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Turbomole

TURBOMOLE is a modular program suite for ab initio quantum-chemical and condensed-matter simulations It includes most standard and state of the art methods for ground state calculations. Properties both for ground and excited states can be obtained. TURBOMOLE has been designed for efficient study of large systems.

Available

  • Puhti: 7.5.1
  • Mahti: 7.5.1

License

  • You may use the Software exclusively for non-profit research purposes.
  • Only users from academic (i.e. degree-granting) institutes are allowed to use the Software

Usage

Initialise Turbomole environment:

module load turbomole/7.5.1

Batch script example for Puhti using MPI parallelization

#!/bin/bash
#SBATCH --partition=test
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=40 # MPI tasks per node
#SBATCH --account=<project>  # insert here the project to be billed 
#SBATCH --time=00:10:00           # time as hh:mm:ss
export PARA_ARCH=MPI         # use MPI 
module load turbomole/7.5.1
export SLURM_CPU_BIND=none
# This setting of TURBOTMPDIR assumes that the job is 
# submitted from a directory below /scratch/<project>
export TURBOTMPDIR=`echo $PWD |cut -d'/' -f1-3`"/TM_TMPDIR/"$SLURM_JOB_ID
mkdir -p $TURBOTMPDIR
export PARNODES=$SLURM_NTASKS  # for MPI
export PATH=$TURBODIR/bin/`$TURBODIR/scripts/sysname`:$PATH
jobex -ri -c 300 > jobex.out

Batch script example for Puhti using SMP parallelization

#!/bin/bash
#SBATCH --partition=test
#SBATCH --nodes=1            # for SMP only 1 is possible
#SBATCH --cpus-per-task=40   # SMP threads
#SBATCH --account=<project>  # insert here the project to be billed
#SBATCH --time=00:10:00      # time as hh:mm:ss
export PARA_ARCH=SMP         # use SMP threads   
module load turbomole/7.5.1
# This setting of TURBOTMPDIR assumes that the job is 
# submitted from a directory below /scratch/<project>
export TURBOTMPDIR=`echo $PWD |cut -d'/' -f1-3`"/TM_TMPDIR/"$SLURM_JOB_ID
mkdir -p $TURBOTMPDIR
export PARNODES=$SLURM_CPUS_PER_TASK  # for SMP
export PATH=$TURBODIR/bin/`$TURBODIR/scripts/sysname`:$PATH
jobex -ri -c 300 > jobex.out

Note

Occasionally mpshift calculations are terminated due to the local /tmp becoming full. The problem can be circumvented by redefining $TMPDIR.

    export TMPDIR=$TURBOTMPDIR

Note

Second-order approximate coupled cluster calculations using the ricc2 module have been reported to suffer from numerical errors resulting in crashed jobs. This applies to Turbomole versions 7.5 and older on Puhti. For reliable performance, we suggest running ricc2 calculations using Turbomole 7.5.1.

Note

Particularly some of the wavefunction-based electron correlation methods can be very disk I/O intensive. Such jobs benefit from using the fast local storage on Puhti. Using local disk for such jobs will also reduce the load on the Lustre parallel file system.

Batch script example for Puhti using MPI parallelization and local disk

#!/bin/bash
#SBATCH --partition=small
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=40 # MPI tasks per node
#SBATCH --account=<project>  # insert here the project to be billed
#SBATCH --time=00:10:00      # time as hh:mm:ss
#SBATCH --gres=nvme:100      # requested local disk in GB
export PARA_ARCH=MPI         # use MPI
module load turbomole/7.5.1
export SLURM_CPU_BIND=none
# define local disk as scratch
export TURBOTMPDIR=$LOCAL_SCRATCH/$SLURM_JOBID
mkdir -p $TURBOTMPDIR
export PARNODES=$SLURM_NTASKS  # for MPI
export PATH=$TURBODIR/bin/`$TURBODIR/scripts/sysname`:$PATH
dscf > dscf.out
ccsdf12 > ccsdt.out

Batch script example for Mahti using MPI parallelization

#!/bin/bash
#SBATCH --partition=medium
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=128 # MPI tasks per node
#SBATCH --account=<project>   # insert here the project to be billed
#SBATCH --time=00:60:00       # time as hh:mm:ss
export PARA_ARCH=MPI          # use MPI
module load turbomole/7.5.1
export SLURM_CPU_BIND=none
# This setting of TURBOTMPDIR assumes that the job is 
# submitted from a directory below /scratch/<project>
export TURBOTMPDIR=`echo $PWD |cut -d'/' -f1-3`"/TM_TMPDIR/"$SLURM_JOB_ID
mkdir -p $TURBOTMPDIR
export PARNODES=$SLURM_NTASKS  # for MPI
export PATH=$TURBODIR/bin/`$TURBODIR/scripts/sysname`:$PATH
jobex -ri -c 300 > jobex.out

NumForce calculations

NumForce is a tool that can be used to calculate second derivatives (molecular Hessian) for all methods for which analytic gradients are available in TURBOMOLE.
A NumForce job spawns 3*N*2 (N = number of atoms ) independent gradient calculations. Usually it is most efficient that the single gradient calculations are run as serial (unset PARA_ARCH). Each serial calculation is expected to take roughly the same time, hence optimally the total number of gradient calculations should be an integer multiple of the allocated cores.

A NumForce step in a job file:

unset PARA_ARCH
export HOSTS_FILE=$PWD/turbomole.machines
rm -f $HOSTS_FILE
srun hostname > $HOSTS_FILE
ulimit -s unlimited
kdg tmpdir
NumForce -ri -central -mfile $HOSTS_FILE > NumForce.out

References

Please quote the usage of the program package under consideration of the version number:

  • TURBOMOLE V7.5.1 2021, a development of University of Karlsruhe andForschungszentrum Karlsruhe GmbH, 1989-2007,TURBOMOLE GmbH, since 2007; available from https://www.turbomole.org
  • Scientific publications require proper citation of methods and procedures employed. The output headers of TURBOMOLE modules include the relevant papers.

More information

Last edited Tue Sep 21 2021