Benchmarks #5
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Benchmarks #5
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Current output: so things seem to be more or less in sync. I still have to do pure Python benchmarks, probably tomorrow, to compare. |
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I can't test it, because I run into some SSL error trying to open it from the python side: julia> py_array = YAXArrays.open_dataset(xr.open_zarr(data_url, decode_times=false))
ERROR: Python: RuntimeError: SSL is not supported.
Python stacktrace:
[1] _get_ssl_context
@ aiohttp.connector ~/.julia/dev/PyYAXArrays/benchmarks/.CondaPkg/env/lib/python3.12/site-packages/aiohttp/connector.py:1015
[2] _create_direct_connection
@ aiohttp.connector ~/.julia/dev/PyYAXArrays/benchmarks/.CondaPkg/env/lib/python3.12/site-packages/aiohttp/connector.py:1285
[3] _create_connection
@ aiohttp.connector ~/.julia/dev/PyYAXArrays/benchmarks/.CondaPkg/env/lib/python3.12/site-packages/aiohttp/connector.py:975
[4] connect
@ aiohttp.connector ~/.julia/dev/PyYAXArrays/benchmarks/.CondaPkg/env/lib/python3.12/site-packages/aiohttp/connector.py:564
[5] _request
@ aiohttp.client ~/.julia/dev/PyYAXArrays/benchmarks/.CondaPkg/env/lib/python3.12/site-packages/aiohttp/client.py:657
[6] __aenter__
@ aiohttp.client ~/.julia/dev/PyYAXArrays/benchmarks/.CondaPkg/env/lib/python3.12/site-packages/aiohttp/client.py:1353
[7] _cat_file
@ fsspec.implementations.http ~/.julia/dev/PyYAXArrays/benchmarks/.CondaPkg/env/lib/python3.12/site-packages/fsspec/implementations/http.py:234
[8] wait_for
@ asyncio.tasks ~/.julia/dev/PyYAXArrays/benchmarks/.CondaPkg/env/lib/python3.12/asyncio/tasks.py:520
[9] _run_coro
@ fsspec.asyn ~/.julia/dev/PyYAXArrays/benchmarks/.CondaPkg/env/lib/python3.12/site-packages/fsspec/asyn.py:245
[10] _cat
@ fsspec.asyn ~/.julia/dev/PyYAXArrays/benchmarks/.CondaPkg/env/lib/python3.12/site-packages/fsspec/asyn.py:461
[11] _runner
@ fsspec.asyn ~/.julia/dev/PyYAXArrays/benchmarks/.CondaPkg/env/lib/python3.12/site-packages/fsspec/asyn.py:56
[12] sync
@ fsspec.asyn ~/.julia/dev/PyYAXArrays/benchmarks/.CondaPkg/env/lib/python3.12/site-packages/fsspec/asyn.py:103
[13] wrapper
@ fsspec.asyn ~/.julia/dev/PyYAXArrays/benchmarks/.CondaPkg/env/lib/python3.12/site-packages/fsspec/asyn.py:118
[14] __getitem__
@ fsspec.mapping ~/.julia/dev/PyYAXArrays/benchmarks/.CondaPkg/env/lib/python3.12/site-packages/fsspec/mapping.py:155
[15] __getitem__
@ zarr.storage ~/.julia/dev/PyYAXArrays/benchmarks/.CondaPkg/env/lib/python3.12/site-packages/zarr/storage.py:1446
[16] __init__
@ zarr.storage ~/.julia/dev/PyYAXArrays/benchmarks/.CondaPkg/env/lib/python3.12/site-packages/zarr/storage.py:3046
[17] open_consolidated
@ zarr.convenience ~/.julia/dev/PyYAXArrays/benchmarks/.CondaPkg/env/lib/python3.12/site-packages/zarr/convenience.py:1360
[18] _get_open_params
@ xarray.backends.zarr ~/.julia/dev/PyYAXArrays/benchmarks/.CondaPkg/env/lib/python3.12/site-packages/xarray/backends/zarr.py:1313
[19] open_group
@ xarray.backends.zarr ~/.julia/dev/PyYAXArrays/benchmarks/.CondaPkg/env/lib/python3.12/site-packages/xarray/backends/zarr.py:483
[20] open_dataset
@ xarray.backends.zarr ~/.julia/dev/PyYAXArrays/benchmarks/.CondaPkg/env/lib/python3.12/site-packages/xarray/backends/zarr.py:1173
[21] open_dataset
@ xarray.backends.api ~/.julia/dev/PyYAXArrays/benchmarks/.CondaPkg/env/lib/python3.12/site-packages/xarray/backends/api.py:588
[22] open_zarr
@ xarray.backends.zarr ~/.julia/dev/PyYAXArrays/benchmarks/.CondaPkg/env/lib/python3.12/site-packages/xarray/backends/zarr.py:1103
Stacktrace:
[1] pythrow()
@ PythonCall.Core ~/.julia/packages/PythonCall/Nr75f/src/Core/err.jl:92
[2] errcheck
@ ~/.julia/packages/PythonCall/Nr75f/src/Core/err.jl:10 [inlined]
[3] pycallargs
@ ~/.julia/packages/PythonCall/Nr75f/src/Core/builtins.jl:222 [inlined]
[4] pycall(f::Py, args::String; kwargs::@Kwargs{decode_times::Bool})
@ PythonCall.Core ~/.julia/packages/PythonCall/Nr75f/src/Core/builtins.jl:237
[5] pycall
@ ~/.julia/packages/PythonCall/Nr75f/src/Core/builtins.jl:233 [inlined]
[6] #_#11
@ ~/.julia/packages/PythonCall/Nr75f/src/Core/Py.jl:357 [inlined]
[7] top-level scope
@ REPL[49]:1 |
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See the comment at the top of the file, it looks like Python's SSL must be loaded first. Maybe there's a hard linking going on instead of dynamic during the build process for Python? That's the only thing I can think of... |
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I did load PythonCall as first package. So I am not sure, what is going on. |
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Huh, interesting. What system are you on? |
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And what's the output of: ]st -m OpenSSL OpenSSL_jll
]conda run conda list? |
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System: julia> versioninfo()
Julia Version 1.10.4
Commit 48d4fd48430 (2024-06-04 10:41 UTC)
Build Info:
Official https://julialang.org/ release
Platform Info:
OS: Linux (x86_64-linux-gnu)
CPU: 16 × AMD Ryzen 7 PRO 5850U with Radeon Graphics
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 10 default, 0 interactive, 5 GC (on 16 virtual cores)
Environment:
JULIA_EDITOR = code
JULIA_NUM_THREADS = 10packages: DetailsDetails
(benchmarks) pkg> st -m OpenSSL OpenSSL_jll
Status `~/.julia/dev/PyYAXArrays/benchmarks/Manifest.toml`
[4d8831e6] OpenSSL v1.4.3
[458c3c95] OpenSSL_jll v3.0.14+0
(benchmarks) pkg> conda run conda list
List of packages in environment: "/home/fcremer/.julia/dev/PyYAXArrays/benchmarks/.CondaPkg/env"
Name Version Build Channel
────────────────────────────────────────────────────────────────────────────────────
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
aiohappyeyeballs 2.4.0 pyhd8ed1ab_0 conda-forge
aiohttp 3.10.5 py312h41a817b_0 conda-forge
aiosignal 1.3.1 pyhd8ed1ab_0 conda-forge
asciitree 0.3.3 py_2 conda-forge
attrs 24.2.0 pyh71513ae_0 conda-forge
aws-c-auth 0.7.25 h15d0e8c_6 conda-forge
aws-c-cal 0.7.3 h8dac057_2 conda-forge
aws-c-common 0.9.27 h4bc722e_0 conda-forge
aws-c-compression 0.2.18 h038f3f9_10 conda-forge
aws-c-event-stream 0.4.3 h570d160_0 conda-forge
aws-c-http 0.8.7 ha1f794c_4 conda-forge
aws-c-io 0.14.18 h0040ed1_5 conda-forge
aws-c-mqtt 0.10.4 hc14a930_17 conda-forge
aws-c-s3 0.6.4 h558cea2_8 conda-forge
aws-c-sdkutils 0.1.19 h038f3f9_2 conda-forge
aws-checksums 0.1.18 h038f3f9_10 conda-forge
aws-crt-cpp 0.27.5 h6e4e78f_8 conda-forge
aws-sdk-cpp 1.11.379 hce093eb_4 conda-forge
azure-core-cpp 1.13.0 h935415a_0 conda-forge
azure-identity-cpp 1.8.0 hd126650_2 conda-forge
azure-storage-blobs-cpp 12.12.0 hd2e3451_0 conda-forge
azure-storage-common-cpp 12.7.0 h10ac4d7_1 conda-forge
azure-storage-files-datalake-cpp 12.11.0 h325d260_1 conda-forge
bokeh 3.5.1 pyhd8ed1ab_0 conda-forge
brotli-python 1.1.0 py312h30efb56_1 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.33.0 ha66036c_0 conda-forge
ca-certificates 2024.7.4 hbcca054_0 conda-forge
certifi 2024.7.4 pyhd8ed1ab_0 conda-forge
cffi 1.17.0 py312h1671c18_0 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
click 8.1.7 unix_pyh707e725_0 conda-forge
cloudpickle 3.0.0 pyhd8ed1ab_0 conda-forge
contourpy 1.2.1 py312h8572e83_0 conda-forge
cytoolz 0.12.3 py312h98912ed_0 conda-forge
dask 2024.8.1 pyhd8ed1ab_0 conda-forge
dask-core 2024.8.1 pyhd8ed1ab_0 conda-forge
dask-expr 1.1.11 pyhd8ed1ab_0 conda-forge
distributed 2024.8.1 pyhd8ed1ab_0 conda-forge
fasteners 0.17.3 pyhd8ed1ab_0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
frozenlist 1.4.1 py312h98912ed_0 conda-forge
fsspec 2024.6.1 pyhff2d567_0 conda-forge
gflags 2.2.2 he1b5a44_1004 conda-forge
glog 0.7.1 hbabe93e_0 conda-forge
h2 4.1.0 pyhd8ed1ab_0 conda-forge
hpack 4.0.0 pyh9f0ad1d_0 conda-forge
hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge
icu 75.1 he02047a_0 conda-forge
idna 3.7 pyhd8ed1ab_0 conda-forge
importlib-metadata 8.4.0 pyha770c72_0 conda-forge
importlib_metadata 8.4.0 hd8ed1ab_0 conda-forge
jinja2 3.1.4 pyhd8ed1ab_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
lcms2 2.16 hb7c19ff_0 conda-forge
ld_impl_linux-64 2.40 hf3520f5_7 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libabseil 20240116.2 cxx17_he02047a_1 conda-forge
libarrow 17.0.0 h8756180_8_cpu conda-forge
libarrow-acero 17.0.0 he02047a_8_cpu conda-forge
libarrow-dataset 17.0.0 he02047a_8_cpu conda-forge
libarrow-substrait 17.0.0 hc9a23c6_8_cpu conda-forge
libblas 3.9.0 23_linux64_openblas conda-forge
libbrotlicommon 1.1.0 hd590300_1 conda-forge
libbrotlidec 1.1.0 hd590300_1 conda-forge
libbrotlienc 1.1.0 hd590300_1 conda-forge
libcblas 3.9.0 23_linux64_openblas conda-forge
libcrc32c 1.1.2 h9c3ff4c_0 conda-forge
libcurl 8.9.1 hdb1bdb2_0 conda-forge
libdeflate 1.21 h4bc722e_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libevent 2.1.12 hf998b51_1 conda-forge
libexpat 2.6.2 h59595ed_0 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 12.4.0 h77fa898_0 conda-forge
libgfortran-ng 13.2.0 h69a702a_0 conda-forge
libgfortran5 13.2.0 ha4646dd_0 conda-forge
libgomp 12.4.0 h77fa898_0 conda-forge
libgoogle-cloud 2.28.0 h26d7fe4_0 conda-forge
libgoogle-cloud-storage 2.28.0 ha262f82_0 conda-forge
libgrpc 1.62.2 h15f2491_0 conda-forge
libiconv 1.17 hd590300_2 conda-forge
libjpeg-turbo 3.0.0 hd590300_1 conda-forge
liblapack 3.9.0 23_linux64_openblas conda-forge
libnghttp2 1.58.0 h47da74e_1 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libopenblas 0.3.27 pthreads_hac2b453_1 conda-forge
libparquet 17.0.0 haa1307c_8_cpu conda-forge
libpng 1.6.43 h2797004_0 conda-forge
libprotobuf 4.25.3 h08a7969_0 conda-forge
libre2-11 2023.09.01 h5a48ba9_2 conda-forge
libsqlite 3.46.0 hde9e2c9_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx-ng 12.4.0 hc0a3c3a_0 conda-forge
libthrift 0.20.0 hb90f79a_0 conda-forge
libtiff 4.6.0 h46a8edc_4 conda-forge
libutf8proc 2.8.0 h166bdaf_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libwebp-base 1.4.0 hd590300_0 conda-forge
libxcb 1.16 hd590300_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxml2 2.12.7 he7c6b58_4 conda-forge
libzlib 1.3.1 h4ab18f5_1 conda-forge
locket 1.0.0 pyhd8ed1ab_0 conda-forge
lz4 4.3.3 py312h03f37cb_0 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
markupsafe 2.1.5 py312h98912ed_0 conda-forge
msgpack-python 1.0.8 py312h2492b07_0 conda-forge
multidict 6.0.5 py312h98912ed_0 conda-forge
ncurses 6.5 h59595ed_0 conda-forge
numcodecs 0.13.0 py312h1df14c2_0 conda-forge
numpy 2.1.0 py312h1103770_0 conda-forge
openjpeg 2.5.2 h488ebb8_0 conda-forge
openssl 3.3.1 h4bc722e_2 conda-forge
orc 2.0.2 h669347b_0 conda-forge
packaging 24.1 pyhd8ed1ab_0 conda-forge
pandas 2.2.2 py312h1d6d2e6_1 conda-forge
partd 1.4.2 pyhd8ed1ab_0 conda-forge
pillow 10.4.0 py312h287a98d_0 conda-forge
pip 24.2 pyhd8ed1ab_0 conda-forge
psutil 6.0.0 py312h9a8786e_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pyarrow 17.0.0 py312h9cebb41_1 conda-forge
pyarrow-core 17.0.0 py312h9cafe31_1_cpu conda-forge
pyarrow-hotfix 0.6 pyhd8ed1ab_0 conda-forge
pycparser 2.22 pyhd8ed1ab_0 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.12.5 h2ad013b_0_cpython conda-forge
python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge
python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge
python_abi 3.12 5_cp312 conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.2 py312h41a817b_0 conda-forge
re2 2023.09.01 h7f4b329_2 conda-forge
readline 8.2 h8228510_1 conda-forge
requests 2.32.3 pyhd8ed1ab_0 conda-forge
s2n 1.5.0 h3400bea_0 conda-forge
setuptools 72.2.0 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
snappy 1.2.1 ha2e4443_0 conda-forge
sortedcontainers 2.4.0 pyhd8ed1ab_0 conda-forge
tblib 3.0.0 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
toolz 0.12.1 pyhd8ed1ab_0 conda-forge
tornado 6.4.1 py312h9a8786e_0 conda-forge
tzdata 2024a h0c530f3_0 conda-forge
urllib3 2.2.2 pyhd8ed1ab_1 conda-forge
wheel 0.44.0 pyhd8ed1ab_0 conda-forge
xarray 2024.7.0 pyhd8ed1ab_0 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xyzservices 2024.6.0 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yarl 1.9.4 py312h98912ed_0 conda-forge
zarr 2.18.2 pyhd8ed1ab_0 conda-forge
zict 3.0.0 pyhd8ed1ab_0 conda-forge
zipp 3.20.0 pyhd8ed1ab_0 conda-forge
zstandard 0.23.0 py312h3483029_0 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forge |
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Openssl is 3.3.1 in Python but 3.0.14 in Julia, maybe that plays a role... You can also set |
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If we want to use this for more than benchmarking, we would need to find a more robust setup. |
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Yeah, I'm not sure what we can do beyond very strict instructions though. This may not be a sustainable workflow, but I expect that it could serve pretty well as a semi-experimental backend, and if people need some feature that is in Xarray but not in Julia. |
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Currently it looks like there's a lot of type instability deep in the |
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Note that this code is not runnable on your local machine since it needs a CairoMakie patch... |
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FSSpec is from https://github.com/asinghvi17/FSSpec.jl - if you have fsspec in your global condapkg env, this already works! |
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Continuation of #4 but as a local branch.
Still getting that FileNotFound error from Python specifically if I've loaded the datasets a couple times - curious if you guys can replicate.