Different versions are available via loading a module

Code Block

[salexan5@mblog2 ~]$ module spider python
----------------------------------------------------------------------------
  python:
----------------------------------------------------------------------------
     Versions:
        python/3.10.6
        python/3.12.0
     Other possible modules matches:
        python2

[]$ module purge        
[salexan5@mblog2 ~]$ module load gcc/13.2.0 python/3.10.6
[salexan5@mblog2 ~]$ python --version
Python 3.10.6
[salexan5@mblog2 ~]$ which pip
/apps/u/spack/gcc/13.2.0/python/3.10.6-jh3qs5v/bin/pip

...

Pip Install Numpy - Python 3.10.6

Info
Let’s `pip install numpy` and then run a test to verify that it works.

Code Block

# Using python/3.10.6
[salexan5@mblog2 ~]$ pip install numpy
Defaulting to user installation because normal site-packages is not writeable
Collecting numpy
  Downloading numpy-2.0.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.9/60.9 kB 2.0 MB/s eta 0:00:00
Downloading numpy-2.0.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (19.3 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 19.3/19.3 MB 131.3 MB/s eta 0:00:00
Installing collected packages: numpy
Successfully installed numpy-2.0.0

[notice] A new release of pip is available: 24.0 -> 24.1
[notice] To update, run: pip install --upgrade pip

Expand

title	py_test.py

Code Block
import sys import numpy print("Python version: " + sys.version) print("Numpy: " + str(numpy.version.version))

Code Block

salexan5@mblog2 ~

]$ python py_test.py
Python: 3.10.6 (main, Apr 30 2024, 11:23:04) [GCC 13.2.0]
Numpy: 2.0.0

...

Use Python 3.12.0 - Is numpy available?

Code Block

[salexan5@mblog2 ~]$ module purge
[salexan5@mblog2 ~]$ module load gcc/13.2.0 python/3.12.0
[salexan5@mblog2 ~]$ python --version
Python 3.12.0
[salexan5@mblog2 ~]$ which python
/apps/u/spack/gcc/13.2.0/python/3.12.0-ovfqpv2/bin/python

[salexan5@mblog2 ~]$ python py_test.py
Traceback (most recent call last):
  File "/cluster/medbow/home/salexan5<username>/py_test.py", line 2, in <module>
    import numpy
ModuleNotFoundError: No module named 'numpy

...

sysconfig: The sysconfig module provides access to Python’s configuration information like the list of installation paths and the configuration variables relevant for the current platform.

Code Block

[salexan5@mblog2 ~]$ module purge
[salexan5@mblog2 ~]$ module load gcc/13.2.0 python/3.10.6
[salexan5@mblog2 ~]$ python -m sysconfig
Platform: "linux-x86_64"
Python version: "3.10"
Current installation scheme: "posix_prefix"
Paths:
        ...
		scripts = "/apps/u/spack/gcc/13.2.0/python/3.10.6-jh3qs5v/bin"
        stdlib = "/apps/u/spack/gcc/13.2.0/python/3.10.6-jh3qs5v/lib/python3.10"
...
Variables:
        ...   
        py_version = "3.10.6"
        ...
        py_version_short = "3.10"
        ...
        userbase = "/home/salexan5<username>/.local"   
# Full list has over 700 lines!

...

What is under the userbase?

Code Block

[salexan5@mblog2 ~]$ ls .local
bin  lib  share

[salexan5@mblog2 ~]$ ls -al .local/bin
total 1
drwxr-xr-x 2 salexan5<username> salexan5<username> 4096 Jun 24 11:16 .
drwxr-xr-x 2 salexan5<username> salexan5<username> 4096 Jun 24 11:16 ..
-rwxr-xr-x 1 salexan5<username> salexan5<username>  257 Jun 24 11:16 f2py
-rwxr-xr-x 1 salexan5<username> salexan5<username>  257 Jun 24 11:16 numpy-config

[salexan5@mblog2 ~]$ ls .local/lib/
python3.10
[salexan5@mblog2 ~]$ ls .local/lib/python3.10/site-packages/
numpy  numpy-2.0.0.dist-info  numpy.libs

# ~/.local/lib/python3.10

...

Note
Because you have not pip installed anything for this particular version.

Info

When using python/3.12.0 it is looking under ~/.local/lib/python3.12 for pip installed packages.

Since we have not pip installed numpy using version 3.12.0, no package exists under this folder.

...

Pip Install Numpy - Python 3.12.0

Code Block

[salexan5@mblog2 ~]$ module purge
[salexan5@mblog2 ~]$ module load gcc/13.2.0 python/3.12.0
[salexan5@mblog2 ~]$ pip install numpy==1.26.4
[salexan5@mblog2 ~]$ python py_test.py
Python: 3.12.0 (main, Apr 30 2024, 11:30:37) [GCC 13.2.0]
Numpy: 1.26.4

[salexan5@mblog2 ~]$ ls .local/lib/
python3.10  python3.12

[salexan5@mblog2 ~]$ ls .local/lib/python3.12/site-packages/
numpy  numpy-1.26.4.dist-info  numpy.libs

...

Code Block

# Previously when installing numpy for python/3.10.6
[salexan5@mblog2 ~]$ ls -al .local/bin
total 1
-rwxr-xr-x 1 salexan5 salexan5  257 Jun 24 11:16 f2py
-rwxr-xr-x 1 salexan5 salexan5  257 Jun 24 11:16 numpy-config
[salexan5@mblog2 ~]$ cat .local/bin/f2py
#!/apps/u/spack/gcc/13.2.0/python/3.10.6-jh3qs5v/bin/python
...

# Now after installing numpy for python/3.12.0
[salexan5@mblog2 ~]$ ls -al .local/bin/
-rwxr-xr-x 1 salexan5 salexan5  257 Jun 24 11:45 f2py
-rwxr-xr-x 1 salexan5 salexan5  257 Jun 24 11:16 numpy-config
[salexan5@mblog2 ~]$ cat .local/bin/f2py
#!/apps/u/spack/gcc/13.2.0/python/3.12.0-ovfqpv2/bin/python
...

Note
The `python/3.10.6` `numpy` related files have been overridden.

...

Remember: Pip Installs and Package Locations

Info
In general: Using `python/X.Y.Z` will `pip install` packages under `~/.local/lib/pythonX.Y/`

...

Workshop Home

Using Python, Conda and Pip on the Cluster

Next

Pip Install within a Conda Environment

...

Versions Compared

Old Version 9

New Version Current

Key

Pip Install Numpy - Python 3.10.6

Use Python 3.12.0 - Is numpy available?

What is under the userbase?

Pip Install Numpy - Python 3.12.0

Remember: Pip Installs and Package Locations

Page Comparison

Versions Compared

Old Version 9

New Version Current

Key

Pip Install Numpy - Python 3.10.6

Use Python 3.12.0 - Is numpy available?

What is under the userbase?

Pip Install Numpy - Python 3.12.0

Remember: Pip Installs and Package Locations