lookups in apache





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<pre>





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$ sudo nano /etc/httpd/conf/httpd.conf





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</pre>





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* turn _HostnameLookups_ to On





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<pre>





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HostnameLookups On





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</pre>





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* restart the webserver





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<pre>





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$ sudo /sbin/service httpd restart





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</pre>





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h4. configure project_1_2, dbem_1_5_1, and dbem_1_5_1/processing 





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





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h3. Initialize database tables from the web tools 





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





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h3. Potential problems 





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h4. Firewall settings 





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





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<pre>





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$ system-config-securitylevel





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h4. Security-enhanced linux 





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"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:





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<pre>





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





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





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h2. 8 Install external packages 





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*Please follow individual package installation instruction provided with them*





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h3. Compile Xmipp for OpenMPI 





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[[Install Xmipp]]





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h2. 9 Install a PBS job submission system





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[[Install PBS]]





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