To remove some of the limitations of g03 we also have Gaussian Linda, a version of g03 that can use multiple nodes.

To run Gaussian 03 on any of our clusters:

1. type: module load gaussian
2. Edit your gaussian input script file (filename.com) to put "%NProc=n" on the top line, where n may be 2 or 4 or 8. Gaussian will create no more than n threads during the job. Your nproc shouldn't exceed the number of cpus you'll reserve in your PBS script file. On your next line put "%mem=nmb" which tells Gaussian how much memory to allocate. Typical amounts are 1800 or 3800. Nyx has nodes with 2,4,6,8, 16 or 64GB. Requesting a maximum allocation of 1800mb leaves room on a 2gb node for the OS, the application,etc.

    

   example of top lines of input file

    

   %nproc=4

   %mem=3600mb

    

3. Write an appropriate PBS script file for your job. Set the queue to route if you need no more than 7600mb; otherwise set it to bigmem, e.g.

    

   #PBS -q route

    

   or

    

   #PBS -q bigmem

    

   Next set the nodes resource to the minimum number of CPUs you'll need. Remember that all the nodes on nyx have at least two CPUs each. Since gaussian is an SMP code you'll need all the CPUs required on one node. So on nyx your choices are:

    

   #PBS -l nodes=1:ppn=2

    

   or

    

   #PBS -l nodes=1:ppn=4

    

   or

    

   #PBS -l nodes=1:ppn=8

    

   if you need more than 3600mb you should set the pmem resource as well, e.g.

    

   #PBS -l pmem=6600mb

   If you need more than 16GB (asking for 15000mb in your PBS script) you'll need to submit to the bigmem queue, then you can ask for up to 63GB (63000mb in your PBS script) but you can only use up to 72 hours of time (walltime=72:00:00 or less).

    

   example of a PBS script file for gaussian:

    

   #PBS -N g03_test
   #PBS -q route
   #PBS -l nodes=1:ppn=4,pmem=5600mb,walltime=24:00:00
   #PBS -M your-email-address
   #PBS -m abe
   #PBS -V
   #
   echo "I ran on:"
   cat $PBS_NODEFILE
   #
   #cd to your execution directory first
   cd /home/your-user-name
   #
   #
   g03 < gaussian.input > gaussian.output

   another example of a PBS script file for gaussian:

    

   #PBS -N g03_bigtest
   #PBS -q bigmem
   #PBS -l nodes=1:ppn=8,mem=1gb,walltime=24:00:00
   #PBS -M your-email-address
   #PBS -m abe
   #PBS -V
   #
   echo "I ran on:"
   cat $PBS_NODEFILE
   #
   #cd to the directory you were in when you submitted the job
   cd $PBS_O_WORKDIR
   #
   #
   g03 < gaussian.input > gaussian.output
   

    

4. submit the job with: qsub name_of_script_file