Else on-heap allocated RAM object is leaked. Fixes e.g. the following
error on ASAN:

	Direct leak of 56 byte(s) in 1 object(s) allocated from:
	    #0 0x7fc9ef390518 in calloc (/usr/lib/x86_64-linux-gnu/libasan.so.5+0xe9518)
	    #1 0x555ca792f309 in zalloc include/wendelin/utils.h:67
	    #2 0x555ca7935f9a in ram_limited_new bigfile/tests/../../t/t_utils.c:35
	    #3 0x555ca793a0ba in test_file_access_synthetic bigfile/tests/test_virtmem.c:292
	    #4 0x555ca7967bc4 in main bigfile/tests/test_virtmem.c:1121
	    #5 0x7fc9ef0e909a in __libc_start_main ../csu/libc-start.c:308

Only one place that was using ram_new was missing to call ram_close in
the end.

For failing case compiler-rt support was added in 2014 - 5 years ago
(see links in removed code).

-> Use .[test] to refer to them.
https://stackoverflow.com/a/41398850/9456786

Just an update to latest CCAN - there is actually no changes to modules
that we use (tap, array_size, minmax, bitmap, build_assert)

Let's keep on test coverage for last 2 stable Python releases.

Starting from Python 3.7 the place to keep exception state was changed:
https://github.com/python/cpython/commit/ae3087c638

NOTE ZEO4 does not wok with Python3.7, because ZEO4 uses "async" for a
variable and that breaks because starting from Python3.7 "async" became
a keyword.

After the fix wendelin.core tests pass under all python2.7, python3.6
and python3.7.

Dependency added here:

	https://github.com/zopefoundation/ZODB/commit/e0bc8bd567

If we don't provide mock, e.g. py27-ZODB5-*-zeo-* breaks:

	    def setup_module():
	        global testdb
	>       testdb = getTestDB()

	bigarray/tests/test_arrayzodb.py:38:
	_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
	.tox/py27-ZODB5-zblk1-zeo-numpy115/lib/python2.7/site-packages/wendelin/lib/testing.py:342: in getTestDB
	    testdb = testdb_factory(testdb_uri)
	.tox/py27-ZODB5-zblk1-zeo-numpy115/lib/python2.7/site-packages/wendelin/lib/testing.py:245: in __init__
	    from ZEO.tests import forker
	.tox/py27-ZODB5-zblk1-zeo-numpy115/lib/python2.7/site-packages/ZEO/tests/forker.py:29: in <module>
	    import ZODB.tests.util
	_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

	    """
	    from ZODB.MappingStorage import DB

	    import atexit
	    import os
	    import persistent
	    import re
	    import tempfile
	    import time
	    import transaction
	    import unittest
	    import warnings
	    import ZODB.utils
	    from ZODB.Connection import TransactionMetaData
	    import zope.testing.setupstack
	    from zope.testing import renormalizing

	    try:
	        from unittest import mock
	    except ImportError:
	>       import mock
	E       ImportError: No module named mock

	.tox/py27-ZODB5-zblk1-zeo-numpy115/lib/python2.7/site-packages/ZODB/tests/util.py:35: ImportError

This continues c7c01ce4 (bigfile/zodb: ZODB.Connection can migrate
between threads on close/open and we have to care): Until now we were
retrieving zconn.transaction_manager on _ZBigFileH init, and further using
that transaction manager for every connection reopen. However that is
not correct because on every reopen connection can be given new
transaction manager.

We were not practically hitting the bug because until recently ZODB was,
by default, using the same ThreadTransactionManager manager instance as
Connection.transaction_manager for all connections, and not doing all
steps needed to keep _ZBigFileH.transaction_manager in sync to
Connection was forgiven - a particular transaction manager that was used
was TransactionManager instance implicitly associated with current
thread by global threading.Local transaction.manager . However starting
from ZODB 5.5.0 Connection code was changed to remember as
.transaction_manager the particular TransactionManager instance without
any threading.Local games:

    https://github.com/zopefoundation/ZODB/commit/b6ac40f153
    https://github.com/zopefoundation/ZODB/issues/208
    https://github.com/zopefoundation/ZODB/pull/226

Given that we were not syncing properly that broke wendelin.core tests, for
example:

    bigfile/tests/test_filezodb.py::test_bigfile_filezodb_vs_conn_migration Exception in thread Thread-1:
    Traceback (most recent call last):
      File "/usr/lib/python2.7/threading.py", line 801, in __bootstrap_inner
        self.run()
      File "/usr/lib/python2.7/threading.py", line 754, in run
        self.__target(*self.__args, **self.__kwargs)
      File "/home/kirr/src/wendelin/wendelin.core/bigfile/tests/test_filezodb.py", line 401, in T11
        transaction.commit()    # should be nothing
      File "/home/kirr/src/wendelin/venv/z-dev/local/lib/python2.7/site-packages/transaction/_manager.py", line 252, in commit
        return self.manager.commit()
      File "/home/kirr/src/wendelin/venv/z-dev/local/lib/python2.7/site-packages/transaction/_manager.py", line 131, in commit
        return self.get().commit()
      File "/home/kirr/src/wendelin/venv/z-dev/local/lib/python2.7/site-packages/transaction/_transaction.py", line 298, in commit
        self._synchronizers.map(lambda s: s.beforeCompletion(self))
      File "/home/kirr/src/wendelin/venv/z-dev/local/lib/python2.7/site-packages/transaction/weakset.py", line 61, in map
        f(elt)
      File "/home/kirr/src/wendelin/venv/z-dev/local/lib/python2.7/site-packages/transaction/_transaction.py", line 298, in <lambda>
        self._synchronizers.map(lambda s: s.beforeCompletion(self))
      File "/home/kirr/src/wendelin/wendelin.core/bigfile/file_zodb.py", line 671, in beforeCompletion
        assert txn is zconn.transaction_manager.get()
    AssertionError

What is happening here is that one thread used the connection and
ZBigFile/_ZBigFileH associated with it, then the connection was closed
and released to DB pool. Then the connection was reopened but by another
thread and thus with different TransactionManager instance and oops -
_ZBigFileH.transaction_manager is different because it is
TransactionManager instance that was used by the first thread.

Fix it by resyncing _ZBigFileH.transaction_manager on every
connection reopen. No new test as existing tests already cover the
problem when run with ZODB >= 5.5.0 .

This continues 6ab95220 (t/qemu-runlinux: Issue terminal resize before
running program) and fully initializes terminal before spawning user
application.

This has practical effect to restore line wrapping for xterm, as kernel,
initially assuming it has "linux" type terminal, somehow messes xterm
settings: before the patch lines that were wider than terminal width were
not wrapped and characters in the last position were printed over each
other. After the patch printed lines are automatically wrapped and test
output is not lost.

Tput hint found here:

	https://unix.stackexchange.com/questions/105958

	0: ERROR+ on boot/run
	1: INFO+  on      run
	2: INFO+  on boot/run
	3: DEBUG+ on boot/run

It is convenient not to see large kernel boot log on every test run. "1"
(single -v) is also convenient: one can skip the boot log but still see
details of what is going on when test workload is run. -vv and -vvv are
there to see full picture.

bpf is needed for tools like bpftrace.
fusectl is needed to observe things like /sys/fs/fuse/connections/X/waiting.

Else program inside sees default terminal settings to be 80x25,
while after the patch it sees correct settings.

Still something is not completely right with terminal settings, as e.g.
vsplit is not working correctly in vim (vertical ruler is not straight).

Graphics mode runs in another window with its own terminal emulation,
so propagating e.g. TERM=xterm to where it is emulated as TERM=linux is
not correct.

Continuing 76d8f76d (Script to run compiled linux kernel with root fs
mounted from host) update the script to run/debug linux inside QEMU:

- teach it to run specified program + args, instead of hardcoded /bin/sh;
- before tailing to user program, builtin init mounts /proc, /sys, ...
  inside - previously it was /proc, /sys from host seen on those
  mountpoints and it was very misleading - e.g. ps was showing processes
  from host, not inside, etc.
- builtin init also cares to run specified program with the same current
  directory that was current on host, and environments such as $HOME,
  $PATH, $TERM, ... are also propagated.
- allow to optionally run QEMU with graphics, instead of stdout only;
- increase available RAM from 128M to 512M (with 128M running py.test
  inside is failing with fork: not enough memory).

This updated version was useful to debug WCFS(*) & FUSE issues by running

	kirr@deco:~/src/wendelin/wendelin.core/wcfs$ ../t/qemu-runlinux ~/src/linux/linux/arch/x86_64/boot/bzImage py.test -vsx -k test_wcfs

See https://marc.info/?l=linux-fsdevel&m=155000277921155&w=2 for details.

(*) WCFS is still being draft and worked on t branch.

On a testing instance we started to see segfaults in pyvma_dealloc()
with inside calls to vma_unmap but with NULL pyvma->fileh. That was
strange, becuse before calling vma_unmap(), the code explicitly checks
whether pyvma->fileh is !NULL.

That was, as it turned out, due to pyvma_dealloc being called twice at the
same time from two python threads. Here is how that was possible:

T1 decrefs pyvma and finds its reference count drops to zero. It calls
pyvma_dealloc. From there vma_unmap() is called, which calls virt_lock()
and that releases GIL first. Another thread T2 was waiting for GIL, it
acquires it, does some work at python level and somehow triggers GC.
Since PyVMA supports cyclic GC, it was on GC list and thus GC calls
dealloc for the same vma again. Here is how it looks in the backtraces:

T1:

	#0  0x00007f6aefc57827 in futex_abstimed_wait_cancelable (private=0, abstime=0x0, expected=0, futex_word=0x1e011d0) at ../sysdeps/unix/sysv/linux/futex-internal.h:205
	#1  do_futex_wait (sem=sem@entry=0x1e011d0, abstime=0x0) at sem_waitcommon.c:111
	#2  0x00007f6aefc578d4 in __new_sem_wait_slow (sem=0x1e011d0, abstime=0x0) at sem_waitcommon.c:181
	#3  0x00007f6aefc5797a in __new_sem_wait (sem=<optimized out>) at sem_wait.c:29
	#4  0x00000000004ffbc4 in PyThread_acquire_lock ()
	#5  0x00000000004dbe8a in PyEval_RestoreThread ()
	#6  0x00007f6ac6d3b8fc in py_gil_retake_if_waslocked (arg=0x4f18f00) at bigfile/_bigfile.c:1048
	#7  0x00007f6ac6d3dcfc in virt_gil_retake_if_waslocked (gilstate=0x4f18f00) at bigfile/virtmem.c:78
	#8  0x00007f6ac6d3dd30 in virt_lock () at bigfile/virtmem.c:92
	#9  0x00007f6ac6d3e724 in vma_unmap (vma=0x7f6a7e0c4100) at bigfile/virtmem.c:271
	#10 0x00007f6ac6d3a0bc in pyvma_dealloc (pyvma0=0x7f6a7e0c40e0) at bigfile/_bigfile.c:284
	...
	#13 0x00000000004d76b0 in PyEval_EvalFrameEx ()

T2:

	#5  0x00007f6ac6d3a081 in pyvma_dealloc (pyvma0=0x7f6a7e0c40e0) at bigfile/_bigfile.c:276
	#6  0x0000000000500450 in ?? ()
	#7  0x00000000004ffd82 in _PyObject_GC_New ()
	#8  0x0000000000485392 in PyList_New ()
	#9  0x00000000004d3bff in PyEval_EvalFrameEx ()

T2 does the work of vma_unmap and clears C-level vma. Then, when T1 wakes up and
returns to vma_unmap, it sees vma->file and all other fields cleared -> oops
segfault.

Fix it by removing pyvma from GC list before going to do actual destruction.
This way if a concurrent GC triggers, it won't see the vma object on its list,
and thus won't have a chance to invoke its destructor the second time.

The bug was introduced in 450ad804 (bigarray: ArrayRef support for BigArray)
when PyVMA was changed to be cyclic-GC aware. However at that time, even Python
documentation itself was not saying PyObject_GC_UnTrack is needed, as it was
added only in 2.7.15 after finding that many types in CPython itself are
vulnerable to similar segfaults:

https://github.com/python/cpython/commit/4cde4bdcc86
https://bugs.python.org/issue31095

It is pity, that CPython took the approach to force all type authors to
care to invoke PyObject_GC_UnTrack explicitly, instead of doing that
automatically in Python runtime before calling tp_dealloc.

/cc @Tyagov, @klaus
/reviewed-on nexedi/wendelin.core!11

Structured creates view of the array interpreting its minor axis as fully covered by a dtype.

It is similar to arr.view(dtype) + corresponding reshape, but does
not have limitations of ndarray.view(). For example:

  In [1]: a = np.arange(3*3, dtype=np.int32).reshape((3,3))

  In [2]: a
  Out[2]:
  array([[0, 1, 2],
         [3, 4, 5],
         [6, 7, 8]], dtype=int32)

  In [3]: b = a[:2,:2]

  In [4]: b
  Out[4]:
  array([[0, 1],
         [3, 4]], dtype=int32)

  In [5]: dtxy = np.dtype([('x', np.int32), ('y', np.int32)])

  In [6]: dtxy
  Out[6]: dtype([('x', '<i4'), ('y', '<i4')])

  In [7]: b.view(dtxy)
  ---------------------------------------------------------------------------
  ValueError                                Traceback (most recent call last)
  <ipython-input-66-af98529aa150> in <module>()
  ----> 1 b.view(dtxy)

  ValueError: To change to a dtype of a different size, the array must be C-contiguous

  In [8]: structured(b, dtxy)
  Out[8]: array([(0, 1), (3, 4)], dtype=[('x', '<i4'), ('y', '<i4')])

Structured always creates view and never copies data.

Here is original context where separately playing with .shape and .dtype
was not enough, since it was creating array copy and OOM'ing the machine:

klaus/wendelin@cbe4938b

We are going to use this code in another place, so move this out to
dommon place as a preparatory step first.

On a related note: Since ArrayRef is generic and quite independent from
BigArray (it only supports it, but equally it supports just other - e.g.
plain arrays), the proper place for it might be also to be lib/xnumpy.py .
We might get to this topic a bit later.

RAMArray is compatible to ZBigArray in API and semantic, but stores its
data in RAM only. It is useful in situations where ZBigArray compatible
data type is needed, but the amount of data is small and the data itself
is needed only temporarily - e.g. in a simulation.

Please see details in individual patches.

Original merge request by @klaus (nexedi/wendelin.core!8).

/cc @Tyagov
/reviewed-on nexedi/wendelin.core!9

RAMArray is compatible to ZBigArray in API and semantic, but stores its
data in RAM only. It is useful in situations where ZBigArray compatible
data type is needed, but the amount of data is small and the data itself
is needed only temporarily - e.g. in a simulation.

Implementation is based on mmapping temporary files from /dev/shm/... and
passing them as file handles, similarly to how ZBigArray works, to BigArray.
We don't use just numpy.ndarray because of append - for ZBigArray append
works in O(1), but more importantly it does not copy data. This way
mmapings previously created for ZBigArray views, continue to correctly
alias array data. If we would be using ndarray directly, since
ndarray.resize copies data, that property would not be preserved.

Original patch by Klaus Wölfel <klaus@nexedi.com>
(nexedi/wendelin.core!8)

bigarray/tests: Factor out a way to spcify on which BigFile/BigFileH an array is tested into fixture parameter

Currently we have only one BigFile and its BigFileH handle. However in
the next patch, for RAMArray, we'll be adding handles for opened RAM
files, and it would be good to test whole BigArray functionality on
data served by those handles too.

Prepare for this and first factor out into testbig fixture the way to
open such handles.

So that it can be available to everyone and in particular B & friends to
be available from introduced importable golang.testing package. The move
itself:

	pygolang@9bf03d9c

While moving the code was restructured / improved a bit and py.bench
interface reworked to mimic `go test -bench` in defaults.

bigfile/tests/test_filezodb.py ........W: testdb: teardown: <Connection at 7f8fe2b43b90> left not closed by test code; opened by:
  ...
  File "/home/kirr/src/wendelin/wendelin.core/bigfile/tests/test_filezodb.py", line 754, in test_bigfile_zblk1_zdata_reuse
    _test_bigfile_zblk1_zdata_reuse()
  File "/home/kirr/src/wendelin/wendelin.core/bigfile/tests/test_filezodb.py", line 759, in _test_bigfile_zblk1_zdata_reuse
    root = dbopen()
  File "/home/kirr/src/wendelin/wendelin.core/bigfile/tests/test_filezodb.py", line 47, in dbopen
    return testdb.dbopen()
  File "/home/kirr/src/wendelin/wendelin.core/lib/testing.py", line 188, in dbopen
    self.connv.append( (weakref.ref(conn), ''.join(traceback.format_stack())) )

lib/tests/test_zodb.py .W: testdb: teardown: <Connection at 7f8fe26f13d0> left not closed by test code; opened by:
  ...
  File "/home/kirr/src/wendelin/wendelin.core/lib/tests/test_zodb.py", line 49, in test_deactivate_btree
    root = dbopen()
  File "/home/kirr/src/wendelin/wendelin.core/lib/tests/test_zodb.py", line 30, in dbopen
    return testdb.dbopen()
  File "/home/kirr/src/wendelin/wendelin.core/lib/testing.py", line 188, in dbopen
    self.connv.append( (weakref.ref(conn), ''.join(traceback.format_stack())) )

If a test forgets to explicitly close ZODB connection it was using, this
connection stays alive in transaction synchronizers (it is a weakset),
and continues to be used on e.g. transaction.commit() when all
synchronizers are invoked. This could lead to crashes like below when
underlying ZODB storage was closed by test module teardown and testing
moved on to another test module:

    $ WENDELIN_CORE_TEST_DB="<neo>" py.test  bigfile/tests/test_filezodb.py::test_bigfile_zblk1_zdata_reuse lib/tests/test_zodb.py
    ======= test session starts ========
    platform linux2 -- Python 2.7.14+, pytest-3.5.0, py-1.5.3, pluggy-0.6.0
    rootdir: /home/kirr/src/wendelin/wendelin.core, inifile:
    collected 2 items

    bigfile/tests/test_filezodb.py .                                     [ 50%]
    lib/tests/test_zodb.py F                                             [100%]

    ______ test_deactivate_btree _______

        def test_deactivate_btree():
            root = dbopen()
            # init btree with many leaf nodes
            leafv = []
            root['btree'] = B = IOBTree()
            for i in range(10000):
                B[i] = xi = XInt(i)
                leafv.append(xi)
    >       transaction.commit()

    lib/tests/test_zodb.py:56:
    _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
    ../venv/z5/local/lib/python2.7/site-packages/transaction/_manager.py:131: in commit
        return self.get().commit()
    ../venv/z5/local/lib/python2.7/site-packages/transaction/_transaction.py:316: in commit
        self._synchronizers.map(lambda s: s.afterCompletion(self))
    ../venv/z5/local/lib/python2.7/site-packages/transaction/weakset.py:62: in map
        f(elt)
    ../venv/z5/local/lib/python2.7/site-packages/transaction/_transaction.py:316: in <lambda>
        self._synchronizers.map(lambda s: s.afterCompletion(self))
    ../venv/z5/local/lib/python2.7/site-packages/ZODB/Connection.py:757: in afterCompletion
        self.newTransaction(transaction, False)
    ../venv/z5/local/lib/python2.7/site-packages/ZODB/Connection.py:737: in newTransaction
        invalidated = self._storage.poll_invalidations()
    ../venv/z5/local/lib/python2.7/site-packages/ZODB/mvccadapter.py:131: in poll_invalidations
        self._start = p64(u64(self._storage.lastTransaction()) + 1)
    _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

    self = <neo.client.Storage.Storage object at 0x7ffa1be8d410>

        def lastTransaction(self):
            # Used in ZODB unit tests
    >       return self.app.last_tid
    E       AttributeError: 'NoneType' object has no attribute 'last_tid'

    ../../neo/src/lab.nexedi.com/kirr/neo/neo/client/Storage.py:181: AttributeError

where NEO's Storage.app is None because the storage was closed.

----

To avoid such kind of failures make sure TestDB.teardown() always closes
all ZODB connections that were ever opened via TestDB.dbopen().

Add a warning about such force-closing with information about corresponding
connection and code place that created it, so that it is easy to
understand which test needs a fix.

/suggested-by @jm

- start testing NEO with ZODB4 and ZODB5. ZODB4-*-NEO works while
  ZODB5-*-NEO currently fails [1].
- update NumPy to latest releases.
- update Python 3 to latest releases.

Since 7fc4ec66 (tests: Allow to test with ZEO & NEO ZODB storages) we
can run the tests with either FileStorage, ZEO or NEO. But ZEO test
adapter started to fail with ZEO5:

	self = <wendelin.lib.testing.TestDB_ZEO object at 0x7f1feb5091d0>

	    def setup(self):
	        port  = self.zeo_forker.get_port()
	        zconf = self.zeo_forker.ZEOConfig(('', port))
	        self.addr, self.adminaddr, self.pid, self.path = \
	>               self.zeo_forker.start_zeo_server(zeo_conf=zconf, port=port)
	E       ValueError: need more than 2 values to unpack

This is because in ZEO5 forker.start_zeo_server() was reworked to return only
addr and stop closure instead of returning all details and relying on caller to
implement stop itself.

Adapt the test to detect ZEO5 and use new calling convention.

With ZConfig==3.2.0 (released 2017-06-22) ZEO started to get file names
as unicode, which eventually breaks on assert in ZODB3.FileStorage code:

    Traceback (most recent call last):
      File "/home/kirr/src/wendelin/r/work/venv/local/lib/python2.7/site-packages/ZEO/tests/zeoserver.py", line 215, in <module>
        main()
      File "/home/kirr/src/wendelin/r/work/venv/local/lib/python2.7/site-packages/ZEO/tests/zeoserver.py", line 188, in main
        server = ZEO.runzeo.create_server({"1": storage}, zo)
      File "/home/kirr/src/wendelin/r/work/venv/local/lib/python2.7/site-packages/ZEO/runzeo.py", line 366, in create_server
        auth_realm = options.auth_realm,
      File "/home/kirr/src/wendelin/r/work/venv/local/lib/python2.7/site-packages/ZEO/StorageServer.py", line 890, in __init__
        self._setup_invq(name, storage)
      File "/home/kirr/src/wendelin/r/work/venv/local/lib/python2.7/site-packages/ZEO/StorageServer.py", line 928, in _setup_invq
        self.invq[name] = list(lastInvalidations(self.invq_bound))
      File "/home/kirr/src/wendelin/r/work/venv/local/lib/python2.7/site-packages/ZODB/FileStorage/FileStorage.py", line 1238, in lastInvalidations
        for trans in FileIterator(self._file_name, pos=pos)]
      File "/home/kirr/src/wendelin/r/work/venv/local/lib/python2.7/site-packages/ZODB/FileStorage/FileStorage.py", line 1640, in __init__
        assert isinstance(filename, str), `filename`
    AssertionError: u'/home/kirr/src/wendelin/r/work/wendelin.core/Data.fs'

-> So for ZODB3 pin ZConfig to ZConfig <3.2.0 which is known to work with ZODB3.

ArrayRef is a reference to NumPy array.

The reference is represented by root array object and instructions how to
create original array as some view of the root.

Such reference could be useful in situations where one needs to pass arrays
between processes and instead of copying array data, leverage the fact that
top-level array, for example ZBigArray, is already persisted separately, and
only send small amount of information referencing data in question.

Use `ArrayRef(array)` to create reference to an ndarray.

Use `.deref()` to convert ArrayRef to pointed array object.

NOTE

don't send ArrayRef unconditionally - for example when array object is
small regular ndarray with also regular, but big, root ndarray, sending
ArrayRef will send whole data for root object, not for small leaf.

Sending ArrayRef only makes sense when root object is known to be already
persisted by other means, for example something like below in ZODB context:

```python
  aref = ArrayRef(a)
  if isinstance(aref.root, Persistent):
      send aref
  else:
      send a 
```

Please see individual patches for more details.

/reviewed-on !6

Rationale
---------

Array reference could be useful in situations where one needs to pass arrays
between processes and instead of copying array data, leverage the fact that
top-level array, for example ZBigArray, is already persisted separately, and
only send small amount of information referencing data in question.

Implementation
--------------

BigArray is not regular NumPy array and so needs explicit support in
ArrayRef code to find root object and indices. This patch adds such
support via the following way:

- when BigArray.__getitem__ creates VMA, it remembers in the VMA
  the top-level BigArray object under which this VMA was created.

- when ArrayRef is finding root, it can detect such VMAs, because it will
  be pointed to by the most top regular ndarray's .base, and in turn gets
  top-level BigArray object from the VMA.

- further all indices computations are performed, similarly to complete regular
  ndarrays case, on ndarrays root and a. But in the end .lo and .hi are
  adjusted for the corresponding offset of where root is inside whole
  BigArray.

- there is no need to adjust .deref() at all.

For remembering information into a VMA and also to be able to get
(readonly) its mapping addresses _bigfile.c extension has to be extended
a bit. Since we are now storing arbitrary python object attached to
PyVMA - it can create cycles - and so PyVMA accordingly adjusted to
support cyclic garbage collector.

Please see the patch itself for more details and comments.

ArrayRef is a tool to find out for a NumPy array its top-level root
parent and remember instructions how to recreate original array from
the root. For example if

	root = arange(1E7)
	z = root[1000:2000]
	a = z[10:20]

`ArrayRef(a)` will find out that the root array for `a` is `root` and
that `a` occupies 1010:1020 bytes in it. The vice versa operation is
also possible, for example given

	aref = ArrayRef(a)

it is possible to restore original `a` from `aref`:

	a_ = aref.deref()
	assert array_equal(a_, a)

the restoration works without copying by creating appropriate view of
root.

ArrayRef should work reliably for arrays of arbitrary dimensions,
strides etc - even fancy arrays created via stride tricks such as arrays
whose elements overlap each other should be supported.

This patch adds ArrayRef with support for regular ndarrays only.

The next patch will add ArrayRef support for BigArray and description
for ArrayRef rationale.

This allows e.g. to open `neo://cluster@master?compress=false` - in
other words with using options, which our current simplified opening
code does not support.

Keep old dbstoropen around as the fallback to work when
zodbtools/zodburi are not available, since we still want to try to
support ZODB 3.10.

It was

	bigfile/pagefault.c:45:36: warning: ‘struct ucontext’ declared inside parameter list will not be visible outside of this definition or declaration
	 static int faulted_by(const struct ucontext *uc);
	                                    ^~~~~~~~
	bigfile/pagefault.c: In function ‘on_pagefault’:
	bigfile/pagefault.c:59:24: warning: passing argument 1 of ‘faulted_by’ from incompatible pointer type [-Wincompatible-pointer-types]
	     write = faulted_by(uc);
	                        ^~
	bigfile/pagefault.c:45:12: note: expected ‘const struct ucontext *’ but argument is of type ‘struct ucontext *’
	 static int faulted_by(const struct ucontext *uc);
	            ^~~~~~~~~~
	bigfile/pagefault.c: At top level:
	bigfile/pagefault.c:208:36: warning: ‘struct ucontext’ declared inside parameter list will not be visible outside of this definition or declaration
	 static int faulted_by(const struct ucontext *uc)
	                                    ^~~~~~~~
	bigfile/pagefault.c:208:12: error: conflicting types for ‘faulted_by’
	 static int faulted_by(const struct ucontext *uc)
	            ^~~~~~~~~~
	bigfile/pagefault.c:45:12: note: previous declaration of ‘faulted_by’ was here
	 static int faulted_by(const struct ucontext *uc);
	            ^~~~~~~~~~
	bigfile/pagefault.c: In function ‘faulted_by’:
	bigfile/pagefault.c:217:15: error: dereferencing pointer to incomplete type ‘const struct ucontext’
	     write = uc->uc_mcontext.gregs[REG_ERR] & 0x2;
	               ^~
	bigfile/pagefault.c: At top level:
	bigfile/pagefault.c:45:12: warning: ‘faulted_by’ used but never defined
	 static int faulted_by(const struct ucontext *uc);
	            ^~~~~~~~~~
	bigfile/pagefault.c:208:12: warning: ‘faulted_by’ defined but not used [-Wunused-function]
	 static int faulted_by(const struct ucontext *uc)
	            ^~~~~~~~~~

Change to using ucontext_t because apparently there is no `struct
ucontext` anymore (and man for sigaction says 3rd parameter to hander is
of type `ucontext_t *` - not `struct ucontext *` - cast to `void *`)

Explicitly include <ucontext.h> because we are dereferencing ucontext_t,
even though today it appears to be included by <signal.h>.

Benchmark the time it takes for virtmem to handle pagefault with noop
loadblk for loadblk both implemented in C and in Python.

On my computer it is:

	name          µs/op
	PagefaultC    269 ± 0%
	pagefault_py  291 ± 0%

Quite a big time in other words.

It turned out to be mostly spent in fallocate'ing pages on tmpfs from
/dev/shm. Part of the above 269 µs/op is taken by freeing (reclaiming)
pages back when benchmarking work size exceed /dev/shm size, and part to
allocating.

If I limit the work size (via npage in benchmem.c) to be less than whole
/dev/shm it starts to be ~ 170 µs/op and with additional tracing it
shows as something like this:

    	.. on_pagefault_start   0.954 µs
    	.. vma_on_pagefault_pre 0.954 µs
    	.. ramh_alloc_page_pre  0.954 µs
    	.. ramh_alloc_page      169.992 µs
    	.. vma_on_pagefault     172.853 µs
    	.. vma_on_pagefault_pre 172.853 µs
    	.. vma_on_pagefault     174.046 µs
    	.. on_pagefault_end     174.046 µs
    	.. whole:               171.900 µs

so almost all time is spent in ramh_alloc_page which is doing the fallocate:

	https://lab.nexedi.com/nexedi/wendelin.core/blob/f11386a4/bigfile/ram_shmfs.c#L125

Simple benchmark[1] confirmed it is indeed the case for fallocate(tmpfs) to be
relatively slow[2] (and that for recent kernels it regressed somewhat
compared to Linux 3.16). Profile flamegraph for that benchmark[3] shows
internal loading of shmem_fallocate which for 1 hardware page is not
that too slow (e.g. <1µs) but when a request comes for a region
internally performs it page by page and so accumulates that ~ 170µs for 2M.

I've tried to briefly rerun the benchmark with huge pages activated on /dev/shm via

	mount /dev/shm -o huge=always,remount

as both regular user and as root but it was executing several times
slower. Probably something to investigate more later.

[1] https://lab.nexedi.com/kirr/misc/blob/4f84a06e/tmpfs/t_fallocate.c
[2] https://lab.nexedi.com/kirr/misc/blob/4f84a06e/tmpfs/1.txt
[3] https://lab.nexedi.com/kirr/misc/raw/4f84a06e/tmpfs/fallocate-2M-nohuge.svg

Rework py.bench output to match output of Go benchmarking[1] so that go
tools like benchstat & friends could be used to analyze and compare the
timings.

Before patch:

============================= test session starts ==============================
platform linux2 -- Python 2.7.14, pytest-3.3.2.dev2+g88f2cc9b.d20171206, py-1.5.2, pluggy-0.6.0
rootdir: /home/kirr/src/wendelin/wendelin.core, inifile:
collected 11 items

pymod: bigfile/tests/bench_0virtmem.py
bench_file_mmapread_hole	0.21  (0.39 0.22 0.21)
bench_file_read_hole    	0.24  (0.24 0.24 0.24)
bench_file_readbig_hole 	0.30  (0.30 0.31 0.31)
bench_bigf_read_hole    	0.44  (0.44 0.45 0.44)
bench_file_mmapwrite0   	0.13  (0.13 0.13 0.13)
bench_file_write55      	0.08  (0.08 0.08 0.08)
bench_bigf_writeff      	0.47  (0.47 0.48 0.47)
bench_file_mmapread     	0.22  (0.22 0.22 0.22)
bench_file_read         	0.25  (0.25 0.25 0.26)
bench_file_readbig      	0.31  (0.31 0.31 0.31)
bench_bigf_read         	0.44  (0.45 0.44 0.44)

========================== 11 passed in 12.92 seconds ==========================

After patch:

============================= test session starts ==============================
platform linux2 -- Python 2.7.14, pytest-3.3.2.dev2+g88f2cc9b.d20171206, py-1.5.2, pluggy-0.6.0
rootdir: /home/kirr/src/wendelin/wendelin.core, inifile:
collected 11 items

pymod: bigfile/tests/bench_0virtmem.py
Benchmarkfile_mmapread_hole	1	385839.939 µs/op
Benchmarkfile_mmapread_hole	1	219214.916 µs/op
Benchmarkfile_mmapread_hole	1	210209.131 µs/op
Benchmarkfile_read_hole    	1	238974.094 µs/op
Benchmarkfile_read_hole    	1	237294.197 µs/op
Benchmarkfile_read_hole    	1	238043.070 µs/op
Benchmarkfile_readbig_hole 	1	301330.090 µs/op
Benchmarkfile_readbig_hole 	1	301767.111 µs/op
Benchmarkfile_readbig_hole 	1	301135.063 µs/op
Benchmarkbigf_read_hole    	1	434718.132 µs/op
Benchmarkbigf_read_hole    	1	435019.970 µs/op
Benchmarkbigf_read_hole    	1	434729.099 µs/op
Benchmarkfile_mmapwrite0   	1	126471.996 µs/op
Benchmarkfile_mmapwrite0   	1	125886.917 µs/op
Benchmarkfile_mmapwrite0   	1	125730.038 µs/op
Benchmarkfile_write55      	1	86760.044 µs/op
Benchmarkfile_write55      	1	87507.010 µs/op
Benchmarkfile_write55      	1	87735.891 µs/op
Benchmarkbigf_writeff      	1	448369.980 µs/op
Benchmarkbigf_writeff      	1	448238.850 µs/op
Benchmarkbigf_writeff      	1	447322.845 µs/op
Benchmarkfile_mmapread     	1	207049.131 µs/op
Benchmarkfile_mmapread     	1	207813.978 µs/op
Benchmarkfile_mmapread     	1	210857.868 µs/op
Benchmarkfile_read         	1	238364.935 µs/op
Benchmarkfile_read         	1	236908.913 µs/op
Benchmarkfile_read         	1	238602.161 µs/op
Benchmarkfile_readbig      	1	303429.842 µs/op
Benchmarkfile_readbig      	1	302191.973 µs/op
Benchmarkfile_readbig      	1	304115.057 µs/op
Benchmarkbigf_read         	1	435079.098 µs/op
Benchmarkbigf_read         	1	434193.850 µs/op
Benchmarkbigf_read         	1	434813.976 µs/op

========================== 11 passed in 12.54 seconds ==========================

benchstat of new output:

	name                µs/op
	file_mmapread_hole   272k ±42%
	file_read_hole       238k ± 0%
	file_readbig_hole    301k ± 0%
	bigf_read_hole       435k ± 0%
	file_mmapwrite0      126k ± 0%
	file_write55        87.3k ± 1%
	bigf_writeff         448k ± 0%
	file_mmapread        209k ± 1%
	file_read            238k ± 0%
	file_readbig         303k ± 0%
	bigf_read            435k ± 0%

--------

Not only the output format is reworked here, but also b fixture is added
to BenchPlugin so that functions which accept it as arg, can run the
benchmark b.N times, can stop/restart timer etc - similar to
https://golang.org/pkg/testing/#B . If a bench_* func does not accept b,
B is still created, but b.N is assumed to be always 1.

The first benchmark which actually uses b will come in the next patch.

[1] https://github.com/golang/proposal/blob/master/design/14313-benchmark-format.md