QuantumPatch Command Line Usage

Setup

To allow for commandline execution export the Nanomatch directory and source the quantumpatch config file:

export NANOMATCH=/path/to/your/nanomatch
export NANOVER=V4 # or your respective release
source $NANOMATCH/$NANOVER/configs/quantumpatch.config

As a side note it is very much advised to export the NANOMATCH directory and NANOVER in your .bashrc file and source the config file during the batch job.

General remarks

QuantumPatch contains lots of parameters, review settings.yml for most of them. For beginning we will provide you with a set of template settings.yml files.

Running a simulation

After setting up your settings.yml file it is best to adapt the following queueing script to run QuantumPatch: Queueing Script. The script exports all necessary environment variables and starts QuantumPatch with the hostfile setup in customer.config. Many different queueing systems require the manual export of the environment variables (as done in the script). You can use it for QuantumPatch and Excitonic Preprocessing.

Only if your queueing system does export the environment variables on it own, you can run QP without exporting them like this:

#For V4
$OPENMPI_PATH/bin/mpirun -x OMP_NUM_THREADS --bind-to none --hostfile $HOSTFILE --mca btl self,vader,tcp python -m mpi4py $SHREDDERPATH/QuantumPatchNG.py >> progress.txt 2> shredder_mpi_stderr
# or in case of Excitonic Preprocessing
$OPENMPI_PATH/bin/mpirun --oversubscribe -x OMP_NUM_THREADS --bind-to none --hostfile $HOSTFILE --mca btl self,vader,tcp python -m mpi4py $SHREDDERPATH/QuantumPatchNG.py >> progress.txt 2> shredder_mpi_stderr
#or For V3 and below
$MPI_PATH/bin/mpirun -n 32 python -m mpi4py $SHREDDERPATH/QuantumPatchNG.py > qp_mpi_stderr

to run QuantumPatch. QuantumPatch scales upwards to the number of molecules in the simulation. If you do not run it using a queueing system you can replace --hostfile $HOTSFILE with -n 32 for 32 processes.

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