8000 BUG: Fix ndarray.tofile large file corruption in append mode. by charris · Pull Request #8339 · numpy/numpy · GitHub
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BUG: Fix ndarray.tofile large file corruption in append mode. #8339

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Merged
merged 1 commit into from
Dec 5, 2016
Merged

BUG: Fix ndarray.tofile large file corruption in append mode. #8339

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13 changes: 12 additions & 1 deletion numpy/core/src/multiarray/convert.c
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Original file line number Diff line number Diff line change
Expand Up @@ -44,10 +44,21 @@ npy_fallocate(npy_intp nbytes, FILE * fp)
if (nbytes < 16 * 1024 * 1024) {
return 0;
}

/* btrfs can take a while to allocate making release worthwhile */
NPY_BEGIN_ALLOW_THREADS;
r = fallocate(fileno(fp), 0, npy_ftell(fp), nbytes);
/*
* flush in case there might be some unexpected interactions between the
* fallocate call and unwritten data in the descriptor
*/
fflush(fp);
/*
* the flag "1" (=FALLOC_FL_KEEP_SIZE) is needed for the case of files
* opened in append mode (issue #8329)
*/
r = fallocate(fileno(fp), 1, npy_ftell(fp), nbytes);
NPY_END_ALLOW_THREADS;

/*
* early exit on no space, other errors will also get found during fwrite
*/
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13 changes: 11 additions & 2 deletions numpy/core/tests/test_multiarray.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3843,6 +3843,15 @@ def test_largish_file(self):
f.seek(d.nbytes)
d.tofile(f)
assert_equal(os.path.getsize(self.filename), d.nbytes * 2)
# check append mode (gh-8329)
open(self.filename, "w").close() # delete file contents
with open(self.filename, "ab") as f:
d.tofile(f)
assert_array_equal(d, np.fromfile(self.filename))
with open(self.filename, "ab") as f:
d.tofile(f)
assert_equal(os.path.getsize(self.filename), d.nbytes * 2)


def test_file_position_after_fromfile(self):
# gh-4118
Expand Down Expand Up @@ -4106,7 +4115,7 @@ def test_int_shape(self):
x = np.eye(3)
if IS_PYPY:
x.resize(3, refcheck=False)
else:
else:
x.resize(3)
assert_array_equal(x, np.eye(3)[0,:])

Expand Down Expand Up @@ -4135,7 +4144,7 @@ def test_zeros_appended(self):
x = np.eye(3)
if IS_PYPY:
x.resize(2, 3, 3, refcheck=False)
else:
else:
x.resize(2, 3, 3)
assert_array_equal(x[0], np.eye(3))
assert_array_equal(x[1], np.zeros((3, 3)))
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