- 07 Jun, 2024 1 commit
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Carlos Ramos Carreño authoredWhen building an editable wheel it is not necessary that `build_packages` (or even `run`) is called before calling `get_outputs` (notice the following in https://setuptools.pypa.io/en/latest/userguide/extension.html#supporting-sdists-and-editable-installs-in-build-sub-commands : "Please note that custom sub-commands SHOULD NOT rely on `run()` being executed (or not) to provide correct return values for `get_outputs()`, `get_output_mapping()` or `get_source_files()`. The `get_*` methods should work independently of `run()."). Our implementation relied in the call to `build_packages` to set the name of the synthetic init file. This commit uses a property of the object instead, to compute that name whenever it is necessary. With this change, it is now possible to make editable wheels. -------- kirr: Without the fix `pip install -e` fails as follows on py3: Traceback (most recent call last): File "/home/kirr/src/wendelin/venv/py39.venv/lib/python3.9/site-packages/setuptools/command/editable_wheel.py", line 155, in run self._create_wheel_file(bdist_wheel) File "/home/kirr/src/wendelin/venv/py39.venv/lib/python3.9/site-packages/setuptools/command/editable_wheel.py", line 357, in _create_wheel_file files, mapping = self._run_build_commands(dist_name, unpacked, lib, tmp) File "/home/kirr/src/wendelin/venv/py39.venv/lib/python3.9/site-packages/setuptools/command/editable_wheel.py", line 281, in _run_build_commands files, mapping = self._collect_build_outputs() File "/home/kirr/src/wendelin/venv/py39.venv/lib/python3.9/site-packages/setuptools/command/editable_wheel.py", line 266, in _collect_build_outputs files.extend(cmd.get_outputs() or []) File "<string>", line 137, in get_outputs File "/home/kirr/src/wendelin/venv/py39.venv/lib/python3.9/site-packages/setuptools/command/build_py.py", line 78, in __getattr__ return orig.build_py.__getattr__(self, attr) File "/home/kirr/src/wendelin/venv/py39.venv/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 107, in __getattr__ raise AttributeError(attr) AttributeError: initfile /reviewed-by @kirr /reviewed-on nexedi/wendelin.core!25
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- 31 May, 2024 2 commits
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Carlos Ramos Carreño authored
The interface of the function `search_include_directories` has changed in Cython 3.0a7 in https://github.com/cython/cython/commit/f3f7b612. This updates the replacement used by wendelin so that it works for both newer and older versions. Note that wendelin.core still does not work with Cython >= 3, as that version refuses to compile Python functions that can throw C++ exceptions (apparently, mixing C++ exceptions and Cython-generated code is not considered safe). /reviewed-by @kirr /reviewed-on nexedi/wendelin.core!24
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Carlos Ramos Carreño authored
NEO is still not ported to Python 3, so Python 3 tests should not use this backend. /reviewed-by @kirr /reviewed-on nexedi/wendelin.core!24
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- 03 Apr, 2024 2 commits
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Levin Zimmermann authored
If a user doesn't explicitly declare a ZBlk format, it can be assumed that this user wants to have the best ratio between consumed storage space and data access speed. Currently the best ratio between these two is provided by the new 'auto' (heuristic) format. In case of small appends this format helps reducing storage space, and in any other case it just behaves like ZBlk0 [1]. Therefore this default ensures a fast access speed [2], but also avoids a massive data growth in case of many small appends [3]. [1] An exception to this is: in its current implementation a block behaves like ZBlk1 (slow access) in case it isn't fully filled up yet. [2] As this was stated as a reason why ZBlk1 as a default format was reverted in nexedi/wendelin.core@0b68f178. [3] This was perhaps the reason why ZBlk1 was set to be the default format in nexedi/wendelin.core@9ae42085. The massive storage space consumption can already be a problem with few array to which regularly small data is appended to, as it can easily happen with Wendelin development instances. /reviewed-by @kirr /reviewed-on nexedi/wendelin.core!20
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Levin Zimmermann authored
There are two formats to save data with a ZBigFile: ZBlk0 and ZBlk1. They differ by adjusting the ratio between access-time and growing disk-space, where ZBlk1 is better regarding to disk space, while ZBlk0 has a better access-time. Wendelin.core users may not always know yet or care which format fits better for their data. In this case it may be easier for users to just let the program automatically select the ZBlk format. With this patch and the new 'auto' (for heuristic) option of the 'ZBlk' argument of ZBigFile, this is now possible. The 'auto' option isn't really a new ZBlk format in itself, but it just tries to automatically select the best ZBlk format option according to the characteristics of the changes that the user applies to the ZBigFile. In its current implementation, the heuristic tackles the use-case of large arrays with many small append-only changes. In this case 'auto' is smaller in space than ZBlk0, but faster to read than ZBlk1. It does so, by initially using ZBlk1 until a blk is filled up. Once a blk is full, it switches to ZBlk1, as it was recommended by @kirr in nexedi/wendelin.core!20 (comment 196084). With this patch comes a test (bigfile/tests/bench_zblkfmt) that creates benchmarks for different combinations and zblk formats. The test aims to check how the 'heuristic' format performs in contrast to 'ZBlk0' and 'ZBlk1': BenchmarkAppendSize/zblk=ZBlk0/change_count=500/change_percentage_set=[0.014] 1 538.1 MB BenchmarkAppendRandRead/zblk=ZBlk0/change_count=500/change_percentage_set=[0.014] 6 2.085 ms/blk BenchmarkAppendSize/zblk=ZBlk1/change_count=500/change_percentage_set=[0.014] 1 16.8 MB BenchmarkAppendRandRead/zblk=ZBlk1/change_count=500/change_percentage_set=[0.014] 6 14.564 ms/blk BenchmarkAppendSize/zblk=auto/change_count=500/change_percentage_set=[0.014] 1 29.4 MB BenchmarkAppendRandRead/zblk=auto/change_count=500/change_percentage_set=[0.014] 6 2.119 ms/blk BenchmarkRandWriteSize/zblk=ZBlk0/arrsize=1000000/change_count=500/change_percentage_set=[0.2] 1 1021.1 MB BenchmarkRandWriteRandRead/zblk=ZBlk0/arrsize=1000000/change_count=500/change_percentage_set=[0.2] 3 2.324 ms/blk BenchmarkRandWriteSize/zblk=ZBlk1/arrsize=1000000/change_count=500/change_percentage_set=[0.2] 1 216.2 MB BenchmarkRandWriteRandRead/zblk=ZBlk1/arrsize=1000000/change_count=500/change_percentage_set=[0.2] 3 15.317 ms/blk BenchmarkRandWriteSize/zblk=auto/arrsize=1000000/change_count=500/change_percentage_set=[0.2] 1 219.8 MB BenchmarkRandWriteRandRead/zblk=auto/arrsize=1000000/change_count=500/change_percentage_set=[0.2] 3 14.027 ms/blk BenchmarkRandWriteSize/zblk=ZBlk0/arrsize=1000000/change_count=500/change_percentage_set=[1] 1 1048.6 MB BenchmarkRandWriteRandRead/zblk=ZBlk0/arrsize=1000000/change_count=500/change_percentage_set=[1] 3 2.126 ms/blk BenchmarkRandWriteSize/zblk=ZBlk1/arrsize=1000000/change_count=500/change_percentage_set=[1] 1 1070.4 MB BenchmarkRandWriteRandRead/zblk=ZBlk1/arrsize=1000000/change_count=500/change_percentage_set=[1] 3 14.284 ms/blk BenchmarkRandWriteSize/zblk=auto/arrsize=1000000/change_count=500/change_percentage_set=[1] 1 1070.3 MB BenchmarkRandWriteRandRead/zblk=auto/arrsize=1000000/change_count=500/change_percentage_set=[1] 3 14.072 ms/blk BenchmarkRandWriteSize/zblk=ZBlk0/arrsize=1000000/change_count=500/change_percentage_set=[0.2,1] 1 1046.4 MB BenchmarkRandWriteRandRead/zblk=ZBlk0/arrsize=1000000/change_count=500/change_percentage_set=[0.2,1] 3 2.137 ms/blk BenchmarkRandWriteSize/zblk=ZBlk1/arrsize=1000000/change_count=500/change_percentage_set=[0.2,1] 1 638.2 MB BenchmarkRandWriteRandRead/zblk=ZBlk1/arrsize=1000000/change_count=500/change_percentage_set=[0.2,1] 3 14.083 ms/blk BenchmarkRandWriteSize/zblk=auto/arrsize=1000000/change_count=500/change_percentage_set=[0.2,1] 1 639.5 MB BenchmarkRandWriteRandRead/zblk=auto/arrsize=1000000/change_count=500/change_percentage_set=[0.2,1] 3 13.937 ms/blk and post-processed with benchstat from 3 such runs: │ x.log │ │ B │ AppendSize/zblk=ZBlk0/change_count=500/change_percentage_set=[0.014] 513.2Mi ± 0% AppendSize/zblk=ZBlk1/change_count=500/change_percentage_set=[0.014] 16.02Mi ± 0% AppendSize/zblk=auto/change_count=500/change_percentage_set=[0.014] 28.04Mi ± 0% RandWriteSize/zblk=ZBlk0/arrsize=1000000/change_count=500/change_percentage_set=[0.2] 973.8Mi ± 0% RandWriteSize/zblk=ZBlk1/arrsize=1000000/change_count=500/change_percentage_set=[0.2] 206.2Mi ± 0% RandWriteSize/zblk=auto/arrsize=1000000/change_count=500/change_percentage_set=[0.2] 209.6Mi ± 0% RandWriteSize/zblk=ZBlk0/arrsize=1000000/change_count=500/change_percentage_set=[1] 1000.0Mi ± 0% RandWriteSize/zblk=ZBlk1/arrsize=1000000/change_count=500/change_percentage_set=[1] 1020.8Mi ± 0% RandWriteSize/zblk=auto/arrsize=1000000/change_count=500/change_percentage_set=[1] 1020.7Mi ± 0% RandWriteSize/zblk=ZBlk0/arrsize=1000000/change_count=500/change_percentage_set=[0.2,1] 997.9Mi ± 0% RandWriteSize/zblk=ZBlk1/arrsize=1000000/change_count=500/change_percentage_set=[0.2,1] 608.6Mi ± 0% RandWriteSize/zblk=auto/arrsize=1000000/change_count=500/change_percentage_set=[0.2,1] 609.9Mi ± 0% geomean 353.0Mi │ x.log │ │ ms/blk │ AppendRandRead/zblk=ZBlk0/change_count=500/change_percentage_set=[0.014] 2.094 ± 12% AppendRandRead/zblk=ZBlk1/change_count=500/change_percentage_set=[0.014] 14.47 ± 1% AppendRandRead/zblk=auto/change_count=500/change_percentage_set=[0.014] 2.168 ± 2% RandWriteRandRead/zblk=ZBlk0/arrsize=1000000/change_count=500/change_percentage_set=[0.2] 2.324 ± 1% RandWriteRandRead/zblk=ZBlk1/arrsize=1000000/change_count=500/change_percentage_set=[0.2] 13.73 ± 12% RandWriteRandRead/zblk=auto/arrsize=1000000/change_count=500/change_percentage_set=[0.2] 13.60 ± 3% RandWriteRandRead/zblk=ZBlk0/arrsize=1000000/change_count=500/change_percentage_set=[1] 2.125 ± 2% RandWriteRandRead/zblk=ZBlk1/arrsize=1000000/change_count=500/change_percentage_set=[1] 14.18 ± 3% RandWriteRandRead/zblk=auto/arrsize=1000000/change_count=500/change_percentage_set=[1] 14.17 ± 1% RandWriteRandRead/zblk=ZBlk0/arrsize=1000000/change_count=500/change_percentage_set=[0.2,1] 2.118 ± 1% RandWriteRandRead/zblk=ZBlk1/arrsize=1000000/change_count=500/change_percentage_set=[0.2,1] 13.85 ± 2% RandWriteRandRead/zblk=auto/arrsize=1000000/change_count=500/change_percentage_set=[0.2,1] 13.80 ± 1% geomean 6.423 See nexedi/wendelin.core!20 and da765ef7...0c6f0850 for the preliminary history of this patch. Co-authored-by:
Kirill Smelkov <kirr@nexedi.com>
Fix typo.
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- 29 Mar, 2024 1 commit
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Kirill Smelkov authoredThis is utility function that we will need to use in the next patch to see how data of two blocks are similar to each other. We use numpy for the implementation because this code will be hot and if we don't use optimized C routines writeout will become very slow. Quoting draft patch 3f631932 : -> Also optimize ndelta computation - when done in plain python just this part was taking a lot of time as timing for initial writeup showed: writeup with ZBlk0: ~20-25s writeup with ZBlk1: ~20-30s writeup with auto: was ~ 120s now, after switching to numpy for ndelta computation, whole runtime with 'auto' is taking ~ 35s. The whole runtime, if I observe benchmark execution correctly, is dominated by database writeup. /reviewed-by @levin.zimmermann /reviewed-on nexedi/wendelin.core!20
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- 11 Dec, 2023 2 commits
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Kirill Smelkov authored
3636242f does not talk about go-fuse, which is wcfs's direct dependency and was actually updated by upstream: kirr/go-fuse@9f9ad4a1 -> Update it as well.
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Levin Zimmermann authored
Update all dependencies of WCFS to their recent versions: - neo/go: Update to pick up support for NEO/go to handle multiple master nodes - go123: Add support for Go1.21 The following dependencies were updated, but depend on higher go versions than supported by wendelin.core - glog: v1.1.0 needs go 1.19, but we still support go 1.18 The following dependencies were not updated by upstream at all: - overflow - og-rek - errors - testify /reviewed-by @kirr /reviewed-on nexedi/wendelin.core!22
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- 01 Aug, 2023 1 commit
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Kirill Smelkov authored
Update all dependencies of WCFS to their recent versions: - go-fuse: update to pick up https://github.com/hanwen/go-fuse/commit/265a3926 and https://github.com/hanwen/go-fuse/commit/90b055af. The first patch potentially improves performance, while the second fixes support for neo:// with multiple masters. - go123: add support for go1.20 - testify: some bugfixes (we use this package only during tests) The following dependencies were not updated by upstream at all: - glog - overflow - ogórek - pkg/errors . /reviewed-by @levin.zimmermann /reviewed-on nexedi/wendelin.core!16
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- 30 Jul, 2023 5 commits
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Levin Zimmermann authored
If a NEO cluster has multiple master nodes, there is no agreed on order in which the master node addresses appear in the URI. In order to insure we always get the same normalized URI among different clients of a NEO cluster with more than one master node, we explicitly sort the master node address order with this patch. /reviewed-by @kirr /reviewed-on !17
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Levin Zimmermann authored
In the old source code we already filtered NEO URI by dropping credentials, but we applied this filter to any URI, not only the NEO one. This patch adds a mechanism to apply various filter according to the specific storage type. Starting with this new patch, 'zurl_normalize_main' also refuses to normalize an URI with an unknown scheme. /reviewed-by @kirr /reviewed-on nexedi/wendelin.core!17
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Levin Zimmermann authored
After moving zurl filtering to a dedicated function, we can now test this function for correctness. It's important that different clients which point to the same storage always result in the same zodburi, even if their initial user-specified zodburi slightly differs (e.g. due to different client-side parameters or different paths of encryption). /reviewed-by @kirr /reviewed-on !17
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Levin Zimmermann authored
The WCFS mountpoint of any ZODB storage must be a unique, persistent, repeatable hash. This means any client which uses the same storage must always calculate the same WCFS mountpoint (independent from client-only parameters etc.). Therefore the WCFS mountpoint calculation must be robust for all supported ZODB storage types (at least NEO, ZEO, filestorage). It was recently decided [1] that in order to provide this robustness, WCFS mountpoint calculation should filter the parsed URI in order to drop parts, which prevents the repeatability/persistence across different clients (e.g. parts which can differ between clients although the same storage is accessed). In order to make this filtering implementation a bit easier to read and the wcfs/__init__.py less dense, the first step is to move the zurl filtering ("normalization") into lib/zodb.py This also makes sense since this normalization can be regarded as a general zodb tool which may be useful for other solutions which use zodburi. [1] neoppod!18 (comment 184671) /reviewed-by @kirr /reviewed-on !17 -
Levin Zimmermann authored
Kirill noted that nexedi/wendelin.core@fb620301 introduced a regression [1]: 'test_zstor_2zurl' sometimes passes and sometimes fails. The reason for this is that there is no deterministic order of master nodes in 'NodeManager.getMasterList()', which is why there is no specified order of master node addresses in a zurl [2]. We don't want to normalize a zurl returned by 'zstor_2zurl' as we need some of the client-specific parameters as SSL file paths, so we rather fix the test to allow any possible order of NEO master nodes in the zurl. [1] nexedi/wendelin.core!17 (comment 188102) [2] https://lab.nexedi.com/nexedi/wendelin.core/blob/fb620301/lib/zodb.py#L414 /reviewed-by @kirr /reviewed-on nexedi/wendelin.core!17
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- 19 Jun, 2023 1 commit
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Levin Zimmermann authored
The old code raised an explicit exception when converting a NEO storage with > 1 master nodes into a URI. Perhaps the rationale for this exception was that there isn't any agreed on order of master nodes in a NEO URI, which means that building a URI from such a storage could potentially break the invariant that any client which points to the same storage should result in the same WCFS mountpoint. With levin.zimmermann/wendelin.core@6f5196fa we can now rely on WCFS mountpoint calculation to always return the same mountpoint even if the order of master node addresses differ. Therefore we can drop this exception and allow WCFS to support NEO clusters with more than one master. -------- kirr: support for multiple masters was simply not implemented because in a05db040 (lib/zodb: Teach zstor_2zurl about ZEO, NEO and Demo storages) I though that we do not yet actually need it and wanted to have something minimal first. I agree that in WCFS context it is ok and makes sense to normalize zurl to have masters coming in particular order. But at zstor_2zurl level we rely on the order of masters that app.nm.getMasterList gives us. The normalization is separate function. /reviewed-by @kirr /reviewed-on !17
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- 21 Dec, 2022 3 commits
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Kirill Smelkov authored
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Kirill Smelkov authored
The function to do it was there, but I missed to add corresponding defer. Fixes 6f0cdaff (wcfs: Provide isolation to clients).
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Kirill Smelkov authored
Update all dependencies of WCFS to their recent versions: - go123: add support for go1.18 and go1.19 - neo: update to latest draft - go-fuse: update to pick up https://github.com/hanwen/go-fuse/commit/4a0e6eb5 - ogórek: no change, just the version we already had was released as v1.2.0 - testify: some bugfixes (we use this package only during tests) The following dependencies were not updated by upstream at all: - glog - overflow - pkg/errors .
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- 26 Nov, 2022 3 commits
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Levin Zimmermann authored
This patch allows using WCFS with a NEO or ZEO storage which is reachable by a URL which contains an ipv6 host. Without this patch the following example doesn't work: >>> from wendelin.lib.zodb import dbopen >>> root = dbopen("neo://cluster-name@[::1]:2051") >>> # "abc" points to a ZBigArray >>> root["abc"][0] It doesn't work because the parser missed adding square brackets around ipv6 hosts, due to which unparsing the resulting URL resulted in a wrong interpretation where a port starts. This patch furthermore amends 'test_zstor_2zurl' to test ZEO and NEO storages with ipv6 hosts. --- /reviewed-by @kirr /reviewed-on nexedi/wendelin.core!13 -
Levin Zimmermann authored
This patch adds comprehensive tests for 'wendelin.lib.zodb.zstor_2zurl'. Before this patch only one related test existed ('test_zurlstable'). This test only lightly checked correct functionality of 'zstor_2zurl'. Therefore we added the new tests 'test_zstor_2zurl' and 'test_zurlsamedb'. The new tests only cover existing functionality. --- Co-authored-by: kirr /reviewed-by @kirr /reviewed-on nexedi/wendelin.core!13 -
Levin Zimmermann authored
Before this patch 'zsync(storage)' was effectless for ZEO storages, it didn't synchronize the client with the server. This patch fixes 'zsync', so that it also performs synchronization of ZEO clients. Background information: ======================= 2006 the sync mode of ZEO has been removed: nexedi/ZEO@629b0667 and only async mode was supported from then. This means, that the "sync" method of ZEO.ClientStorage was in fact effectless. In ZEO 5 the "server-sync" option has been added: https://github.com/zopefoundation/ZEO/pull/63 Setting this option to 'True' makes the 'sync' method performing a "server round trip, thus causing client to wait for outstanding invalidations" [1]. In this patch we imitate the effect of this flag for both ZEO 4 and ZEO 5. [1] https://github.com/zopefoundation/ZEO/blob/423cb8563be3e1ee0bb4297ee980d9b74f09c710/src/ZEO/ClientStorage.py#L225-L226 --- /reviewed-by @kirr /reviewed-on nexedi/wendelin.core!13
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- 10 Nov, 2022 1 commit
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Levin Zimmermann authored
The 'shape' argument of 'numpy.ndarray's initialization method accepts integer and sequences of integers. But the 'shape' property of 'numpy.ndarray' always returns tuple[int, ...], so numpy manually casts any legal argument into tuple[int, ...]. In 'BigArray' and 'ZBigArray' this internal casting didn't exist yet. This patch adds the casting. Before: ZBigArray(shape=[1, 2, 3], dtype=float).shape == [1, 2, 3] After: ZBigArray(shape=[1, 2, 3], dtype=float).shape == (1, 2, 3) In this way BigArray and ZBigArray API behaves closer to numpy.ndaray, which should help avoiding confusion when people are using BigArray / ZBigArray. ----- See issue #9 and MR !14 for additional context. /reviewed-by @kirr /reviewed-on !14
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- 18 May, 2022 1 commit
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Kirill Smelkov authored
Wendelin.core already supports Python3 relatively well, but demo_zbigarray.py, that is invoked only manually, was missing compatibility bits for xrange: (neo) (py3.venv) (g.env) kirr@deca:~/src/neo/src/lab.nexedi.com/nexedi/wendelin.core$ ./demo/demo_zbigarray.py gen 1.fs I: RAM: 15.29GB I: WORK: 30.57GB gen signal t=0...4.10e+09 float64 (= 30.57GB) Traceback (most recent call last): File "/home/kirr/src/wendelin/wendelin.core/./demo/demo_zbigarray.py", line 154, in <module> main() File "/home/kirr/src/wendelin/venv/py3.venv/lib/python3.9/site-packages/decorator.py", line 232, in fun return caller(func, *(extras + args), **kw) File "/home/kirr/src/tools/go/pygolang/golang/__init__.py", line 103, in _ return f(*argv, **kw) File "/home/kirr/src/wendelin/wendelin.core/./demo/demo_zbigarray.py", line 142, in main gen(sig) File "/home/kirr/src/wendelin/wendelin.core/./demo/demo_zbigarray.py", line 74, in gen for t0 in xrange(0, len(a), blocksize): NameError: name 'xrange' is not defined -> Fix it.
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- 02 Feb, 2022 1 commit
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Kirill Smelkov authored
Arnaud reports that wendelin.core currently cannot be installed on Python3: /opt/slapgrid/3f9add9291086dee302fc478df4b3130/parts/python3/bin/python3 /tmp/tmp1fuxchsb -q develop -mN -d /opt/slapgrid/3f9add9291086dee302fc478df4b3130/develop-eggs/tmps5jr7ymsbuild /opt/slapgrid/3f9add9291086dee302fc478df4b3130/eggs/setuptools-44.1.1-py3.7.egg/setuptools/dist.py:476: UserWarning: Normalizing '2.0.alpha2.post1' to '2.0a2.post1' package init file '__init__.py' not found (or not a regular file) Traceback (most recent call last): File "/tmp/tmp1fuxchsb", line 19, in <module> exec(compile(f.read(), '/opt/slapgrid/3f9add9291086dee302fc478df4b3130/parts/wendelin.core/setup.py', 'exec')) File "/opt/slapgrid/3f9add9291086dee302fc478df4b3130/parts/wendelin.core/setup.py", line 426, in <module> """.splitlines()] File "/opt/slapgrid/3f9add9291086dee302fc478df4b3130/develop-eggs/pygolang-0.1-py3.7-linux-x86_64.egg/golang/pyx/build.py", line 118, in setup setuptools_dso.setup(**kw) File "/opt/slapgrid/3f9add9291086dee302fc478df4b3130/eggs/setuptools_dso-1.7-py3.7.egg/setuptools_dso/__init__.py", line 37, in setup _setup(**kws) File "/opt/slapgrid/3f9add9291086dee302fc478df4b3130/eggs/setuptools-44.1.1-py3.7.egg/setuptools/__init__.py", line 162, in setup File "/opt/slapgrid/3f9add9291086dee302fc478df4b3130/parts/python3/lib/python3.7/distutils/core.py", line 148, in setup dist.run_commands() File "/opt/slapgrid/3f9add9291086dee302fc478df4b3130/parts/python3/lib/python3.7/distutils/dist.py", line 966, in run_commands self.run_command(cmd) File "/opt/slapgrid/3f9add9291086dee302fc478df4b3130/parts/python3/lib/python3.7/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/opt/slapgrid/3f9add9291086dee302fc478df4b3130/eggs/setuptools-44.1.1-py3.7.egg/setuptools/command/develop.py", line 38, in run File "/opt/slapgrid/3f9add9291086dee302fc478df4b3130/eggs/setuptools-44.1.1-py3.7.egg/setuptools/command/develop.py", line 136, in install_for_development File "/opt/slapgrid/3f9add9291086dee302fc478df4b3130/parts/python3/lib/python3.7/distutils/cmd.py", line 313, in run_command self.distribution.run_command(command) File "/opt/slapgrid/3f9add9291086dee302fc478df4b3130/parts/python3/lib/python3.7/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/opt/slapgrid/3f9add9291086dee302fc478df4b3130/eggs/setuptools-44.1.1-py3.7.egg/setuptools/command/egg_info.py", line 296, in run File "/opt/slapgrid/3f9add9291086dee302fc478df4b3130/eggs/setuptools-44.1.1-py3.7.egg/setuptools/command/egg_info.py", line 303, in find_sources File "/opt/slapgrid/3f9add9291086dee302fc478df4b3130/eggs/setuptools-44.1.1-py3.7.egg/setuptools/command/egg_info.py", line 537, in run File "/opt/slapgrid/3f9add9291086dee302fc478df4b3130/eggs/setuptools-44.1.1-py3.7.egg/setuptools/command/egg_info.py", line 591, in prune_file_list File "/opt/slapgrid/3f9add9291086dee302fc478df4b3130/eggs/setuptools-44.1.1-py3.7.egg/setuptools/command/egg_info.py", line 452, in prune File "/opt/slapgrid/3f9add9291086dee302fc478df4b3130/eggs/setuptools-44.1.1-py3.7.egg/setuptools/command/egg_info.py", line 405, in _remove_files TypeError: cannot use a string pattern on a bytes-like object While: Installing wendelin.core. The problem turned out to be that git-lsfiles output, that we add into list of source files, is bytes and it breaks when those bytes get intermixed into strings. -> Fix it by always returning from runcmd the str type of current python. /reported-by @arnau
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- 27 Jan, 2022 3 commits
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Kirill Smelkov authored
Similarly to build_ext we need ccan/config.h to be present for dso to build. It was not the case and so pip install wendelin.core was failing: $ pip install wendelin.core-2.0a2.tar.gz Processing ./wendelin.core-2.0a2.tar.gz Installing build dependencies ... done Getting requirements to build wheel ... done Preparing wheel metadata ... done Collecting ZODB>=4 ... Building wheels for collected packages: wendelin.core Building wheel for wendelin.core (PEP 517) ... error ERROR: Command errored out with exit status 1: ... running build_dso Building DSOs building 'wendelin.bigfile.libvirtmem' DSO as build/lib.linux-x86_64-2.7/wendelin/bigfile/liblibvirtmem.so creating build/temp.linux-x86_64-2.7 creating build/temp.linux-x86_64-2.7/bigfile creating build/temp.linux-x86_64-2.7/lib x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -ffile-prefix-map=/build/python2.7-vgIf7a/python2.7-2.7.18=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_GNU_SOURCE -I/tmp/pip-build-env-lfVr7E/overlay/lib/python2.7/site-packages -I. -I./include -I./3rdparty/ccan -I./3rdparty/include -Ibuild/lib.linux-x86_64-2.7/. -c bigfile/pagefault.c -o build/temp.linux-x86_64-2.7/bigfile/pagefault.o -fno-strict-aliasing -std=gnu99 -fplan9-extensions -Wno-declaration-after-statement -Wno-error=declaration-after-statement In file included from ./include/wendelin/list.h:11, from ./include/wendelin/bigfile/virtmem.h:50, from bigfile/pagefault.c:29: ./3rdparty/ccan/ccan/array_size/array_size.h:4:10: fatal error: config.h: Нет такого файла или каталога 4 | #include "config.h" | ^~~~~~~~~~ compilation terminated. error: command 'x86_64-linux-gnu-gcc' failed with exit status 1 ---------------------------------------- ERROR: Failed building wheel for wendelin.core Failed to build wendelin.core ERROR: Could not build wheels for wendelin.core which use PEP 517 and cannot be installed directly -> Fix it by making build_dso also first come through `make all`. NOTE we cannot fix it in exactly the same way as for build_ext: if we split build_dso into build_dso and ll_build_dso, `make all` will still go to infinite recursion: build_dso -> ll_build_dso -> build_dso (not ll_build_dso, this is controlled by setuptools_dso) -> oops. -
Kirill Smelkov authored
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Kirill Smelkov authored
Starting from version 0.1 pygolang provides File out of the box: pygolang@4690460b https://pypi.org/project/pygolang/#pygolang-change-history -> Use it and remove our custom File implementation that originally served as POC for that pygolang functionality.
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- 26 Jan, 2022 2 commits
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Kirill Smelkov authored
Don't use golang::* namespaces to avoid clashes with pygolang adding something in there and getting compilation error due to conflict, when e.g. nexedi/pygolang!17 lands. -> use xgolang:: as top-level namespace for what was previously living in golang:: shipped in wendelin.core. Inside that xgolang:: namespace don't use the same package names that might be used inside golang:: in pygolang. This avoids ambiguation and compile error in the future on e.g. os::AfterFork - is `using namespace golang` and `using namespace xgolang` were both activated. -> Prefix all namespaces inside xgolang:: also with "x".
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Kirill Smelkov authored
See pygolang!17
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- 21 Jan, 2022 8 commits
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Kirill Smelkov authored
The problem is similar to a7bf0311 (wcfs: Fix crash if on invalidation handledδZ needs to access ZODB) - I forgot to put zhead's transaction into context. Without the fix added test fails as: wcfs_test.py::test_wcfs_crash_old_data ---------------- live log call ----------------- WARNING ZODB.FileStorage:FileStorage.py:413 Ignoring index for /tmp/testdb_fs.OV0rS6/1.fs M: commit -> @at0 (03e5a3342bc5ab22) M: commit -> @at1 (03e5a3342bc88899) M: f<0000000000000002> [0] INFO wcfs:__init__.py:293 starting for file:///tmp/testdb_fs.OV0rS6/1.fs ... I0120 17:12:10.274379 704327 wcfs.go:2393] start "/dev/shm/wcfs/556fa61a9f9675f34c6b44e1f978842c37176c59" "file:///tmp/testdb_fs.OV0rS6/1.fs" I0120 17:12:10.274409 704327 wcfs.go:2399] (built with go1.17.6) W0120 17:12:10.274560 704327 storage.go:152] zodb: FIXME: open file:///tmp/testdb_fs.OV0rS6/1.fs: raw cache is not ready for invalidations -> NoCache forced INFO wcfs:__init__.py:334 started pid704327 @ /dev/shm/wcfs/556fa61a9f9675f34c6b44e1f978842c37176c59 C: setup watch f<0000000000000002> @at1 (03e5a3342bc88899) # pinok: {} M: commit -> @at2 (03e5a3342c895777) M: f<0000000000000002> [1] M: commit -> @at3 (03e5a3342ca5ef55) M: f<0000000000000002> [0] C: setup watch f<0000000000000002> @at2 (03e5a3342c895777) # pinok: {0: @at1 (03e5a3342bc88899)} panic: transaction: no current transaction goroutine 88 [running]: lab.nexedi.com/kirr/neo/go/transaction.currentTxn({0x969718, 0xc0000b6240}) /home/kirr/src/neo/src/lab.nexedi.com/kirr/neo/go/transaction/transaction.go:59 +0x77 lab.nexedi.com/kirr/neo/go/transaction.Current(...) /home/kirr/src/neo/src/lab.nexedi.com/kirr/neo/go/transaction/api.go:206 lab.nexedi.com/kirr/neo/go/zodb.(*Connection).checkTxnCtx(...) /home/kirr/src/neo/src/lab.nexedi.com/kirr/neo/go/zodb/connection.go:374 lab.nexedi.com/kirr/neo/go/zodb.(*Connection).Get(0xc0000c25a0, {0x969718, 0xc0000b6240}, 0x4) /home/kirr/src/neo/src/lab.nexedi.com/kirr/neo/go/zodb/connection.go:331 +0x73 lab.nexedi.com/nexedi/wendelin.core/wcfs/internal/zdata.(*ΔFtail).BlkRevAt(0xc00009dd40, {0x969718, 0xc0000b6240}, 0xc000100540, 0x30, 0x3e5a3342c895777) /home/kirr/src/neo/src/lab.nexedi.com/nexedi/wendelin.core/wcfs/internal/zdata/δftail.go:1140 +0x39d main.(*WatchLink).setupWatch(0xc0000120a0, {0x969718, 0xc0000b6240}, 0x2, 0x3e5a3342c895777) /home/kirr/src/neo/src/lab.nexedi.com/nexedi/wendelin.core/wcfs/wcfs.go:1754 +0xe3f main.(*WatchLink)._handleWatch(0x0, {0x969718, 0xc0000b6240}, {0xc0000a0122, 0x0}) /home/kirr/src/neo/src/lab.nexedi.com/nexedi/wendelin.core/wcfs/wcfs.go:1973 +0x65 main.(*WatchLink).handleWatch(0x0, {0x969718, 0xc0000b6240}, 0x0, {0xc0000a0122, 0x28}) /home/kirr/src/neo/src/lab.nexedi.com/nexedi/wendelin.core/wcfs/wcfs.go:1955 +0x10c main.(*WatchLink)._serve.func3({0x969718, 0xc0000b6240}) /home/kirr/src/neo/src/lab.nexedi.com/nexedi/wendelin.core/wcfs/wcfs.go:1944 +0x3c lab.nexedi.com/kirr/go123/xsync.(*WorkGroup).Go.func1() /home/kirr/src/neo/src/lab.nexedi.com/kirr/go123/xsync/xsync.go:86 +0x68 created by lab.nexedi.com/kirr/go123/xsync.(*WorkGroup).Go /home/kirr/src/neo/src/lab.nexedi.com/kirr/go123/xsync/xsync.go:83 +0x92 >>> Change history by file: f<0000000000000002>: 0 1 2 3 4 5 6 7 a b c d e f g h @at0 (03e5a3342bc5ab22) @at1 (03e5a3342bc88899) 0 @at2 (03e5a3342c895777) 1 @at3 (03e5a3342ca5ef55) 0 ---------------------------------------- # wcfs was crashing in setting up watch because of "1" and "2" from above, and # 3. setupWatch was calling ΔFtail.BlkRevAt without putting zhead's transaction into ctx. wl2 = t.openwatch() > wl2.watch(zf, at2, {0:at1})
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Kirill Smelkov authored
- put into if block to avoid collision with already-defined-elsewhere blkv - show revisions in symbolic form Noticed while working on recent change to allow ΔFtail/ΔBtail point-queries with at=tail.
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Kirill Smelkov authored
Watching with at=tail is inevitable as explained in the previous patch.
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Kirill Smelkov authored
This is needed because when e.g. wcfs is just started the coverage of ΔFtail is (head,head] i.e. empty, and if user wants to setup a watch with at=head, it becomes watch with at=tail. Then that at is used in a query and if point-queries with at=tail are disallowed it panics with "at out of bounds". This fixes crashes in test_wcfs_watch_setup (see 339f1884 "wcfs: tests: Always start tDB with ZBigFile pre-created before WCFS startup") and in test_wcfs_crash_old_data (see 97ce5105 "wcfs: tests: Add test do demonstrate "at out of bounds" crash on readPinWatchers -> ΔFtail.BlkRevAt") For the reference zodb.ΔTail already allows point queries with at=tail: https://lab.nexedi.com/kirr/neo/blob/1193c44e/go/zodb/δtail.go#L202-206 https://lab.nexedi.com/kirr/neo/blob/1193c44e/go/zodb/δtail.go#L225-228
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Kirill Smelkov authored
The codepath that sends pin messages to watchers on FUSE READ, similarly to what was showed in 339f1884 is also vulnerable to "at out of bounds" panic if at=ΔFtail.tail: wcfs_test.py::test_wcfs_crash_old_data ---------------- live log call ----------------- WARNING ZODB.FileStorage:FileStorage.py:413 Ignoring index for /tmp/testdb_fs.nbSKXu/1.fs M: commit -> @at0 (03e5a31e5e5ef6bb) M: commit -> @at1 (03e5a31e5e63fa77) M: f<0000000000000002> [0] INFO wcfs:__init__.py:293 starting for file:///tmp/testdb_fs.nbSKXu/1.fs ... I0120 16:50:22.136098 697106 wcfs.go:2393] start "/dev/shm/wcfs/93026d44ef96f87df2cc0e2e451c5aabee91b652" "file:///tmp/testdb_fs.nbSKXu/1.fs" I0120 16:50:22.136127 697106 wcfs.go:2399] (built with go1.17.6) W0120 16:50:22.136233 697106 storage.go:152] zodb: FIXME: open file:///tmp/testdb_fs.nbSKXu/1.fs: raw cache is not ready for invalidations -> NoCache forced INFO wcfs:__init__.py:334 started pid697106 @ /dev/shm/wcfs/93026d44ef96f87df2cc0e2e451c5aabee91b652 C: setup watch f<0000000000000002> @at1 (03e5a31e5e63fa77) # pinok: {} panic: at out of bounds: at: @03e5a31e5e63fa77, (tail, head] = (@03e5a31e5e63fa77, @03e5a31e5e63fa77] goroutine 7 [running]: lab.nexedi.com/nexedi/wendelin.core/wcfs/internal/zdata.panicf(...) /home/kirr/src/neo/src/lab.nexedi.com/nexedi/wendelin.core/wcfs/internal/zdata/misc.go:47 lab.nexedi.com/nexedi/wendelin.core/wcfs/internal/zdata.(*ΔFtail).BlkRevAt(0xc0000a5d40, {0x969718, 0xc000076140}, 0xc0001a22a0, 0xc0001c0200, 0x3e5a31e5e63fa77) /home/kirr/src/neo/src/lab.nexedi.com/nexedi/wendelin.core/wcfs/internal/zdata/δftail.go:1077 +0xa45 main.(*BigFile).readPinWatchers(0xc0001d0200, {0x969718, 0xc000076140}, 0x0, 0xffffffffffffffff) /home/kirr/src/neo/src/lab.nexedi.com/nexedi/wendelin.core/wcfs/wcfs.go:1559 +0x2a5 main.(*BigFile).readBlk(0xc0001d0200, {0x969718, 0xc000076140}, 0x0, {0xc000320000, 0x200000, 0x0}) /home/kirr/src/neo/src/lab.nexedi.com/nexedi/wendelin.core/wcfs/wcfs.go:1281 +0x4d2 main.(*BigFile).Read.func1({0x969718, 0xc000076140}) /home/kirr/src/neo/src/lab.nexedi.com/nexedi/wendelin.core/wcfs/wcfs.go:1223 +0x71 lab.nexedi.com/kirr/go123/xsync.(*WorkGroup).Go.func1() /home/kirr/src/neo/src/lab.nexedi.com/kirr/go123/xsync/xsync.go:86 +0x68 created by lab.nexedi.com/kirr/go123/xsync.(*WorkGroup).Go /home/kirr/src/neo/src/lab.nexedi.com/kirr/go123/xsync/xsync.go:83 +0x92 >>> Change history by file: f<0000000000000002>: 0 1 2 3 4 5 6 7 a b c d e f g h @at0 (03e5a31e5e5ef6bb) @at1 (03e5a31e5e63fa77) 0 ... @func def test_wcfs_crash_old_data(): # start wcfs with ΔFtail/ΔBtail not covering that initial data. t = tDB(old_data=[{0:'a'}]); zf = t.zfile; at1 = t.head defer(t.close) f = t.open(zf) # ΔFtail coverage is currently (at1,at1] wl = t.openwatch() wl.watch(zf, at1, {}) # wcfs is crashing on readPinWatcher -> ΔFtail.BlkRevAt with # "at out of bounds: at: @at1, (tail,head] = (@at1,@at1] # because BlkRevAt(at=tail) query was disallowed. > f.assertBlk(0, 'a') # [0] becomes tracked Still also crashing in test_wcfs_watch_setup.
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Kirill Smelkov authored
Soon this test will also exercise functionality from isolation protocol as well and so it will stop to be basic. Move plus rename test_wcfs_basic_invalidation_wo_dFtail_coverage -> test_wcfs_crash_old_data. Still crashing in test_wcfs_watch_setup.
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Kirill Smelkov authored
This semantically moves initialization code from test_wcfs_basic_invalidation_wo_dFtail_coverage (see a7bf0311 "wcfs: Fix crash if on invalidation handledδZ needs to access ZODB") to tDB itself, and will be useful to exercise similar scenarios in other tests. Still crashing in test_wcfs_watch_setup.
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Kirill Smelkov authored
This should hopefully exercise codepaths in wcfs.go a bit more for mistakes similar to a7bf0311 (wcfs: Fix crash if on invalidation handledδZ needs to access ZODB) where the code on server side forgets to put zhead's transaction into context. Currently, because watching @tail is disallowed, this leads to panic triggered by test_wcfs_watch_setup: @at0 (03e59e3e606b89bb) -> @at1 (03e59e3e610692bb) -> @at2 (03e59e3e612a5811) -> @at3 (03e59e3e614fa9cc) -> @at4 (03e59e3e6189c3ee) -> @at5 (03e59e3e61af0baa) C: setup watch f<0000000000000002> @at0 (03e59e3e606b89bb) # pinok: {0: @at0 (03e59e3e606b89bb), 2: @at0 (03e59e3e606b89bb), 3: @at0 (03e59e3e606b89bb), 5: @at0 (03e59e3e606b89bb)} panic: at out of bounds: at: @03e59e3e606b89bb, (tail, head] = (@03e59e3e606b89bb, @03e59e3e61af0baa] goroutine 187 [running]: lab.nexedi.com/nexedi/wendelin.core/wcfs/internal/zdata.panicf(...) /home/kirr/src/neo/src/lab.nexedi.com/nexedi/wendelin.core/wcfs/internal/zdata/misc.go:47 lab.nexedi.com/nexedi/wendelin.core/wcfs/internal/zdata.(*ΔFtail).BlkRevAt(0xc000077d40, {0x969718, 0xc000062940}, 0xc0003060c0, 0x4174f4, 0x3e59e3e606b89bb) /home/kirr/src/neo/src/lab.nexedi.com/nexedi/wendelin.core/wcfs/internal/zdata/δftail.go:1077 +0xa45 main.(*WatchLink).setupWatch(0xc000108050, {0x969718, 0xc000062940}, 0x2, 0x3e59e3e606b89bb) /home/kirr/src/neo/src/lab.nexedi.com/nexedi/wendelin.core/wcfs/wcfs.go:1754 +0xe3f main.(*WatchLink)._handleWatch(0x0, {0x969718, 0xc000062940}, {0xc00001c812, 0xa00000}) /home/kirr/src/neo/src/lab.nexedi.com/nexedi/wendelin.core/wcfs/wcfs.go:1973 +0x65 main.(*WatchLink).handleWatch(0x74039b, {0x969718, 0xc000062940}, 0xc0000a4280, {0xc00001c812, 0x28}) /home/kirr/src/neo/src/lab.nexedi.com/nexedi/wendelin.core/wcfs/wcfs.go:1955 +0x10c main.(*WatchLink)._serve.func3({0x969718, 0xc000062940}) /home/kirr/src/neo/src/lab.nexedi.com/nexedi/wendelin.core/wcfs/wcfs.go:1944 +0x3c lab.nexedi.com/kirr/go123/xsync.(*WorkGroup).Go.func1() /home/kirr/src/neo/src/lab.nexedi.com/kirr/go123/xsync/xsync.go:86 +0x68 created by lab.nexedi.com/kirr/go123/xsync.(*WorkGroup).Go /home/kirr/src/neo/src/lab.nexedi.com/kirr/go123/xsync/xsync.go:83 +0x92 >>> Change history by file: f<0000000000000002>: 0 1 2 3 4 5 6 7 a b c d e f g h @at0 (03e59e3e606b89bb) @at1 (03e59e3e610692bb) 2 @at2 (03e59e3e612a5811) 2 3 4 5 @at3 (03e59e3e614fa9cc) 0 2 5 @at4 (03e59e3e6189c3ee) 2 4 5 @at5 (03e59e3e61af0baa) 3 5 However next we will anyway need to allow to setup watches @tail, and so we will be fixing this and other errors in followup commits. NOTE: we don't loose coverage for the case when ZBigFile is created after wcfs startup due to test_wcfs_watch_2files, where that scenario is tested. ΔFtail/ΔBtail tests also exercise ZBigFile/BTree epochs (creation/deletion) well.
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- 19 Jan, 2022 3 commits
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Kirill Smelkov authored
tDB.commit always creates only one transaction and so wcfs should be expected to catch up with only that single one -> no need to loop. No need to keep tDB._wc_zheadv as we have information about all committed transactions in t.dFtail.
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Kirill Smelkov authored
.commit is the only caller of ._wcsync. .commit is also the only place via which tests are intended to modify ZODB.
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Kirill Smelkov authored
- .commit performs ZODB commit and synchronizes WCFS to database changes; - ._commit performs ZODB commit without WCFS synchronization. We will soon need ._commit to create initial revisions for ZBigFile while WCFS is not yet started.
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