def runtest(nout, repeat=5, path=None, nprocs=4, model=None, log_dir=None):
"""Run `model` in `path` `repeat` times, returning the mean runtime
and its standard deviation
"""
if path is None:
path = DEFAULT_MODEL_PATH
if model is None:
model = DEFAULT_MODEL_EXE
os.chdir(path)
shell_safe("make")
command = "mpirun -n {nprocs} ./{model} NOUT={nout} >/dev/null".format(
model=model, nout=nout, nprocs=nprocs)
runtime = []
for run_number in range(repeat):
runtime.append(timeit.timeit(lambda: shell_safe(command), number=1))
backup_log_file(log_dir, subdir="run{:02d}".format(run_number))
return {
"mean": np.mean(runtime),
"std": np.std(runtime),
"low": np.min(runtime)
}
def git_info():
"""Return a dict of the commit hash and the date on which it was committed
"""
_, git_commit = shell_safe("git rev-parse HEAD", pipe=True)
_, commit_date = shell_safe("git --no-pager show -s --format=%ci",
pipe=True)
return {"commit": git_commit[:7], "date": commit_date.strip()}
def cleanup():
"""Make sure BOUT++ directory is clean and submodules correct
"""
shell("make distclean")
shell_safe(r'find src -type f -name "*\.o" -delete')
shutil.rmtree("googletest", ignore_errors=True)
shutil.rmtree("externalpackages/googletest", ignore_errors=True)
shutil.rmtree("externalpackages/mpark.variant", ignore_errors=True)
shell_safe("git submodule update --init --recursive")
def configure_bout(configure_line=None):
"""Configure BOUT++
"""
if configure_line is None:
configure_line = (
"./configure -C "
"CXXFLAGS='-std=c++11 -fdiagnostics-color=always' "
"--with-netcdf --enable-optimize=3 --enable-checks=no "
"--disable-backtrace")
print(configure_line)
shell_safe(configure_line)
def test_git_hash(self):
# Try to get git hash directly instead of through versioneer's get_versions()
from boututils.run_wrapper import shell, shell_safe
# check if git exists
retval, git_version = shell("git --version")
if retval == 0:
# git exists
from pathlib import Path
from hypnotoad.__init__ import __file__ as hypnotoad_init_file
hypnotoad_path = Path(hypnotoad_init_file).parent
# check if hypnotoad is in it's own git repo. hypnotoad.__init__.py
# should be in the hypnotoad/ subdirectory of the git repo if it is.
# So the parent directory of hypnotoad_path should contain a '.git'
# directory if hypnotoad is in a git repo
if hypnotoad_path.parent.joinpath(".git").is_dir():
retval, git_hash = shell_safe(
"cd "
+ str(hypnotoad_path)
+ '&& git describe --always --abbrev=0 --dirty --match "NOT A TAG"',
pipe=True,
)
git_hash = git_hash.strip()
# found a git hash, check it is consistent with the one from versioneer
dirty_pos = git_hash.find("-dirty")
if dirty_pos != -1:
# Check versioneer says the repo is dirty
assert get_versions()["dirty"]
# remove "-dirty" from git_hash
git_hash = git_hash[:dirty_pos]
else:
# repo is clean
assert not get_versions()["dirty"]
assert git_hash == get_versions()["full-revisionid"]
elif retval == 127:
# git not installed
pass
else:
raise RuntimeError(
"'git --version' failed with {retval}. Output was {git_version}"
)
gamma_tol = 1e-2
from boututils.run_wrapper import shell, shell_safe, launch_safe, getmpirun
from boututils.file_import import file_import
from boututils.calculus import deriv
from boututils.linear_regression import linear_regression
from boutdata.collect import collect
import numpy as np
from sys import exit ,argv
nthreads=1
MPIRUN = getmpirun()
print("Making resistive drift instability test")
shell_safe("make > make.log")
zlist = [2, 32, 256] # Just test a few
# Values from revision c4f7ec92786b333a5502c5256b5e602ba867090f
# 26th Oct 2011
omega_orig = {1:1.00819536681,
2:0.975756752742,
4:0.888269347989,
8:0.741253948437,
16:0.574003058717,
32:0.428644078148, #0.430745728591, Changed 25th April 2014, revision fd032da
64:0.336073734175,
128:0.2208085,
256:0.155890075514} #0.156853396108} Changed 25th April 2014
gamma_orig = {1:0.0784576199501,
#,("../fci-wave-logn/div-integrate", "Model 5 (velocity, log density, area integration)")
]
data_boundary = [
("boundary", "Model 2 (density, momentum)")
,("boundary-logn", "Model 3 (log density, momentum)")
#,("../fci-wave-logn/boundary", "Model 5 (log density, velocity)")
]
# Change this to select no boundary or boundary cases
data = data_noboundary
if run:
from boututils.run_wrapper import shell_safe, launch_safe, getmpirun
shell_safe("make > make.log")
MPIRUN=getmpirun()
for path,label in data:
launch_safe("./fci-wave -d "+path, runcmd=MPIRUN, nproc=nproc, pipe=False)
# Collect the results into a dictionary
sum_n_B = {}
for path,label in data:
n = collect("n", path=path)
Bxyz = collect("Bxyz", path=path)
time = collect("t_array", path=path)
nt, nx, ny, nz = n.shape
#,("../fci-wave-logn/div-integrate", "Model 5 (velocity, log density, area integration)")
]
data_boundary = [
("boundary", "Model 2 (density, momentum)"),
("boundary-logn", "Model 3 (log density, momentum)")
#,("../fci-wave-logn/boundary", "Model 5 (log density, velocity)")
]
# Change this to select no boundary or boundary cases
data = data_noboundary
if run:
from boututils.run_wrapper import shell_safe, launch_safe, getmpirun
shell_safe("make > make.log")
MPIRUN = getmpirun()
for path, label in data:
launch_safe("./fci-wave -d " + path,
runcmd=MPIRUN,
nproc=nproc,
pipe=False)
# Collect the results into a dictionary
sum_n_B = {}
for path, label in data:
n = collect("n", path=path)
Bxyz = collect("Bxyz", path=path)
def build_bout(configure_line=None):
"""Build BOUT++
"""
shell_safe("make -j8")