Installation error on pyfnntw==0.4.0 #5
Comments
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I will switch it back to >3.7. I believe I also accidentally left out a feature... I will fix these |
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go ahead and try again. If it doesn't work... try disabling |
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4.1 is out with >3.7 and no |
I have successfully installed pytnntw==0.4.1 and everything works well. My test script is as below: import numpy as np
from time import time
from scipy.spatial import KDTree
import pyfnntw
N = 10**7
k = 12
pos = np.random.random((N, 3))
start = time()
kdt = KDTree(pos, 32, boxsize=[1.0, 1.0, 1.0])
print(f"Scipy build tree time: {time()-start} s.")
start1 = time()
dis, indices = kdt.query(pos, k, workers=-1)
end = time()
print(f"Scipy query time: {end-start1} s.")
print(f"Scipy total time: {end-start} s.")
print(indices[0])
start = time()
kdt = pyfnntw.Treef64(
pos, leafsize=32, par_split_level=4, boxsize=np.array([1.0, 1.0, 1.0])
)
print(f"Pyfnntw build tree time: {time()-start} s.")
start1 = time()
dis, indices = kdt.query(pos, k)
end = time()
print(f"Pyfnntw query time: {end-start1} s.")
print(f"Pyfnntw total time: {end-start} s.")
print(indices[0])In my computer, Intel Xeon E5-2630 @2.2GHz (20 cores), the output is as below: Scipy build tree time: 17.172202825546265 s.
Scipy query time: 10.185096025466919 s.
Scipy total time: 27.357298851013184 s.
[ 0 635729 4951542 2569924 7108333 5208854 3171473 9350673 3314987
1842148 5125748 2983723]
Parallelism activated: 40 threads
Pyfnntw build tree time: 1.5725889205932617 s.
Pyfnntw query time: 10.762544393539429 s.
Pyfnntw total time: 12.336133241653442 s.
[ 0 635729 4951542 2569924 7108333 5208854 3171473 9350673 3314987
1842148 5125748 2983723]The pyfnntw shows excellent performance on building KDtree aginst that in Scipy. Thanks for your significant work, and I have add pyfnntw to my library to accelerate the NearestNeighbor Search. |
I install pyfnntw by:
I use Conda environment and the PYTHON version is 3.11.0 (as required in pyproject.toml) ans OS is windows10.
The output is as below:
Collecting pyfnntw==0.4.0 Downloading pyfnntw-0.4.0.tar.gz (71 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 71.1/71.1 kB 647.0 kB/s eta 0:00:00 Installing build dependencies ... done Getting requirements to build wheel ... done Preparing metadata (pyproject.toml) ... done Building wheels for collected packages: pyfnntw Building wheel for pyfnntw (pyproject.toml) ... error error: subprocess-exited-with-error × Building wheel for pyfnntw (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [84 lines of output] Running `maturin pep517 build-wheel -i D:\Anaconda\envs\py311\python.exe --compatibility off` 馃敆 Found pyo3 bindings 馃悕 Found CPython 3.11 at D:\Anaconda\envs\py311\python.exe Compiling autocfg v1.1.0 Compiling proc-macro2 v1.0.51 Compiling quote v1.0.21 Compiling unicode-ident v1.0.3 Compiling syn v1.0.109 Compiling thiserror v1.0.39 Compiling cfg-if v1.0.0 Compiling target-lexicon v0.12.4 Compiling scopeguard v1.1.0 Compiling crossbeam-utils v0.8.15 Compiling version_check v0.9.4 Compiling once_cell v1.13.1 Compiling ucd-trie v0.1.5 Compiling windows_x86_64_msvc v0.36.1 Compiling rayon-core v1.11.0 Compiling num_cpus v1.15.0 Compiling libc v0.2.132 Compiling parking_lot_core v0.9.3 Compiling const_fn v0.4.9 Compiling tcmalloc-sys v0.3.0 Compiling either v1.8.1 Compiling arrayvec v0.4.12 Compiling smallvec v1.9.0 Compiling Inflector v0.11.4 Compiling rawpointer v0.2.1 Compiling nodrop v0.1.14 Compiling itoa v0.4.8 Compiling unindent v0.1.10 Compiling aliasable v0.1.3 Compiling indoc v1.0.7 Compiling permutation v0.4.1 Compiling sync-unsafe-cell v0.1.0 Compiling matrixmultiply v0.3.2 Compiling memoffset v0.8.0 Compiling num-traits v0.2.15 Compiling crossbeam-epoch v0.9.14 Compiling lock_api v0.4.7 Compiling num-integer v0.1.45 Compiling proc-macro-error-attr v1.0.4 Compiling proc-macro-error v1.0.4 Compiling windows-sys v0.36.1 Compiling tcmalloc v0.3.0 Compiling num-format v0.4.0 Compiling pyo3-build-config v0.16.5 Compiling crossbeam-channel v0.5.7 Compiling crossbeam-deque v0.8.3 Compiling num-complex v0.4.3 Compiling ordered-float v3.0.0 Compiling rayon v1.7.0 Compiling parking_lot v0.12.1 Compiling pyo3-ffi v0.16.5 Compiling pyo3 v0.16.5 Compiling ndarray v0.15.6 Compiling pyo3-macros-backend v0.16.5 Compiling thiserror-impl v1.0.39 Compiling ouroboros_macro v0.15.6 Compiling concat-idents v1.1.4 Compiling pest v2.5.6 Compiling ouroboros v0.15.6 Compiling pyo3-macros v0.16.5 Compiling semver-parser v0.10.2 Compiling semver v0.11.0 Compiling rustc_version v0.3.3 Compiling likely_stable v0.1.2 Compiling fnntw v0.4.0 (C:\Users\Administrator\AppData\Local\Temp\pip-install-uv8o5oyw\pyfnntw_89a06f849e7240068ea92b3e9ceaee94\local_dependencies\fnntw) Compiling numpy v0.16.2 Compiling pyfnntw v0.4.0 (C:\Users\Administrator\AppData\Local\Temp\pip-install-uv8o5oyw\pyfnntw_89a06f849e7240068ea92b3e9ceaee94) error: could not compile `pyfnntw` due to 2 previous errors 馃挜 maturin failed Caused by: Failed to build a native library through cargo Caused by: Cargo build finished with "exit code: 101": `"cargo" "rustc" "--release" "--manifest-path" "C:\\Users\\Administrator\\AppData\\Local\\Temp\\pip-install-uv8o5oyw\\pyfnntw_89a06f849e7240068ea92b3e9ceaee94\\Cargo.toml" "--message-format" "json" "--lib"` error: linking with `link.exe` failed: exit code: 1181 | = note: "C:\\Program Files (x86)\\Microsoft Visual Studio\\2022\\BuildTools\\VC\\Tools\\MSVC\\14.33.31629\\bin\\HostX64\\x64\\link.exe" "/DEF:C:\\Users\\ADMINI~1\\AppData\\Local\\Temp\\rustc25OP3V\\lib.def" "/NOLOGO" "C:\\Users\\ADMINI~1\\AppData\\Local\\Temp\\rustc25OP3V\\symbols.o" "C:\\Users\\Administrator\\AppData\\Local\\Temp\\pip-install-uv8o5oyw\\pyfnntw_89a06f849e7240068ea92b3e9ceaee94\\target\\release\\deps\\pyfnntw.pyfnntw.5efcba88-cgu.0.rcgu.o" "/LIBPATH:C:\\Users\\Administrator\\AppData\\Local\\Temp\\pip-install-uv8o5oyw\\pyfnntw_89a06f849e7240068ea92b3e9ceaee94\\target\\release\\deps" "/LIBPATH:C:\\Users\\Administrator\\.cargo\\registry\\src\\github.com-1ecc6299db9ec823\\windows_x86_64_msvc-0.36.1\\lib" "/LIBPATH:D:\\Anaconda\\envs\\py311\\libs" "/LIBPATH:C:\\Users\\Administrator\\.rustup\\toolchains\\stable-x86_64-pc-windows-msvc\\lib\\rustlib\\x86_64-pc-windows-msvc\\lib" "C:\\Users\\Administrator\\.rustup\\toolchains\\stable-x86_64-pc-windows-msvc\\lib\\rustlib\\x86_64-pc-windows-msvc\\lib\\libcompiler_builtins-3f0eed38bcc54ffc.rlib" "windows.lib" "python311.lib" "legacy_stdio_definitions.lib" "tcmalloc.lib" "kernel32.lib" "advapi32.lib" "userenv.lib" "kernel32.lib" "ws2_32.lib" "bcrypt.lib" "msvcrt.lib" "legacy_stdio_definitions.lib" "/NXCOMPAT" "/LIBPATH:C:\\Users\\Administrator\\.rustup\\toolchains\\stable-x86_64-pc-windows-msvc\\lib\\rustlib\\x86_64-pc-windows-msvc\\lib" "/OUT:C:\\Users\\Administrator\\AppData\\Local\\Temp\\pip-install-uv8o5oyw\\pyfnntw_89a06f849e7240068ea92b3e9ceaee94\\target\\release\\deps\\pyfnntw.dll" "/OPT:REF,ICF" "/DLL" "/IMPLIB:C:\\Users\\Administrator\\AppData\\Local\\Temp\\pip-install-uv8o5oyw\\pyfnntw_89a06f849e7240068ea92b3e9ceaee94\\target\\release\\deps\\pyfnntw.dll.lib" "/DEBUG" "/NATVIS:C:\\Users\\Administrator\\.rustup\\toolchains\\stable-x86_64-pc-windows-msvc\\lib\\rustlib\\etc\\intrinsic.natvis" "/NATVIS:C:\\Users\\Administrator\\.rustup\\toolchains\\stable-x86_64-pc-windows-msvc\\lib\\rustlib\\etc\\liballoc.natvis" "/NATVIS:C:\\Users\\Administrator\\.rustup\\toolchains\\stable-x86_64-pc-windows-msvc\\lib\\rustlib\\etc\\libcore.natvis" "/NATVIS:C:\\Users\\Administrator\\.rustup\\toolchains\\stable-x86_64-pc-windows-msvc\\lib\\rustlib\\etc\\libstd.natvis" = note: Non-UTF-8 output: LINK : fatal error LNK1181: \xce\xde\xb7\xa8\xb4\xf2\xbf\xaa\xca\xe4\xc8\xeb\xce\xc4\xbc\xfe\xa1\xb0tcmalloc.lib\xa1\xb1\r\n error: aborting due to previous error Error: command ['maturin', 'pep517', 'build-wheel', '-i', 'D:\\Anaconda\\envs\\py311\\python.exe', '--compatibility', 'off'] returned non-zero exit status 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyfnntw Failed to build pyfnntw ERROR: Could not build wheels for pyfnntw, which is required to install pyproject.toml-based projects NativeCommandExitException: Program "pip.exe" ended with non-zero exit code: 1.In my WSL, the error seems to be related to tcmalloc-sys v0.3.0.
Can you tell me how to solve it?
BTW., why the PYTHON version is required larger than 3.11.0? It would be helpful to change it to >=3.7.0.
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