Comanche intends to gather and format MD topologies in order to extend the number of available lipids and build membranes in an automated way based on a CG2AT flow. More complex lipid compositions will then be available. This project will provide a web interface where you can input a molecule (and its topology if needed) and choose a membrane composition to compute their interaction with the Gromacs software on distant nodes.
Install the latest Ubuntu Gnome Desktop on all computers with a common user name and password on all systems. In a first development step Virtualbox will be used. comanche will be our common user name on all systems. sudo password should match on all systems. MySQL and phpmyadmin passwords will match system root password (master only). Make sure all systems have time settings synchronized.
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Install the following components on Master
apache2 (web directory /var/www/) mysql-server (create root user and password “comanche”) php5 php5-gd (for image to text engine - captcha) phmypadmin (create root user and password ) munge (create authentication key on Master and copy to all nodes) slurm-llnl (create slurm.conf from web page and copy to all nodes and Master) nfs-kernel-server nfs-common ntp build-essential cmake python-pip libmysqlclient-dev python-dev python-mysqldb python3-mysql.connector
pip install mysql pip install MySQL-python pip install mysql-connector-python --allow-external mysql-connector-python
if the last command doesn't work: cd ~/Software wget https://cdn.mysql.com/Downloads/Connector-Python/mysql-connector-python-2.0.3.zip unzip mysql-connector-python-2.0.3.zip cd mysql-connector-python-2.0.3 python setup.py install
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Configure /etc/hosts (in sudo mode)
-----hosts---start---------- 127.0.0.1 localhost linux1 127.0.1.1 comancheM
192.168.1.2 comancheN1 -----hosts---end------------ -
Configure /etc/network/interfaces (in sudo mode)
-----interfaces---start---------- auto lo iface lo inet loopback
auto eth1 iface eth1 inet static address 192.168.1.1 netmask 255.255.255.0 -----interfaces---end------------
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Configure the nfs
Add the following line to /etc/export /home/ 192.168.1.2(rw,all_squash,anonuid=1000,anongid=1000,sync) and start the service /etc/init.d/nfs-kernel-server start
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Configure the ntp
Remplace the default servers in /etc/ntp.conf by server 0.fr.pool.ntp.org iburst dynamic server 1.fr.pool.ntp.org iburst dynamic server 2.fr.pool.ntp.org iburst dynamic server 3.fr.pool.ntp.org iburst dynamic and start the service sudo /etc/init.d/ntp restart
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Test apache works and copy the comanche web site
In firefox goto http://localhost/index.html and you should see message “It works” now delete index.html page
Replace /var/www/html by the comanche www directory
In firefox goto: http://localhost/ you should see comanche login page
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Configure sql (in sudo mode)
Edit /etc/mysql/my.cnf and change the following line bind-address = 192.168.1.1
Launch phpmyadmin by going to http://localhost/myphpadmin/ Import the comanche_db.sql file
In /etc/apache2/conf.d/phpmyadmin.conf edit line "Allow from 127.0.0.1/24" to "Allow from 192.168.1.1/24" This change will limit access via “eth1” and will not be visible on internet
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Create /home/comanche/Job_run.sh:
This script will be launch by the web interface and has for job to submit the computation script comanche.sh to slurm
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Setup Munge
create a munge key and copy it to /etc/munge/munge.key on master and all nodes
#/usr/sbin/create-munge-key
Add the option –-force in /etc/default/munge
#/etc/init.d/munge start
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Setup slurm
run the provided configurator and copy slurm.conf in /etc/slurm-llnl
In firefox goto : file:///usr/share/doc/slurm-llnl/slurm-llnl-configurator.html
fill in the form and copy text into /etc/slurm-llnl/slurm.conf
or copy the provided slurm.conf
Test slurm with commands like
#/etc/init.d/slurm-llnl start
#scontrol show daemons
#sinfo
- Secureimage download and steup
Copy secureimage directory to /var/www/
http://www.phpcaptcha.org/documentation/quickstart-guide/
- Install gromacs
bash instal_gmx507.bash
Add the following alias in .bashrc
alias gmx507="source /home/comanche/Software/gmx507/build/bin/GMXRC && export GMXLIB='/home/comanche/Software/gmx507/build/share/gromacs/top'"
alias gmx467="source /home/comanche/Software/gmx467/build/bin/GMXRC && export GMXLIB='/home/comanche/Software/gmx467/build/share/gromacs/top'"
The 4.6.7 verison need to be installed now for the reverse step
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Installed components on Nodes:
libnet-daemon-perl libplrpc-perl libdbi-perl libdbd-mysql-perl mysql-client-core-5.6 mysql-client-5.6 munge (must copy munge key from master to /etc/munge/ dir) slurm-llnl (must copy slurm.conf from master to /etc/slurm-llnl/ dir ) build-essential cmake nfs-common ntp
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configure /etc/hosts: (in sudo mode)
-----hosts---start---------- 172.0.0.1 localhost 192.168.1.1 comancheM 192.168.1.2 comancheN1 192.168.1.3 comancheN2
192.168.1.4 comancheN3
-----hosts---end------------Note: slurm uses host file to resolve node IP address
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configure /etc/network/interfaces (in sudo mode)
-----interface---start---------- auto lo iface lo inet loopback
auto eth0 iface eth0 inet static address 192.168.1.2 netmask 255.255.255.0 -----interface---end------------
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Modified /etc/fstab to mount home at boot time: (in sudo mode)
192.168.1.1:/home /home nfs4 rw,noatime 0 2
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Configure ntp
remplace default serveurs in /etc/ntp.conf by server 0.fr.pool.ntp.org iburst dynamic server 1.fr.pool.ntp.org iburst dynamic server 2.fr.pool.ntp.org iburst dynamic server 3.fr.pool.ntp.org iburst dynamic and restart the service sudo /etc/init.d/ntp restart
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Created remote script comanche.sh on all nodes:
copy the script to /home/comanche/
This script is the main script of the comanche project
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Install gromacs versions 4.6.7 and 5.0.7
bash instal_gmx507.bash
Add the following alias in .bashrc alias gmx507="source /home/comanche/Software/gmx507/build/bin/GMXRC && export GMXLIB='/home/comanche/Software/gmx507/build/share/gromacs/top'" alias gmx467="source /home/comanche/Software/gmx467/build/bin/GMXRC && export GMXLIB='/home/comanche/Software/gmx467/build/share/gromacs/top'"
The 4.6.7 verison need to be installed now for the reverse step