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Start with existing CentOS installation » History » Version 51

Amber Herold, 03/17/2010 02:21 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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h3. 3.1 Install the additional package repositories 
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*NOTE*
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There are several additional CentOS repositories that you can install.
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These repositories provide additional packages, such as patented software (MP3 players),
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closed source applications (Flash plugin, Adobe Acrobat Reader)
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and lesser used packages (python numpy, Gnu Scientific Library).
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But some repositories install packages over other packages,
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which can cause problems and conflicts (ATrpms is bad at this). So I recommend only installing
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EPEL and RPM Fusion. Read more here:
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"CentOS Additional Repositories":http://wiki.centos.org/AdditionalResources/Repositories 
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h4. 3.1.1 Extra Packages for Enterprise Linux (EPEL) 
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* http://fedoraproject.org/wiki/EPEL
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* contains a wealth of packages required for appion
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.Download repository rpm and install
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<pre>
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$ sudo rpm -Uvh http://download.fedora.redhat.com/pub/epel/5/`uname -i`/epel-release-5-3.noarch.rpm
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</pre>
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h4. 3.1.2 RPM Fusion 
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* http://rpmfusion.org/
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* good for mp3 and other patent limited software
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.Download repository rpms and install
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<pre>
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$ sudo rpm -Uhv http://download1.rpmfusion.org/free/el/updates/testing/5/`uname -i`/rpmfusion-free-release-5-0.1.noarch.rpm
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$ sudo rpm -Uvh http://download1.rpmfusion.org/nonfree/el/updates/testing/5/`uname -i`/rpmfusion-nonfree-release-5-0.1.noarch.rpm
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</pre>
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h3. 3.2 Update current packages 
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.Update the updater to make life easier
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<pre>
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$ sudo yum -y update yum
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</pre>
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.Update all packages
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<pre>
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$ sudo yum -y update
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</pre>
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*NOTE*
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Download was over 129 MB (in July 2009). If you have a slow internet connection you can setup presto/deltarpms, "see this email]":http://www.linux-archive.org/centos-development/222706-presto-deltarpm.html 
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You may want to restart your computer when this completes.
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h4. .Install Complete list of additional packages:
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* *python tools*: python-tools python-devel
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* *general applications*: subversion ImageMagick grace gnuplot python-matplotlib
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* *Tilt Picker*: wxPython numpy scipy python-imaging
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* *FindEM*: gcc-gfortran compat-gcc-34-g77
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* *Ace 2*: gcc-objc fftw3-devel gsl-devel
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* *Sinedon*: mysql mysql-server MySQL-python
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* *DBEM*: httpd php php-mysql phpMyAdmin
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* *Xmipp MPI*: gcc-c++ openmpi-devel libtiff-devel
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* *MRC tools*: php-devel gd-devel re2c fftw2-devel php-gd
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* *UCSF Chimera imaging*: xorg-x11-server-Xvfb
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<pre>
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$ sudo yum -y install \
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python-tools python-devel python-matplotlib \
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subversion ImageMagick grace gnuplot \
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wxPython numpy scipy python-imaging \
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gcc-gfortran compat-gcc-34-g77 \
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gcc-objc fftw3-devel gsl-devel \
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mysql mysql-server MySQL-python \
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httpd php php-mysql phpMyAdmin  \
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gcc-c++ openmpi-devel libtiff-devel \
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php-devel gd-devel re2c fftw2-devel php-gd \
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xorg-x11-server-Xvfb
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</pre>
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If you have an nVidia video card and setup RPM fusion, install the nVidia binary, will speed things up especially for UCSF Chimera
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<pre>
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$ sudo yum -y install nvidia-x11-drv
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</pre>
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.Clean up packages to save drive space
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<pre>
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$ sudo yum clean all
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</pre>
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.Re-index the hard drive, this will come in handy later
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<pre>
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$ sudo updatedb
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</pre>
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.Enable servers on reboot
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<pre>
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$ sudo /sbin/chkconfig httpd on
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</pre>
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<pre>
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$ sudo /sbin/chkconfig mysqld on
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</pre>
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You can further configure this with the GUI and turn off unnecessary items
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<pre>
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$ system-config-services
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</pre>
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.Reboot the computer
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<pre>
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$ sudo reboot
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</pre>
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----
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h2. 4 MRC PHP Extension Installation and Testing
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h3. 4.1 Build the MRC module
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Download "php_mrc_src_1_5_1.tgz":http://emg.nysbc.org/software/dwd.php?id=N1HDb4ac22efb5b38b05fd3575d42d3e4adc2
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h4. cd to your php devel directory
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<pre>
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> cd /usr/include/php/ext/
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> mv [downloads]/php_mrc_src_1_5_1.tgz .
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</pre>
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h4. Untar the archive
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<pre>
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> tar zxvf php_mrc_src_1_5_1.tgz
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> cd mrc/
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</pre>
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h4. Make sure that GD and FFTW 3 devel libraries are installed
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<pre>
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> phpize
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> ./configure 
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> make
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> make install
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</pre>
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h3. 4.2 Install MRC module
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h4.  Check that mrc.so is in your php extension directory
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<pre>
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> ls /usr/lib/php/extensions
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</pre>
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You should see mrc.so listed.
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h4. Make sure that GD and FFTW 3 libraries are installed
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* edit your  php configuration file php.ini to add "mrc.so" extension.
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* You might also increase the memory_limit field. It is set to 8M by default. The more the merrier!
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* 4kx4k float MRC image is about 64MB
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<pre>
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> vi /etc/php.ini
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</pre>
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* increase memory
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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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* Create the mrc.ini file
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<pre>
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> cd /etc/php.d
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vi mrc.ini
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</pre>
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* add the following lines
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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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*NOTE:* If PHP modules are already listed in PHP.ini do the following:
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* check extension_dir value
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<pre>
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 extension_dir = /usr/lib64/php/extensions
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</pre>
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* add the following at the end of the [extension section]
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<pre>
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 extension=mrc.so
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</pre>
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h4. Restart your webserver
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<pre>
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/etc/init.d/apache2 restart
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</pre>
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OR
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<pre>
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/etc/init.d/httpd restart
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</pre>
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h3. 4.3 Test the MRC module installation
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Download this MRC file "mymrc.mrc":http://emg.nysbc.org/attachments/55/mymrc.mrc and the following 2 scripts into the same directory to test the PHP mrc extension. 
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* gd module testing script "ex1.php":http://emg.nysbc.org/attachments/53/ex1.php
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* fftw module testing script "ex2.php":http://emg.nysbc.org/attachments/54/ex2.php
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Run the scripts with the following commands:
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The expected results are shown below. If you get the same images, you've installed the extension properly.
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> php -q ex1.php | display
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</pre>
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* gd module test result:
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!http://emg.nysbc.org/attachments/57/ex1.php.png!
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<pre>
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> php -q ex2.php | display
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</pre>
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* fftw module test result:
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!http://emg.nysbc.org/attachments/58/ex2.php.png!
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----
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h2. 5 Setup MySQL (appiondata) databases 
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[[Setup MySQL database]]
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----
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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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</pre>
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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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</pre>
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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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; 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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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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$ 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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$ system-config-securitylevel
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</pre>
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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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</pre>
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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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----
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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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* For more info, see http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/InstallingTheSoftware
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* Go into Xmipp source directory
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* Find openmpi directory
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$ locate libmpi.so
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</pre>
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/usr/lib/openmpi/1.2.7-gcc/lib/libmpi.so
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</pre>
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* Setup Xmipp to use openmpi by changing three lines in SConstruct
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$ cp SConstruct SConstruct.orig
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</pre>
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$ nano SConstruct
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</pre>
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<pre>
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opts.Add('MPI_INCLUDE', 'MPI headers dir ', '/usr/lib/openmpi/1.2.7-gcc/include/')
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opts.Add('MPI_LIBDIR', 'MPI libraries dir ', '/usr/lib/openmpi/1.2.7-gcc/lib/')
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opts.Add('MPI_LIB', 'MPI library', 'mpi')
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</pre>
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* Compile
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$ sudo mpi-selector --yes --system --set `rpm --qf '%{NAME}-%{VERSION}-gcc-%{ARCH}\n' -q openmpi`
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</pre>
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$ export PATH=$PATH:/usr/lib/openmpi/1.2.7-gcc/bin
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</pre>
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$ ./scons.configure
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you should see the line:
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<pre>
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* Checking for MPI ... yes
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</pre>
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<pre>
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$ ./scons.compile
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</pre>
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h2. 9 Install a PBS job submission system
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You'll need to install a "Portable Batch System":http://en.wikipedia.org/wiki/Portable_Batch_System for job submission, such as "TORQUE":http://en.wikipedia.org/wiki/TORQUE_Resource_Manager . I know Torque comes with Fedora 10, but not CentOS.
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* An RPM is available in the EPEL testing section
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$ sudo yum -y --enablerepo=epel-testing install torque
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</pre>
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or another way to get packages
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<pre>
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$ wget http://centos.karan.org/el5/extras/testing/`uname -i`/RPMS/torque-2.1.9-1.el5.kb.`uname -i`.rpm
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$ sudo yum -y localinstall --nogpgcheck torque-2.1.9-1.el5.kb.`uname -i`.rpm
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$ #sudo rpm -Uhv torque-2.1.9-1.el5.kb.`uname -i`.rpm
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</pre>
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After installing torque it needs to be configured. Sorry, we have no documentation for configuring torque at this time. You may try http://www.clusterresources.com/products/torque-resource-manager.php