software:cp2k

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
software:cp2k [2018/03/29 15:12]
henkela
— (current)
Line 1: Line 1:
-====== CP2K ====== 
- 
-//"CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. CP2K provides a general framework for different modeling methods such as DFT using the mixed Gaussian and plane waves approaches GPW and GAPW. Supported theory levels include DFTB, LDA, GGA, MP2, RPA, semi-empirical methods (AM1, PM3, PM6, RM1, MNDO, …), and classical force fields (AMBER, CHARMM, …). CP2K can do simulations of molecular dynamics, metadynamics, Monte Carlo, Ehrenfest dynamics, vibrational analysis, core level spectroscopy, energy minimization, and transition state optimization using NEB or dimer method. (Detailed overview of features.) 
- 
-CP2K is written in Fortran 2003 and can be run efficiently in parallel using a combination of multi-threading, MPI, and CUDA. It is freely available under the GPL license. It is therefore easy to give the code a try, and to make modifications as needed." // [[https://www.cp2k.org/about|About CP2K]] 
- 
-You can check for available version on Mogon I/II using 
-<code bash> 
-module av chem/CP2K 
-</code> 
- 
-We ran [[https://www.cp2k.org/performance#h2o-64|H2O-64 benchmark]] and H20- 
-In the simplest case you can submit a cp2k-job like this:  
- 
-<file myjobscript> 
-#!/bin/bash 
-#----------------------------------------------------------------- 
-# Example SLURM job script to run GROMACS with MPI on Mogon I. 
-# 
-# This script requests 128 cores on two node. The job 
-# will have access to all the memory in the nodes.   
-#----------------------------------------------------------------- 
- 
-#SBATCH -J mycp2kjob          # Job name 
-#SBATCH -o mycp2kjob.%j.out   # Specify stdout output file (%j expands to jobId) 
-#SBATCH -p nodeshort          # Parition name 
-#SBATCH -N 2                  # Total number of nodes requested (64 cores/node) 
-#SBATCH -t 00:30:00           # Run time (hh:mm:ss) - 0.5 hours 
- 
-#SBATCH -A <account>             # Specify allocation to charge against 
- 
-# Load all necessary modules if needed (these are examples) 
-# Loading modules in the script ensures a consistent environment. 
-module purge  
-module load chem/GROMACS/5.1.4-foss-2016b-hybrid 
- 
-# Launch the executable 
-srun -n 64 -c 2 cp2k.popt <options> -i <inputfile> -o <outputfile> 
-</file> 
- 
- 
- 
- 
-====== Discussion ====== 
- 
-[[discussion:software:cp2k|Discussion page]] 
- 
-This is a job script that I am using to run on mogon. In this script we can use the localscratch of node and then get the results back to the same directory that we submitted a job! 
- 
-<code bash> 
-#BSUB -q long              # Job queue 
-#BSUB -o job%J.output              # output is sent to file job${LSB_JOBID}.output 
-#BSUB -e job%J.error              #error output is sent to file job.error 
-#BSUB -J BIG_JOB                # name of the job 
-#BSUB -n 64                      # number of procs 
-#BSUB -R 'span[hosts=1]' 
-##BSUB -W 400 
-#BSUB -W 7200 
-#BSUB -app Reserve1900M  
-##BSUB -R 'mem>1000' 
-##BSUB -M 1000000 
-##BSUB -I  
-#BSUB -N        # send job report by email 
-#!/bin/bash 
- 
-## Store working directory to be safe 
-SAVEDPWD=`pwd` 
- 
-## We define a bash function to do the cleaning when the signal is caught 
-cleanup(){ 
-    cp /jobdir/${LSB_JOBID}/* ${SAVEDPWD} 
-        exit 0 
-        } 
- 
-#        # Register the cleanup function when SIGUSR2 is sent, or when the script is terminating successfully 
-        trap 'cleanup' SIGUSR2 EXIT 
- 
-module add gcc/4.7.0 
-module add mpi/intelmpi/4.0.3.008 
-module add acml/5.1.0/gfortran/gfortran64_fma4 
- 
- 
-#copy input files 
-cp BASIS_MOLOPT GTH_POTENTIALS dftd3.dat 4ace-70water-1.restart 4ace-70water.inp  /jobdir/${LSB_JOBID}/ 
- 
- 
-pushd /jobdir/${LSB_JOBID} 
-mpiexec.hydra -genvall /cluster/Apps/cp2k/2.3/gfortran_4.7.0_intelmpi_4_acml_5.1.0/cp2k.popt 4ace-70water.inp 
-popd 
- 
-#copy output back 
-cp  /jobdir/${LSB_JOBID}/ . 
- 
-</code> 
-By: Leila Salimi 
  
  • software/cp2k.1522329124.txt.gz
  • Last modified: 2018/03/29 15:12
  • by henkela