When we serve indexing request, we first compute page range in backing
file, which contains the result based on major index range, then mmap
that file range and pick up result from there.

Page range math was however not correct: e.g. for positive strides, last
element's byte is (byte0_stop-1), NOT (byte0_stop - byte0_stride) which
for cases where byte0_stop is just a bit after page boundary, can make a
difference - page_max will be 1 page less what it should be and then
whole ndarray view creation breaks:

    ...
    Module wendelin.bigarray, line 381, in __getitem__
      view0 = ndarray(view0_shape, self._dtype, vma0, view0_offset, view0_stridev)
  ValueError: strides is incompatible with shape of requested array and size of buffer

( because vma0 was created less in size than what is needed to create view0_shape
  shaped array starting from view0_offset in vma0. )

Similar story for negative strides math - it was not correct neither.

Fix it.

/reported-by @Camata

We'll need this class in tests in the next patch.

It was already done from the beginning in 4174b84a (bigfile: BigFile
backend to store data in ZODB).

bigfile/zodb/tests: Make sure _p_invalidate() in Zblk.loadblk() does not lead to reloading data updated

Thanks to ZODB being MVCC this does not happen, but we better test
explicitly.

We'll need it in other places in the next patch.

e.g. on .shape

When there is a conflict (on any object, but on ZBlk in particular) ZODB
machinery calls its ._p_invalidate() twice:

  File ".../wendelin.core/bigfile/tests/test_filezodb.py", line 661, in test_bigfile_filezodb_vs_conflicts
    tm2.commit()    # this should raise ConflictError and stay at 11 state
  File ".../transaction/_manager.py", line 111, in commit
    return self.get().commit()
  File ".../transaction/_transaction.py", line 271, in commit
    self._commitResources()
  File ".../transaction/_transaction.py", line 414, in _commitResources
    self._cleanup(L)
  File ".../transaction/_transaction.py", line 426, in _cleanup
    rm.abort(self)
  File ".../ZODB/Connection.py", line 436, in abort
    self._abort()
  File ".../ZODB/Connection.py", line 479, in _abort
    self._cache.invalidate(oid)
  File ".../wendelin.core/bigfile/file_zodb.py", line 148, in _p_invalidate
    traceback.print_stack()

and

  File ".../wendelin.core/bigfile/tests/test_filezodb.py", line 661, in test_bigfile_filezodb_vs_conflicts
    tm2.commit()    # this should raise ConflictError and stay at 11 state
  File ".../transaction/_manager.py", line 111, in commit
    return self.get().commit()
  File ".../transaction/_transaction.py", line 271, in commit
    self._commitResources()
  File ".../transaction/_transaction.py", line 416, in _commitResources
    self._synchronizers.map(lambda s: s.afterCompletion(self))
  File ".../transaction/weakset.py", line 59, in map
    f(elt)
  File ".../transaction/_transaction.py", line 416, in <lambda>
    self._synchronizers.map(lambda s: s.afterCompletion(self))
  File ".../ZODB/Connection.py", line 831, in _storage_sync
    self._flush_invalidations()
  File ".../ZODB/Connection.py", line 539, in _flush_invalidations
    self._cache.invalidate(invalidated)
  File ".../wendelin.core/bigfile/file_zodb.py", line 148, in _p_invalidate
    traceback.print_stack()

i.e. first invalidation is done by commit cleanup:

    https://github.com/zopefoundation/transaction/blob/1.4.4/transaction/_transaction.py#L414
    https://github.com/zopefoundation/ZODB/blob/3.10/src/ZODB/Connection.py#L479

and then Connection.afterCompletion() flushes invalidation again:

    https://github.com/zopefoundation/transaction/blob/1.4.4/transaction/_transaction.py#L416
    https://github.com/zopefoundation/ZODB/blob/3.10/src/ZODB/Connection.py#L833
    https://github.com/zopefoundation/ZODB/blob/3.10/src/ZODB/Connection.py#L539

If there was no conflict - there will be no ConflictError raised and
thus no Transaction._cleanup() done in its ._commitResources() ->
invalidation called only once. But with ConflictError - it is twice.

Adjust ZBlk._p_invalidate() not to delve into real invalidation more
than once - else we will fail, as ZBlk._v_zfile becomes unbound after
invalidation done the first time.

All is currently handled correctly, but an observation is made that upon
such invalidation we through away ._v_fileh i.e. we through away whole
data cache just because an array was resized.

LivePersistent can go to ghost state, because invalidation cannot be
ignored, i.e. they indicate the object has been changed externally.

This does not break our logic for ZBigFile and ZBigArray as
invalidations can happen only at transaction boundary, so during the
course of transaction those classes are guaranteed to stay uptodate and
thus not loose ._v_file and ._v_fileh (which is the reason they inherit
from LivePersistent).

it is ok to loose ._v_file and ._v_fileh at transaction boundary and
become ghost - those objects will be recreated upon going back uptodate
and will stay alive again during the whole transaction window.

We care only not to loose e.g. ._v_fileh inside transaction, because
loosing that data manager and thus data it manages inside transaction
can break synchronization logic and forget changed-through-mmap data.

If we do - ZBigFileH objects just don't get garbage collected, and
sooner or later this way it leaks enough filedescriptors so that main
zope loop breaks:

    Traceback (most recent call last):
      File ".../bin/runzope", line 194, in <module>
        sys.exit(Zope2.Startup.run.run())
      File ".../eggs/Zope2-2.13.22-py2.7.egg/Zope2/Startup/run.py", line 26, in run
        starter.run()
      File ".../eggs/Zope2-2.13.22-py2.7.egg/Zope2/Startup/__init__.py", line 105, in run
        Lifetime.loop()
      File ".../eggs/Zope2-2.13.22-py2.7.egg/Lifetime/__init__.py", line 43, in loop
        lifetime_loop()
      File ".../eggs/Zope2-2.13.22-py2.7.egg/Lifetime/__init__.py", line 53, in lifetime_loop
        asyncore.poll(timeout, map)
      File ".../parts/python2.7/lib/python2.7/asyncore.py", line 145, in poll
        r, w, e = select.select(r, w, e, timeout)
    ValueError: filedescriptor out of range in select()

    $ lsof -p <runzope-pid> |grep ramh | wc -l
    950

So continuing 64d1f40b (bigfile/zodb: Monkey-patch for ZODB.Connection
to support callback on .open()) let's change the implementation to use
WeakSet for callbacks list.

Yes, because weakref to bound methods release immediately, we give up
flexibility to subscribe to arbitrary callbacks. If it become an issue,
something like WeakMethod from py3 or recipes from the net how to do it
are there.

ZODB 3.10.4 was released almost 4 years ago, and contains significant
change how ghost objects coming from DB are initially setup.

Continuing theme from the previous patch, here is propagation of
invalidation messages from ZODB to BigFileH memory.

The use-case here is that e.g. one fileh mapping was created in one
connection, another in another, and after doing changes in second
connection and committing there, the first fileh has to invalidate
appropriate already-loaded pages, so its next transaction won't work
with stale data.

To do it, we hook into ZBlk._p_invalidate() and propagate the
invalidation message to ZBigFile which then notifies all
opened-through-it ZBigFileH to invalidate a page.

ZBlk -> ZBigFile lookup is done without storing backpointer in ZODB -
instead, every time ZBigFile touches ZBlk object (and thus potentially
does GHOST -> Live transition to it), we (re-)bind it back to ZBigFile.
Since ZBigFile is the only class that works with ZBlk objects it is safe
to do so.

For ZBigFile to notify "all-opened-through-it" ZBigFileH, a weakset is
introduced to track them.

Otherwise the real page invalidation work is done by virtmem (see
previous patch).

FileH is a handle representing snapshot of a file. If, for a pgoffset,
fileh already has loaded page, but we know the content of the file has
changed externally after loading has been done, we need to propagate to
fileh that such-and-such page should be invalidated (and reloaded on
next access).

This patch introduces

    fileh_invalidate_page(fileh, pgoffset)

to do just that.

In the next patch we'll use this facility to propagate invalidations of
ZBlk ZODB objects to virtmem subsystem.

NOTE

Since invalidation removes "dirtiness" from a page state, several
subsequent invalidations can make a fileh completely non-dirty
(invalidating all dirty page). Previously fileh->dirty was just a one
bit, so we needed to improve how we track dirtiness.

One way would be to have a dirty list for fileh pages and operate on
that. This has advantage to even optimize dirty pages processing like
fileh_dirty_writeout() where we currently scan through all fileh pages
just to write only PAGE_DIRTY ones.

Another simpler way is to make fileh->dirty a counter and maintain that.

Since we are going to move virtmem subsystem back into the kernel, here,
a simpler less-intrusive approach is used.

Intro
-----

ZODB maintains pool of opened-to-DB connections. For each request Zope
opens 1 connection and, after request handling is done, returns the
connection back to ZODB pool (via Connection.close()). The same
connection will be opened again for handling some future next request at
some future time. This next open can happen in different-from-first
request worker thread.

TransactionManager  (as accessed by transaction.{get,commit,abort,...})
is thread-local, that is e.g. transaction.get() returns different
transaction for threads T1 and T2.

When _ZBigFileH hooks into txn_manager to get a chance to run its
.beforeCompletion() when transaction.commit() is run, it hooks into
_current_ _thread_ transaction manager.

Without unhooking on connection close, and circumstances where
connection migrates to different thread this can lead to
dissynchronization between ZBigFileH managing fileh pages and Connection
with ZODB objects. And even to data corruption, e.g.

    T1              T2

    open
    zarray[0] = 11
    commit
    close

                    open                # opens connection as closed in T1
    open
                    zarray[0] = 21
    commit
                    abort

    close           close

Here zarray[0]=21 _will_ be committed by T1 as part of T1 transaction -
because when T1 does commit .beforeCompletion() for zarray is invoked,
sees there is dirty data and propagate changes to zodb objects in
connection for T2, joins connection for T2 into txn for T1, and then txn
for t1 when doing two-phase-commit stores modified objects to DB ->
oops.

----------------------------------------

To prevent such dissynchronization _ZBigFileH needs to be a DataManager
which works in sync with the connection it was initially created under -
on connection close, unregister from transaction_manager, and on
connection open, register to transaction manager in current, possibly
different, thread context. Then there won't be incorrect
beforeCompletion() notification and corruption.

This issue, besides possible data corruption, was probably also exposing
itself via following ways we've seen in production (everywhere
connection was migrated from T1 to T2):

1. Exception ZODB.POSException.ConnectionStateError:
        ConnectionStateError('Cannot close a connection joined to a transaction',)
        in <bound method Cleanup.__del__ of <App.ZApplication.Cleanup instance at 0x7f10f4bab050>> ignored

     T1          T2

                 modify zarray
                 commit/abort    # does not join zarray to T2.txn,
                                 # because .beforeCompletion() is
                                 # registered in T1.txn_manager

     commit                      # T1 invokes .beforeCompletion()
     ...                         # beforeCompletion() joins ZBigFileH and zarray._p_jar (=T2.conn) to T1.txn
     ...                         # commit is going on in progress
     ...
     ...         close           # T2 thinks request handling is done and
     ...                         # and closes connection. But T2.conn is
     ...                         # still joined to T1.txn

2. Traceback (most recent call last):
     File ".../wendelin/bigfile/file_zodb.py", line 121, in storeblk
       def storeblk(self, blk, buf):   return self.zself.storeblk(blk, buf)
     File ".../wendelin/bigfile/file_zodb.py", line 220, in storeblk
       zblk._v_blkdata = bytes(buf)    # FIXME does memcpy
     File ".../ZODB/Connection.py", line 857, in setstate
       raise ConnectionStateError(msg)
   ZODB.POSException.ConnectionStateError: Shouldn't load state for 0x1f23a5 when the connection is closed

   Similar to "1", but close in T2 happens sooner, so that when T1 does
   the commit and tries to store object to database, Connection refuses to
   do the store:

     T1          T2

                 modify zarray
                 commit/abort

     commit
     ...         close
     ...
     ...
     . obj.store()
     ...
     ...

3. Traceback (most recent call last):
     File ".../wendelin/bigfile/file_zodb.py", line 121, in storeblk
       def storeblk(self, blk, buf):   return self.zself.storeblk(blk, buf)
     File ".../wendelin/bigfile/file_zodb.py", line 221, in storeblk
       zblk._p_changed = True          # if zblk was already in DB: _p_state -> CHANGED
     File ".../ZODB/Connection.py", line 979, in register
       self._register(obj)
     File ".../ZODB/Connection.py", line 989, in _register
       self.transaction_manager.get().join(self)
     File ".../transaction/_transaction.py", line 220, in join
       Status.ACTIVE, Status.DOOMED, self.status))
   ValueError: expected txn status 'Active' or 'Doomed', but it's 'Committing'

  ( storeblk() does zblk._p_changed -> Connection.register(zblk) ->
    txn.join() but txn is already committing

    IOW storeblk() was invoked with txn.state being already 'Committing' )

    T1          T2

                modify obj      # this way T2.conn joins T2.txn
                modify zarray

    commit                      # T1 invokes .beforeCompletion()
    ...                         # beforeCompletion() joins only _ZBigFileH to T1.txn
    ...                         # (because T2.conn is already marked as joined)
    ...
    ...         commit/abort    # T2 does commit/abort - this touches only T2.conn, not ZBigFileH
    ...                         # in particular T2.conn is now reset to be not joined
    ...
    . tpc_begin                 # actual active commit phase of T1 was somehow delayed a bit
    . tpc_commit                # when changes from RAM propagate to ZODB objects associated
    .  storeblk                 # connection (= T2.conn !) is notified again,
    .   zblk = ...              # wants to join txn for it thinks its transaction_manager,
                                # which when called from under T1 returns *T1* transaction manager for
                                # which T1.txn is already in state='Committing'

4. Empty transaction committed to NEO

   ( different from doing just transaction.commit() without changing
     any data - a connection was joined to txn, but set of modified
     object turned out to be empty )

   This is probably a race in Connection._register when both T1 and T2
   go to it at the same time:

   https://github.com/zopefoundation/ZODB/blob/3.10/src/ZODB/Connection.py#L988

   def _register(self, obj=None):
        if self._needs_to_join:
            self.transaction_manager.get().join(self)
            self._needs_to_join = False

    T1                          T2

                                modify zarray
    commit
    ...
    .beforeCompletion           modify obj
    . if T2.conn.needs_join      if T2.conn.needs_join      # race here
    .   T2.conn.join(T1.txn)       T2.conn.join(T2.txn)     # as a result T2.conn joins both T1.txn and T2.txn
    .
    commit finishes             # T2.conn registered-for-commit object list is now empty

                                commit
                                 tpc_begin
                                  storage.tpc_begin
                                 tpc_commit
                                  # no object stored, because for-commit-list is empty

/cc @jm, @klaus, @Tyagov, @vpelletier

ZODB.Connection has support for calling callbacks on .close() but not on
.open() . We'll need to hook into both Connection open/close process in the
next patch (for _ZBigFileH to stay in sync with Connection state).

NOTE

on-open  callbacks are setup once and fire many times on every open,
on-close callbacks are setup once and fire only once on next close.

The reason for this is that on-close callbacks are useful for scheduling
current connection cleanup, after its processing is done. But on-open
callback is for future connection usage, which is generally not related
to current connection.

/cc @jm, @vpelletier

( without dbclose, next test will not be able to open database - will
  timeout on open on waiting for FileStorage lock )

Previously we were limited to printing traceback starting down from just
storeblk() via explicit PyErr_PrintEx() - because pybuf was attached to
memory which could go away right after return from C function - so we
had to destroy that object for sure, not letting any traceback to hold a
reference to it.

This turned out to be too limiting and not showing full context where
errors happen.

So do the following trick: before returning, reattach pybuf to empty
region at NULL, and this way we don't need to worry about pybuf pointing
to memory which can go away -> thus instead of printing exception locally
- just return it the usual way it is done with C api in Python.

NOTE In contrast to PyMemoryViewObject, PyBufferObject definition is not
public, so to support Python2 - had to copy its definition to PY2 compat
header.

NOTE2 loadblk() is not touched - the loading is done from sighandler
context, which simulates as if it work in separate python thread, so it
is leaved as is for now.

At present several threads running can corrupt internal virtmem
datastructures (e.g. ram->lru_list, fileh->pagemap, etc).

This can happen even if we have zope instances only with 1 worker thread
- because there are other "system" thread, and python garbage collection
can trigger at any thread, so if a virtmem object, e.g. VMA or FileH was
there sitting at GC queue to be collected, their collection, and thus
e.g. vma_unmap() and fileh_close() will be called from
different-from-worker thread.

Because of that virtmem just has to be aware of threads not to allow
internal datastructure corruption.

On the other hand, the idea of introducing userspace virtual memory
manager turned out to be not so good from performance and complexity
point of view, and thus the plan is to try to move it back into the
kernel. This way it does not make sense to do a well-optimised locking
implementation for userspace version.

So we do just a simple single "protect-all" big lock for virtmem.

Of a particular note is interaction with Python's GIL - any long-lived
lock has to be taken with GIL released, because else it can deadlock:

    t1  t2

    G
    V   G
   !G   V
    G

so we introduce helpers to make sure the GIL is not taken, and to retake
it back if we were holding it initially.

Those helpers (py_gil_ensure_unlocked / py_gil_retake_if_waslocked) are
symmetrical opposites to what Python provides to make sure the GIL is
locked (via PyGILState_Ensure / PyGILState_Release).

Otherwise, the patch is more-or-less straightforward application for
one-big-lock to protect everything idea.

Mutex lock/unlock should not fail if mutex was correctly initialized/used.

And specifically that GC'ed object __del__ calls into virtmem
(vma_dealloc and fileh_dealloc) again.

NOTE not sure it is a good idea to do GC from under sighandle, but
     currently it happens in practice, because we did not cared to
     protect against it.

We factored out SIGSEGV block/restore from fileh_dirty_writeout() to all
functions in cb7a7055 (bigfile/virtmem: Block/restore SIGSEGV in
non-pagefault-handling function). The restoration however just sets
whole thread sigmask.

It could be possible that between block/restore calls procmask for other
signals could be changed, and this way - setting procmask directly - we
will overwrite them.

So be careful, and when restoring SIGSEGV mask, touch mask bit for only
that signal.

( we need xsigismember helper to get this done, which is also introduced
  in this patch )

The mistake was there from the beginning - from 3e5e78cd (lib/utils:
Small C utilities we'll use).

We'll need this for function which return error not in errno - e.g.
pthread_sigmask().

http://mail.tiolive.com/pipermail/neo-users/20150713/000027.html

Non on-pagefault code should not access any not-mmapped memory.

Here we just refactor the code we already had to block/restore
SIGSEGV from fileh_dirty_writeout() and use it in all functions called
from non-pagefaulting context, as promised.

This way, if there is an error in virtmem implementation which
incorrectly accesses prepared for BigFile maps memory, we'll just die
with coredump instead of trying to incorrectly handle the pagefault.

ca064f75 (bigarray: Support resizing in-place) added O(1) in-place
BigArray.resize() which makes possible for users to append data to BigArray in
O(δ) time.

But it is easy for people to make off-by-one mistakes when calculating
indices for append.

So provide a convenient BigArray.append() which simplifies the following

    A                               # ZBigArray e.g. of shape       (N, 3)
    values                          # ndarray to append of shape    (δ, 3)
    n, δ = len(A), len(values)      # length of A's major index  =N
    A.resize((n+δ, A.shape[1:]))    # add δ new entries ; now len(A) =N+δ
    A[-δ:] = values                 # set data for last new δ entries

into

    A.append(values)

/cc @klaus

We stopped using numpy.multiply in 73926487 (*: It is not safe to use
multiply.reduce() - it overflows).

We compare A_[10*PS-1] (which is A_[1]) to 0, but

    A_= ndarray ((10*PS,), uint8)

and that means the array memory is not initialized. So the comparison
works sometimes and sometimes it does not.

Initialize compared element explicitly.

NOTE: A (without _) element does not need to be initialized -
because not-initialized BigArray parts read as zeros.

/cc @jm

Previously we were always testing with DBs backed up by FileStorage. Now
we provide a way to run the testsuite with user selected storage
backend:

    $ WENDELIN_CORE_TEST_DB="<fs>"   make test.py     # test with temporary db with FileStorage
    $ WENDELIN_CORE_TEST_DB="<zeo>"  make test.py     # ----------//---------- with ZEO
    $ WENDELIN_CORE_TEST_DB="<neo>"  make test.py     # ----------//---------- with NEO

    $ WENDELIN_CORE_TEST_DB=neo://db@master  make test.py     # test with externally provided DB

Default is still to run tests with FileStorage.

/cc @jm

And this way, because dbopen() supports opening various kind of
databases (see previous commit) we can now specify type of database on
command line, e.g.

    /path/to/db
    neo://db@master
    zeo://host:port

/cc @jm

Done via manual hacky way for now. The clean solution would be to reuse
e.g. repoze.zodbconn[1] or zodburi[2] and teach them to support NEO.

But for now we can't -- those eggs depend on ZODB, and we still use
ZODB3 for maintaining compatibility with both ZODB3.10 and ZODB4.

/cc @jm

[1] https://pypi.python.org/pypi/repoze.zodbconn
[2] https://pypi.python.org/pypi/zodburi

Factor out those routines to open a ZODB database to common place.

The reason for doing so is that we'll soon teach dbopen to automatically
recognize several protocols, e.g. neo:// and zeo:// and this way,
clients who use dbopen() could automatically access storages besides
FileStorage.

Because numpy.ndarray does not accept it as buffer= argument

    https://github.com/numpy/numpy/issues/5935

and our memcpy crashes.

NOTE if we'll need to use memoryview, we can adapt our memcpy to use
array() directly which works with memoryview, as outlined in the above
numpy issue.