Linux Installation Instructions for the SMP client

Table of contents

- Requirements
- Installation of the SMP client
- How to start the linux SMP client as a service

Requirements

Before you install the Linux SMP client, here is some requirements to check :

  • You must be running a 64 bit Linux OS. The client is not supported on 32 bit (this is due to the MPI layer SMP is using for inter-core communications).
  • Even though the core requires a 64 bit OS, the client needs the 32 bit library so you will have to install it.

Note: With some distributions, you may need to add su or sudo to execute the command if you are not logged as root.

Debian-based distributions : 

 apt-get install ia32-libs

Redhat-based distributions : 

 yum install compat-libstdc++

Installation of the SMP client

We are in the process of making an installer to make this process much easier. For now, here are detailed instructions to setup the client.

  • Go to Terminal. Depending of your desktop engine (KDE, GNOME, ...) the Terminal application can be at different places, but you'll find it. GNOME has it at "Applications->Accessories->Terminal". Open Terminal.
  • In the Terminal window you should see a prompt that looks something like this: yourusername@yourcomputername ~ $
  • To download the FAH client type in (or copy/paste) the following commands: 
 mkdir -p ~/folding
 cd ~/folding
 curl -O http://www.stanford.edu/group/pandegroup/folding/release/FAH6.02-Linux.tgz
 tar xzf FAH6.02-Linux.tgz
Note: If you don't have curl available on your machine, use wget instead: 
 wget http://www.stanford.edu/group/pandegroup/folding/release/FAH6.02-Linux.tgz
  • After the FAH client is downloaded, the client needs to be configured. Please run these 2 commands: 
 chmod +x fah6
 ./fah6 -configonly -smp
  • After the client setup, there are different methods for starting the FAH client. One way is to type in following command: 
 ./fah6 -smp -verbosity 9
  • OPTIONAL: To make it a little easier for yourself, you can make a script by running the following commands: 
 echo "./fah6 -smp -verbosity 9 $* &" > fah
 chmod +x fah
Now you can just just run 
 ./fah
and all those additional FAH client flags will get added automatically.
Note: All those listed commands MUST be typed/pasted from this install GUIDE to the terminal (window) of your machine.

Example: 

 user@box ~ $ mkdir -p ~/folding
 user@box ~ $ cd ~/folding
 user@box FAH $ curl -O http://www.stanford.edu/group/pandegroup/folding/release/FAH6.02-Linux.tgz
 % Total % Received % Xferd Average Speed Time Time Time Current
 Dload Upload Total Spent Left Speed
 100 138k 100 138k 0 0 34461 0 0:00:04 0:00:04 --:--:-- 39789
 user@box FAH $ tar xzf FAH6.02-Linux.tgz
 user@box FAH $ ls -la
 total 960
 drwxr-xr-x 5 user guest 170 Nov 6 23:58 .
 drwx------ 18 user guest 612 Nov 6 23:55 ..
 -rw-r--r-- 1 user guest 138145 Nov 6 23:56 FAH6.02-Linux.tgz
 -rwxr-xr-x 1 user guest 282796 Nov 4 07:04 fah6
 -rwxr-xr-x 1 user guest 60156 Oct 27 16:52 mpiexec
 user@box FAH $ ./fah6 -configonly
 ...
 user@box FAH $ echo "./fah6 -smp -verbosity 9 $*" > fah
 user@box FAH $ chmod +x fah
 user@box FAH $ ./fah
 ...

How to start the linux SMP client as a service

Note: Adding the client as a service in Linux depends on which distribution you are using. The instructions below should work for the majority of distributions available in the market. If nothing works, you might need to do some research to find out what your distribution needs to install as a service.

Do not change accounts or change directory location then create a script named folding by pasting the following commands: 

 echo "# chkconfig: 345 93 14" > ./folding
 echo "# description: will start FAH client as a service" >> ./folding
 echo "su - $USER -c \"cd $PWD; ./fah6 -smp -verbosity 9 < /dev/null > 
  /dev/null 2>&1 &\"" >> ./folding
 chmod +x ./folding

Note: In the following steps, replace [fahdir] with the value you saw on screen during the previous installation steps (don't include the brackets).

To mark down where you installed the FAH client just run: 

 echo "[fahdir] = $PWD"

Note: All the following steps need root privileges to be carried out successfully.

For Debian-based distributions run: 

 sudo cp [fahdir]/folding /etc/init.d/

For other distributions run: 

 su - -c "cp [fahdir]/folding /etc/init.d/"

Note: If you installed the client under root user account, do this instead : 

 echo "# chkconfig: 345 93 14" > ./folding
 echo "# description: will start FAH client as a service" >> ./folding
 echo "cd $PWD; ./fah6 -smp -verbosity 9 < /dev/null > /dev/null 2>&1 &" >>
  /etc/init.d/folding
 chmod +x /etc/init.d/folding

Last step is to register the folding service.

For Debian-based distributions run: 

 sudo update-rc.d folding defaults

For other distributions run: 

 su - -c "chkconfig --add folding"

That's all so reboot the computer to make the new script start the client. To check if it is working fine, just go to your folding folder and open fahlog.txt or run: 

 tail -f [fahdir]/FAHlog.txt


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Last Updated on August 24, 2008, at 05:07 PM