py-numcodecs@0.11.0 fails build on ARM64 and PPC64: gcc: error: unrecognized command line option '-mno-avx2' #40740
Description
Steps to reproduce the issue
py-numcodecs@0.11.0 fails build using:
spack@develop(81172f9 fromThu Oct 26 21:11:43 2023 +0200)- Python 3.11.6
- fails on:
- GGC 9.4.0, PPC64, Ubuntu 20.04
- GCC 11.4.0, ARM64, Ubuntu 20.04
This error is affecting our ability to install libpressio as part of E4S.
It seems like the error is related to changes introduced by 9889a0c
Spack environment: spack.yaml.txt
Concretization
- py-numcodecs@0.11.0%gcc@9.4.0~msgpack build_system=python_pip arch=linux-ubuntu20.04-ppc64le [+] ^py-cython@0.29.36%gcc@9.4.0 build_system=python_pip patches=c4369ad arch=linux-ubuntu20.04-ppc64le [+] ^py-entrypoints@0.4%gcc@9.4.0 build_system=python_pip arch=linux-ubuntu20.04-ppc64le [+] ^py-flit-core@3.9.0%gcc@9.4.0 build_system=python_pip arch=linux-ubuntu20.04-ppc64le [+] ^py-numpy@1.25.2%gcc@9.4.0+blas+lapack build_system=python_pip patches=873745d arch=linux-ubuntu20.04-ppc64le [+] ^openblas@0.3.24%gcc@9.4.0~bignuma~consistent_fpcsr+fortran~ilp64+locking+pic+shared build_system=makefile symbol_suffix=none threads=openmp arch=linux-ubuntu20.04-ppc64le [+] ^gmake@4.4.1%gcc@9.4.0~guile build_system=generic arch=linux-ubuntu20.04-ppc64le [+] ^perl@5.38.0%gcc@9.4.0+cpanm+opcode+open+shared+threads build_system=generic patches=714e4d1 arch=linux-ubuntu20.04-ppc64le [+] ^berkeley-db@18.1.40%gcc@9.4.0+cxx~docs+stl build_system=autotools patches=26090f4,b231fcc arch=linux-ubuntu20.04-ppc64le [+] ^py-setuptools@63.4.3%gcc@9.4.0 build_system=python_pip arch=linux-ubuntu20.04-ppc64le [+] ^py-pip@23.1.2%gcc@9.4.0 build_system=generic arch=linux-ubuntu20.04-ppc64le [+] ^py-py-cpuinfo@9.0.0%gcc@9.4.0 build_system=python_pip arch=linux-ubuntu20.04-ppc64le [+] ^py-setuptools@68.0.0%gcc@9.4.0 build_system=python_pip arch=linux-ubuntu20.04-ppc64le [+] ^py-setuptools-scm@7.1.0%gcc@9.4.0+toml build_system=python_pip arch=linux-ubuntu20.04-ppc64le [+] ^git@2.42.0%gcc@9.4.0+man+nls+perl+subtree~svn~tcltk build_system=autotools arch=linux-ubuntu20.04-ppc64le [+] ^autoconf@2.69%gcc@9.4.0 build_system=autotools patches=35c4492,7793209,a49dd5b arch=linux-ubuntu20.04-ppc64le [+] ^automake@1.16.5%gcc@9.4.0 build_system=autotools arch=linux-ubuntu20.04-ppc64le [+] ^curl@8.4.0%gcc@9.4.0~gssapi~ldap~libidn2~librtmp~libssh~libssh2+nghttp2 build_system=autotools libs=shared,static tls=openssl arch=linux-ubuntu20.04-ppc64le [+] ^nghttp2@1.57.0%gcc@9.4.0 build_system=autotools arch=linux-ubuntu20.04-ppc64le [+] ^gnuconfig@2022-09-17%gcc@9.4.0 build_system=generic arch=linux-ubuntu20.04-ppc64le [+] ^libiconv@1.17%gcc@9.4.0 build_system=autotools libs=shared,static arch=linux-ubuntu20.04-ppc64le [+] ^libidn2@2.3.4%gcc@9.4.0 build_system=autotools arch=linux-ubuntu20.04-ppc64le [+] ^libunistring@1.1%gcc@9.4.0 build_system=autotools arch=linux-ubuntu20.04-ppc64le [+] ^libtool@2.4.7%gcc@9.4.0 build_system=autotools arch=linux-ubuntu20.04-ppc64le [+] ^m4@1.4.19%gcc@9.4.0+sigsegv build_system=autotools patches=9dc5fbd,bfdffa7 arch=linux-ubuntu20.04-ppc64le [+] ^libsigsegv@2.14%gcc@9.4.0 build_system=autotools arch=linux-ubuntu20.04-ppc64le [+] ^openssh@9.5p1%gcc@9.4.0+gssapi build_system=autotools arch=linux-ubuntu20.04-ppc64le [+] ^krb5@1.20.1%gcc@9.4.0+shared build_system=autotools arch=linux-ubuntu20.04-ppc64le [+] ^bison@3.8.2%gcc@9.4.0 build_system=autotools arch=linux-ubuntu20.04-ppc64le [+] ^findutils@4.9.0%gcc@9.4.0 build_system=autotools patches=440b954 arch=linux-ubuntu20.04-ppc64le [+] ^libedit@3.1-20210216%gcc@9.4.0 build_system=autotools arch=linux-ubuntu20.04-ppc64le [+] ^pcre2@10.42%gcc@9.4.0~jit+multibyte build_system=autotools arch=linux-ubuntu20.04-ppc64le [+] ^py-packaging@23.1%gcc@9.4.0 build_system=python_pip arch=linux-ubuntu20.04-ppc64le [+] ^py-tomli@2.0.1%gcc@9.4.0 build_system=python_pip arch=linux-ubuntu20.04-ppc64le [+] ^py-typing-extensions@4.8.0%gcc@9.4.0 build_system=python_pip arch=linux-ubuntu20.04-ppc64le [+] ^py-wheel@0.41.2%gcc@9.4.0 build_system=generic arch=linux-ubuntu20.04-ppc64le [+] ^python@3.11.6%gcc@9.4.0+bz2+crypt+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tkinter+uuid+zlib build_system=generic patches=13fa8bf,b0615b2,ebdca64,f2fd060 arch=linux-ubuntu20.04-ppc64le [+] ^bzip2@1.0.8%gcc@9.4.0~debug~pic+shared build_system=generic arch=linux-ubuntu20.04-ppc64le [+] ^diffutils@3.9%gcc@9.4.0 build_system=autotools arch=linux-ubuntu20.04-ppc64le [+] ^expat@2.5.0%gcc@9.4.0+libbsd build_system=autotools arch=linux-ubuntu20.04-ppc64le [+] ^libbsd@0.11.7%gcc@9.4.0 build_system=autotools arch=linux-ubuntu20.04-ppc64le [+] ^libmd@1.0.4%gcc@9.4.0 build_system=autotools arch=linux-ubuntu20.04-ppc64le [+] ^gdbm@1.23%gcc@9.4.0 build_system=autotools arch=linux-ubuntu20.04-ppc64le [+] ^gettext@0.22.3%gcc@9.4.0+bzip2+curses+git~libunistring+libxml2+pic+shared+tar+xz build_system=autotools arch=linux-ubuntu20.04-ppc64le [+] ^libxml2@2.10.3%gcc@9.4.0+pic~python+shared build_system=autotools arch=linux-ubuntu20.04-ppc64le [+] ^tar@1.34%gcc@9.4.0 build_system=autotools zip=pigz arch=linux-ubuntu20.04-ppc64le [+] ^pigz@2.7%gcc@9.4.0 build_system=makefile arch=linux-ubuntu20.04-ppc64le [+] ^zstd@1.5.5%gcc@9.4.0+programs build_system=makefile compression=none libs=shared,static arch=linux-ubuntu20.04-ppc64le [+] ^libffi@3.4.4%gcc@9.4.0 build_system=autotools arch=linux-ubuntu20.04-ppc64le [+] ^libxcrypt@4.4.35%gcc@9.4.0~obsolete_api build_system=autotools patches=4885da3 arch=linux-ubuntu20.04-ppc64le [+] ^ncurses@6.3%gcc@9.4.0~symlinks+termlib abi=none build_system=autotools arch=linux-ubuntu20.04-ppc64le [+] ^openssl@3.1.3%gcc@9.4.0~docs+shared build_system=generic certs=mozilla arch=linux-ubuntu20.04-ppc64le [+] ^ca-certificates-mozilla@2023-05-30%gcc@9.4.0 build_system=generic arch=linux-ubuntu20.04-ppc64le [+] ^pkgconf@1.9.5%gcc@9.4.0 build_system=autotools arch=linux-ubuntu20.04-ppc64le [+] ^readline@8.2%gcc@9.4.0 build_system=autotools patches=bbf97f1 arch=linux-ubuntu20.04-ppc64le [+] ^sqlite@3.43.2%gcc@9.4.0+column_metadata+dynamic_extensions+fts~functions+rtree build_system=autotools arch=linux-ubuntu20.04-ppc64le [+] ^util-linux-uuid@2.38.1%gcc@9.4.0 build_system=autotools arch=linux-ubuntu20.04-ppc64le [+] ^xz@5.4.1%gcc@9.4.0+pic build_system=autotools libs=shared,static arch=linux-ubuntu20.04-ppc64le [+] ^zlib-ng@2.1.4%gcc@9.4.0+compat+opt build_system=autotools arch=linux-ubuntu20.04-ppc64le
Error reproduced below using spack.yaml from above and Docker container image:
ecpe4s/ubuntu20.04-runner-ppc64-gcc-11.4-mpi-base:2023.08.20
$> spack -e . install /4ssb5a
...
==> Installing py-numcodecs-0.11.0-4ssb5a5eicmjwvx55omsugtaio2xjzkk [46/46]
==> No binary for py-numcodecs-0.11.0-4ssb5a5eicmjwvx55omsugtaio2xjzkk found: installing from source
==> Using cached archive: /spack/var/spack/cache/_source-cache/archive/6c/6c058b321de84a1729299b0eae4d652b2e48ea1ca7f9df0da65cb13470e635eb.tar.gz
==> No patches needed for py-numcodecs
==> py-numcodecs: Executing phase: 'install'
==> Error: ProcessError: Command exited with status 1:
6 errors found in build log:
11 Created temporary directory: /tmp/pip-ephem-wheel-cache-xs9jg0b2
12 Processing /tmp/root/spack-stage/spack-stage-py-numcodecs-0.11.0-4ssb5a5eicmjwvx55omsugtaio2xjzkk/spack-src
13 Added file:///tmp/root/spack-stage/spack-stage-py-numcodecs-0.11.0-4ssb5a5eicmjwvx55omsugtaio2xjzkk/spack-src to build tracker '/tmp/pip-build-tracker-wx3gg3ei'
14 Created temporary directory: /tmp/pip-modern-metadata-irmlmfqf
15 Preparing metadata (pyproject.toml): started
16 Running command Preparing metadata (pyproject.toml)
>> 17 /spack/opt/spack/linux-ubuntu20.04-ppc64le/gcc-9.4.0/py-setuptools-63.4.3-mbykritsmmhgvvf2ver6yb2faqxsdnio/lib/python3.11/site-packages/setuptools/config/pyprojecttoml.py:
108: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*.
18 warnings.warn(msg, _BetaConfiguration)
19 [numcodecs] setting up Blosc extension
20 [numcodecs] compiling Blosc extension without SSE2 support
21 [numcodecs] compiling Blosc extension without AVX2 support
22 [numcodecs] setting up Zstandard extension
23 [numcodecs] setting up LZ4 extension
24 [numcodecs] setting up compat extension
25 [numcodecs] setting up shuffle extension
26 [numcodecs] setting up vlen extension
27 running dist_info
28 creating /tmp/pip-modern-metadata-irmlmfqf/numcodecs.egg-info
29 writing /tmp/pip-modern-metadata-irmlmfqf/numcodecs.egg-info/PKG-INFO
>> 30 /spack/opt/spack/linux-ubuntu20.04-ppc64le/gcc-9.4.0/py-setuptools-63.4.3-mbykritsmmhgvvf2ver6yb2faqxsdnio/lib/python3.11/site-packages/setuptools/dist.py:160: UserWarning
: newlines not allowed and will break in the future
31 warnings.warn("newlines not allowed and will break in the future")
32 writing dependency_links to /tmp/pip-modern-metadata-irmlmfqf/numcodecs.egg-info/dependency_links.txt
33 writing requirements to /tmp/pip-modern-metadata-irmlmfqf/numcodecs.egg-info/requires.txt
34 writing top-level names to /tmp/pip-modern-metadata-irmlmfqf/numcodecs.egg-info/top_level.txt
35 writing manifest file '/tmp/pip-modern-metadata-irmlmfqf/numcodecs.egg-info/SOURCES.txt'
36 [1/6] Cythonizing numcodecs/_shuffle.pyx
...
51 Created temporary directory: /tmp/pip-unpack-16ahaysr
52 Building wheels for collected packages: numcodecs
53 Created temporary directory: /tmp/pip-wheel-afj84kd3
54 Destination directory: /tmp/pip-wheel-afj84kd3
55 Building wheel for numcodecs (pyproject.toml): started
56 Running command Building wheel for numcodecs (pyproject.toml)
>> 57 /spack/opt/spack/linux-ubuntu20.04-ppc64le/gcc-9.4.0/py-setuptools-63.4.3-mbykritsmmhgvvf2ver6yb2faqxsdnio/lib/python3.11/site-packages/setuptools/config/pyprojecttoml.py:
108: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*.
58 warnings.warn(msg, _BetaConfiguration)
59 [numcodecs] setting up Blosc extension
60 [numcodecs] compiling Blosc extension without SSE2 support
61 [numcodecs] compiling Blosc extension without AVX2 support
62 [numcodecs] setting up Zstandard extension
63 [numcodecs] setting up LZ4 extension
...
124 copying ./numcodecs/tests/test_blosc.py -> build/lib.linux-ppc64le-cpython-311/numcodecs/tests
125 copying ./numcodecs/tests/test_lz4.py -> build/lib.linux-ppc64le-cpython-311/numcodecs/tests
126 copying ./numcodecs/tests/test_vlen_utf8.py -> build/lib.linux-ppc64le-cpython-311/numcodecs/tests
127 copying ./numcodecs/tests/test_entrypoints.py -> build/lib.linux-ppc64le-cpython-311/numcodecs/tests
128 running egg_info
129 writing numcodecs.egg-info/PKG-INFO
>> 130 /spack/opt/spack/linux-ubuntu20.04-ppc64le/gcc-9.4.0/py-setuptools-63.4.3-mbykritsmmhgvvf2ver6yb2faqxsdnio/lib/python3.11/site-packages/setuptools/dist.py:160: UserWarning
: newlines not allowed and will break in the future
131 warnings.warn("newlines not allowed and will break in the future")
132 writing dependency_links to numcodecs.egg-info/dependency_links.txt
133 writing requirements to numcodecs.egg-info/requires.txt
134 writing top-level names to numcodecs.egg-info/top_level.txt
135 [1/6] Cythonizing numcodecs/_shuffle.pyx
136 [2/6] Cythonizing numcodecs/blosc.pyx
...
155 creating build/temp.linux-ppc64le-cpython-311/c-blosc/internal-complibs/zstd-1.4.8/common
156 creating build/temp.linux-ppc64le-cpython-311/c-blosc/internal-complibs/zstd-1.4.8/compress
157 creating build/temp.linux-ppc64le-cpython-311/c-blosc/internal-complibs/zstd-1.4.8/decompress
158 creating build/temp.linux-ppc64le-cpython-311/c-blosc/internal-complibs/zstd-1.4.8/dictBuilder
159 creating build/temp.linux-ppc64le-cpython-311/numcodecs
160 /spack/lib/spack/env/gcc/gcc -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -fPIC -DHAVE_LZ4=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ic-blosc/blosc -Ic-blosc/internal-complibs/zlib-1.2.8 -I
c-blosc/internal-complibs/zstd-1.4.8 -Ic-blosc/internal-complibs/lz4-1.9.3 -Ic-blosc/internal-complibs/zstd-1.4.8/deprecated -Ic-blosc/internal-complibs/zstd-1.4.8/compres
s -Ic-blosc/internal-complibs/zstd-1.4.8/dll -Ic-blosc/internal-complibs/zstd-1.4.8/decompress -Ic-blosc/internal-complibs/zstd-1.4.8/common -Ic-blosc/internal-complibs/zs
td-1.4.8/legacy -Ic-blosc/internal-complibs/zstd-1.4.8/dictBuilder -Ic-blosc/internal-complibs/zstd-1.4.8/dll/example -I/spack/opt/spack/linux-ubuntu20.04-ppc64le/gcc-9.4.
0/python-3.11.6-ghm4v2sxvxv7cvblmyvwjklodrypfky5/include/python3.11 -c c-blosc/blosc/bitshuffle-generic.c -o build/temp.linux-ppc64le-cpython-311/c-blosc/blosc/bitshuffle-
generic.o -mno-sse2 -mno-avx2
>> 161 gcc: error: unrecognized command line option '-mno-sse2'; did you mean '-mno-isel'?
>> 162 gcc: error: unrecognized command line option '-mno-avx2'
163 [numcodecs] command '/spack/lib/spack/env/gcc/gcc' failed with exit code 1
164 Traceback (most recent call last):
165 File "/spack/opt/spack/linux-ubuntu20.04-ppc64le/gcc-9.4.0/py-setuptools-63.4.3-mbykritsmmhgvvf2ver6yb2faqxsdnio/lib/python3.11/site-packages/setuptools/_distutils/uni
xccompiler.py", line 186, in _compile
166 self.spawn(compiler_so + cc_args + [src, '-o', obj] + extra_postargs)
167 File "/spack/opt/spack/linux-ubuntu20.04-ppc64le/gcc-9.4.0/py-setuptools-63.4.3-mbykritsmmhgvvf2ver6yb2faqxsdnio/lib/python3.11/site-packages/setuptools/_distutils/cco
mpiler.py", line 986, in spawn
168 spawn(cmd, dry_run=self.dry_run, **kwargs)
Error message
Error message
... see above
Information on your system
- Spack: 0.21.0.dev0 (81172f9)
- Python: 3.8.10
- Platform: linux-ubuntu20.04-power9le
- Concretizer: clingo
Additional information
spack-build-env.txt
spack-build-out.txt
General information
- I have run
spack debug reportand reported the version of Spack/Python/Platform - I have run
spack maintainers <name-of-the-package>and @mentioned any maintainers - I have uploaded the build log and environment files
- I have searched the issues of this repo and believe this is not a duplicate