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

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.

Consider e.g. this for pyvma:

    1. in pyfileh_mmap() pyvma is created

    2. next fileh_mmap(pyvma, pyfileh, ...) fails

    3. we need to deallocate pyvma which was not mapped

    4. in pyvma_dealloc() we unmap pyvma unconditionally -> boom.

The same story goes for pyfileh dealloc vs not fully constructing it in
pyfileh_open().

Currently we always raise RuntimeError for problems, which is
more-or-less ok for humans, but soon we'll need to distinguish "no
memory" errors from other error conditions in upper layers in code.

Introduce helper function for choosing appropriate exception type for an
error - MemoryError for when errno=ENOMEM and RuntimeError otherwise,
and use it where appropriate.

( Unfortunately Python does not provide such a helper... )

For example on Debian 7 Wheezy the kernel (linux 3.2) supports holepunching,
because holepunching was added in linux 2.6.38:

    http://git.kernel.org/linus/79124f18b335172e1916075c633745e12dae1dac

but glibc does not provide fallocate mode constants, and compilation fails:

    gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -D_GNU_SOURCE -I./include -I./3rdparty/ccan -I./3rdparty/include -I/opt/slapgrid/f2a5f59d0d2b521681b9333ee76a2859/parts/python2.7/include/python2.7 -c bigfile/ram_shmfs.c -o build/temp.linux-x86_64-2.7/bigfile/ram_shmfs.o -std=gnu99 -fplan9-extensions -fvisibility=hidden -Wno-declaration-after-statement -Wno-error=declaration-after-statement
    bigfile/ram_shmfs.c: In function ‘shmfs_drop_memory’:
    bigfile/ram_shmfs.c:135:31: error: ‘FALLOC_FL_PUNCH_HOLE’ undeclared (first use in this function)
    bigfile/ram_shmfs.c:135:31: note: each undeclared identifier is reported only once for each function it appears in
    bigfile/ram_shmfs.c:135:54: error: ‘FALLOC_FL_KEEP_SIZE’ undeclared (first use in this function)
    error: command 'gcc' failed with exit status 1

Try to fix it via fallbacking to provide the needed defines on older systems ourselves.

Cc: Klaus Wölfel <klaus@nexedi.com>
Cc: Ivan Tyagov <ivan@tyagov.com>

    - for virtual memory subsytem
    - for ZBigFiles

They are not currently great, e.g. for virtmem we have in-kernel
overhead of page clearing - in perf profiles, for bigfile_mmap compared
to file_read kernel's clear_page_c raises significantly.

That is the worker for clearing page memory and we currently cannot
avoid that - any memory obtained from kernel (MAP_ANONYMOUS, mmap(file)
with hole, etc...) comes pre-initialized to zeros to userspace.

This can be seen in the benchmarks as well: file_readbig differs from
file_read in only that the latter uses 1 small buffer and the first
allocates large memory (cleared by kernel + python does the memset).

    bigfile/tests/bench_virtmem.py@125::bench_file_mmap_adler32     0.47  (0.86 0.49 0.47)
    bigfile/tests/bench_virtmem.py@126::bench_file_read_adler32     0.69  (1.11 0.71 0.69)
    bigfile/tests/bench_virtmem.py@127::bench_file_readbig_adler32  1.41  (1.70 1.42 1.41)
    bigfile/tests/bench_virtmem.py@128::bench_bigfile_mmap_adler32  1.42  (1.45 1.42 1.51)

    bigfile/tests/bench_virtmem.py@130::bench_file_mmap_md5         1.52  (1.91 1.54 1.52)
    bigfile/tests/bench_virtmem.py@131::bench_file_read_md5         1.73  (2.10 1.75 1.73)
    bigfile/tests/bench_virtmem.py@132::bench_file_readbig_md5      2.44  (2.73 2.46 2.44)
    bigfile/tests/bench_virtmem.py@133::bench_bigfile_mmap_md5      2.40  (2.48 2.40 2.53)

There is MAP_UNINITIALIZED which works only for non-mmu targets and only
if explicitly allowed when configuring kernel (off by default).

There were patches to disable that pages zeroing, as it gives
significant speedup for people's workloads, e.g. [1,2] but all of them
did not got merged for security reasons.

[1] http://marc.info/?t=132691315900001&r=1&w=2
[2] http://thread.gmane.org/gmane.linux.kernel/548926

~~~~

For ZBigFile - it is the storage who is dominating in profiles.

This adds transactionality and with e.g. NEO[1] allows to distribute
objects to nodes into cluster.

We hook into ZODB two-phase commit process as a separate data manager,
and synchronize changes to memory, to changes to object only at that
time.

Alternative would be to get notified on every page change, and mark
appropriate object as dirty right at that moment.

But I wanted to stay close to filesystem design (we don't get
notification for every file change from kernel) - that's why it is done
the first way.

[1] http://www.neoppod.org/

In Python. To demonstrate how backends could be implemented and test
system on simple things.

Exposes BigFile - this way users can define BigFile backend in Python.

Also exposed are BigFile handles, and VMA objects which are results of
mmaping.

Does similar things to what kernel does - users can mmap file parts into
address space and access them read/write. The manager will be getting
invoked by hardware/OS kernel for cases when there is no page loaded for
read, or when a previousle read-only page is being written to.

Additionally to features provided in kernel, it support to be used to
store back changes in transactional way (see fileh_dirty_writeout()) and
potentially use huge pages for mappings (though this is currently TODO)

This thing allows to get aliasable RAM from OS kernel and to manage it.
Currently we get memory from a tmpfs mount, and hugetlbfs should also
work, but is TODO because hugetlbfs in the kernel needs to be improved.

We need aliasing because we'll need to be able to memory map the same
page into several places in address space, e.g. for taking two slices
overlapping slice of the same array at different times.

Comes with test programs that show we aliasing does not work for
anonymous memory.

This will be the core of virtual memory subsystem. For now we just
define a structure to describe pages of memory and add utility to
allocate address space from OS.

We hook into SIGSEGV and handle read/write pagefaults this way.

In this patch there goes stub code that only detects faults and
determines (in arch specific way) whether fault was for read or write
and there is a TODO to pass that information to higher level.

It also comes with tests to detect we still crash if we access something
incorrectly, so people could have coredumps and investigate them.

For BigFiles we'll needs to maintain `{} offset-in-file -> void *` mapping. A
hash or a binary tree could be used there, but since we know files are
most of the time accessed sequentially and locally in pages-batches, we
can also organize the mapping in batches of keys.

Specifically offset bits are so divided into parts, that every part
addresses 1 entry in a table of hardware-page in size. To get to the actual
value, the system lookups first table by first part of offset, then from
first table and next part from address - second table, etc.

To clients this looks like a dictionary with get/set/del & clear methods,
but lookups are O(1) time always, and in contrast to hashes values are
stored with locality (= adjacent lookups almost always access the same tables).

It is an early project decision to use gnu99 & Plan9 C extensions, to
simplify C code.

So far we only build stub wendelin/bigfile/_bigfile.so .

Makefile is introduced because there will be targets which are easier to
handle at make level. For end users no make knowledge is required -
usual `python setup.py build|install|...` work, redirecting to make
where necessary.

As was promised (e870781d "Top-level in-tree import redirector")
setup.py contains install-time hooks to handle in-tree wendelin.py and
install it as a module namespace.

For sdist, we just use `git ls-files` info if we are in a checkout.

This will be a module to allow users to program custom file-like
backends and latter memory-map content of files from the backend.

For now just start the module structure.