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abinit/tasks.py

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"""
Pyinvoke file for automating build/config stuff.
Example:
invoke abichecks
invoke --list
Can be executed everywhere inside the Abinit directory, including build directories.
Use: `pip install invoke --user` to install invoke package.
"""
import os
import sys
import webbrowser
from contextlib import contextmanager
try:
from invoke import task
except ImportError:
raise ImportError("Cannot import invoke package. Use `pip install invoke --user`")
from tests.pymods.testsuite import find_top_build_tree
from tests.pymods.devtools import number_of_cpus
from tests.pymods.termcolor import cprint
ABINIT_ROOTDIR = os.path.dirname(__file__)
ABINIT_SRCDIR = os.path.join(ABINIT_ROOTDIR, "src")
# Set ABI_PSPDIR env variable to point to the absolute path of Psps_for_tests
#os.environ["ABI_PSPDIR"] = os.path.abspath(os.path.join(ABINIT_ROOTDIR, "Psps_for_tests"))
#print("ABI_PSPDIR:", os.environ["ABI_PSPDIR"])
ALL_BINARIES = [
"abinit",
"abitk",
"aim",
"anaddb",
"band2eps",
"conducti",
"cut3d",
"dummy_tests",
"fftprof",
"fold2Bloch",
"ioprof",
"lapackprof",
"macroave",
"mrgddb",
"mrgdv",
"mrggkk",
"mrgscr",
"multibinit",
"optic",
"atdep",
"testtransposer",
"lruj",
]
import platform
SYSTEM = platform.system()
@contextmanager
def cd(path):
"""
A Fabric-inspired cd context that temporarily changes directory for
performing some tasks, and returns to the original working directory
afterwards. E.g.,
with cd("/my/path/"):
do_something()
Args:
path: Path to cd to.
"""
# Taken from monty.os
cwd = os.getcwd()
os.chdir(path)
try:
yield
finally:
os.chdir(cwd)
@task
def make(ctx, jobs="auto", touch=False, clean=False, binary=""):
"""
Touch all modified files and recompile the code
Args:
jobs: Use `jobs` threads for make -jNUM
touch: Touch all changed files
clean: Issue `make clean` before `make`.
binary: Binary to recompile, default: all
"""
if touch:
with cd(ABINIT_ROOTDIR):
cmd = "./abisrc.py touch"
cprint("Executing: %s" % cmd, "yellow")
result = ctx.run(cmd, pty=True)
if not result.ok:
cprint("`%s` failed. Aborting now!" % cmd, "red")
return 1
top = find_top_build_tree(".", with_abinit=False)
jobs = max(1, number_of_cpus() // 2) if jobs == "auto" else int(jobs)
with cd(top):
if clean:
ctx.run("cd src && make clean && cd ..", pty=True)
ctx.run("cd shared && make clean && cd ..", pty=True)
cmd = "make -j%d %s > >(tee -a make.log) 2> >(tee -a make.stderr >&2)" % (jobs, binary)
cprint("Executing: %s" % cmd, "yellow")
results = ctx.run(cmd, pty=True)
# TODO Check for errors in make.stderr
#cprint("Exit code: %s" % retcode, "green" if retcode == 0 else "red")
#if SYSTEM == "Darwin":
# for binary in ALL_BINARIES:
# cmd = f"codesign -v --force --deep src/98_main/{binary}"
# cprint("Executing: %s" % cmd, "yellow")
# ctx.run(cmd, pty=True)
@task
def clean(ctx):
"""Remove object files in src and shared. Do not remove object files in fallbacks"""
top = find_top_build_tree(".", with_abinit=False)
with cd(top):
ctx.run("cd src && make clean && cd ..", pty=True)
ctx.run("cd shared && make clean && cd ..", pty=True)
@task
def runemall(ctx, make=True, jobs="auto", touch=False, clean=False, keywords=None):
"""Run all tests (sequential and parallel). Exit immediately if errors"""
make(ctx, jobs=jobs, touch=touch, clean=clean)
top = find_top_build_tree(".", with_abinit=True)
jobs = max(1, number_of_cpus() // 2) if jobs == "auto" else int(jobs)
kws = "" if keywords is None else "-k %s" % keywords
with cd(os.path.join(top, "tests")):
cmd = "./runtests.py -j%d %s" % (jobs, kws)
cprint("Executing: %s" % cmd, "yellow")
ctx.run(cmd, pty=True)
# Now run the parallel tests.
for n in [2, 4, 10]:
j = jobs // n
if j == 0: continue
cmd = "./runtests.py paral mpiio -j%d -n%d %s" % (j, n, kws)
cprint("Executing: %s" % cmd, "yellow")
ctx.run(cmd, pty=True)
@task
def makemake(ctx):
"""Invoke makemake"""
with cd(ABINIT_ROOTDIR):
ctx.run("./config/scripts/makemake", pty=True)
@task
def makedeep(ctx, jobs="auto"):
"""Execute `makemake && make clean && make`"""
makemake(ctx)
make(ctx, jobs=jobs, clean=True)
@task
def abichecks(ctx):
"""Execute (some of the) abichecks scripts."""
import time
retcode = 0
with cd(ABINIT_ROOTDIR):
script_dir = os.path.join("abichecks", "scripts")
exclude = ["check-libpaw.py", "warningschk.py", "abirules_tools.py", "__init__.py"]
for py_script in [f for f in os.listdir(script_dir) if f.endswith(".py")]:
if py_script in exclude: continue
py_script = os.path.join(script_dir, py_script)
print("Running", py_script, "... ")
start = time.time()
result = ctx.run(py_script, warn=True, pty=True)
#print(result.ok)
msg, color = ("[OK]", "green") if result.ok else ("[FAILED]", "red")
cprint("%s (%.2f s)" % (msg, time.time() - start), color=color)
if not result.ok: retcode += 1
if retcode != 0:
cprint("%d FAILED TESTS" % retcode, "red")
else:
cprint("ALL TESTS OK", "green")
return retcode
@task
def robodoc(ctx):
with cd(ABINIT_ROOTDIR):
result = ctx.run("./mkrobodoc.sh", pty=True)
if result.ok:
cprint("ROBODOC BUILD OK", "green")
# https://stackoverflow.com/questions/44447469/cannot-open-an-html-file-from-python-in-a-web-browser-notepad-opens-instead
html_path = os.path.join(ABINIT_ROOTDIR, "./tmp-robodoc/www/robodoc/masterindex.html")
print("Trying to open %s in browser ..." % html_path)
return webbrowser.open_new_tab(html_path)
else:
cprint("ROBODOC BUILD FAILED", "red")
return result.ok
@task
def mksite(ctx):
"""
Build the Abinit documentation by running the mksite.py script and open the main page in the browser.
"""
with cd(ABINIT_ROOTDIR):
webbrowser.open_new_tab("http://127.0.0.1:8000")
ctx.run("./mksite.py serve --dirtyreload", pty=True)
@task
def links(ctx):
"""
Create symbolic links to Abinit executables in current working directory.
"""
top = find_top_build_tree(".", with_abinit=True)
main98 = os.path.join(top, "src", "98_main")
for dest in ALL_BINARIES:
if os.path.islink(os.path.join(os.getcwd(), dest)): continue
source = os.path.join(main98, dest)
if os.path.isfile(source):
os.symlink(source, dest)
else:
cprint("Cannot find `%s` in dir `%s" % (source, main98), "yellow")
@task
def ctags(ctx):
"""
Update ctags file.
"""
with cd(ABINIT_ROOTDIR):
cmd = "ctags -R --langmap=fortran:+.finc.f90,c:.c.cu shared/ src/"
print("Executing:", cmd)
ctx.run(cmd, pty=True)
#ctx.run('ctags -R --exclude="_*"', pty=True)
@task
def fgrep(ctx, pattern):
"""
Grep for `pattern` in all F90 files contained in `src` and `shared` directories.
"""
# grep -r -i --include \*.h
# Syntax notes:
# -r - search recursively
# -i - case-insensitive search
# --include=\*.${file_extension} - search files that match the extension(s) or file pattern only
with cd(ABINIT_ROOTDIR):
cmd = 'grep -r -i --color --include "*[.F90,.f90,.finc,.c,.cu,.cpp]" "%s" src shared' % pattern
#cmd = 'grep -r -i --color --include "*.F90" "%s" src shared' % pattern
print("Executing:", cmd)
ctx.run(cmd, pty=True)
@task
def cgrep(ctx, pattern):
"""
Grep for `pattern` in all C files contained in `src` and `shared` directories.
"""
with cd(ABINIT_ROOTDIR):
cmd = 'grep -r -i --color --include "*.c" "%s" src shared' % pattern
print("Executing:", cmd)
ctx.run(cmd, pty=True)
@task
def tgrep(ctx, pattern):
"""
Grep for `pattern` in all input files contained in the `tests` directory.
"""
with cd(ABINIT_ROOTDIR):
cmd = 'grep -r -i --color "%s" tests/*/Input/*' % pattern
print("Executing:", cmd)
ctx.run(cmd, pty=True)
@task
def vimt(ctx, tagname):
"""
Execute `vim -t tagname` with tagname a ctags tag.
"""
with cd(ABINIT_ROOTDIR):
if which("mvim") is not None:
cmd = "mvim -t %s" % tagname
else:
cmd = "vim -t %s" % tagname
print("Executing:", cmd)
ctx.run(cmd, pty=True)
@task
def env(ctx):
"""Print sh code to set $PATH and $ABI_PSPDIR in order to work with build directory."""
print("\nExecute the following lines in the shell to set the env:\n")
top = find_top_build_tree(".", with_abinit=True)
binpath = os.path.join(top, "src", "98_main")
print(f"export ABI_PSPDIR={ABINIT_ROOTDIR}/tests/Psps_for_tests")
print(f"export PATH={binpath}:$PATH")
@task
def diff2(ctx, filename="run.abo"):
"""
Execute `vimdiff` to compare run.abo with the last run.abo0001 found in the cwd.
"""
vimdiff = "vimdiff"
if which("mvimdiff") is not None: vimdiff = "mvimdiff"
files = sorted([f for f in os.listdir(".") if f.startswith(filename)])
if not files: return
cmd = "%s %s %s" % (vimdiff, filename, files[-1])
print("Executing:", cmd)
ctx.run(cmd, pty=True)
@task
def diff3(ctx, filename="run.abo"):
"""
Execute `vimdiff` to compare run.abo with the last run.abo0001 found in the cwd.
"""
vimdiff = "vimdiff"
if which("mvimdiff") is not None: vimdiff = "vimdiff"
files = sorted([f for f in os.listdir(".") if f.startswith(filename)])
if not files: return
if len(files) > 2:
cmd = "%s %s %s %s" % (vimdiff, filename, files[-2], files[-1])
else:
cmd = "%s %s %s" % (vimdiff, filename, files[-1])
print("Executing:", cmd)
ctx.run(cmd, pty=True)
@task
def add_trunk(ctx):
"""Register trunk as remote."""
cmd = "git remote add trunk git@gitlab.abinit.org:trunk/abinit.git"
print("Executing:", cmd)
ctx.run(cmd, pty=True)
@task
def remote_add(ctx, remote):
"""Register `remote` as remote branch and fetch it"""
cmd = f"git remote add {remote} git@gitlab.abinit.org:{remote}/abinit.git"
print("Executing:", cmd)
ctx.run(cmd, pty=True)
cmd = f"git fetch {remote}"
print("Executing:", cmd)
ctx.run(cmd, pty=True)
#@task
#def gdb(ctx, input_name, exec_name="abinit", run_make=False):
# """
# Execute `lldb` debugger with the given `input_name`.
# """
# if run_make: make(ctx)
#
# top = find_top_build_tree(".", with_abinit=True)
# binpath = os.path.join(top, "src", "98_main", exec_name)
# cprint(f"Using binpath: {binpath}", "green")
# cmd = f"gdb {binpath} --one-line 'settings set target.run-args {input_name}'"
# cprint(f"Executing gdb command: {cmd}", color="green")
# # mpirun -np 2 xterm -e gdb fftprof --command=dbg_file
# #cprint("Type run to start lldb debugger", color="green")
# #cprint("Then use `bt` to get the backtrace\n\n", color="green")
# ctx.run(cmd, pty=True)
@task
def lldb(ctx, input_name, exec_name="abinit", run_make=False):
"""
Execute `lldb` debugger with the given `input_name`.
"""
if run_make: make(ctx)
top = find_top_build_tree(".", with_abinit=True)
binpath = os.path.join(top, "src", "98_main", exec_name)
cprint(f"Using binpath: {binpath}", "green")
cmd = f"lldb {binpath} --one-line 'settings set target.run-args {input_name}'"
cprint(f"Executing lldb command: {cmd}", color="green")
cprint("Type run to start lldb debugger", color="green")
cprint("Then use `bt` to get the backtrace\n\n", color="green")
ctx.run(cmd, pty=True)
@task
def abinit(ctx, input_name, run_make=False):
"""
Execute `abinit` with the given `input_name`.
"""
_run(ctx, input_name, exec_name="abinit", run_make=run_make)
@task
def anaddb(ctx, input_name, run_make=False):
""""execute `anaddb` with the given `input_name`."""
_run(ctx, input_name, exec_name="anaddb", run_make=run_make)
def _run(ctx, input_name, exec_name, run_make):
""""Execute `exec_name input_name`"""
if run_make: make(ctx)
top = find_top_build_tree(".", with_abinit=True)
binpath = os.path.join(top, "src", "98_main", exec_name)
cprint(f"Using binpath: {binpath}", "green")
cmd = f"{binpath} {input_name}"
cprint(f"Executing {cmd}", color="green")
ctx.run(cmd, pty=True)
@task
def pull_trunk(ctx):
""""Execute `git stash && git pull trunk develop && git stash apply`"""
ctx.run("git stash")
ctx.run("git pull trunk develop")
ctx.run("git stash apply")
@task
def pull(ctx):
""""Execute `git stash && git pull --recurse-submodules && git stash apply`"""
ctx.run("git stash")
ctx.run("git pull --recurse-submodules")
ctx.run("git stash apply")
@task
def submodules(ctx):
"""Update submodules."""
with cd(ABINIT_ROOTDIR):
# https://stackoverflow.com/questions/1030169/easy-way-to-pull-latest-of-all-git-submodules
ctx.run("git submodule update --remote --init", pty=True)
ctx.run("git submodule update --recursive --remote", pty=True)
@task
def branchoff(ctx, start_point):
""""Checkout new branch from start_point e.g. `trunk/release-9.0` and set default upstream to origin."""
try:
remote, branch = start_point.split("/")
except:
remote = "trunk"
def run(cmd):
cprint(f"Executing: `{cmd}`", color="green")
ctx.run(cmd)
run(f"git fetch {remote}")
# Create new branch `test_v9.0` using trunk/release-9.0 as start_point:
# git checkout [-q] [-f] [-m] [[-b|-B|--orphan] <new_branch>] [<start_point>]
my_branch = "my_" + start_point.replace("/", "-")
run(f"git checkout -b {my_branch} {start_point}")
# Change default upstream. If you forget this step, you will be pushing to trunk
run("git branch --set-upstream-to origin")
run("git push origin HEAD")
@task
def dryrun_merge(ctx, start_point):
""""Merge `remote/branch` in dry-run mode."""
def run(cmd):
cprint(f"Executing: `{cmd}`", color="green")
ctx.run(cmd)
run(f"git merge --no-commit --no-ff {start_point}")
print("""
To examine the staged changes:
$ git diff --cached
And you can undo the merge, even if it is a fast-forward merge:
$ git merge --abort
""")
@task
def watchdog(ctx, jobs="auto", sleep_time = 5):
"""
Start watchdog service to watch F90 files and execute `make` when changes are detected.
"""
cprint("Starting watchdog service to watch F90 files and execute `make` when changes are detected", color="green")
cprint("Enter <CTRL + C> in the terminal to kill the service.", color="green")
cprint(f"Start watching F90 files with sleep_time {sleep_time} s ....", color="green")
top = find_top_build_tree(".", with_abinit=True)
jobs = max(1, number_of_cpus() // 2) if jobs == "auto" else int(jobs)
# http://thepythoncorner.com/dev/how-to-create-a-watchdog-in-python-to-look-for-filesystem-changes/
# https://stackoverflow.com/questions/19991033/generating-multiple-observers-with-python-watchdog
import time
from watchdog.observers import Observer
from watchdog.events import PatternMatchingEventHandler
event_handler = PatternMatchingEventHandler(patterns="*.F90", ignore_patterns="",
ignore_directories=False, case_sensitive=True)
def on_created(event):
print(f"hey, {event.src_path} has been created!")
def on_deleted(event):
print(f"what the f**k! Someone deleted {event.src_path}!")
def on_modified(event):
print(f"hey buddy, {event.src_path} has been modified")
cmd = "make -j%d > >(tee -a make.log) 2> >(tee -a make.stderr >&2)" % jobs
cprint("Executing: %s" % cmd, color="yellow")
with cd(top):
try:
result = ctx.run(cmd, pty=True)
if result.ok:
cprint("Make completed successfully", color="green")
cprint("Watching for changes ...", color="green")
except Exception:
cprint(f"Make returned non-zero exit status", color="red")
cprint(f"Keep on watching for changes hoping you get it right ...", color="red")
def on_moved(event):
print(f"ok ok ok, someone moved {event.src_path} to {event.dest_path}")
event_handler.on_created = on_created
event_handler.on_deleted = on_deleted
event_handler.on_modified = on_modified
event_handler.on_moved = on_moved
observer = Observer()
path = ABINIT_SRCDIR
observer.schedule(event_handler, path, recursive=True)
observer.start()
try:
while True:
time.sleep(sleep_time)
except KeyboardInterrupt:
observer.stop()
observer.join()
def which(cmd):
"""
Returns full path to a executable.
Args:
cmd (str): Executable command to search for.
Returns:
(str) Full path to command. None if it is not found.
Example::
full_path_to_python = which("python")
Take from monty.path. See https://github.com/materialsvirtuallab/monty
"""
def is_exe(fp):
return os.path.isfile(fp) and os.access(fp, os.X_OK)
fpath, fname = os.path.split(cmd)
if fpath:
if is_exe(cmd):
return cmd
else:
for path in os.environ["PATH"].split(os.pathsep):
exe_file = os.path.join(path, cmd)
if is_exe(exe_file):
return exe_file
return None
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