add hdf5 output option

This commit is contained in:
Magnus Ulimoen 2020-04-04 22:14:15 +02:00
parent 358f831513
commit c17ef20c76
4 changed files with 138 additions and 4 deletions

View File

@ -13,3 +13,7 @@ members = [
[profile.bench] [profile.bench]
debug = true debug = true
[patch]
[patch.crates-io]
hdf5 = { git = "https://github.com/mulimoen/hdf5-rust.git", branch = "feature/resizable_idx" }

View File

@ -22,6 +22,7 @@ criterion = "0.3.0"
structopt = "0.3.12" structopt = "0.3.12"
indicatif = "0.14.0" indicatif = "0.14.0"
rayon = "1.3.0" rayon = "1.3.0"
hdf5 = "0.6.0"
[[bench]] [[bench]]
name = "maxwell" name = "maxwell"
@ -30,3 +31,4 @@ harness = false
[[bench]] [[bench]]
name = "euler" name = "euler"
harness = false harness = false

View File

@ -2,6 +2,7 @@
import matplotlib as mpl import matplotlib as mpl
import matplotlib.pyplot as plt import matplotlib.pyplot as plt
import numpy as np import numpy as np
import h5py
import os import os
@ -195,6 +196,29 @@ def plot_pressure(grids, save: bool, filename="figure.png"):
def read_from_file(filename): def read_from_file(filename):
grids = [] grids = []
file = h5py.File(filename, "r")
for groupname in file:
group = file[groupname]
if not isinstance(group, h5py.Group):
continue
grids.append(
{
"x": group["x"][:],
"y": group["y"][:],
"rho": group["rho"][-1, :, :],
"rhou": group["rhou"][-1, :, :],
"rhov": group["rhov"][-1, :, :],
"e": group["e"][-1, :, :],
}
)
return grids
def read_from_legacy_file(filename):
grids = []
with open(filename, "rb") as f: with open(filename, "rb") as f:
ngrids = int(np.fromfile(f, dtype=np.uint32, count=1)) ngrids = int(np.fromfile(f, dtype=np.uint32, count=1))
for i in range(ngrids): for i in range(ngrids):

View File

@ -283,6 +283,12 @@ struct Options {
/// Number of simultaneous threads /// Number of simultaneous threads
#[structopt(short, long)] #[structopt(short, long)]
jobs: Option<Option<usize>>, jobs: Option<Option<usize>>,
/// Name of output file
#[structopt(default_value = "output")]
output: std::path::PathBuf,
/// Output on the legacy format
#[structopt(long)]
legacy: bool,
} }
fn main() { fn main() {
@ -326,7 +332,7 @@ fn main() {
}; };
let dt = 0.2 / (max_n as Float); let dt = 0.2 / (max_n as Float);
let ntime = (integration_time / dt).round() as usize; let ntime = (integration_time / dt).round() as u64;
let pool = if let Some(j) = opt.jobs { let pool = if let Some(j) = opt.jobs {
let builder = rayon::ThreadPoolBuilder::new(); let builder = rayon::ThreadPoolBuilder::new();
@ -340,6 +346,15 @@ fn main() {
None None
}; };
let output = if opt.legacy {
None
} else {
Some(create_hdf(&opt.output, sys.grids.as_slice()).unwrap())
};
if let Some(file) = output.as_ref() {
add_timestep_to_file(&file, 0, sys.fnow.as_slice()).unwrap();
}
let bar = if opt.no_progressbar { let bar = if opt.no_progressbar {
indicatif::ProgressBar::hidden() indicatif::ProgressBar::hidden()
} else { } else {
@ -359,12 +374,19 @@ fn main() {
} }
bar.finish(); bar.finish();
dump_to_file(&sys); if let Some(file) = output.as_ref() {
add_timestep_to_file(&file, ntime, sys.fnow.as_slice()).unwrap();
} else {
legacy_output(&opt.output, &sys);
}
} }
fn dump_to_file<T: sbp::operators::UpwindOperator>(sys: &System<T>) { fn legacy_output<T: sbp::operators::UpwindOperator, P: AsRef<std::path::Path>>(
path: &P,
sys: &System<T>,
) {
use std::io::prelude::*; use std::io::prelude::*;
let file = std::fs::File::create("output").unwrap(); let file = std::fs::File::create(path).unwrap();
let mut file = std::io::BufWriter::new(file); let mut file = std::io::BufWriter::new(file);
let ngrids = sys.grids.len(); let ngrids = sys.grids.len();
file.write_all(&(ngrids as u32).to_le_bytes()).unwrap(); file.write_all(&(ngrids as u32).to_le_bytes()).unwrap();
@ -391,3 +413,85 @@ fn dump_to_file<T: sbp::operators::UpwindOperator>(sys: &System<T>) {
} }
} }
} }
fn create_hdf<P: AsRef<std::path::Path>>(
path: P,
grids: &[sbp::grid::Grid],
) -> Result<hdf5::File, Box<dyn std::error::Error>> {
let gzip = 7;
let file = hdf5::File::create(path.as_ref())?;
let _tds = file
.new_dataset::<u64>()
.resizable(true)
.chunk((1,))
.create("t", (0,))?;
for (i, grid) in grids.iter().enumerate() {
let g = file.create_group(&i.to_string())?;
g.link_soft("/t", "t").unwrap();
let add_dim = |name| {
g.new_dataset::<f64>()
.gzip(gzip)
.create(name, (grid.ny(), grid.nx()))
};
let xds = add_dim("x")?;
xds.write(grid.x())?;
let yds = add_dim("y")?;
yds.write(grid.y())?;
let add_var = |name| {
g.new_dataset::<f64>()
.gzip(gzip)
.chunk((1, grid.ny(), grid.nx()))
.resizable_idx(&[true, false, false])
.create(name, (0, grid.ny(), grid.nx()))
};
add_var("rho")?;
add_var("rhou")?;
add_var("rhov")?;
add_var("e")?;
}
Ok(file)
}
fn add_timestep_to_file(
file: &hdf5::File,
t: u64,
fields: &[euler::Field],
) -> Result<(), Box<dyn std::error::Error>> {
let tds = file.dataset("t")?;
let tpos = tds.size();
tds.resize((tpos + 1,))?;
tds.write_slice(&[t], ndarray::s![tpos..tpos + 1])?;
for (i, fnow) in fields.iter().enumerate() {
let g = file.group(&i.to_string())?;
let (tpos, ny, nx) = {
let ds = g.dataset("rho")?;
let shape = ds.shape();
(shape[0], shape[1], shape[2])
};
let rhods = g.dataset("rho")?;
let rhouds = g.dataset("rhou")?;
let rhovds = g.dataset("rhov")?;
let eds = g.dataset("e")?;
let (rho, rhou, rhov, e) = fnow.components();
rhods.resize((tpos + 1, ny, nx))?;
rhods.write_slice(rho, ndarray::s![tpos, .., ..])?;
rhouds.resize((tpos + 1, ny, nx))?;
rhouds.write_slice(rhou, ndarray::s![tpos, .., ..])?;
rhovds.resize((tpos + 1, ny, nx))?;
rhovds.write_slice(rhov, ndarray::s![tpos, .., ..])?;
eds.resize((tpos + 1, ny, nx))?;
eds.write_slice(e, ndarray::s![tpos, .., ..])?;
}
Ok(())
}