1. 12 Jun, 2015 1 commit
  2. 02 Jun, 2015 2 commits
  3. 01 Jun, 2015 2 commits
  4. 28 May, 2015 1 commit
  5. 25 May, 2015 2 commits
  6. 14 May, 2015 1 commit
    • Kirill Smelkov's avatar
      Fix build with non-std "python" · a280b53d
      Kirill Smelkov authored
      In 5755a6b3 (Basic setup.py / Makefile to build/install/sdist stuff +
      bigfile.so skeleton) we overlooked one thing:
      
          when tailing from setup.py to make level, we forgot to setup the
          PYTHON env variable properly, and that leads to changing building
          with std python.
      
      Look e.g.
      
          $ python3 setup.py build_ext -i
          running build_ext
          python setup.py ll_build_ext --inplace
          ^^^
      
      which is obviously not correct.
      
      Fix it.
      
      The tox setup we have setup for testing with multiple interpreters
      (7af2b2d7 "Tox setup to test things with py27 & py34 and several
      versions of ZODB") did not caught this, because for every python and
      environment versions tox initializes separate virtualenv, in which
      .../bin/python is a link to chosen python, and this way both python and
      my-selected-for-build-python are the same.
      
      Cc: @Tyagov
      a280b53d
  7. 15 Apr, 2015 1 commit
    • Kirill Smelkov's avatar
      Fix build with Python that enables -Werror=declaration-after-statement · e0b25398
      Kirill Smelkov authored
      In C99 declaration after statement is ok, and we explicitly compile with -std=gnu99.
      
      Python >= 3.4 however adds -Werror=declaration-after-statement even for extension
      modules irregardless of their compilation flags:
      
        https://bugs.python.org/issue21121
      
      and the build fails this way:
      
          building 'wendelin.bigfile._bigfile' extension
          creating build/temp.linux-x86_64-3.4
          creating build/temp.linux-x86_64-3.4/bigfile
          creating build/temp.linux-x86_64-3.4/lib
          gcc -pthread -Wno-unused-result -Werror=declaration-after-statement -DNDEBUG -fmessage-length=0 -grecord-gcc-switches -O2 -Wall
      -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -DOPENSSL_LOAD_CONF -fPIC -D_GNU_SOURCE
      -I./include -I./3rdparty/ccan -I./3rdparty/include -I/usr/include/python3.4m -c bigfile/_bigfile.c -o build/temp.linux-x86_64-3.4/bigfile/_bigfile.o
      -std=gnu99 -fplan9-extensions -fvisibility=hidden
          bigfile/_bigfile.c: In function ‘pyfile_new’:
          bigfile/_bigfile.c:679:5: error: ISO C90 forbids mixed declarations and code [-Werror=declaration-after-statement]
               static char *kw_list[] = {"blksize", NULL};
               ^
          cc1: some warnings being treated as errors
          error: command 'gcc' failed with exit status 1
      
      Ensure we turn off this warning and error because we already rely on compiling in C99 mode.
      Reported-and-tested-by: 's avatarIvan Tyagov <ivan@tyagov.com>
      e0b25398
  8. 03 Apr, 2015 16 commits
    • Kirill Smelkov's avatar
      wendelin.core v0.1 · 4b6821f4
      Kirill Smelkov authored
      4b6821f4
    • Kirill Smelkov's avatar
      Demo program that shows how to work with ZBigArrays bigger than RAM in size · 1ee72371
      Kirill Smelkov authored
      This shows how to first generate such arrays (in steps, as every
      transaction change should fit in memory), and then gather data from
      whole array using C/Fortran/etc code.
      
      It shows how to compute mean via NumPy's ndarray.mean()
      
      It also shows that e.g. ndarray.var() wants to create temporaries in
      size of original ndarray and that would fail, because it does not fit
      into RAM.
      
      ndarray.var() should not need to create such temporaries in principle -
      all it has to do is to first compute mean, and then compute
      
          sum (Xi - <X>)^2
      
      in a loop.
      
      <X> is scalar, Xi - is just access to original array.
      
      ~~~~
      
      So this also show NumPy can be incrementally improved to avoid creating
      such temporaries, and then it will work.
      1ee72371
    • Kirill Smelkov's avatar
      Prepare to benchmark python code with py.test · bcab1246
      Kirill Smelkov authored
      For this, a small wrapper over py.test is developed (to discover/collect
      functions to benchmar, etc) and then it runs such functions several
      times in a boxed enveronment.
      
      Benchmarks should be named bench_*.py
      bcab1246
    • Kirill Smelkov's avatar
      BigArray: An ndarray-like on top of BigFile memory mappings · 0c826d5c
      Kirill Smelkov authored
      I.e. something like numpy.memmap for numpy.ndarray and OS files. The whole
      bigarray cannot be used as a drop-in replacement for numpy arrays, but BigArray
      _slices_ are real ndarrays and can be used everywhere ndarray can be used,
      including in C/Fortran code. Slice size is limited by mapping-size (=
      address-space size) limit, i.e. to ~ max 127TB on Linux/amd64.
      
      Changes to bigarray memory are changes to bigfile memory mapping and as such
      can be discarded or saved back to bigfile using mapping (= BigFileH) dirty
      discard/writeout interface.
      
      For the same reason the whole amount of changes to memory is limited by amount
      of physical RAM.
      0c826d5c
    • Kirill Smelkov's avatar
      bigfile: BigFile backend to store data in ZODB · 4174b84a
      Kirill Smelkov authored
      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/
      4174b84a
    • Kirill Smelkov's avatar
      bigfile: Python wrapper around virtual memory subsystem · 35eb95c2
      Kirill Smelkov authored
      Exposes BigFile - this way users can define BigFile backend in Python.
      
      Also exposed are BigFile handles, and VMA objects which are results of
      mmaping.
      35eb95c2
    • Kirill Smelkov's avatar
      Prepare to test python code with py.test · 8ba39a60
      Kirill Smelkov authored
      We'll use py.test for unit-testing of Python part.
      8ba39a60
    • Kirill Smelkov's avatar
      bigfile: RAM subsystem · 8c935a5f
      Kirill Smelkov authored
      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.
      8c935a5f
    • Kirill Smelkov's avatar
      bigfile: Stub for virtmem · 77d61533
      Kirill Smelkov authored
      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.
      77d61533
    • Kirill Smelkov's avatar
      Low-level pagefault handler · 6f7d4d64
      Kirill Smelkov authored
      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.
      6f7d4d64
    • Kirill Smelkov's avatar
      bigfile/pagemap: specialized {} uint64 -> void * mapping · 45af76e6
      Kirill Smelkov authored
      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).
      45af76e6
    • Kirill Smelkov's avatar
      Prepare to unit-test C stuff · cd5646af
      Kirill Smelkov authored
      We'll be testing C code in a similiar-to-python way - keep test_*.c
      files nearby and compile/executing them as needed.
      
      Tests are run several times in several ways - as plainly compiled and
      also with additional error checkers:
      
       - AddressSanitizer
       - ThreadSanitizer
       - and similiar checkers from Valgrind
      cd5646af
    • Kirill Smelkov's avatar
      lib/mem: Python utilities to zero, set & copy memory · 699b1375
      Kirill Smelkov authored
      Like C bzero / memset & memcopy - but work on python buffers. We
      leverage NumPy for doing actual work, and this way NumPy becomes a
      depenency.
      
      Having NumPy as a dependency is ok - we'll for sure need it later as we
      are trying to build out-of-core ndarrays.
      699b1375
    • Kirill Smelkov's avatar
      lib/utils: Small C utilities we'll use · 3e5e78cd
      Kirill Smelkov authored
      Like taking an exact integer log2, upcasting pointers for C-style
      inheritance done in a Plan9 way, and wrappers to functions which should
      never fail.
      3e5e78cd
    • Kirill Smelkov's avatar
      lib/bug: Small utilities to say there is a warning, or a todo, or a bug on condition · db28e53f
      Kirill Smelkov authored
      Modelled by ones used in Linux kernel.
      db28e53f
    • Kirill Smelkov's avatar
      Basic setup.py / Makefile to build/install/sdist stuff + bigfile.so skeleton · 5755a6b3
      Kirill Smelkov authored
      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.
      5755a6b3