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| How To: Setup PVM for LeadIT |
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Prepare PVM Environment
- Choose a machine as a PVM daemon machine, accessible from any cluster node
- Configure ssh, so that my user can login to the PVM daemon machine; in the following steps, as an example this user is called bit
- Download PVM from http://www.csm.ornl.gov/pvm, compile it
- Set up the following environment variables
- export PVM_ROOT=/home/bit/pvm3
- export PVM_ARCH=LINUX64
- export PVM_DPATH=$PVM_ROOT/lib/pvmd
- export PATH=$PATH:$PVM_ROOT/lib
- export PATH=$PATH:$PVM_ROOT/lib/$PVM_ARCH
- export PATH=$PATH:$PVM_ROOT/bin/$PVM_ARCH
- Start PVM daemon
echo quit | pvm
- Edit execution host list in
Leadit -> Global Preferences -> Parallel Computing
Note: You need a docking license (typically from a license server) for each cluster node.
- For PVM_TMP enter a path which can be reached by each cluster machine in
Leadit -> Global Preferences -> Parallel Computing
- Check that USE_PVM_FEATURE is enabled in
Leadit -> Global Preferences -> Parameters & Flags
- Set parameter FLEXX to leadit in
Leadit -> Global Preferences -> Parameters & Flags
- Add a link to the leadit executable to the PVM bin path, e.g.
ln -s $PWD/leadit /home/bit/pvm3/bin/$PVM_ARCH/leadit
- Download the attached script screen.bat and save it as a template for your future screening runs
Prepare and Start Screening
- Start LeadIT and prepare your receptor with the receptor wizard, then save your project
Note: The protein will be enclosed in the project
- Adapt screen.bat concerning project and library file name
- Start LeadIT with this screening script
leadit -b screen.bat
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