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from __future__ import print_function, division, unicode_literals
import time
from pprint import pprint
from itertools import groupby
from collections import namedtuple, deque
# OrderedDict was added in 2.7. ibm6 still uses python2.6
try:
from collections import OrderedDict
except ImportError:
from .ordereddict import OrderedDict
from .plotting import add_fig_kwargs, get_ax_fig_plt
from .tools import lazy_property
class Entry(namedtuple("Entry", "vname, ptr, action, size, file, line, tot_memory")):
"""
vname: Variable name.
prt: Address of variable.
action: "A" for allocation, "D" for deallocation.
size: Size of allocation in bits.
file: Name of Fortran file in which allocation/deallocation is performed.
line: Line number in file.
tot_memory: Total memory in bits allocated so far.
"""
@classmethod
def from_line(cls, line):
"""Build entry from line."""
vname = line[:59].strip().replace(" ", "")
args = [vname] + line[59:].split()
return cls(*args)
def __new__(cls, *args):
"""Extends the base class adding type conversion of arguments."""
# write(logunt,'(a,t60,a,1x,2(i0,1x),2(a,1x),2(i0,1x))')&
# trim(vname), trim(act), addr, isize, trim(abimem_basename(file)), line, memtot_abi%memory
return super(cls, Entry).__new__(cls,
vname=args[0],
action=args[1],
ptr=int(args[2]),
size=int(args[3]),
file=args[4],
line=int(args[5]),
tot_memory=int(args[6]),
)
def __repr__(self):
return self.to_repr(with_addr=True)
def to_repr(self, with_addr=True):
if with_addr:
return "<var=%s, %s@%s:%s, addr=%s, size_mb=%.3f>" % (
self.vname, self.action, self.file, self.line, hex(self.ptr), self.size_mb)
else:
return "<var=%s, %s@%s:%s, size_mb=%.3f>" % (
self.vname, self.action, self.file, self.line, self.size_mb)
@lazy_property
def size_mb(self):
"""Size in Megabytes."""
sign = {"A": +1, "D": -1}[self.action]
return sign * self.size / (8 * 1024 ** 2)
@lazy_property
def tot_memory_mb(self):
"""Total memory in Mb."""
return self.tot_memory / (8 * 1024 ** 2)
@lazy_property
def isalloc(self):
"""True if entry represents an allocation."""
return self.action == "A"
@lazy_property
def isfree(self):
"""True if entry represents a deallocation."""
return self.action == "D"
@lazy_property
def iszerosized(self):
"""True if this is a zero-sized alloc/free."""
return self.size == 0
@lazy_property
def locus(self):
"""Location of the entry. This is (hopefully) unique."""
return "%s:%s@%s:%s" % (self.action, self.vname, self.file, self.line)
def __hash__(self):
return hash(self.locus, self.size)
def __eq__(self, other):
return self.locus == other.locus and self.size == other.size
def __neq__(self, other):
return not (self == other)
def frees_onheap(self, other):
if (not self.isfree) or other.isalloc: return False
if self.size + other.size != 0: return False
return True
def frees_onstack(self, other):
if (not self.isfree) or other.isalloc: return False
if self.size + other.size != 0: return False
if self.locus != other.locus: return False
return True
def entries_to_dataframe(entries):
"""
Convert list of entries to pandas DataFrame.
"""
import pandas as pd
rows, index = [], []
for e in entries:
rows.append(OrderedDict([
("locus", e.locus),
("vname", e.vname),
("file", e.file),
("line", e.line),
("action", e.action),
("size_mb", e.size_mb),
("tot_memory_mb", e.tot_memory_mb),
("ptr", e.ptr),
]))
index.append(e.locus)
return pd.DataFrame(rows, index=index, columns=list(rows[0].keys()))
class AbimemFile(object):
def __init__(self, path):
self.path = path
def __str__(self):
return self.to_string()
def to_string(self, verbose=0):
lines = []
app = lines.append
df = self.get_intense_dataframe()
app(df.to_string())
return "\n".join(lines)
def find_small_allocs(self, nbits=160*8):
"""Zero sized allocations are not counted."""
smalles = []
for e in self.all_entries:
if not e.isalloc: continue
if 0 < e.size <= nbits: smalles.append(e)
pprint(smalles)
return smalles
def find_large_allocs(self, nbits=10 *8*1024*1024):
"""Allocations below 10 Mbytes are not counted."""
larges = []
for e in self.all_entries:
if not e.isalloc: continue
if e.size > nbits: larges.append(e)
pprint(larges)
return larges
def get_intense_dataframe(self):
"""
Return DataFrame with intensive spots i.e. variables that are allocated/freed many times.
"""
df = self.dataframe
index, rows = [], []
for locus, g in self.dataframe.groupby(by="locus"):
this_action = g.action.values[0]
assert all(g.action.values == this_action)
malloc_mb = g.size_mb.sum()
rows.append(OrderedDict([
("ncalls", len(g)),
("malloc_mb", malloc_mb),
("mem_per_call_mb", malloc_mb / len(g)),
]))
index.append(locus)
import pandas as pd
df = pd.DataFrame(rows, index=index, columns=list(rows[0].keys()))
return df.sort_values(by="ncalls", ascending=False)
def find_zerosized(self, as_dataframe=False):
"""
Find zero-sized allocations.
Args:
as_dataframe: True to return a pandas dataframe instead of a deque.
"""
elist = []
eapp = elist.append
for e in self.all_entries:
if e.size == 0: eapp(e)
return entries_to_dataframe(elist) if as_dataframe else elist
def find_weird_ptrs(self):
"""Find negative or zero pointers."""
elist = []
eapp = elist.append
for e in self.all_entries:
if e.ptr <= 0: eapp(e)
if elist:
print("Found %d weird entries:" % len(elist))
pprint(elist)
else:
print("No weird entries found")
return elist
@lazy_property
def all_entries(self):
"""Parse file and create list of Entries."""
all_entries = []
app = all_entries.append
with open(self.path, "rt") as fh:
for lineno, line in enumerate(fh):
# skip header line of abimem files
if line.startswith("#"): continue
try:
entry = Entry.from_line(line)
#if entry.size > 1024 * 8
app(entry)
except Exception as exc:
print("Error while parsing lineno %d, line:\n%s" % (lineno, line))
raise exc
return all_entries
def get_peaks(self, maxlen=30, as_dataframe=False):
"""
Find peaks in the allocation with the corresponding variable.
Args:
maxlen: Maximum number of peaks
as_dataframe: True to return a pandas dataframe instead of a deque.
"""
# The deque is bounded to the specified maximum length. Once a bounded length deque is full,
# when new items are added, a corresponding number of items are discarded from the opposite end.
peaks = deque(maxlen=maxlen)
visited = set()
for e in self.all_entries:
# Avoid redundant entries:
#k = (e.locus, e.size)
k = e.locus
if e.size == 0 or not e.isalloc or k in visited: continue
if len(peaks) == 0:
peaks.append(e)
visited.add(k)
continue
if e.size > peaks[0].size:
peaks.append(e)
visited.add(k)
# Keep peaks sorted
peaks = deque(sorted(peaks, key=lambda x: x.size), maxlen=maxlen)
peaks = deque(sorted(peaks, key=lambda x: x.size, reverse=True), maxlen=maxlen)
return entries_to_dataframe(peaks) if as_dataframe else peaks
@lazy_property
def dataframe(self):
"""
Return a |pandas-DataFrame| with **all** entries.
"""
return entries_to_dataframe(self.all_entries)
@add_fig_kwargs
def plot_memory_usage(self, ax=None, **kwargs):
"""
Plot total allocated memory in Mb on axis `ax`.
"""
memory = [e.tot_memory_mb for e in self.all_entries]
ax, fig, plt = get_ax_fig_plt(ax=ax)
ax.plot(memory)
ax.grid(True)
ax.set_ylabel("Total Memory (Mb)")
return fig
@add_fig_kwargs
def plot_peaks(self, ax=None, maxlen=20, fontsize=4, rotation=25, **kwargs):
"""
Plot memory peaks as vertical bars.
Args:
ax: |matplotlib-Axes| or None if a new figure should be created.
maxlen: Maximum number of peaks
fontsize: fontsize for legends and titles
rotation: Rotation angle for xticklabels.
Returns: |matplotlib-Figure|
"""
ax, fig, plt = get_ax_fig_plt(ax=ax)
peaks = self.get_peaks(maxlen=maxlen)
data = [e.size_mb for e in peaks]
names = ["%s\n%s" % (e.vname, e.locus) for e in peaks]
xs = list(range(len(data)))
ax.bar(xs, data)
ax.grid(True)
ax.set_xticks(xs)
ax.set_xticklabels(names, fontsize=fontsize, rotation=rotation)
ax.set_ylabel("Memory (Mb)")
return fig
@add_fig_kwargs
def plot_hist(self, ax=None, **kwargs):
"""
Plot histogram with the number of arrays allocated for a given size
Args:
ax: |matplotlib-Axes| or None if a new figure should be created.
Returns: |matplotlib-Figure|
"""
ax, fig, plt = get_ax_fig_plt(ax=ax)
data = [e.size_mb for e in self.all_entries]
ax.hist(data) #, bins=n_bins)
ax.grid(True)
ax.set_ylabel("Number of arrays")
ax.set_xlabel("Memory (Mb)")
return fig
def get_hotspots_dataframe(self):
"""
Return DataFrame with total memory allocated per Fortran file.
"""
index, rows = [], []
for filename, g in self.dataframe.groupby(by="file"):
malloc_mb = g[g["action"] == "A"].size_mb.sum()
free_mb = g[g["action"] == "D"].size_mb.sum()
nalloc = len(g["action"] == "A")
nfree = len(g["action"] == "D")
rows.append(OrderedDict([
("malloc_mb", malloc_mb),
("free_mb", free_mb),
#("diff_mb", malloc_mb + free_mb),
("nalloc", nalloc),
("nfree", nfree),
#("npall", nalloc - nfree),
]))
index.append(filename)
import pandas as pd
df = pd.DataFrame(rows, index=index, columns=list(rows[0].keys()))
return df.sort_values(by="malloc_mb", ascending=False)
def expose(self, slide_mode=False, slide_timeout=None, **kwargs):
"""
Shows a predefined list of matplotlib figures with minimal input from the user.
"""
#from abipy.tools.plotting import MplExpose
with MplExpose(slide_mode=slide_mode, slide_timeout=slide_mode, verbose=1) as e:
e(self.plot_memory_usage(show=False))
#e(self.plot_peaks(show=False))
#e(self.plot_hist(show=False))
def find_memleaks(self, verbose=0):
"""
Try to find memory leaks using the address of the arrays and the action performed (allocation/free).
"""
heap, stack = Heap(), Stack()
reallocs = []
for newe in self.all_entries:
p = newe.ptr
if newe.size == 0: continue
# Store new entry in list if the ptr is not in d
# else we check if there's an allocation that matches a previous allocation
# (zero-sized arrays are not included)
# else there's a possible memory leak or some undected problems.
if p not in heap:
if newe.isalloc:
heap[p] = [newe]
# isfree found but ptr has not been allocated:
else:
# Likely comes from a reallocation
reallocs.append(newe)
else:
if newe.isfree and len(heap[p]) == 1 and heap[p][0].size + newe.size == 0:
heap.pop(p)
else:
# In principle this should never happen but there are exceptions:
#
# 1) The compiler may decide to put the allocatable on the stack
# In this case the ptr reported by gfortran is 0.
#
# 2) The allocatable variable is "reallocated" by the compiler (F2003).
# Example:
#
# allocate(foo(2,1)) ! p0 = &foo
# foo = reshape([0,0], [2,1]) ! p1 = &foo. Reallocation of the LHS.
# ! Use foo(:) to avoid that
# deallocate(foo) ! p2 = &foo
#
# In this case, p2 != p0
if verbose:
print("WARN:", newe.ptr, newe, "ptr already on the heap ", len(heap[p]), \
" sizes = ", heap[p][0].size, newe.size)
#print("HEAP:", heap[newe.ptr])
locus = newe.locus
if locus not in stack:
stack[locus] = [newe]
else:
#if newe.ptr != 0: print(newe)
stack_loc = stack[locus]
ifind = -1
for i, olde in enumerate(stack_loc):
if newe.frees_onstack(olde):
ifind = i
break
if ifind != -1:
stack_loc.pop(ifind)
#else:
# print(newe)
#if p == 0:
# stack[p] = newe
#else:
# print("varname", newe.vname, "in heap with size ",newe.size)
# for weirde in heap[p]:
# print("\tweird entry:", weirde)
# heap[p].append(newe)
if False and heap:
# Possible memory leaks.
count = -1
keyfunc = lambda e: abs(e.size)
for a, entries in heap.items():
count += 1
entries = [e for e in entries if e.size != 0]
entries = sorted(entries, key=keyfunc)
#if any(int(e.size) != 0 for e in l):
#msizes = []
for key, group in groupby(entries, keyfunc):
group = list(group)
#print([e.name for e in g])
pos_size = [e for e in group if e.size >0]
neg_size = [e for e in group if e.size <0]
if len(pos_size) != len(neg_size):
print("key", key)
for e in group:
print(e)
#print(list(g))
#for i, e in enumerate(entries):
# print("\t[%d]" % i, e)
#print("Count=%d" % count, 60 * "=")
if heap: heap.show()
if stack: stack.show()
if verbose and reallocs:
print("Possible reallocations:")
pprint(reallocs)
return len(heap) + len(stack) + len(reallocs)
def get_panel(self):
"""
Build panel with widgets to interact with the memocc file either in a notebook or in panel app.
"""
from .memprof_panel import MoccViewer
return MoccViewer(self).get_panel()
class Heap(dict):
def show(self):
print("=== HEAP OF LEN %s ===" % len(self))
if not self: return
# for p, elist in self.items():
pprint(self, indent=4)
print("")
def pop_alloc(self, entry):
if not entry.isfree: return 0
elist = self.get[entry.ptr]
if elist is None: return 0
for i, olde in elist:
if entry.size + olde.size != 0:
elist.pop(i)
return 1
return 0
class Stack(dict):
def show(self):
print("=== STACK OF LEN %s ===" % len(self))
if not self: return
pprint(self)
print("")
# Copied from abipy.tools.plotting
class MplExpose(object): # pragma: no cover
"""
Example:
with MplExpose() as e:
e(obj.plot1(show=False))
e(obj.plot2(show=False))
"""
def __init__(self, slide_mode=False, slide_timeout=None, verbose=1):
"""
Args:
slide_mode: If true, iterate over figures. Default: Expose all figures at once.
slide_timeout: Close figure after slide-timeout seconds Block if None.
verbose: verbosity level
"""
self.figures = []
self.slide_mode = bool(slide_mode)
self.timeout_ms = slide_timeout
self.verbose = verbose
if self.timeout_ms is not None:
self.timeout_ms = int(self.timeout_ms * 1000)
assert self.timeout_ms >= 0
if self.verbose:
if self.slide_mode:
print("\nSliding matplotlib figures with slide timeout: %s [s]" % slide_timeout)
else:
print("\nLoading all matplotlib figures before showing them. It may take some time...")
self.start_time = time.time()
def __call__(self, obj):
"""
Add an object to MplExpose. Support mpl figure, list of figures or
generator yielding figures.
"""
import types
if isinstance(obj, (types.GeneratorType, list, tuple)):
for fig in obj:
self.add_fig(fig)
else:
self.add_fig(obj)
def add_fig(self, fig):
"""Add a matplotlib figure."""
if fig is None: return
if not self.slide_mode:
self.figures.append(fig)
else:
#print("Printing and closing", fig)
import matplotlib.pyplot as plt
if self.timeout_ms is not None:
# Creating a timer object
# timer calls plt.close after interval milliseconds to close the window.
timer = fig.canvas.new_timer(interval=self.timeout_ms)
timer.add_callback(plt.close, fig)
timer.start()
plt.show()
fig.clear()
def __enter__(self):
return self
def __exit__(self, exc_type, exc_val, exc_tb):
"""Activated at the end of the with statement. """
self.expose()
def expose(self):
"""Show all figures. Clear figures if needed."""
if not self.slide_mode:
print("All figures in memory, elapsed time: %.3f s" % (time.time() - self.start_time))
import matplotlib.pyplot as plt
plt.show()
for fig in self.figures:
fig.clear()
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