Run Tinker On Joe

In the lab TINKER is installed on joe in the /local/tinker folder and please do not modify this version but instead copy it in your personal folder and use your personal copy to run the calculations.

The script tinker.pbs
To run TINKER calculations you should pass trough the queue system of the server submitting the job with a pbs script: below an example of script.

#PBS -q long
#PBS -l nodes=1:p4:ppn=1
#PBS -A minoiaa
#export all my environment variables to the job
#here we define the directory where the calculation has to be run
#set variables and creation of a WORKDIR
setenv INITIALDIR /home/output/minoiaa/tinker setenv input 4cisGR20x50
mkdir /scratch/minoiaa/$input
setenv WORKDIR /scratch/minoiaa/$input
#Copy the files of your project into the WORKDIR
cp /home/output/minoiaa/tinker/$ $WORKDIR
cp /home/output/minoiaa/tinker/$input.key $WORKDIR
#Launch the tinker analyze program and redirect the standard output in the .out file
/home/output/minoiaa/tinker/bin/analyze $ E > $input.out
find . | cpio -pd $INITIALDIR
rm -rf ${WORKDIR}

In the script you need to check the path of your files and change the command line as requested by the calculation to run and… don’t forget all the required parameters.

Run the script and manage the job
To launch a calculation (i.e. to submit a job) use the following command:

localhost$: qsub tinker.pbs

which return the number of your job in the queue and writes a file tinker.oXXXX in your directory, where XXXX is the number of the job submitted. To control the status of your job in the queue (wait, running, …) use the following command:

localhost$: qstat -u username

To delete the job use

localhost$: qdel job number


  • the file in which you have redirected the screen output is not written frequently, so do not worry if it is empty for long time;
  • it is possible you have to modify your /.bashrc to load the modules requests by the compiler;
  • to find the node on which your calculation is running type localhost$: qstat -f job number | grep exec_host then you can connect to the node, i.e. joe-xx, and check your file in the scratch folder;

Compile TINKER on joe
To compile TINKER on joe we can follow the same steps seen in the case of local linux installation with the VM or Cygwin and you can referred to that section. Here the steps to do are listed:

  1. cd /tinker/bin
  2. rm -f *.o
  3. make all
  4. make rename

Please note that you should work with a copy of the installation already present on joe because the script you use to recompile the source has some flags to optimize the program for the architecture of the server. These flags are different from those used for a pc desktop machine.

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