1. 02 Jun, 2015 1 commit
    • Kirill Smelkov's avatar
      setup: Fix for py3 · 25dbf467
      Kirill Smelkov authored
      py2-only syntax introduced in acf7e91d (setup/runcmd: Properly report
      errors, if running command is missing):
      
            File "setup.py", line 168
              except Exception, e:
                              ^
          SyntaxError: invalid syntax
      25dbf467
  2. 01 Jun, 2015 4 commits
  3. 28 May, 2015 4 commits
    • Kirill Smelkov's avatar
      setup: Ensure setuptools.file_finders entry-point group is registered · 11d130d1
      Kirill Smelkov authored
      If setuptools.file_finders group is not registered,
      dist.get_entry_map('setuptools.file_finders') returns just {} not
      connected to entry map, and further modifications of this dict go
      nowhere (and thus, our git_lsfiles() is not hooked -> sdist fails to
      produce correct source archive).
      
      This is a workaround for setuptools 9.0 dropping
      `setuptools.file_finders` entrypoint group registration:
      
          https://bitbucket.org/pypa/setuptools/commits/f191c8a1225bd58a5fb5aa9abb31b06dc710f0b9#Lsetup.pyF175
          https://bitbucket.org/pypa/setuptools/issue/313
      
      issue reported back:
      
          https://bitbucket.org/pypa/setuptools/issue/313#comment-18430008
      11d130d1
    • Kirill Smelkov's avatar
      bigarray: Test that asarray(BigArray(...)) does not hang · 0e25b01c
      Kirill Smelkov authored
      It was hanging with NumPy-1.9 before 425dc5d1 (bigarray: Raise
      IndexError for out-of-bound element access), because of the following
      correct NumPy commit:
      
          https://github.com/numpy/numpy/commit/d36f8227
      
      and in particular
      
          https://github.com/numpy/numpy/commit/d36f8227#diff-6d326badc0872de91e025cbfb0be1aafR522
      
      That PySequence_Fast(obj)    (with obj being BigArray)
      
      creates iterator on top of obj and before our previous IndexError fix in
      425dc5d1, this was looping forever.
      
      Test explicitly with both NumPy 1.8 and NumPy 1.9, that this construct
      does not hang.
      
      /cc @Tyagov
      0e25b01c
    • Kirill Smelkov's avatar
      bigarray: Raise IndexError for out-of-bound element access · 425dc5d1
      Kirill Smelkov authored
      The way BigArray.__getitem__ works for element access is that for e.g.
      
          A[i]
      
      it translates the request to
      
          A[i:i+1]
      
      and remembers to lower the dimensionality at scalar index
      
          dim_adjust = (0,)
      
      so, in full, A[i] is computed this way:
      
          A[i] -> A[i:i+1](0,)
      
      ( it is done this way to unify code for scalar / slice access in
        __getitem__ - see 0c826d5c "BigArray: An ndarray-like on top of
        BigFile memory mappings" )
      
      The code for slice access also has a shortcut - if it sees that slice
      results in empty array (e.g. for out-of-bound slice), we can avoid
      spending time to create a file vma mapping only to create empty view on
      top of it.
      
      In 0c826d5c, that optimization, however forgot to apply the "lower the
      dimensionality" step on top of resulting empty view, and that turned out
      for not raising IndexError for out-of-bounds scalar access:
      
          A = BigArray((10,), uint8)
          In [1]: A[0]
          Out[1]: 0
      
          In [2]: A[1]
          Out[2]: 0
      
          In [3]: A[2]
          Out[3]: 0
      
          In [4]: A[9]
          Out[4]: 0
      
          In [5]: A[10]
          Out[5]: array([], dtype=uint8)
      
      NOTE that A[10] returns empty array instead of raising IndexError.
      
      So do not forget to apply the "reduce dimensionality" step for empty
      views, and this way we get proper IndexError (because for empty view,
      scalar access results in IndexError).
      
      NOTE:
      
      this bug was also preventing for e.g.
      
          list(A)
      
      to work, because list(A) internally works this way:
      
          l = []
          i = iter(A)
          for _ in i:
              l.append(_)
      
      but iterating would not stop after 10 elements - after array end, _ will
      be always array([], dtype=uint8), and thus the loop never finished and
      memory usage grow to infinity.
      
      /cc @Tyagov
      425dc5d1
    • Kirill Smelkov's avatar
      bigarray: Be explicit about not-supporting advanced indexing · 4680c0cd
      Kirill Smelkov authored
      In NumPy speak advanced indexing is picking up arbitrarily requested
      elemtnts, e.g.
      
          a = arange(10)
          a[[0,3,2]]  -> array([0, 3, 2])
      
      The way this indexing schem works is - it creates a new array with
      len = len(key), and picks up requested elements sequentially into new
      area.
      
      So it is very not the same as creating _view_ to original array data by
      using basic indexing [1]
      
      BigArray does not support advanced indexing, because its main job is to
      organize an ndarray _view_ backed up by BigFile data and give that view
      to clients, and then it is up to clients how to use that view with full
      numpy api available with it.
      
      So be explicit, and reject advanced indexing in __getitem__ right at the
      beginning.
      
      [1] http://docs.scipy.org/doc/numpy/reference/arrays.indexing.html
      4680c0cd
  4. 25 May, 2015 3 commits
    • Kirill Smelkov's avatar
    • Kirill Smelkov's avatar
      wendelin.core v0.2 · c877184f
      Kirill Smelkov authored
      c877184f
    • Kirill Smelkov's avatar
      tests: Don't forget to depend on ccan's config.h · dcdb0302
      Kirill Smelkov authored
      Else, in a clean repo the tests do not build from scratch:
      
          $ make test
          x86_64-linux-gnu-gcc -pthread -g -Wall -D_GNU_SOURCE -std=gnu99 -fplan9-extensions -Wno-declaration-after-statement -Wno-error=declaration-after-statement  -Iinclude -I3rdparty/ccan -I3rdparty/include   bigfile/tests/test_virtmem.c lib/bug.c lib/utils.c 3rdparty/ccan/ccan/tap/tap.c  -o bigfile/tests/test_virtmem.t
          In file included from include/wendelin/list.h:11:0,
                           from include/wendelin/bigfile/virtmem.h:33,
                           from bigfile/tests/../virtmem.c:23,
                           from bigfile/tests/test_virtmem.c:21:
          3rdparty/ccan/ccan/array_size/array_size.h:4:20: fatal error: config.h: No such file or directory
           #include "config.h"
                              ^
          compilation terminated.
          3rdparty/ccan/ccan/tap/tap.c:26:20: fatal error: config.h: No such file or directory
           #include "config.h"
                              ^
          compilation terminated.
          Makefile:99: recipe for target 'bigfile/tests/test_virtmem.t' failed
          make: *** [bigfile/tests/test_virtmem.t] Error 1
      dcdb0302
  5. 20 May, 2015 4 commits
    • Kirill Smelkov's avatar
      bigarray: Support resizing in-place · ca064f75
      Kirill Smelkov authored
      In NumPy, ndarray has .resize() but actually it does a whole array
      copy into newly allocated larger segment which makes e.g. appending O(n).
      
      For BigArray, we don't have that internal constraint NumPy has - to
      keep the array itself contiguously _stored_ (compare to contiguously
      _presented_ in memory). So we can have O(1) resize for big arrays.
      
      NOTE having O(1) resize, here is how O(δ) append can be done:
      
          A                               # ZBigArray e.g. of shape   (N, 3)
          n = len(A)                      # lengh of A's major index  =N
          A.resize((n+δ, A.shape[1:]))    # add δ new entries ; now len(A) =N+δ
          A[-δ:] = <new-data>             # set data for last new δ entries
      
      /cc @klaus
      ca064f75
    • Kirill Smelkov's avatar
      bigarray/tests: Factor-out generic BigFile connected to numpy array · 929922fa
      Kirill Smelkov authored
      test_bigarray_indexing_Nd() contains useful class to have a BigFile
      connected to ndarray storage. Factor it out so that all tests could use
      it.
      
      BigFile_Data.storeblk() is newly introduced and is currently unused, but
      will be convenient to have later.
      929922fa
    • Kirill Smelkov's avatar
    • Kirill Smelkov's avatar
      bigarray: Fix typos · 3c7abddb
      Kirill Smelkov authored
      3c7abddb
  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. 29 Apr, 2015 2 commits
    • Kirill Smelkov's avatar
    • Kirill Smelkov's avatar
      bigfile/ram_shmfs: Try to support compiling on older systems · 48defba0
      Kirill Smelkov authored
      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>
      48defba0
  8. 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: default avatarIvan Tyagov <ivan@tyagov.com>
      e0b25398
  9. 03 Apr, 2015 20 commits
    • Kirill Smelkov's avatar
      wendelin.core v0.1 · 4b6821f4
      Kirill Smelkov authored
      4b6821f4
    • Kirill Smelkov's avatar
    • 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
      bigfile: Basic benchmarks · bb9d8bf1
      Kirill Smelkov authored
          - 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.
      bb9d8bf1
    • 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
      ZBigArray: in-ZODB stored BigArray · 90d32e51
      Kirill Smelkov authored
      This is like to BigArray, like ZBigFile is to BigFile (4174b84a
      "bigfile: BigFile backend to store data in ZODB")
      90d32e51
    • 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: BackFile backend to store data in an OS file · b3910de8
      Kirill Smelkov authored
      In Python. To demonstrate how backends could be implemented and test
      system on simple things.
      b3910de8
    • 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/virtmem: Userspace Virtual Memory Manager · 9a293c2d
      Kirill Smelkov authored
      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)
      9a293c2d
    • Kirill Smelkov's avatar
      bigfile/file.h: C interface for defining BigFile backends · 9065e2b9
      Kirill Smelkov authored
      Users can inherit from BigFile and provide custom ->loadblk() and
      ->storeblk() to load/store file blocks from a database or some other
      storage. The system then could use such files to memory map them into
      user address space (see next patch).
      9065e2b9
    • Kirill Smelkov's avatar
      Script to run compiled linux kernel with root fs mounted from host · 76d8f76d
      Kirill Smelkov authored
      Useful to debug (via either printk or gdb) the kernel - one can boot it,
      and tweak compile test program on host and be ready to test it inside
      qemu on tested kernel. Another use case is to add tracing printk to
      kernel and to boot it on each iteration. Booting via qemu means the
      workflow is not disrupted as would with rebooting the hardware.
      
      With this tool it was straightforward to find out why mmap-alias through
      mremap does not work for huge pages:
      
      static struct vm_area_struct *vma_to_resize(unsigned long addr,
              unsigned long old_len, unsigned long new_len, unsigned long *p)
      {
              struct mm_struct *mm = current->mm;
              struct vm_area_struct *vma = find_vma(mm, addr);
      
              if (!vma || vma->vm_start > addr)
                      goto Efault;
      
              if (is_vm_hugetlb_page(vma))            <--
                      goto Einval;
      
      mremap_to(...)
      {
              /* lots of checks, then */
              vma_to_resize(...)
      76d8f76d
    • 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
    • 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
      bigfile/types.h: Type's we'll use · 8114ad6c
      Kirill Smelkov authored
      8114ad6c