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
Set up environment and generate TURBOMOLE coordinate file:
module load turbomole7.0 x2t inputfile.xyz > start-coord
Run define to create the input files needed.
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
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.