Create a Dockerfile
FROM fedora
RUN sudo yum install -y python3-devel
RUN sudo pip3 install -U Cython && \
sudo pip3 install -U pybind11 && \
sudo pip3 install -U pythran && \
sudo pip3 install -U numpy && \
sudo pip3 install -U scipy
docker build --pull --rm -f "Dockerfile" -t fedoratest:latest "."
Sending build context to Docker daemon 2.048kB
Step 1/3 : FROM fedora
latest: Pulling from library/fedora
Digest:
sha256:3487c98481d1bba7e769cf7bcecd6343c2d383fdd6bed34ec541b6b23ef07664
Status: Image is up to date for fedora:latest
---> 95b7a2603d3a
Step 2/3 : RUN sudo yum install -y python3-devel
---> Running in a7c648ae7014
Fedora 37 - x86_64 7.5 MB/s | 64 MB 00:08
Fedora 37 openh264 (From Cisco) - x86_64 418 B/s | 2.5 kB 00:06
Fedora Modular 37 - x86_64 471 kB/s | 3.0 MB 00:06
Fedora 37 - x86_64 - Updates 3.0 MB/s | 20 MB 00:06
Fedora Modular 37 - x86_64 - Updates 179 kB/s | 1.1 MB 00:06
Last metadata expiration check: 0:00:01 ago on Fri Jan 6 17:37:59 2023.
Dependencies resolved.
================================================================================
Package Architecture Version Repository
Size
================================================================================
Installing:
python3-devel x86_64 3.11.1-1.fc37 updates
269 k
Upgrading:
python3 x86_64 3.11.1-1.fc37 updates
27 k
python3-libs x86_64 3.11.1-1.fc37 updates
9.6 M
Installing dependencies:
libpkgconf x86_64 1.8.0-3.fc37 fedora
36 k
pkgconf x86_64 1.8.0-3.fc37 fedora
41 k
pkgconf-m4 noarch 1.8.0-3.fc37 fedora
14 k
pkgconf-pkg-config x86_64 1.8.0-3.fc37 fedora
10 k
Installing weak dependencies:
python3-pip noarch 22.2.2-3.fc37 updates
3.1 M
python3-setuptools noarch 62.6.0-2.fc37 fedora
1.6 M
Transaction Summary
================================================================================
Install 7 Packages
Upgrade 2 Packages
Total download size: 15 M
Downloading Packages:
(1/9): pkgconf-m4-1.8.0-3.fc37.noarch.rpm 2.9 kB/s | 14 kB 00:05
(2/9): libpkgconf-1.8.0-3.fc37.x86_64.rpm 7.1 kB/s | 36 kB 00:05
(3/9): pkgconf-1.8.0-3.fc37.x86_64.rpm 8.2 kB/s | 41 kB 00:05
(4/9): pkgconf-pkg-config-1.8.0-3.fc37.x86_64.r 143 kB/s | 10 kB 00:00
(5/9): python3-devel-3.11.1-1.fc37.x86_64.rpm 458 kB/s | 269 kB 00:00
(6/9): python3-3.11.1-1.fc37.x86_64.rpm 442 kB/s | 27 kB 00:00
(7/9): python3-setuptools-62.6.0-2.fc37.noarch. 2.1 MB/s | 1.6 MB 00:00
(8/9): python3-pip-22.2.2-3.fc37.noarch.rpm 4.0 MB/s | 3.1 MB 00:00
(9/9): python3-libs-3.11.1-1.fc37.x86_64.rpm 7.2 MB/s | 9.6 MB 00:01
--------------------------------------------------------------------------------
Total 1.8 MB/s | 15 MB 00:08
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
Preparing :
1/1
Upgrading : python3-libs-3.11.1-1.fc37.x86_64
1/11
Upgrading : python3-3.11.1-1.fc37.x86_64
2/11
Installing : python3-setuptools-62.6.0-2.fc37.noarch
3/11
Installing : python3-pip-22.2.2-3.fc37.noarch
4/11
Installing : pkgconf-m4-1.8.0-3.fc37.noarch
5/11
Installing : libpkgconf-1.8.0-3.fc37.x86_64
6/11
Installing : pkgconf-1.8.0-3.fc37.x86_64
7/11
Installing : pkgconf-pkg-config-1.8.0-3.fc37.x86_64
8/11
Installing : python3-devel-3.11.1-1.fc37.x86_64
9/11
Cleanup : python3-3.11.0-1.fc37.x86_64
10/11
Cleanup : python3-libs-3.11.0-1.fc37.x86_64
11/11
Running scriptlet: python3-libs-3.11.0-1.fc37.x86_64
11/11
Verifying : libpkgconf-1.8.0-3.fc37.x86_64
1/11
Verifying : pkgconf-1.8.0-3.fc37.x86_64
2/11
Verifying : pkgconf-m4-1.8.0-3.fc37.noarch
3/11
Verifying : pkgconf-pkg-config-1.8.0-3.fc37.x86_64
4/11
Verifying : python3-setuptools-62.6.0-2.fc37.noarch
5/11
Verifying : python3-devel-3.11.1-1.fc37.x86_64
6/11
Verifying : python3-pip-22.2.2-3.fc37.noarch
7/11
Verifying : python3-3.11.1-1.fc37.x86_64
8/11
Verifying : python3-3.11.0-1.fc37.x86_64
9/11
Verifying : python3-libs-3.11.1-1.fc37.x86_64
10/11
Verifying : python3-libs-3.11.0-1.fc37.x86_64
11/11
Upgraded:
python3-3.11.1-1.fc37.x86_64 python3-libs-3.11.1-1.fc37.x86_64
Installed:
libpkgconf-1.8.0-3.fc37.x86_64
pkgconf-1.8.0-3.fc37.x86_64
pkgconf-m4-1.8.0-3.fc37.noarch
pkgconf-pkg-config-1.8.0-3.fc37.x86_64
python3-devel-3.11.1-1.fc37.x86_64
python3-pip-22.2.2-3.fc37.noarch
python3-setuptools-62.6.0-2.fc37.noarch
Complete!
Removing intermediate container a7c648ae7014
---> 593ffbdb0c08
Step 3/3 : RUN sudo pip3 install -U Cython && sudo pip3 install -U pybind11
&& sudo pip3 install -U pythran && sudo pip3 install -U numpy && sudo pip3
install -U scipy
---> Running in 97aa856851b4
Collecting Cython
Downloading
Cython-0.29.33-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl
(1.9 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.9/1.9 MB 21.0 MB/s eta
0:00:00
Installing collected packages: Cython
Successfully installed Cython-0.29.33
WARNING: Running pip as the 'root' user can result in broken permissions
and conflicting behaviour with the system package manager. It is
recommended to use a virtual environment instead:
https://pip.pypa.io/warnings/venv
Collecting pybind11
Downloading pybind11-2.10.3-py3-none-any.whl (222 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 222.4/222.4 kB 4.4 MB/s eta
0:00:00
Installing collected packages: pybind11
Successfully installed pybind11-2.10.3
WARNING: Running pip as the 'root' user can result in broken permissions
and conflicting behaviour with the system package manager. It is
recommended to use a virtual environment instead:
https://pip.pypa.io/warnings/venv
Collecting pythran
Downloading pythran-0.12.0-py3-none-any.whl (4.2 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.2/4.2 MB 26.8 MB/s eta
0:00:00
Collecting ply>=3.4
Downloading ply-3.11-py2.py3-none-any.whl (49 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 49.6/49.6 kB 7.1 MB/s eta
0:00:00
Collecting gast~=0.5.0
Downloading gast-0.5.3-py3-none-any.whl (19 kB)
Collecting numpy
Downloading
numpy-1.24.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
(17.3 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 17.3/17.3 MB 34.8 MB/s eta
0:00:00
Collecting beniget~=0.4.0
Downloading beniget-0.4.1-py3-none-any.whl (9.4 kB)
Installing collected packages: ply, numpy, gast, beniget, pythran
Successfully installed beniget-0.4.1 gast-0.5.3 numpy-1.24.1 ply-3.11
pythran-0.12.0
WARNING: Running pip as the 'root' user can result in broken permissions
and conflicting behaviour with the system package manager. It is
recommended to use a virtual environment instead:
https://pip.pypa.io/warnings/venv
Requirement already satisfied: numpy in
/usr/local/lib64/python3.11/site-packages (1.24.1)
WARNING: Running pip as the 'root' user can result in broken permissions
and conflicting behaviour with the system package manager. It is
recommended to use a virtual environment instead:
https://pip.pypa.io/warnings/venv
Collecting scipy
Downloading
scipy-1.10.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
(34.1 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 34.1/34.1 MB 30.8 MB/s eta
0:00:00
Requirement already satisfied: numpy<1.27.0,>=1.19.5 in
/usr/local/lib64/python3.11/site-packages (from scipy) (1.24.1)
Installing collected packages: scipy
Successfully installed scipy-1.10.0
WARNING: Running pip as the 'root' user can result in broken permissions
and conflicting behaviour with the system package manager. It is
recommended to use a virtual environment instead:
https://pip.pypa.io/warnings/venv
Removing intermediate container 97aa856851b4
---> 9b2a51c94efe
Successfully built 9b2a51c94efe
Successfully tagged fedoratest:latest
[root@afebdea35f7c /]# python
bash: python: command not found
[root@afebdea35f7c /]# python3
Python 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat
12.2.1-4)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from scipy.stats import norm
>>>
fre. 6. jan. 2023 kl. 18:12 skrev Oliver Ruebenacker <
oliv...@broadinstitute.org>:
> Thank you for the link. I already tried most of what was suggested there,
> but without success.
>
> On Fri, Jan 6, 2023 at 11:35 AM Bjørn Jørgensen <bjornjorgen...@gmail.com>
> wrote:
>
>>
>>
>>
>> https://stackoverflow.com/questions/66060487/valueerror-numpy-ndarray-size-changed-may-indicate-binary-incompatibility-exp
>>
>>
>>
>>
>> fre. 6. jan. 2023, 16:01 skrev Oliver Ruebenacker <
>> oliv...@broadinstitute.org>:
>>
>>>
>>> Hello,
>>>
>>> I'm trying to install SciPy using a bootstrap script and then use it
>>> to calculate a new field in a dataframe, running on AWS EMR.
>>>
>>> Although the SciPy website states that only NumPy is needed, when I
>>> tried to install SciPy using pip, pip kept failing, complaining about
>>> missing software, until I ended up with this bootstrap script:
>>>
>>>
>>>
>>>
>>>
>>>
>>> *sudo yum install -y python3-develsudo pip3 install -U Cythonsudo pip3
>>> install -U pybind11sudo pip3 install -U pythransudo pip3 install -U
>>> numpysudo pip3 install -U scipy*
>>>
>>> At this point, the bootstrap seems to be successful, but then at this
>>> line:
>>>
>>> *from scipy.stats import norm*
>>>
>>> I get the following error:
>>>
>>> *ValueError: numpy.ndarray size changed, may indicate binary
>>> incompatibility. Expected 88 from C header, got 80 from PyObject*
>>>
>>> Any advice on how to proceed? Thanks!
>>>
>>> Best, Oliver
>>>
>>> --
>>> Oliver Ruebenacker, Ph.D. (he)
>>> Senior Software Engineer, Knowledge Portal Network <http://kp4cd.org/>,
>>> Flannick
>>> Lab <http://www.flannicklab.org/>, Broad Institute
>>> <http://www.broadinstitute.org/>
>>>
>>
>
> --
> Oliver Ruebenacker, Ph.D. (he)
> Senior Software Engineer, Knowledge Portal Network <http://kp4cd.org/>,
> Flannick
> Lab <http://www.flannicklab.org/>, Broad Institute
> <http://www.broadinstitute.org/>
>
--
Bjørn Jørgensen
Vestre Aspehaug 4, 6010 Ålesund
Norge
+47 480 94 297
