python-glmnet
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Published
20 hours ago •
civisanalytics
civisanalytics
Python 3.9 Compatibility
I'd also love a 3.9 wheel!
fwiw i was able to build my own wheel on 3.9 after apt-get install build-essential gfortran
I had no luck building wheels for 3.9 (also I do not have root privileges)/ I run in the following error:
ERROR: Command errored out with exit status 1:
command: /zfs/projects/faculty/ldblatt-mistreatment/blackbox_2.0/assets/blackbox_v2/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-j1g6z3bg/glmnet_2a4b2922fe5a4660b6e4a169242c965e/setup.py'"'"'; __file__='"'"'/tmp/pip-install-j1g6z3bg/glmnet_2a4b2922fe5a4660b6e4a169242c965e/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-djq55rki
cwd: /tmp/pip-install-j1g6z3bg/glmnet_2a4b2922fe5a4660b6e4a169242c965e/
Complete output (343 lines):
/tmp/pip-install-j1g6z3bg/glmnet_2a4b2922fe5a4660b6e4a169242c965e/setup.py:14: DeprecationWarning:
`numpy.distutils` is deprecated since NumPy 1.23.0, as a result
of the deprecation of `distutils` itself. It will be removed for
Python >= 3.12. For older Python versions it will remain present.
It is recommended to use `setuptools < 60.0` for those Python versions.
For more details, see:
https://numpy.org/devdocs/reference/distutils_status_migration.html
from numpy.distutils.core import Extension, setup
<...>
INFO: compile options: '-I/zfs/projects/faculty/ldblatt-mistreatment/blackbox_2.0/assets/blackbox_v2/include -I/home/users/georgyk/miniconda3/include/python3.9 -c'
extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mno-mmx -mavx512cd -mavx512vl -mavx512bw -mavx512dq -Werror'
WARN: CCompilerOpt.dist_test[630] : CCompilerOpt._dist_test_spawn[764] : Command (gcc -pthread -B /home/users/georgyk/miniconda3/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/users/georgyk/miniconda3/include -fPIC -O2 -isystem /home/users/georgyk/miniconda3/include -fPIC -I/zfs/projects/faculty/ldblatt-mistreatment/blackbox_2.0/assets/blackbox_v2/include -I/home/users/georgyk/miniconda3/include/python3.9 -c /zfs/projects/faculty/ldblatt-mistreatment/blackbox_2.0/assets/blackbox_v2/lib/python3.9/site-packages/numpy/distutils/checks/cpu_avx512_clx.c -o /tmp/tmpfppa577g/zfs/projects/faculty/ldblatt-mistreatment/blackbox_2.0/assets/blackbox_v2/lib/python3.9/site-packages/numpy/distutils/checks/cpu_avx512_clx.o -MMD -MF /tmp/tmpfppa577g/zfs/projects/faculty/ldblatt-mistreatment/blackbox_2.0/assets/blackbox_v2/lib/python3.9/site-packages/numpy/distutils/checks/cpu_avx512_clx.o.d -msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mno-mmx -mavx512cd -mavx512vl -mavx512bw -mavx512dq -Werror) failed with exit status 1 output ->
/zfs/projects/faculty/ldblatt-mistreatment/blackbox_2.0/assets/blackbox_v2/lib/python3.9/site-packages/numpy/distutils/checks/cpu_avx512_clx.c: In function ‘main’:
/zfs/projects/faculty/ldblatt-mistreatment/blackbox_2.0/assets/blackbox_v2/lib/python3.9/site-packages/numpy/distutils/checks/cpu_avx512_clx.c:20:17: error: implicit declaration of function ‘_mm512_dpbusd_epi32’; did you mean ‘_mm512_4dpwssd_epi32’? [-Werror=implicit-function-declaration]
a = _mm512_dpbusd_epi32(a, _mm512_setzero_si512(), a);
^~~~~~~~~~~~~~~~~~~
_mm512_4dpwssd_epi32
/zfs/projects/faculty/ldblatt-mistreatment/blackbox_2.0/assets/blackbox_v2/lib/python3.9/site-packages/numpy/distutils/checks/cpu_avx512_clx.c:20:15: error: incompatible types when assigning to type ‘__m512i {aka __vector(8) long long int}’ from type ‘int’
a = _mm512_dpbusd_epi32(a, _mm512_setzero_si512(), a);
^
cc1: all warnings being treated as errors
WARN: CCompilerOpt.feature_test[1563] : testing failed
INFO: CCompilerOpt.feature_test[1547] : testing feature 'AVX512_SKX' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mno-mmx -mavx512cd -mavx512vl -mavx512bw -mavx512dq)
INFO: C compiler: gcc -pthread -B /home/users/georgyk/miniconda3/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/users/georgyk/miniconda3/include -fPIC -O2 -isystem /home/users/georgyk/miniconda3/include -fPIC
INFO: compile options: '-I/zfs/projects/faculty/ldblatt-mistreatment/blackbox_2.0/assets/blackbox_v2/include -I/home/users/georgyk/miniconda3/include/python3.9 -c'
extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mno-mmx -mavx512cd -mavx512vl -mavx512bw -mavx512dq -Werror'
INFO: CCompilerOpt.cc_test_flags[1073] : testing flags (-mavx512er -mavx512pf)
INFO: C compiler: gcc -pthread -B /home/users/georgyk/miniconda3/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/users/georgyk/miniconda3/include -fPIC -O2 -isystem /home/users/georgyk/miniconda3/include -fPIC
INFO: compile options: '-I/zfs/projects/faculty/ldblatt-mistreatment/blackbox_2.0/assets/blackbox_v2/include -I/home/users/georgyk/miniconda3/include/python3.9 -c'
extra options: '-mavx512er -mavx512pf'
INFO: CCompilerOpt.feature_test[1547] : testing feature 'AVX512_KNL' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mno-mmx -mavx512cd -mavx512er -mavx512pf)
INFO: C compiler: gcc -pthread -B /home/users/georgyk/miniconda3/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/users/georgyk/miniconda3/include -fPIC -O2 -isystem /home/users/georgyk/miniconda3/include -fPIC
INFO: compile options: '-I/zfs/projects/faculty/ldblatt-mistreatment/blackbox_2.0/assets/blackbox_v2/include -I/home/users/georgyk/miniconda3/include/python3.9 -c'
extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mno-mmx -mavx512cd -mavx512er -mavx512pf -Werror'
INFO: CCompilerOpt.cc_test_flags[1073] : testing flags (-mavx512ifma -mavx512vbmi)
INFO: C compiler: gcc -pthread -B /home/users/georgyk/miniconda3/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/users/georgyk/miniconda3/include -fPIC -O2 -isystem /home/users/georgyk/miniconda3/include -fPIC
INFO: compile options: '-I/zfs/projects/faculty/ldblatt-mistreatment/blackbox_2.0/assets/blackbox_v2/include -I/home/users/georgyk/miniconda3/include/python3.9 -c'
extra options: '-mavx512ifma -mavx512vbmi'
INFO: CCompilerOpt.feature_test[1547] : testing feature 'AVX512_CNL' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mno-mmx -mavx512cd -mavx512vl -mavx512bw -mavx512dq -mavx512ifma -mavx512vbmi)
INFO: C compiler: gcc -pthread -B /home/users/georgyk/miniconda3/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/users/georgyk/miniconda3/include -fPIC -O2 -isystem /home/users/georgyk/miniconda3/include -fPIC
INFO: compile options: '-I/zfs/projects/faculty/ldblatt-mistreatment/blackbox_2.0/assets/blackbox_v2/include -I/home/users/georgyk/miniconda3/include/python3.9 -c'
extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mno-mmx -mavx512cd -mavx512vl -mavx512bw -mavx512dq -mavx512ifma -mavx512vbmi -Werror'
INFO: CCompilerOpt.cc_test_flags[1073] : testing flags (-mavx5124fmaps -mavx5124vnniw -mavx512vpopcntdq)
INFO: C compiler: gcc -pthread -B /home/users/georgyk/miniconda3/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/users/georgyk/miniconda3/include -fPIC -O2 -isystem /home/users/georgyk/miniconda3/include -fPIC
INFO: compile options: '-I/zfs/projects/faculty/ldblatt-mistreatment/blackbox_2.0/assets/blackbox_v2/include -I/home/users/georgyk/miniconda3/include/python3.9 -c'
extra options: '-mavx5124fmaps -mavx5124vnniw -mavx512vpopcntdq'
INFO: CCompilerOpt.feature_test[1547] : testing feature 'AVX512_KNM' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mno-mmx -mavx512cd -mavx512er -mavx512pf -mavx5124fmaps -mavx5124vnniw -mavx512vpopcntdq)
INFO: C compiler: gcc -pthread -B /home/users/georgyk/miniconda3/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/users/georgyk/miniconda3/include -fPIC -O2 -isystem /home/users/georgyk/miniconda3/include -fPIC
INFO: compile options: '-I/zfs/projects/faculty/ldblatt-mistreatment/blackbox_2.0/assets/blackbox_v2/include -I/home/users/georgyk/miniconda3/include/python3.9 -c'
extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mno-mmx -mavx512cd -mavx512er -mavx512pf -mavx5124fmaps -mavx5124vnniw -mavx512vpopcntdq -Werror'
INFO: CCompilerOpt.__init__[1803] : skip features (SSE SSE3 SSE2) since its part of baseline
INFO: CCompilerOpt.__init__[1807] : initialize targets groups
INFO: CCompilerOpt.__init__[1809] : parse target group simd_test
INFO: CCompilerOpt._parse_target_tokens[2020] : skip targets (VXE XOP VSX3 VSX4 ASIMD NEON VXE2 VSX2 FMA4 VSX VX) not part of baseline or dispatch-able features
INFO: CCompilerOpt._parse_policy_not_keepbase[2132] : skip baseline features (SSE2)
INFO: CCompilerOpt.generate_dispatch_header[2353] : generate CPU dispatch header: (build/src.linux-x86_64-3.9/numpy/distutils/include/npy_cpu_dispatch_config.h)
INFO: CCompilerOpt.feature_extra_checks[1627] : Testing extra checks for feature 'AVX512F' (AVX512F_REDUCE)
INFO: C compiler: gcc -pthread -B /home/users/georgyk/miniconda3/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/users/georgyk/miniconda3/include -fPIC -O2 -isystem /home/users/georgyk/miniconda3/include -fPIC
INFO: compile options: '-I/zfs/projects/faculty/ldblatt-mistreatment/blackbox_2.0/assets/blackbox_v2/include -I/home/users/georgyk/miniconda3/include/python3.9 -c'
extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mno-mmx -Werror'
INFO: CCompilerOpt.feature_extra_checks[1627] : Testing extra checks for feature 'AVX512_SKX' (AVX512BW_MASK AVX512DQ_MASK)
INFO: C compiler: gcc -pthread -B /home/users/georgyk/miniconda3/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/users/georgyk/miniconda3/include -fPIC -O2 -isystem /home/users/georgyk/miniconda3/include -fPIC
INFO: compile options: '-I/zfs/projects/faculty/ldblatt-mistreatment/blackbox_2.0/assets/blackbox_v2/include -I/home/users/georgyk/miniconda3/include/python3.9 -c'
extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mno-mmx -mavx512cd -mavx512vl -mavx512bw -mavx512dq -Werror'
INFO: C compiler: gcc -pthread -B /home/users/georgyk/miniconda3/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/users/georgyk/miniconda3/include -fPIC -O2 -isystem /home/users/georgyk/miniconda3/include -fPIC
INFO: compile options: '-I/zfs/projects/faculty/ldblatt-mistreatment/blackbox_2.0/assets/blackbox_v2/include -I/home/users/georgyk/miniconda3/include/python3.9 -c'
extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mno-mmx -mavx512cd -mavx512vl -mavx512bw -mavx512dq -Werror'
INFO: get_default_fcompiler: matching types: '['arm', 'gnu95', 'intel', 'lahey', 'pg', 'nv', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor', 'fujitsu']'
INFO: customize ArmFlangCompiler
WARN: Could not locate executable armflang
INFO: customize Gnu95FCompiler
WARN: Could not locate executable gfortran
WARN: Could not locate executable f95
INFO: customize IntelFCompiler
WARN: Could not locate executable ifort
WARN: Could not locate executable ifc
INFO: customize LaheyFCompiler
WARN: Could not locate executable lf95
INFO: customize PGroupFCompiler
WARN: Could not locate executable pgfortran
INFO: customize NVHPCFCompiler
WARN: Could not locate executable nvfortran
INFO: customize AbsoftFCompiler
WARN: Could not locate executable f90
WARN: Could not locate executable f77
INFO: customize NAGFCompiler
INFO: customize VastFCompiler
INFO: customize CompaqFCompiler
WARN: Could not locate executable fort
INFO: customize IntelItaniumFCompiler
WARN: Could not locate executable efort
WARN: Could not locate executable efc
INFO: customize IntelEM64TFCompiler
INFO: customize GnuFCompiler
WARN: Could not locate executable g77
INFO: customize G95FCompiler
WARN: Could not locate executable g95
INFO: customize PathScaleFCompiler
WARN: Could not locate executable pathf95
INFO: customize NAGFORCompiler
WARN: Could not locate executable nagfor
INFO: customize FujitsuFCompiler
WARN: Could not locate executable frt
WARN: don't know how to compile Fortran code on platform 'posix'
warning: build_ext: f77_compiler=None is not available.
INFO: building '_glmnet' extension
error: extension '_glmnet' has Fortran sources but no Fortran compiler found
INFO:
########### EXT COMPILER OPTIMIZATION ###########
INFO: Platform :
Architecture: x64
Compiler : gcc
CPU baseline :
Requested : 'min'
Enabled : SSE SSE2 SSE3
Flags : -msse -msse2 -msse3
Extra checks: none
CPU dispatch :
Requested : 'max -xop -fma4'
Enabled : SSSE3 SSE41 POPCNT SSE42 AVX F16C FMA3 AVX2 AVX512F AVX512CD AVX512_KNL AVX512_KNM AVX512_SKX AVX512_CNL
Generated : none
INFO: CCompilerOpt.cache_flush[857] : write cache to path -> /tmp/pip-install-j1g6z3bg/glmnet_2a4b2922fe5a4660b6e4a169242c965e/build/temp.linux-x86_64-3.9/ccompiler_opt_cache_ext.py
----------------------------------------
ERROR: Command errored out with exit status 1: /zfs/projects/faculty/ldblatt-mistreatment/blackbox_2.0/assets/blackbox_v2/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-j1g6z3bg/glmnet_2a4b2922fe5a4660b6e4a169242c965e/setup.py'"'"'; __file__='"'"'/tmp/pip-install-j1g6z3bg/glmnet_2a4b2922fe5a4660b6e4a169242c965e/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-ismq92dd/install-record.txt --single-version-externally-managed --compile --install-headers /zfs/projects/faculty/ldblatt-mistreatment/blackbox_2.0/assets/blackbox_v2/include/site/python3.9/glmnet Check the logs for full command output.
@jacksonlee-civis Would you let us know if you are able to release a new version with updated dependency and prolly support Python 3.8, 3.9, ... I am not sure if lower versions of Python is necessary
I'm not on this project anymore. To my knowledge, this project isn't currently staffed for either maintenance or feature work. Since this codebase lives under the Civis corporate umbrella, I'm afraid there's not much else I could say or do.
@jacksonlee-civis Thanks; how can I tag someone from Civis to get more info?