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machines_FabMD_user.yml
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# This is the user personal configuration for job submission and execution for FabCovid19 plugin
# All given variable here will be override machine settings loaded from (a) FabSim3/deploy/machines.yml and (b) FabSim3/deploy/machines_user.yml
#
# Here, you can find some examples for pre-defined remote machines
# All env variable can be modified here and will overwrite setting in machines.yml and machines_user.yml
required_py_packages: &PY_PKG ["easyvvuq"]
default:
# example :
# exe_file: "app.py"
# exe_prefix: "python3"
# or
# exe_file: "app.sh"
# exe_prefix: "bash"
# this env variables will be used in case of env.script=generic_app
# exe_file should be located inside the target config_files folder
exe_file: ""
exe_prefix: ""
lammps_params:
lammps_input: "in.lammps"
#wall_time: "0:10:00"
sweep_dir_name: "SWEEP"
namd_params:
namd_input: "eq0.conf"
#wall_time: "0:10:00"
sweep_dir_name: "SWEEP"
gromacs_params:
sweep_dir_name: "SWEEP"
required_files:
grompp: nvt.mdp
conf: npt4b.gro
topol: top.top
checkpoint:
index: index.ndx
# possible inputs are: ["delete","ignore","warn_only"]
# 1- delete : delte the exist results folder
# 2- ignore : ignore the exist results folder
# 2- warn_only : warn user and keep the exist results folder
prevent_results_overwrite: "delete"
localhost:
# location of lmp_serial in your local PC
lammps_exec: "/usr/bin/lmp"
gromacs_exec: "/usr/local/gromacs/bin/gmx"
# used core for executing lmp_serial on your local PC
lammps_params:
lammps_input: "in.lammps"
#wall_time: "0:10:00"
sweep_dir_name: "SWEEP"
cores: 1
eagle_hidalgo:
# location of lmp_serial on the remote machine
lammps_exec: "/home/users/hamid/lammps/src/lmp_serial"
gromacs_exec: "/opt/exp_soft/local/generic/gromacs/2018/mpi/bin/gmx_mpi_openmp"
cores: 1
# format days-hours:minutes:seconds
job_wall_time : "0-0:10:00"
partition_name: "fast"
fabric_dir: "FabMD_tests"
py_pkg: *PY_PKG
modules:
# list of modules to be loaded on remote machine
loaded: ["python/3.7.3", "openmpi/4.0.0_gcc620", "namd/2.12-verbs-smp", "lammps/15Apr2020", "gromacs/2018_mpi", "amber/16"]
# list of modules to be unloaded on remote machine
unloaded: ["python"]
eagle_vecma:
# location of lmp_serial on the remote machine
lammps_exec: "/home/plgrid/plgvassaux/source/lammps-17Nov16/src/lmp_mpi"
namd_exec: "/opt/exp_soft/local/generic/namd/NAMD_2.12_Linux-x86_64-verbs-smp/namd2"
gromacs_exec: "/opt/exp_soft/local/generic/gromacs/2018/mpi/bin/gmx_mpi_openmp"
cores: 28
# format days-hours:minutes:seconds
job_wall_time : "0-0:10:00"
partition_name: "fast"
modules:
# list of modules to be loaded on remote machine
loaded: ["openmpi/4.0.0_gcc620", "lammps/15Apr2020", "gromacs/2018_mpi", "namd", "amber"]
# list of modules to be unloaded on remote machine
unloaded: ["python"]
cirrus:
# location of lmp_serial on the remote machine
lammps_exec: "/lustre/sw/LAMMPS/3March20_intel19_mpt222/bin/lmp_mpi"
modules:
# list of modules to be loaded on remote machine
loaded: [ "lammps"]
ohm:
# location of lmp_serial on the remote machine
lammps_exec: "/home/kevinb/lammps-17Nov16/src/lmp_serial"
cores: 2
# list of modules to be loaded on remote machine
# loaded: [ "lammps/13Apr17/intel-2017", "gromacs/2018/intel-2017", "fftw/2.1.5/intel-2015-update2", "namd/2.12/intel-2018-update3" ]
Kathleen:
# location of lmp_serial on the remote machine
lammps_exec: "/shared/ucl/apps/lammps/16Mar18/USERINTEL/intel-2018/lammps-16Mar18/bin/lmp_default"
cores: 28
modules:
# list of modules to be loaded on remote machine
loaded: [ "python/3.7.4", "lammps/16Mar18/userintel/intel-2018", "gromacs/2018/intel-2017", "fftw/2.1.5/intel-2015-update2", "namd/2.12/intel-2018-update3" ]