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TURBOMOLE

** This manual is work in progress, please check regularly for updates **

Important note: To run TURBOMOLE, user must be a member of the TURBOMOLE user group or have purchased TURBOMOLE licenses.




TURBOMOLE short introduction


  1. Set up environment and generate TURBOMOLE coordinate file:

     module load turbomole7.0
     x2t inputfile.xyz > start-coord
    
  2. Run define to create the input files needed.

  3. Download TURBOMOLE.slurm batch script:

     #!/bin/bash
     #SBATCH --nodes=1
     #SBATCH --ntasks=1
     #SBATCH --cpus-per-task=1
     #SBATCH --job-name=test
     #SBATCH --mem-per-cpu=1GB
     #SBATCH -t 1:00:00
     #SBATCH --partition=common 
    
     module load turbomole7.0
    
     #Directory where you run the script
     CALCULATIONDIR=`pwd`
    
     #Create scratch directory
     SCRATCHDIRNAME=/state/partition1/$SLURM_JOBID
     mkdir $SCRATCHDIRNAME
     cp * $SCRATCHDIRNAME
     cd $SCRATCHDIRNAME 
    
     #Run calculations 
      jobex -ri > jobex.out 2>jobex.err  # TURBOMOLE commands
      t2x -c > final.xyz
    
     #Clean after yourself
     mv $SCRATCHDIRNAME/* $CALCULATIONDIR 
     rm -rf $SCRATCHDIRNAME
    
  4. Submit the job:

        sbatch TURBOMOLE.slurm
    

NB! More cores does not mean faster!!! See Benchmarks.




TURBOMOLE long version


Environment

There are currently several versions of TURBOMOLE (6.3 - 7.0) are available on HPC, and most of them can be run as parallel jobs. Environment is set up by the command:

module load turbomole7.0
module load turbomole7.0-mpi    # for parallel run 

Running TURBOMOLE jobs

TURBOMOLE uses its own coordinate file coord, which can be generated from .xyz file by TURBOMOLE command (when some TURBOMOLE version is already loaded):

x2t inputfile.xyz > start-coord

Example of TURBOMOLE coordinate file:

 $coord
 1.27839972889714      0.80710203135546      0.00041573974923       c
 1.42630859331810      2.88253155131977      0.00372276048178       h
 3.06528696563114     -0.57632867600746     -0.00069919866917       o
-1.91446264796512     -0.31879679861781      0.00039684248791       s
-2.98773260513752      1.98632893279876     -0.00701088395301       h
 $end

In addition to coordinate file, TURBOMOLE uses a special interactive program define to create the input files, which determines molecules’ parameters, levels of theory used and calculation types.

define

The answers to the define’s questions can be presented as a separate file. More about define can be read in ‘Quick and Dirty’ Tutorial and TURBOMOLE tutorial. Some examples of define files can be found here.

To include solvent effects into calculations interactive program cosmoprep should be run after define.

cosmoprep 

TURBOMOLE includes the Conductor-like Screening Model (COSMO), where the solvent is described as dielectric continuum with permittivity ε. An example of cosmoprep file with acetonitrile as a solvent.

After input files are created TURBOMOLE calculations are executed by one of the following commands: dscf, ridft, jobex, aoforce, NumForce, escf, egrad, mpshift, raman, ricc2 etc. For example,

dscf           # for Hartree-Fock energy calculation (single point calculation)
jobex -ri      # geometry optimization using RI-approximation
aoforce        # analytical force constant calculations
NumForce -ri   # numerical force constant calculations using RI-approximation

More about TURBOMOLE commands used can be found in TURBOMOLE tutorial.

Single core calculations

Example of Slurm script for single point HF calculation performed on a single core:

#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --job-name=test
#SBATCH --mem-per-cpu=1GB
#SBATCH -t 1:00:00
#SBATCH --partition=common 

module load turbomole7.0

#Directory where you run the script
CALCULATIONDIR=`pwd`

#Create scratch directory
SCRATCHDIRNAME=/state/partition1/$SLURM_JOBID
mkdir $SCRATCHDIRNAME

cp * $SCRATCHDIRNAME
cd $SCRATCHDIRNAME 

#Run calculations 
dscf > JOB.out 2>JOB.err  
    
#Clean after yourself
mv $SCRATCHDIRNAME/* $CALCULATIONDIR 
rm -rf $SCRATCHDIRNAME

Parallel jobs SMP

Example of Slurm script for geometry optimization using RI-approximation performed by SMP run:

#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=24
#SBATCH --job-name=test
#SBATCH --mem-per-cpu=1GB
#SBATCH -t 1:00:00
#SBATCH --partition=common 

module load turbomole7.0-mpi

#Directory where you run the script
CALCULATIONDIR=`pwd`

#Create scratch directory
SCRATCHE=/state/partition1/$SLURM_JOBID
mkdir $SCRATCH

cp * $SCRATCH
cd $SCRATCH 

export PARA_ARCH=SMP
export PATH=$TURBODIR/bin/`sysname`:$PATH 
export PARNODES=$SLURM_NTASKS 
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK

#Run calculations 
jobex -ri -c 600 > jobex.out 2>jobex.err 
t2x -c > final.xyz

#Clean after yourself
mv $SCRATCH/* $CALCULATIONDIR 
rm -rf $SCRATC

Memory

For common calculations (e.g. optimization, frequency etc.) it is enough 1 GB per 1 CPU. However, some calculations can require more memory (e.g TD-DFT, large SCF calculations, etc.). Data from a slurm-JOBID.stat file can be useful to determine the amount of memory required for a computation. In slurm-JOBID.stat file the efficiency of memory utilization is shown.

Bad example:

Memory Utilized: 3.08 GB 
Memory Efficiency: 11.83% of 26.00 GB

Good example:

Memory Utilized: 63.12 GB 
Memory Efficiency: 98.62% of 64.00 GB

Time

Time limits depend on time partition used taltech user-guides. If the calculation time exceeds the time limit requested in the Slurm script, then the job will be killed. Therefore, it is recommended to request a little more than is usually needed for calculation.

Restarting a failed/interrupted calculation

All TURBOMOLE jobs are restart jobs as default.

Benchmarks for parallel jobs