|CP2K||2.3, 2.4, 2.6, r14075||cp2k|
|Gaussian||g03e01, g09, g09b01||gaussian|
Note that on Taurus, the NAMD installation (ibverbs) does not use MPI anymore but rather uses Infiniband directly. Therefore, you cannot not use srun/mpirun to spawn the processes but have to use the supplied "charmrun" command instead. Also, since this is batch system agnostic, it has no possiblity of knowing which nodes are reserved for it use, so if you want it to run on more than node, you have to create a hostlist file and feed it to charmrun via the parameter "++nodelist". Otherwise, all processes will be launched on the same node (localhost) and the other nodes remain unused.You can use the following snippet in your batch file to create a hostlist file:
export NODELISTFILE="/tmp/slurm.nodelist.$SLURM_JOB_ID" for LINE in `scontrol show hostname $SLURM_JOB_NODELIST` ; do echo "host $LINE" >> $NODELISTFILE ; done # launch NAMD processes. Note that the environment variable $SLURM_NTASKS is only available if you have # used the -n|--ntasks parameter. Otherwise, you have to specify the number of processes manually, e.g. +p64 charmrun +p$SLURM_NTASKS ++nodelist $NODELISTFILE $NAMD inputfile.namd # clean up afterwards: test -f $NODELISTFILE && rm -f $NODELISTFILE
The current version 2.7b1 of NAMD runs much faster than 2.6. - Especially on the SGI Altix. Since the parallel performance strongly depends on the size of the given problem one cannot give a general advice for the optimum number of CPUs to use. (Please check this by running NAMD with your molecules and just a few time steps.)Any published work which utilizes NAMD shall include the following reference:
module load gaussian(or
gaussian/g09) a number of environment variables are set according to the needs of Gaussian. Please, set the directory for temporary data (GAUSS_SCRDIR) manually to somewhere below
/scratch/<username>/. GAMESS home page. For runs with Slurm, please use a script like this:
#!/bin/bashGAMESS should be cited as: M.W.Schmidt, K.K.Baldridge, J.A.Boatz, S.T.Elbert, M.S.Gordon, J.H.Jensen, S.Koseki, N.Matsunaga, K.A.Nguyen, S.J.Su, T.L.Windus, M.Dupuis, J.A.Montgomery, J.Comput.Chem. 14, 1347-1363(1993). LAMMPS is a classical molecular dynamics code that models an ensemble of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, metallic, granular, and coarse-grained systems using a variety of force fields and boundary conditions. For examples of LAMMPS simulations, documentations, and more visit LAMMPS sites. ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave basis. ABINIT also includes options to optimize the geometry according to the DFT forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate dynamical matrices, Born effective charges, and dielectric tensors. Excited states can be computed within the Time-Dependent Density Functional Theory (for molecules), or within Many-Body Perturbation Theory (the GW approximation). CP2K performs atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. CPMD homepage.
#SBATCH -t 120
#SBATCH -n 8
# you have to make sure that on each node runs an even number of tasks !!
module load gamess
rungms.slurm cTT_M_025.inp /scratch/mark/gamess
# the third parameter is the location of the scratch directory
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.For documentations see Gromacs homepage.
is about to be installed.http://www.uam.es/siesta In any paper or other academic publication containing results wholly or partially derived from the results of use of the SIESTA package, the following papers must be cited in the normal manner: