- 14 Jul, 2016 1 commit
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Kazuhiko authored
If wendelin.core is built under buildout and setuptools exists only in buildout environment, 'python setup.py' called inside make will fail without this change. Building 'wendelin.core' Running easy_install: "/path/to/python2.7" "-c" "import sys; sys.path[0:0] = ['/path/to/setuptools-19.6.2-py2.7.egg']; from setuptools.command.easy_install import main; main()"... path_list=['/path/to/setuptools-19.6.2-py2.7.egg'] ... <<< setup.py: os.system('make %s PYTHON="%s"' % (target, sys.executable)) ... make[1]: Leaving directory '/tmp/xxx/wendelin.core-0.6/3rdparty/ccan' /path/to/python2.7 setup.py ll_build_ext --inplace Traceback (most recent call last): File "setup.py", line 18, in <module> from setuptools import setup, Extension, Command, find_packages ImportError: No module named setuptools Makefile:40: recipe for target 'bigfile/_bigfile.so' failed make: *** [bigfile/_bigfile.so] Error 1 error: Setup script exited with error: Failed to execute `make all` [ @kirr: as a solution we are propagating whole python path via make. This should cover both setuptools case, and any other future potential "preloaded-by-buildout" egg. ] /reviewed-on nexedi/wendelin.core!1
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- 06 Jul, 2016 1 commit
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Kirill Smelkov authored
@kazuhiko reports that wendelin.core build is currently broken on Python 3.5. Indeed it was: In file included from bigfile/_bigfile.c:37:0: ./include/wendelin/compat_py2.h: In function ‘_PyThreadState_UncheckedGetx’: ./include/wendelin/compat_py2.h:66:28: warning: implicit declaration of function ‘_Py_atomic_load_relaxed’ [-Wimplicit-function-declaration] return (PyThreadState*)_Py_atomic_load_relaxed(&_PyThreadState_Current); ^ ./include/wendelin/compat_py2.h:66:53: error: ‘_PyThreadState_Current’ undeclared (first use in this function) return (PyThreadState*)_Py_atomic_load_relaxed(&_PyThreadState_Current); ^ ./include/wendelin/compat_py2.h:66:53: note: each undeclared identifier is reported only once for each function it appears in ./include/wendelin/compat_py2.h:67:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ The story here is that in 3.5 they decided to remove direct access to _PyThreadState_Current and atomic implementations - because that might semantically conflict with other headers implementing atomics - and provide only access by function. Starting from Python 3.5.2rc1 the function to get current thread state without asserting it is !NULL - _PyThreadState_UncheckedGet() - was added: https://github.com/python/cpython/commit/df858591 so for those python versions we can directly use it. After the fix wendelin.core tox tests pass under all python2.7, python3.4 and python3.5. More context here: https://bugs.python.org/issue26154 https://bugs.python.org/issue25150 Fixes: nexedi/wendelin.core#1
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- 01 Jul, 2016 2 commits
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Kirill Smelkov authored
_PyThreadState_Current_GET() is a function to get current python thread state without asserting it is !NULL. It was added as part of d53271b9 (bigfile/virtmem: Big Virtmem lock) We are going to adapt it to Python 3.5 (see next patch), so before doing so move it to our compatibility place. In the new place the name is _PyThreadState_UncheckedGet -- like such function is named in Python 3.5 (again, see next patch). Updates: #1
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Kirill Smelkov authored
Now that ZODB 5.0 eggs are starting to appear (see e.g. [1] for context) let's limit ZODB4 test setup to actually install ZODB4, not 5. [1] https://groups.google.com/forum/#!topic/zodb/P05S0pyUbAM
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- 27 Jun, 2016 2 commits
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Kirill Smelkov authored
Upon @jp request.
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Kirill Smelkov authored
The link is absolute URL, since the readme can be shown in a lot of places (on lab.nexedi.com, on pypi, on github, etc...) We might also change the link to demo_zbigarray.py to be absolute URL because of pypi case in the future.
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- 24 Jun, 2016 1 commit
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Kirill Smelkov authored
Since the beginning of pagemap (45af76e6 "bigfile/pagemap: specialized {} uint64 -> void * mapping") we had a bug sitting in __pagemap_for_each_leaftab() (non-leaf iterating logic behind pagemap_for_each): After entry to stack-down was found, we did not updated tailv[l] accordingly. Thus if there are non-adjacent entries an entry could be e.g. emitted many times: l 3 __down 0x7f79da1ee000 tailv[4]: 0x7f79da1ee000 -> tailv[4] 0x7f79da1ee000 __down 0x7f79da1ed000 l 4 __down 0x7f79da1ed000 tailv[5]: 0x7f79da1ed000 h 5 l 5 leaftab: 0x7f79da1ed000 <-- lvl 5 idx 169 page 0x55aa ok 9 - pagemap_for_each(0) == 21930 l 5 __down (nil) tailv[4]: 0x7f79da1ee008 -> tailv[4] 0x7f79da1ee008 __down 0x7f79da1ed000 l 4 __down 0x7f79da1ed000 tailv[5]: 0x7f79da1ed000 h 5 l 5 leaftab: 0x7f79da1ed000 <-- lvl 5 idx 169 page 0x55aa not ok 10 - pagemap_for_each(1) == 140724106500272 And many-time-emitted entries are not only incorrect, but can also lead to not-handled segmentation faults in e.g. fileh_close(): https://lab.nexedi.com/nexedi/wendelin.core/blob/v0.6-1-gb0b2c52/bigfile/virtmem.c#L179 /* drop all pages (dirty or not) associated with this fileh */ pagemap_for_each(page, &fileh->pagemap) { /* it's an error to close fileh to mapping of which an access is * currently being done in another thread */ BUG_ON(page->state == PAGE_LOADING); page_drop_memory(page); list_del(&page->lru); <-- HERE bzero(page, sizeof(*page)); /* just in case */ free(page); } ( because after first bzero of a page, the page is all 0 bytes including page->lru{.next,.prev} so on the second time when the same page is emitted by pagemap_for_each, list_del(&page->lru) will try to set page->lru.next = ... which will segfault. ) So fix it by properly updating tailv[l] while we scan/iterate current level. NOTE This applies only to non-leaf pagemap levels, as leaf level is scanned with separate loop in pagemap_for_each. That's why we probably did not noticed this earlier - up until now our usual workloads was to change data in adjacent batches and that means adjacent pages. Though today @Tyagov was playing with wendelin.core in some other way and it uncovered the bug.
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- 13 Jun, 2016 5 commits
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Kirill Smelkov authored
In the time when README.rst was initially introduced (58279ac7 "readme: Initial draft") GitLab was not handling relative links well and it was necessary to construct them properly by hand. Nowdays GitLab automatically adds namespace and project and blob/ref/ prefix to relative URL link, so there is no need to specify them manually. Actually specifying the prefix manually makes URL invalid, as it becomes something like https://lab.nexedi.com/nexedi/wendelin.core/blob/master/wendelin.core/blob/master/demo/demo_zbigarray.py Fix it.
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Kirill Smelkov authored
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Kirill Smelkov authored
This continues c7750965 (changelog: Convert it to pretty rst) - without .rst extension gitlab shows this file as plain text.
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Kirill Smelkov authored
>= 1.6 was already using latest in 1.6 series, but >= 1.6.2 is more explicit. Also: in 1.6.2 NEO switched from MySQL-python to mysqlclient: nexedi/neoppod@5f0c93f5 so we switch it too.
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Kirill Smelkov authored
Namely 1.8.x, 1.9.x -> 1.10.x -> 1.11.x
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- 12 Jun, 2016 1 commit
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Kirill Smelkov authored
Just update to latest CCAN for it to be a fresh one. Throught the modules we use there are no real updates, just a fix for one warning in array_size.
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- 20 Apr, 2016 1 commit
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Kirill Smelkov authored
For ZBlk1 we already compare ZData content about whether it was changed compared to data already stored to DB, and do not store it twice if data is the same. However ZBlk itself is always marked as changed, if corresponding memory page was dirtied. This results in transactions like Trans #33915309 tid=03b6944919befeee time=2016-04-17 22:01:06.034237 offset=140320105842 status=' ' user='...' description='...' # ... other parts, but no ZData here data #00002 oid=000000000026fc4c size=79 class=wendelin.bigfile.file_zodb.ZBlk1 where ZBlk1 is committed the same without necessity. NOTE we cannot avoid committing ZBlk in all cases, because it is used to signal other DB clients that a ZBlk needs to be invalidated and this way associated fileh pages are invalidated too. This cannot work via ZData, because ZData don't have back-pointer to ZBlk1 or to corresponding zfile.
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- 05 Apr, 2016 1 commit
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Kirill Smelkov authored
Starting from setuptools 19.4, more concrete from the following commit: https://github.com/pypa/setuptools/commit/ebc54982 setuptools sorts namespaced packages .__path__ to be in sync with sys.path . That however breaks for wendelin.core used from in-tree or installed in development mode, because we are doing tricks in top-level import redirector (see e870781d "Top-level in-tree import redirector"): (z+numpy.v2)kirr@teco:~/tmp/trashme/wendelin.core$ python -c 'import wendelin' Traceback (most recent call last): File "<string>", line 1, in <module> File "wendelin.py", line 39, in <module> __import__('pkg_resources').declare_namespace(__name__) File "/home/kirr/src/wendelin/venv/z+numpy.v2/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2081, in declare_namespace _handle_ns(packageName, path_item) File "/home/kirr/src/wendelin/venv/z+numpy.v2/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2026, in _handle_ns _rebuild_mod_path(path, packageName, module) File "/home/kirr/src/wendelin/venv/z+numpy.v2/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2050, in _rebuild_mod_path orig_path.sort(key=position_in_sys_path) File "/home/kirr/src/wendelin/venv/z+numpy.v2/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2045, in position_in_sys_path return sys_path.index(_normalize_cached(os.sep.join(parts))) ValueError: '/home/kirr/tmp/trashme' is not in list Here wendelin.py added /home/kirr/tmp/trashme/wendelin.core to .__path__ and setuptools' _handle_ns() wants to order that dir's parent in correspondence with sys.path, but parent path is not there - oops. We can workaround the problem, by first not initializing .__path__ and letting __import__('pkg_resources').declare_namespace(__name__) fully handle and initialize it, and only after it is done we make the correction for wendelin modules located not under .../wendelin.core/wendelin/ but under .../wendelin.core/ . Importing was tested to work with the fix with both setuptools 20.6.7 and older setuptools 17.1.1, i.e. here we should not be breaking backward compatibility. /reported-by @tatuya, @Camata, @Tyagov /reviewed-on !1
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- 18 Dec, 2015 1 commit
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Kirill Smelkov authored
Commit ab9ca2df (bigarray: Add support for FORTRAN ordering) added ability to define array order, but there I made a mistake of not caring about how previously-saved to DB arrays would be read back. The thing is BigArray gained new data member ._order which is automatically saved to DB thanks to ZBigArray inheriting from Persistent; on load-from-db path we just read object state from DB, which for ZBigArray is dict, and restore object attributes from it. But for previously-saved data, obviously, there is no 'order' entry and thus this way restored objects are restored not in full to current code expectations and it can boom e.g. this way: zarray.resize((new_one,old_shape[1])) Module wendelin.bigarray, line 190, in resize self._init0(new_shape, self.dtype, order=self._order) AttributeError: 'ZBigArray' object has no attribute '_order' Solution to fix is: on restore-from-DB path, see if a data member is not present on restored object, and if it has default value in BigArray set it to that. ( code to get function defaults is from http://stackoverflow.com/questions/12627118/get-a-function-arguments-default-value ) /cc @Tyagov, @klaus
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- 15 Dec, 2015 6 commits
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Kirill Smelkov authored
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Kirill Smelkov authored
loadblk() calls are potentially slow and external code that serve the cal can take other locks in addition to virtmem lock taken by virtmem subsystem. If that "other locks" are also taken before external code calls e.g. fileh_invalidate_page() in different codepath a deadlock can happen, e.g. T1 T2 page-access invalidation-from-server received V -> loadblk Z <- ClientStorage.invalidateTransaction() Z -> zeo.load V <- fileh_invalidate_page The solution to avoid deadlock is to call loadblk() with virtmem lock released and upon loadblk() completion recheck virtmem data structures carefully. To make that happen: - new page state is introduces: PAGE_LOADING (file content loading is in progress) - virtmem releases virt_lock before calling loadblk() when serving pagefault - because loading is now done with virtmem lock released, now: 1. After loading completes we need to recheck fileh/vma data structures The recheck is done in full - vma_on_pagefault() just asks its driver (see VM_RETRY and VM_HANDLED codes) to retry handling the fault completely. This should work as the freshly loaded page was just inserted into fileh->pagemap and should be found there in the cache on next lookup. On the other hand this also works correctly, if there was concurrent change - e.g. vma was unmapped while we were loading the data - in that case the fault will be also processed correctly - but loaded data will stay in fileh->pagemap (and if not used will be evicted as not-needed eventually by RAM reclaim). 2. Similar to retrying mechanism is used for cases when two threads concurrently access the same page and would both try to load corresponding block - only one thread issues the actual loadblk() and another waits for load to complete with polling and VM_RETRY. 3. To correctly invalidate loading-in-progress pages another new page state is introduced: PAGE_LOADING_INVALIDATED (file content loading was in progress while request to invalidate the page came in) which fileh_invalidate_page() uses to propagate invalidation message to loadblk() caller. 4. Blocks loading can now happen in parallel with other block loading and other virtmem operations - e.g. invalidation. For such cases tests are added to test_thread.py 5. virtmem lock now becomes just regular lock, instead of being previously recursive. For virtmem lock to be recursive was needed for cases, when code under loadblk() could trigger other virtmem calls, e.g. due to GC and calling another VMA dtor that would want to lock virtmem, but virtmem lock was already held. This is no longer needed. 6. To catch double faults we now cannot use just on static variable in_on_pagefault. That variable thus becomes thread-local. 7. Old test in test_thread to "test that access vs access don't overlap" no longer holds true - and is thus removed. /cc @Tyagov, @klaus
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Kirill Smelkov authored
Previously we were doing virt_lock() / virt_unlock() which automatically were making sure to unlock GIL before locking virtmem, and to restore GIL state to previous after virtmem lock happened. virt_unlock() was unlocking just the virtmem lock without touching GIL at all - that works because the running code would eventually release GIL as python regularly does so to allowing multiple threads to run. In the next patch however, we'll need to wait for in-progress-loading page to complete, and that wait has to be done with GIL released (so other python threads could run), and for doing so we'll need functionality to make sure GIL is unlocked and retake it back, not tied to virt_lock(). So factor it out.
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Kirill Smelkov authored
NotifyChannel was introduced in c7c01ce4 (bigfile/zodb: ZODB.Connection can migrate between threads on close/open and we have to care) to test thread interaction specific to ZODB. We'll however need NotifyChannel to do more threading test of virtmem core, and this way the proper place for NotifyChannel is test_thread.py itself. Move it.
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Kirill Smelkov authored
Both comments are from the beginning - from 9a293c2d (bigfile/virtmem: Userspace Virtual Memory Manager) - but d53271b9 patch (bigfile/virtmem: Big Virtmem lock) missed to update them.
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Kirill Smelkov authored
No one was freeing RAMH structure itself, and thus ASAN reports e.g.: ==15935==ERROR: LeakSanitizer: detected memory leaks Direct leak of 32 byte(s) in 1 object(s) allocated from: #0 0x7f29c89f1001 in __interceptor_calloc (/usr/lib/x86_64-linux-gnu/libasan.so.2+0x94001) #1 0x401da1 in zalloc include/wendelin/utils.h:65 #2 0x408128 in shmfs_ramh_open bigfile/tests/../ram_shmfs.c:202 #3 0x407611 in ramh_open bigfile/tests/../ram.c:81 #4 0x402560 in fileh_open bigfile/tests/../virtmem.c:131 #5 0x427ca1 in test_pagefault_savestate bigfile/tests/test_virtmem.c:1022 #6 0x4281ba in main bigfile/tests/test_virtmem.c:1061 #7 0x7f29c83b8b44 in __libc_start_main (/lib/x86_64-linux-gnu/libc.so.6+0x21b44) NOTE similar leak remains open in ram_close(), but it is a bit involved to fix and the effort will be removed anyway after we switch to kernel virtual memory manager. Besides ramh are opened and closed all the time and ram only once.
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- 05 Nov, 2015 1 commit
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Kirill Smelkov authored
Currently wendelin.core does not work on e.g. Debian 7, because that distro has too old kernel without support for fallocate on tmpfs. But the diagnostics of failure is not clear and looks like just being out of memory: bigfile/tests/../virtmem.c:845 OOM BUG! what happens in fact is that - virtmem tries to allocate a page -> calls shmfs_alloc_page(), - fallocate() fails with "operation not supported" error code - virtmem sees this as page allocation failure, - tries to reclaim pages, - but there are no allocated pages at all -> OOM Detect whether fallocate() error is operational error, or simply "fallocate not supported" and if latter, report to user. Now it looks like: bigfile/tests/../ram_shmfs.c:129 shmfs_alloc_page WARN: fallocate() not supported bigfile/tests/../virtmem.c:845 OOM BUG! /cc @Tyagov
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- 02 Nov, 2015 1 commit
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Kirill Smelkov authored
Until now BigArrays could use only C-style ordering - where major index is the first one. Fortran ordering is the opposite - where major index is the last one - and is used in Fortran world and sometimes by scientists in other areas. As people keep on asking for Fortran-ordered BigArrays, let's add support for it. The essential code change is to change 0'th index to major index in __getitem__ and rest of the code. For the reference: ndarray memory layout for different orders is described here: http://docs.scipy.org/doc/numpy/reference/arrays.ndarray.html#internal-memory-layout-of-an-ndarray
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- 02 Oct, 2015 9 commits
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Kirill Smelkov authored
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Kirill Smelkov authored
Since 13c0c17c (bigfile/zodb: Format #1 which is optimized for small changes) each ZBlk is split into chunks, and the procedure to load/save blk data collects/disassembles the chunks. Previously in bigfile/zodb tests, we were testing by verifying only [0] element in each block, so this way most code for chunks collection/disassembling was not tested. Fix this aspect by making sure whole block content is as would-be expected in tests.
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Kirill Smelkov authored
It was reStructuredText already, but links showing was ugly, especially when there were several links in the same line. Use kernelnewbies style to refer to commits, when particular commit url is not shown to user, only hyperlinked. This way it looks nicer.
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Kirill Smelkov authored
With the target being to show it on pypi project page.
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Kirill Smelkov authored
Now we have at least some readme, so this way it is more convenient.
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Kirill Smelkov authored
This is a general readme about what wendelin.core is and how to use ZBigArray from user point of view.
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Kirill Smelkov authored
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Kirill Smelkov authored
It was already there but very brief. Here we add text which tries to explain to reader what is generally going on in the program.
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Kirill Smelkov authored
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- 30 Sep, 2015 1 commit
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Kirill Smelkov authored
ZBlk* objects are intermediate ZODB object in between data stored in ZODB and memory pages managed by virtmem. As such, after they do their job to either load data from DB to memory, or store from memory to DB, it is not needed to keep them alive with duplicate content thus only wasting memory. ZBlk0 cares about this detail via "deactivating" ._v_blkdata in loadblkdata() and __getstate__() prologues. ZBlk1 did the same for load path in loadblkdata() prologue, but for .__getstate__() it was not directly possible, because for ZBlk1 the state is IOBTree, not one non-persistent object, and thus it first needs to be processed by ZODB together with its subobjects on its way to storage and only then all they deactivated. So 13c0c17c (bigfile/zodb: Format #1 which is optimized for small changes) only put TODO for memory-page -> DB path about not wasting memory this way. But the problem is relatively easy to solve: - we can deactivate ZData objects (leaf objects in ZBlk1.chunktab btree) by hooking into ZData.__getstate__() prologue; - we also need to care to deactivate chunks right away, which setblkdata() loaded to compare .data and found them to be not changed This way we do not waste memory keeping intermediate ZData objects alive with the same content as memory page after commit. /cc @Tyagov
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- 28 Sep, 2015 5 commits
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Kirill Smelkov authored
ZBlk1.setblkdata() has logic to detect CHUNKSIZE change, and if so recreate whole chunktab from scratch for simplicity. There was a thinko however - len(chunk.data) == CHUNKSIZE is ok and actually very often happens when data does not have zeroes. Because of this off-by-1 comparison mistake, ZData objects were constantly created and thrown out instead of being reused which led to fast ZODB growth. Fix it. /reported-by @Tyagov
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Kirill Smelkov authored
Our current workloads are mostly a lot of small data changes and this is what ZBlk1 was created for. Yes it has larger overhead for accessing data, but we already painted the way how to handle this in 13c0c17c (bigfile/zodb: Format #1 which is optimized for small changes) -> move data deduplication/management to server side. So be it ZBlk1 the default for now. /cc @Tyagov, @klaus
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Kirill Smelkov authored
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Kirill Smelkov authored
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Kirill Smelkov authored
We check all pairs of possible formats and for every pair write some data at file 0 block, check that it is in source format; then change default format, write another data, check that file.blktab[0] changed its type. I.e. with this test we verify that the we can read data in old format and change it incrementally to new. Or the other way, if data is in new format, and we decide to migrate to old one, it also works. /cc @Tyagov, @klaus
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- 24 Sep, 2015 1 commit
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Kirill Smelkov authored
Our current approach is that each file block is represented by 1 zodb object, with block size being 2M. Even with trailing \0 trimming, which halves the overhead on average, DB size grows very fast if we do a lot of small appends or changes. So another format needs to be introduced which has lower overhead for storing small changes: In general, to represent BigFile as ZODB objects, each file block could be represented separately either as 1) one ZODB object, or (ZBlk0 - this what we have already) 2) group of ZODB objects (ZBlk1 - this is what we introduce) with top-level BTree directory #blk -> objects representing block. For "1" we have - low-overhead access time (only 1 object loaded from DB), but - high-overhead in terms of ZODB size (with FileStorage / ZEO, every change to a block causes it to be written into DB in full again) For "2" we have - low-overhead in terms of ZODB size (only part of a block is overwritten in DB on single change), but - high-overhead in terms of access time (several objects need to be loaded for 1 block) In general it is not possible to have low-overhead for both i) access-time, and ii) DB size, with approach where we do block objects representation / management on *client* side. On the other hand, if object management is moved to DB *server* side, it is possible to deduplicate them there and this way have low-overhead for both access-time and DB size with just client storing 1 object per file block. This will be our future approach after we teach NEO about object deduplication. ~~~~ As shown above in the last paragraph it is not possible to perform optimally on client side. Thus ZBlk1 should be only an intermediate solution until we move data management to DB server side, with main criteria for ZBlk1 to keep it simple. In this patch a simple scheme is used, where every block is divided into chunks organized via BTree. When a block part changes, only corresponding chunk is updated. Chunk size is chosen to be 4K which creates ~ 512 fanout for 2M block. DB size after tests is changed as follows: bigfile bigarray ZBlk0 24K 6200K ZBlk1 36K 36K ( slight size increase for bigfile tests is because of btree structures overhead ) Time to run tests stays approximately the same. /cc @Tyagov, @klaus
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