VASP-MGCM: Difference between revisions
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New page: The VASP-MGCM (Vasp-Multigrid Continuum Model) was compiled in the VASP 5.3.3 version (normal and gamma version). To perform a calculation of a solvated system PLEASE read first the attach... |
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The VASP-MGCM (Vasp-Multigrid Continuum Model) | The VASP-MGCM (Vasp-Multigrid Continuum Model) available in tekla2 corresponds to the VASP 5.3.3 version (normal and gamma version). To perform a calculation of a solvated system PLEASE read first the attached pdf guide. After that, one needs to slightly modify your running script. The two only lines that have to be changed are those corresponding to the modules and executable calls. For some reason (most likely due to the different fortran libraries used in the tekla2 queues) the code runs at a reasonable computational cost in the c8m24.q. If there is enough space in this queue run your calculation there, otherwise use the c24m128ib.q although the speed is much lower there at this moment. | ||
Example of a script to launch a VASP-MGCM calculation in the c8m24.q with the VASP 5.3.3 version: | - Example of a script to launch a VASP-MGCM calculation in the c8m24.q with the VASP 5.3.3 version (normal version): | ||
-------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------- | ||
#!/bin/bash | #!/bin/bash | ||
# - Dr. Nuria Lopez Group - | # - Dr. Nuria Lopez Group - | ||
########################################## | ########################################## | ||
# SGE Parameters | # SGE Parameters | ||
########################################## | ########################################## | ||
#$ -S /bin/bash | #$ -S /bin/bash | ||
#$ -N example1 | #$ -N example1 | ||
#$ -cwd | #$ -cwd | ||
#$ -masterq c8m24.q | #$ -masterq c8m24.q | ||
#$ -pe c8m24_mpi 8 | #$ -pe c8m24_mpi 8 | ||
#$ -m ae | #$ -m ae | ||
#$ -o o_$JOB_NAME.$JOB_ID | #$ -o o_$JOB_NAME.$JOB_ID | ||
#$ -e e_$JOB_NAME.$JOB_ID | #$ -e e_$JOB_NAME.$JOB_ID | ||
########################################## | ########################################## | ||
# Load Evironment Variables | # Load Evironment Variables | ||
########################################## | ########################################## | ||
. /etc/profile.d/modules.sh | . /etc/profile.d/modules.sh | ||
module load vasp/5.3.3-mgarciar | module load vasp/5.3.3-mgarciar | ||
########################################## | ########################################## | ||
# Running Job | # Running Job | ||
########################################## | ########################################## | ||
export OMP_NUM_THREADS=1 | export OMP_NUM_THREADS=1 | ||
echo $PWD >> o_$JOB_NAME.$JOB_ID | |||
echo $TMP >> o_$JOB_NAME.$JOB_ID | |||
mpirun -np $NSLOTS vasp_mgcm | |||
-------------------------------------------------------------------------------------------- | |||
- Example of a script to launch a VASP-MGCM calculation in the c8m24.q with the VASP 5.3.3 version (gamma-version): | |||
-------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------- | ||
#!/bin/bash | |||
# - Dr. Nuria Lopez Group - | |||
########################################## | |||
# SGE Parameters | |||
########################################## | |||
#$ -S /bin/bash | |||
#$ -N example2 | |||
#$ -cwd | |||
#$ -masterq c8m24.q | |||
#$ -pe c8m24_mpi 8 | |||
#$ -m ae | |||
#$ -o o_$JOB_NAME.$JOB_ID | |||
#$ -e e_$JOB_NAME.$JOB_ID | |||
########################################## | |||
# Load Evironment Variables | |||
########################################## | |||
. /etc/profile.d/modules.sh | |||
module load vasp/5.3.3-mgarciar-GAMMA | |||
########################################## | |||
# Running Job | |||
########################################## | |||
export OMP_NUM_THREADS=1 | |||
echo $PWD >> o_$JOB_NAME.$JOB_ID | |||
echo $TMP >> o_$JOB_NAME.$JOB_ID | |||
mpirun -np $NSLOTS vasp_mgcm | |||
-------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------- | ||
For further details about the VASP-MGCM please read: J. Chem. Theory Comput., 2016, 12 (3), pp 1331–1341. | |||
Revision as of 09:13, 23 June 2017
The VASP-MGCM (Vasp-Multigrid Continuum Model) available in tekla2 corresponds to the VASP 5.3.3 version (normal and gamma version). To perform a calculation of a solvated system PLEASE read first the attached pdf guide. After that, one needs to slightly modify your running script. The two only lines that have to be changed are those corresponding to the modules and executable calls. For some reason (most likely due to the different fortran libraries used in the tekla2 queues) the code runs at a reasonable computational cost in the c8m24.q. If there is enough space in this queue run your calculation there, otherwise use the c24m128ib.q although the speed is much lower there at this moment.
- Example of a script to launch a VASP-MGCM calculation in the c8m24.q with the VASP 5.3.3 version (normal version):
#!/bin/bash # - Dr. Nuria Lopez Group - ########################################## # SGE Parameters ########################################## #$ -S /bin/bash #$ -N example1 #$ -cwd #$ -masterq c8m24.q #$ -pe c8m24_mpi 8 #$ -m ae #$ -o o_$JOB_NAME.$JOB_ID #$ -e e_$JOB_NAME.$JOB_ID ########################################## # Load Evironment Variables ########################################## . /etc/profile.d/modules.sh module load vasp/5.3.3-mgarciar ########################################## # Running Job ########################################## export OMP_NUM_THREADS=1 echo $PWD >> o_$JOB_NAME.$JOB_ID echo $TMP >> o_$JOB_NAME.$JOB_ID mpirun -np $NSLOTS vasp_mgcm
- Example of a script to launch a VASP-MGCM calculation in the c8m24.q with the VASP 5.3.3 version (gamma-version):
#!/bin/bash # - Dr. Nuria Lopez Group - ########################################## # SGE Parameters ########################################## #$ -S /bin/bash #$ -N example2 #$ -cwd #$ -masterq c8m24.q #$ -pe c8m24_mpi 8 #$ -m ae #$ -o o_$JOB_NAME.$JOB_ID #$ -e e_$JOB_NAME.$JOB_ID ########################################## # Load Evironment Variables ########################################## . /etc/profile.d/modules.sh module load vasp/5.3.3-mgarciar-GAMMA ########################################## # Running Job ########################################## export OMP_NUM_THREADS=1 echo $PWD >> o_$JOB_NAME.$JOB_ID echo $TMP >> o_$JOB_NAME.$JOB_ID mpirun -np $NSLOTS vasp_mgcm
For further details about the VASP-MGCM please read: J. Chem. Theory Comput., 2016, 12 (3), pp 1331–1341.