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Start with existing CentOS installation » History » Version 5

Amber Herold, 01/19/2010 09:12 PM

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h1. Start with existing CentOS installation
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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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.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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h2. 4. Download and install Leginon and associated packages 
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Refer to [http://code.google.com/p/appion/wiki/AppionInstall_with_Leginon#5._processing_server-side_installation]
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h2. 5. Compile and setup python (pyappion) programs 
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h3. 5.1. Compile FindEM 
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 * Goto pyappion/findem folder to make findem.exe
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 * Compile the libraries and binary
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<pre>
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$ make
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</pre>
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 * Test findem.exe to see if it runs
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<pre>
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$ make test
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</pre>
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*WARNING*
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Only if the first part fails, you must add the path to libg2c.so library file.
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Otherwise skip to next section.
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 * locate libg2c.so library file
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<pre>
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$ ls /usr/lib/gcc/`uname -i`-redhat-linux/3.4.6/libg2c.so
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</pre>
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$ locate libg2c.so
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</pre>
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 * Edit Makefile with location of libg2c.so
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<pre>
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$ nano Makefile
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</pre>
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 * Example: EXLIBS=-L/usr/lib/gcc/i386-redhat-linux/3.4.6/ -lg2c
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 * Re-compile
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h3. 5.2. Compile Ace2 
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*WARNING*
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ace2 typically requires fftw 3.2 or greater, but you can remove the FFTW_WISDOM_ONLY flag in Image.m
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*NOTE*
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64 bit binaries are included with pyappion
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 * Goto pyappion/ace2
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 * compile the libraries and binary
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 * test to see if program runs
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<pre>
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$ make
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$ ./ace2.exe -h
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$ ./ace2correct.exe -h
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$ mv -v ./ace2*.exe ../bin
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</pre>
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h3. 5.3. Compile Radermacher module 
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 * Goto pyappion/radermacher
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 * compile the libraries and binary
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<pre>
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$ python ./setup.py build
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</pre>
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 * install module globally
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<pre>
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$ sudo python ./setup.py install
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</pre>
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 * test installed module
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<pre>
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$ python
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</pre>
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<pre>
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>>> import radermacher
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>>> <Ctrl-D>
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</pre>
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h3. 5.4. Test PyAppion 
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 * Go into pyappion directory
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 * Add leginon to PYTHONPATH if Leginon is built locally
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$ export PYTHONPATH="$LEGINONPATH:$PYTHONPATH"
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</pre>
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 * Add pyappion lib to PYTHONPATH
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<pre>
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$ export PYTHONPATH="/your-complete-path-to-pyappion/lib:$PYTHONPATH"
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</pre>
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 * Run the test script
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$ ./check.sh
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</pre>
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*NOTE*
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You can ignore EMAN, MATLAB, and UCSF Chimera errors at this point
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h2. 6. Setup MySQL (appiondata) databases 
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Refer to [http://code.google.com/p/appion/wiki/AppionInstall_with_Leginon#2._Setup_MySQL_databases]
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h3. Configure MySQL 
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Edit the configuration file:
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$ sudo nano /etc/my.cnf
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</pre>
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Add or edit the following lines:
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query_cache_type = 1
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query_cache_size = 100M
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query_cache_limit= 100M
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</pre>
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Restart MySQL
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$ sudo /sbin/service mysqld restart
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</pre>
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h3. Configure phpMyAdmin 
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Edit the phpMyAdmin config file:
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$ sudo nano /etc/phpMyAdmin/config.inc.php
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</pre> 
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and change the following lines:
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$cfg['Servers'][$i]['AllowRoot']     = FALSE;
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</pre>
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Edit the phpMyAdmin apache config file:
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$ sudo nano /etc/httpd/conf.d/phpMyAdmin.conf
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</pre>
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and change the following lines:
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<pre>
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<Directory /usr/share/phpMyAdmin/>
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   order deny,allow
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   deny from all
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   allow from 127.0.0.1
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   allow from YOUR_IP_ADDRESS
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</Directory>
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</pre>
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h2. 7. Install webpages (appionweb)
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Refer to [http://code.google.com/p/appion/wiki/AppionInstall_with_Leginon#3._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 $USER mrc
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</pre>
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 * Unpackage MRC Tools from http://emg.nysbc.org/software/mrctools/
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$ 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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$ 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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$ 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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memory_limit = 256M; Maximum amount of memory
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</pre>
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 * Turn error display on:
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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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$ 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 [http://code.google.com/p/appion/wiki/AppionInstall_with_Leginon#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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HostnameLookups On
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</pre>
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 * restart the webserver
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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 [http://code.google.com/p/appion/wiki/AppionInstall_with_Leginon#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 [http://code.google.com/p/appion/wiki/AppionInstall_with_Leginon#4._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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</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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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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 * 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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<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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<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=$PATH:/usr/lib/openmpi/1.2.7-gcc/bin
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</pre>
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<pre>
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$ ./scons.configure
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</pre>
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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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$ ./scons.compile
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</pre>
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= 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