Overhaul numpy package by adamjstewart · Pull Request #12170 · spack/spack

adamjstewart · 2019-07-28T20:27:49Z

Fixes #3204
Fixes #5327
Fixes #6634
Fixes #7687
Fixes #8616
Closes #8817
Fixes #10361
Fixes #12237

This PR makes the following changes:

Obviously, any big change to the numpy package, which has already gone through a lot of turmoil, will require extensive testing. Here are the platforms and configurations I would like to test before merging this:

macOS 10.14.5, Clang 10.0.1

+blas+lapack ^intel-mkl

$ cat ./lib/python3.7/site-packages/numpy/distutils/site.cfg
[mkl]
libraries = mkl_rt
library_dirs = /opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib:/usr/lib
rpath = /opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib:/usr/lib
include_dirs = /opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/include
$ otool -l $(find . -name '*.so') | sort | uniq
...
         name /usr/lib/libSystem.B.dylib (offset 24)
         name @rpath/libmkl_rt.dylib (offset 24)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/bzip2-1.0.8-llnc6sqphf7yp4drig6njzzkxctjwfse/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/expat-2.2.5-ivx3l77irr7xnft6v2xduzqier7zlct3/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/gdbm-1.18.1-pvjwideh43qybd2ifi65gjxq2dd6p4nj/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/libffi-3.2.1-rmioaofogfk7efvt3cpb3d433sevjnaf/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/ncurses-6.1-nhodl3ckldkmn6nfzgtymzlsn7mm3htq/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/openssl-1.1.1b-z6erpibfcvzxo5chnvovu3qmet4dzuuv/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/py-numpy-1.17.0-pwyhmfnrnpg264vfofzhyizizwyamjvu/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/py-numpy-1.17.0-pwyhmfnrnpg264vfofzhyizizwyamjvu/lib64 (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/python-3.7.4-jqlxzxpwzdhmrirodxanluofnce5o3ab/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/readline-7.0-kn3u3qhqwktlvjpr47ism2uqqgstvvf2/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/sqlite-3.28.0-mijtevf42dqzctgyaizz44skbyqwxgol/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/xz-5.2.4-snwzcouby3x3ztkutupqzmqwbbxh2tur/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/zlib-1.2.11-nqnlnxddpa4qfz5cnf4grnct57ds25ks/lib (offset 12)
         path /opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib (offset 12)
         path /opt/intel/lib (offset 12)

+blas~lapack ^blis+cblas (fails due to rpath problems: Problems building numpy with BLIS numpy/numpy#14180)

$ cat site.cfg
[blis]
libraries = blis
library_dirs = /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/blis-0.6.0-5adedbjl73c76sqq3izc7d3qxyzksr3t/lib
rpath = /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/blis-0.6.0-5adedbjl73c76sqq3izc7d3qxyzksr3t/lib
include_dirs = /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/blis-0.6.0-5adedbjl73c76sqq3izc7d3qxyzksr3t/include

+blas+lapack ^openblas

$ cat ./lib/python3.7/site-packages/numpy/distutils/site.cfg
[openblas]
libraries = openblas
library_dirs = /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/openblas-0.3.6-3yts3o25cqf437oxaa4qzfhiw3swc7j2/lib
rpath = /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/openblas-0.3.6-3yts3o25cqf437oxaa4qzfhiw3swc7j2/lib
include_dirs = /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/openblas-0.3.6-3yts3o25cqf437oxaa4qzfhiw3swc7j2/include
$ otool -l $(find . -name '*.so') | sort | uniq
...
         name /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/openblas-0.3.6-3yts3o25cqf437oxaa4qzfhiw3swc7j2/lib/libopenblas_sandybridge-r0.3.6.dylib (offset 24)
         name /usr/lib/libSystem.B.dylib (offset 24)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/bzip2-1.0.8-llnc6sqphf7yp4drig6njzzkxctjwfse/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/expat-2.2.5-ivx3l77irr7xnft6v2xduzqier7zlct3/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/gdbm-1.18.1-pvjwideh43qybd2ifi65gjxq2dd6p4nj/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/libffi-3.2.1-rmioaofogfk7efvt3cpb3d433sevjnaf/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/ncurses-6.1-nhodl3ckldkmn6nfzgtymzlsn7mm3htq/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/openblas-0.3.6-3yts3o25cqf437oxaa4qzfhiw3swc7j2/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/openssl-1.1.1b-z6erpibfcvzxo5chnvovu3qmet4dzuuv/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/py-numpy-1.17.0-tt562t4vqgt2jc6j4gkk5rdj6mbakig2/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/py-numpy-1.17.0-tt562t4vqgt2jc6j4gkk5rdj6mbakig2/lib64 (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/python-3.7.4-jqlxzxpwzdhmrirodxanluofnce5o3ab/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/readline-7.0-kn3u3qhqwktlvjpr47ism2uqqgstvvf2/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/sqlite-3.28.0-mijtevf42dqzctgyaizz44skbyqwxgol/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/xz-5.2.4-snwzcouby3x3ztkutupqzmqwbbxh2tur/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/zlib-1.2.11-nqnlnxddpa4qfz5cnf4grnct57ds25ks/lib (offset 12)

~blas+lapack ^libflame@master (unable to build libflame: Add libflame #12193)
+blas+lapack ^atlas (weird build error: Bug in ATLAS version detection numpy/numpy#14212)

$ cat site.cfg
[atlas]
libraries = satlas
library_dirs = /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/atlas-3.10.3-j53o6sg7cswtaak6duqdofi7emddfg6z/lib
rpath = /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/atlas-3.10.3-j53o6sg7cswtaak6duqdofi7emddfg6z/lib
include_dirs = /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/atlas-3.10.3-j53o6sg7cswtaak6duqdofi7emddfg6z/include

+blas+lapack ^veclibfort (I think veclib is enough, veclibfort is not required)

$ cat ./lib/python3.7/site-packages/numpy/distutils/site.cfg
[accelerate]
libraries = vecLibFort
library_dirs = /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/veclibfort-0.4.2-ucgnmbinqkiftt2h2roihqbxezvbiwpv/lib
rpath = /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/veclibfort-0.4.2-ucgnmbinqkiftt2h2roihqbxezvbiwpv/lib
$ otool -l $(find . -name '*.so') | sort | uniq
...
         name /usr/lib/libSystem.B.dylib (offset 24)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/bzip2-1.0.8-llnc6sqphf7yp4drig6njzzkxctjwfse/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/expat-2.2.5-ivx3l77irr7xnft6v2xduzqier7zlct3/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/gdbm-1.18.1-pvjwideh43qybd2ifi65gjxq2dd6p4nj/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/libffi-3.2.1-rmioaofogfk7efvt3cpb3d433sevjnaf/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/ncurses-6.1-nhodl3ckldkmn6nfzgtymzlsn7mm3htq/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/openssl-1.1.1b-z6erpibfcvzxo5chnvovu3qmet4dzuuv/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/py-numpy-1.17.0-bvtdp3tqpak7snvkhnfsutkshtrjk2ri/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/py-numpy-1.17.0-bvtdp3tqpak7snvkhnfsutkshtrjk2ri/lib64 (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/python-3.7.4-jqlxzxpwzdhmrirodxanluofnce5o3ab/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/readline-7.0-kn3u3qhqwktlvjpr47ism2uqqgstvvf2/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/sqlite-3.28.0-mijtevf42dqzctgyaizz44skbyqwxgol/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/veclibfort-0.4.2-ucgnmbinqkiftt2h2roihqbxezvbiwpv/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/xz-5.2.4-snwzcouby3x3ztkutupqzmqwbbxh2tur/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/zlib-1.2.11-nqnlnxddpa4qfz5cnf4grnct57ds25ks/lib (offset 12)

+blas+lapack ^netlib-lapack

$ cat ./lib/python3.7/site-packages/numpy/distutils/site.cfg
[blas]
libraries = blas
library_dirs = /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/netlib-lapack-3.8.0-r242vagzpssq7r5za4wfnfha5hrtcj7d/lib
rpath = /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/netlib-lapack-3.8.0-r242vagzpssq7r5za4wfnfha5hrtcj7d/lib
include_dirs = /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/netlib-lapack-3.8.0-r242vagzpssq7r5za4wfnfha5hrtcj7d/include
[lapack]
libraries = lapack
library_dirs = /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/netlib-lapack-3.8.0-r242vagzpssq7r5za4wfnfha5hrtcj7d/lib
rpath = /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/netlib-lapack-3.8.0-r242vagzpssq7r5za4wfnfha5hrtcj7d/lib
include_dirs = /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/netlib-lapack-3.8.0-r242vagzpssq7r5za4wfnfha5hrtcj7d/include
$ otool -l $(find . -name '*.so') | sort | uniq
...
         name /usr/lib/libSystem.B.dylib (offset 24)
         name @rpath/libblas.3.dylib (offset 24)
         name @rpath/libcblas.3.dylib (offset 24)
         name @rpath/liblapack.3.dylib (offset 24)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/bzip2-1.0.8-llnc6sqphf7yp4drig6njzzkxctjwfse/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/expat-2.2.5-ivx3l77irr7xnft6v2xduzqier7zlct3/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/gdbm-1.18.1-pvjwideh43qybd2ifi65gjxq2dd6p4nj/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/libffi-3.2.1-rmioaofogfk7efvt3cpb3d433sevjnaf/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/ncurses-6.1-nhodl3ckldkmn6nfzgtymzlsn7mm3htq/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/netlib-lapack-3.8.0-r242vagzpssq7r5za4wfnfha5hrtcj7d/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/openssl-1.1.1b-z6erpibfcvzxo5chnvovu3qmet4dzuuv/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/py-numpy-1.17.0-z6fmbjnxdegdbxzavacnimooqg3obs6n/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/py-numpy-1.17.0-z6fmbjnxdegdbxzavacnimooqg3obs6n/lib64 (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/python-3.7.4-jqlxzxpwzdhmrirodxanluofnce5o3ab/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/readline-7.0-kn3u3qhqwktlvjpr47ism2uqqgstvvf2/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/sqlite-3.28.0-mijtevf42dqzctgyaizz44skbyqwxgol/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/xz-5.2.4-snwzcouby3x3ztkutupqzmqwbbxh2tur/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/zlib-1.2.11-nqnlnxddpa4qfz5cnf4grnct57ds25ks/lib (offset 12)

~blas~lapack

$ cat ./lib/python3.7/site-packages/numpy/distutils/site.cfg
cat: ./lib/python3.7/site-packages/numpy/distutils/site.cfg: No such file or directory
$ otool -l $(find . -name '*.so') | sort | uniq
...
         name /usr/lib/libSystem.B.dylib (offset 24)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/bzip2-1.0.8-llnc6sqphf7yp4drig6njzzkxctjwfse/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/expat-2.2.5-ivx3l77irr7xnft6v2xduzqier7zlct3/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/gdbm-1.18.1-pvjwideh43qybd2ifi65gjxq2dd6p4nj/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/libffi-3.2.1-rmioaofogfk7efvt3cpb3d433sevjnaf/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/ncurses-6.1-nhodl3ckldkmn6nfzgtymzlsn7mm3htq/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/openssl-1.1.1b-z6erpibfcvzxo5chnvovu3qmet4dzuuv/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/py-numpy-1.17.0-gkuufd4mljdukrciubhmvpxuiflny22x/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/py-numpy-1.17.0-gkuufd4mljdukrciubhmvpxuiflny22x/lib64 (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/python-3.7.4-jqlxzxpwzdhmrirodxanluofnce5o3ab/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/readline-7.0-kn3u3qhqwktlvjpr47ism2uqqgstvvf2/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/sqlite-3.28.0-mijtevf42dqzctgyaizz44skbyqwxgol/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/xz-5.2.4-snwzcouby3x3ztkutupqzmqwbbxh2tur/lib (offset 12)
         path /Users/Adam/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/zlib-1.2.11-nqnlnxddpa4qfz5cnf4grnct57ds25ks/lib (offset 12)

Linux CentOS 7, GCC 4.8.5

+blas+lapack ^intel-mkl

$ cat ./lib/python3.7/site-packages/numpy/distutils/site.cfg
[mkl]
libraries = mkl_rt
library_dirs = /home/adamjs5/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/intel-mkl-2019.3.199-dwmyyb66bsnoisor6fmvcx4j6akq7cgg/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64:/lib64
rpath = /home/adamjs5/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/intel-mkl-2019.3.199-dwmyyb66bsnoisor6fmvcx4j6akq7cgg/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64:/lib64
include_dirs = /home/adamjs5/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/intel-mkl-2019.3.199-dwmyyb66bsnoisor6fmvcx4j6akq7cgg/compilers_and_libraries_2019.3.199/linux/mkl/include
$ ldd -r $(find . -name '*.so') | sort | uniq
...
	libmkl_rt.so => /home/adamjs5/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/intel-mkl-2019.3.199-dwmyyb66bsnoisor6fmvcx4j6akq7cgg/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_rt.so (0x00007f516259e000)

+blas~lapack ^blis+cblas (fails due to rpath problems: Problems building numpy with BLIS numpy/numpy#14180)

$ cat site.cfg
[blis]
libraries = blis
library_dirs = /home/adamjs5/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/blis-0.6.0-k46gjp3oke6i2z2c3jmhgnfexc3jpkqw/lib
rpath = /home/adamjs5/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/blis-0.6.0-k46gjp3oke6i2z2c3jmhgnfexc3jpkqw/lib
include_dirs = /home/adamjs5/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/blis-0.6.0-k46gjp3oke6i2z2c3jmhgnfexc3jpkqw/include

+blas+lapack ^openblas

$ cat ./lib/python3.7/site-packages/numpy/distutils/site.cfg
[openblas]
libraries = openblas
library_dirs = /home/adamjs5/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/openblas-0.3.6-2wdlwxcbb44em2a2eukduuaqxteko3of/lib
rpath = /home/adamjs5/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/openblas-0.3.6-2wdlwxcbb44em2a2eukduuaqxteko3of/lib
include_dirs = /home/adamjs5/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/openblas-0.3.6-2wdlwxcbb44em2a2eukduuaqxteko3of/include
$ ldd -r $(find . -name "*.so") | sort | uniq
...
	libopenblas.so.0 => /home/adamjs5/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/openblas-0.3.6-2wdlwxcbb44em2a2eukduuaqxteko3of/lib/libopenblas.so.0 (0x00007f1a7769f000)

~blas+lapack ^libflame@master (numpy does not pick up libflame: Can't build with libFLAME numpy/numpy#14205)

$ cat ./lib/python3.7/site-packages/numpy/distutils/site.cfg
[flame]
libraries = flame
library_dirs = /home/adamjs5/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/libflame-master-xmo2dhpugpfgb4zetev2lcccvdgybjog/lib
rpath = /home/adamjs5/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/libflame-master-xmo2dhpugpfgb4zetev2lcccvdgybjog/lib
include_dirs = /home/adamjs5/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/libflame-master-xmo2dhpugpfgb4zetev2lcccvdgybjog/include

+blas+lapack ^atlas

$ cat ./lib/python3.7/site-packages/numpy/distutils/site.cfg
[atlas]
libraries = satlas
library_dirs = /home/adamjs5/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/atlas-3.10.2-a32yghlhsmlartth4vxyrn2cswzbotlu/lib
rpath = /home/adamjs5/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/atlas-3.10.2-a32yghlhsmlartth4vxyrn2cswzbotlu/lib
include_dirs = /home/adamjs5/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/atlas-3.10.2-a32yghlhsmlartth4vxyrn2cswzbotlu/include
$ ldd -r $(find . -name "*.so") | sort | uniq
...
	/home/adamjs5/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/atlas-3.10.2-a32yghlhsmlartth4vxyrn2cswzbotlu/lib/libsatlas.so (0x00007f4ebaf1e000)

+blas+lapack ^netlib-lapack

$ cat ./lib/python3.7/site-packages/numpy/distutils/site.cfg
[blas]
libraries = blas
library_dirs = /home/adamjs5/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/netlib-lapack-3.8.0-c5uo7hykg6txcixdohlsmixphc5ikf4b/lib64
rpath = /home/adamjs5/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/netlib-lapack-3.8.0-c5uo7hykg6txcixdohlsmixphc5ikf4b/lib64
include_dirs = /home/adamjs5/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/netlib-lapack-3.8.0-c5uo7hykg6txcixdohlsmixphc5ikf4b/include
[lapack]
libraries = lapack
library_dirs = /home/adamjs5/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/netlib-lapack-3.8.0-c5uo7hykg6txcixdohlsmixphc5ikf4b/lib64
rpath = /home/adamjs5/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/netlib-lapack-3.8.0-c5uo7hykg6txcixdohlsmixphc5ikf4b/lib64
include_dirs = /home/adamjs5/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/netlib-lapack-3.8.0-c5uo7hykg6txcixdohlsmixphc5ikf4b/include
$ ldd -r $(find . -name "*.so") | sort | uniq
...
	libblas.so.3 => /home/adamjs5/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/netlib-lapack-3.8.0-c5uo7hykg6txcixdohlsmixphc5ikf4b/lib64/libblas.so.3 (0x00007f0034177000)
	libcblas.so.3 => /home/adamjs5/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/netlib-lapack-3.8.0-c5uo7hykg6txcixdohlsmixphc5ikf4b/lib64/libcblas.so.3 (0x00007f00343cf000)
	liblapack.so.3 => /home/adamjs5/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/netlib-lapack-3.8.0-c5uo7hykg6txcixdohlsmixphc5ikf4b/lib64/liblapack.so.3 (0x00007f726f796000)

~blas~lapack

$ cat ./lib/python3.7/site-packages/numpy/distutils/site.cfg
cat: ./lib/python3.7/site-packages/numpy/distutils/site.cfg: No such file or directory
$ ldd -r $(find . -name '*.so') | sort | uniq
...
no linkage to blas/lapack

Caveats

I only plan on testing the latest version of numpy, this PR may break older versions
I only plan on testing Python 3, as numpy no longer supports Python 2
I only plan on testing supported BLAS/LAPACK configurations, not BLAS providers like essl or netlib-xblas
I don't plan on testing mixed BLAS/LAPACK configurations, like ^blis ^libflame, but they should work
This PR does not try to tackle the many build problems that Intel users face. That can be saved for another PR

@scheibelp @huqy @robbmcleod @scottwittenburg @s-sajid-ali

s-sajid-ali · 2019-08-01T06:29:59Z

@adamjstewart : Could numpy+libflame be added to verify the functionality ?

scheibelp · 2019-08-01T19:46:50Z

Reverts Exclude system mkl installs from numpy #10383 which was causing problems with the numexpr installation (Numpy MKL errors during installation pydata/numexpr#340)

Fixes a bug where numpy would pick up the first BLAS/LAPACK it found, regardless of what was asked for (How to force build system to use a particular BLAS/LAPACK? numpy/numpy#14146)

As I mention in #10383 (comment), it is likely worthwhile to:

keep Exclude system mkl installs from numpy #10383 for versions of numpy before 1.17
use the NPY_LAPACK_ORDER logic you added here for 1.17 and later

adamjstewart · 2019-08-01T23:22:50Z

As I mention in #10383 (comment), it is likely worthwhile to:

keep Exclude system mkl installs from numpy #10383 for versions of numpy before 1.17

use the NPY_LAPACK_ORDER logic you added here for 1.17 and later

I'm hesitant to add this back as it greatly increases the complexity of the package and has never been recommended by the developers. I'm afraid it might break more things than we realized, not just in 1.17.0 and not just numexpr. I would rather:

tell users to upgrade to a newer version of numpy, or
tell users they can try to backport BLD: Allow users to specify BLAS and LAPACK library link order numpy/numpy#13132 to older versions of numpy

adamjstewart · 2019-08-02T04:18:11Z

Can someone test another platform/compiler for me? Spack is broken on Blue Waters (#12187) and I'm unable to build even a basic py-numpy~blas~lapack on the other system I have access to (numpy/numpy#14182). I'm also fine with just merging this at this point. I think it's pretty robust.

s-sajid-ali · 2019-08-02T15:38:13Z

I'll re-run the test script I created for #8817 with this branch and get back with the results in a few days.

adamjstewart · 2019-08-02T18:18:34Z

Thanks @s-sajid-ali. You should be able to run:

$ spack install --test=root py-numpy +blas+lapack ^intel-mkl
$ cd $(spack location -i py-numpy +blas+lapack ^intel-mkl)
$ cat ./lib/python3.7/site-packages/numpy/distutils/site.cfg
$ ldd -r $(find . -name '*.so') | sort | uniq

for every combination. We want to make sure that a) the site.cfg is formatted correctly, b) the install passes all unit tests, including import tests, and c) rpath correctly links to the right libraries.

scheibelp · 2019-08-02T18:58:27Z

I would rather:
tell users to upgrade to a newer version of numpy, or

IMO that's problematic because 1.17.x is Python 3 only and Python 2 is still supported for a short while longer.

tell users they can try to backport numpy/numpy#13132 to older versions of numpy

That seems like a big ask

https://github.com/numpy/numpy/commit/0f19dae081e6678902826b195e0d3857c5b4c2b3 minus the .travis.yml changes (attached) appears to apply cleanly.

If we merge this without addressing some 1.16.x version an issue should be opened and hopefully that patch will be sufficient.

adamjstewart · 2019-08-02T19:22:25Z

@scheibelp does the latest commit address your concerns?

scheibelp · 2019-08-02T19:26:34Z

does the latest commit address your concerns?

yes

var/spack/repos/builtin/packages/py-numpy/package.py

s-sajid-ali · 2019-08-06T03:28:27Z

WIP

CentOS/Py 3.6.8	Intel-MKL	OpenBLAS	BLIS	libFLAME	libFLAME+BLIS
GCC 9.1.0	Pass	Pass	Pass	Fail 1,2,3	Fail 1,2,3
Intel19	[]	[]	[]	[]	[]

py-numpy fails to link to any variant of libFLAME (release, master, static, shared) and complains of undefined references of BLAS functions from the libflame library. When I attempted to build py-numpy+blis+libflame, I ended up building py-numpy+blis~libflame

adamjstewart · 2019-08-06T05:13:51Z

Okay, I think this PR is complete from my end. I've tested most common configurations and reported bugs upstream when I wasn't able to get them working. If anyone wants to see any more tests, let me know. Otherwise, I think this PR is finally ready to merge!

…upsream_develop * commit 'f7026a058b63f5a3109691e2c3871ee77c08f756': (1881 commits) Version 19.8.1 of PLASMA (spack#12299) new package: py-exodus (spack#12291) ncurses: fix pic and opt flags (spack#12272) pumi: new version 2.2.1 (spack#12282) tests: explain and test dependency flattening routines (spack#11993) graphviz package: add MacOS fixes and quartz support (spack#11128) Overhaul numpy package (spack#12170) mirrors: mirror config should use spack variable expansions (spack#9027) stacks: fix reference handling in env.write() (spack#12096) fltk: fix about variable types (spack#12292) Avoid sending empty reports to codecov (spack#12293) Packages/musl (spack#12288) c-blosc package: Add -std=gnu99 flag for gcc (spack#11959) Move new packages from tutorial to builtin (spack#12289) Balay/amrex 19.08 (spack#12287) openPMD-api: pre-load depend libs (spack#12279) Add version 19.8.0 of PLASMA (spack#12275) Add version 2.5.1 of MAGMA released today (spack#12274) ginkgo: add maintainers (spack#12273) new package: py-backports-tempfile (spack#12261) ... # Conflicts: # .travis.yml # var/spack/repos/builtin/packages/moab/package.py # var/spack/repos/builtin/packages/mofem-cephas/package.py # var/spack/repos/builtin/packages/mofem-fracture-module/package.py # var/spack/repos/builtin/packages/mofem-users-modules/package.py # var/spack/repos/builtin/packages/petsc/package.py

* Add numpy 1.17.0 * Overhaul numpy package * Flake8 fixes * Undefined reference fix * HeaderList and LibraryList need an arg * veclibfort has no headers * Add patch for older versions of py-numpy * Remove py-meep hack from py-numpy package * libflame: always add max arg hack flag * Fix build with GCC 4.8 * Compiler flags come from self.compiler * Only apply -std=c99 to cflags * Try to fix libflame package * Fix ATLAS build on macOS * --force-clang flag added in 3.10.3

adamjstewart · 2019-09-18T20:31:18Z

Update: the blis issues were finally resolved in #12869

adamjstewart added new-version don't-merge-yet labels Jul 28, 2019

adamjstewart changed the title ~~Add numpy 1.17.0~~ Overhaul numpy package Jul 29, 2019

adamjstewart added blas-lapack-scalapack python labels Jul 29, 2019

adamjstewart force-pushed the packages/py-numpy branch from 94f22c0 to cf29bfd Compare July 29, 2019 22:15

adamjstewart removed the don't-merge-yet label Jul 30, 2019

scheibelp mentioned this pull request Aug 1, 2019

Exclude system mkl installs from numpy #10383

Merged

adamjstewart force-pushed the packages/py-numpy branch from d5b472f to e4c7b8e Compare August 1, 2019 22:23

adamjstewart mentioned this pull request Aug 3, 2019

Fix py-scipy build with intel compilers #8817

Closed

adamjstewart force-pushed the packages/py-numpy branch from 9586dbe to 05cbeec Compare August 3, 2019 19:20

adamjstewart commented Aug 6, 2019

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adamjstewart mentioned this pull request Aug 6, 2019

Add libflame #12193

Merged

s-sajid-ali mentioned this pull request Aug 6, 2019

Can't build with libFLAME numpy/numpy#14205

Closed

adamjstewart force-pushed the packages/py-numpy branch from 36a3dd6 to 6faa6a2 Compare August 6, 2019 04:37

adamjstewart added 4 commits August 6, 2019 13:36

Add numpy 1.17.0

5f3305c

Overhaul numpy package

6fdda24

Flake8 fixes

6798e7e

Undefined reference fix

8f9e731

adamjstewart added 10 commits August 6, 2019 13:36

HeaderList and LibraryList need an arg

e16c1cf

veclibfort has no headers

c30ad90

Add patch for older versions of py-numpy

f7ff903

Remove py-meep hack from py-numpy package

f8539b3

libflame: always add max arg hack flag

38b661c

Fix build with GCC 4.8

90c1e3e

Compiler flags come from self.compiler

613fd60

Only apply -std=c99 to cflags

c99c818

Try to fix libflame package

8bc29dc

Fix ATLAS build on macOS

ded5c88

adamjstewart force-pushed the packages/py-numpy branch from 143b6bc to ded5c88 Compare August 6, 2019 18:36

--force-clang flag added in 3.10.3

4a56102

adamjstewart merged commit 66e9b12 into spack:develop Aug 6, 2019

adamjstewart deleted the packages/py-numpy branch August 6, 2019 23:20

This was referenced Aug 28, 2019

Conditional test dependencies not added to spec #12613

Closed

System paths may get into generated module files #12628

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climbfuji mentioned this pull request Sep 21, 2022

Again py-scipy with Intel issues - undefined symbols #32732

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Overhaul numpy package#12170

Overhaul numpy package#12170
adamjstewart merged 15 commits intospack:developfrom
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macOS 10.14.5, Clang 10.0.1

Linux CentOS 7, GCC 4.8.5

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