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How to load anaconda virtual environment from slurm?
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Using conda activate or specifying python path in bash script?
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Closed 8 months ago.
I'm trying to run some python scripts on a computing cluster.
On the head node of the computing cluster, I have my conda environment activated, all the software loaded that I need and any python modules installed that I need to make the code run and it runs fine.
But after this test on the head node, I am trying to use Slurm to distribute jobs to the nodes. Now my script immediately fails and the error tells me that numpy is not installed etc..
Obviously this is because the node isn't set up properly to deal with my code. How does this work normally? Do I need to include instructions in my bash script to initialise conda and activate a conda environment and install the python modules before running my script? This doesn't seem sensible.
I was hoping that the node would just be used for computing resources but my existing personal head node environment (whatever the correct term is) would be used to execute the job. Could someone explain how people do this please? I've used a different cluster before and never had this problem.
Related
I used apache/airflow:2.3.3 docker image to set up the airflow. I've a pyenv installed in another drive. I've binded the volume with pyenv while creating the airflow containers. I've also updated env variable PATH in the containers to point to the python versions available in pyenv volume mounted. But airflow is still making use of the python (3.7.7) that comes with image apache/airflow:2.3.3. Is it possible to make airflow use a different python environment? I'm looking for if there is some additional environment variables that need to be updated so that airflow will take another python environment.
Have you taken a look at
PythonVirtualenvOperator
ExternalPythonOperator <-- this might require an upgrade to 2.4.0
Both of these offer flexibility call Python callables inside new Python environments.
I am a beginner and I am starting using a local cluster that works with Slurm.
I am able to execute some python codes with the usual modules (numpy, scipy, etc..) but as I try to run a script that includes my own library: myownlib.py, the following message is displayed:
No module named myownlib
I sought a lot for the solution, probably looking in the wrong direction. Hereby what I tried to fix this:
I created an environment file, with conda;
I wrote the following test.sh
(That led to the error mentioned before)
#!/bin/bash
module purge
source myownlib-devel #This is the name I gave into the environment file)
/usr/bin/python ~/filexample.py
Any suggestions?
(Thank you in advance...)
One of the most probable cause could be a difference in Python version between the login node where you created the environment and the compute nodes. If you loaded a specific Python module with module load for creating the virtual env, you should load the same module in the submission script. The default Python version for the login node could be Python 3 while the default version for the compute nodes could be Python 2, depending on the Linux distribution and list of modules loaded.
I faced this silly problem since the last 2 days, and it turns me mad.
Since I installed python 3.9 on my new Windows 10 machine, when I run the command python3 -m venv .\venv, I get the error "Python was not found; run without arguments to install from the Microsoft Store, or disable this shortcut from Settings > Manage App Execution Aliases."
If I switch off the app execution aliases, as mentioned in the message, I got a message:
'python3' is not recognized as an internal or external command,
operable program or batch file.
So, I looked at similar issues on Stackoverflow and fixed the path in the environment variables (in the user variables and in the system variables).
I added to the variable 'paths' the 2 following entries:
C:\Users{myuser}\AppData\Local\Programs\Python\Python39
C:\Users{myuser}\AppData\Local\Programs\Python\Python39\Scripts\
In all cases seen on Stack, that should have been enough. Not in my case.
I rebooted my machine twice, to make sure the new variables were picked up, but it's still the same.
I must add that I am using daily my Jupyter Lab environment, and everything works fine.
It's just this venv that refuses to work.
Does anyone has a hint on other places I should look for ?
Solution found thanks to Michael Vine.
To summarize:
referring to python instead of python3 in the command line
using [virtualenv venv] instead of [python -m venv .\venv] as I did
The Flask official website says that we can run a Flask application by
$ export FLASK_APP=hello.py
$ flask run
The second command doesn't work for me.
$ flask run
Command 'flask' not found, but can be installed with:
sudo apt install python3-flask
Instead this works
python3 -m flask run
How can I make the second command works? If I run sudo apt install python3-flask, will I get two installations of flask?
Can the two commands be combined into one command without using environment variable?
Bear with me as I will try to explain the different pieces and how they all interconnect. export FLASK_APP=hello.py is setting an operating system environment variable called FLASK_APP and is simply pointing to the entry file to start your flask application. This is no different than setting any other environment variable on your operating system. Now the flask team has provided everyone with a command called flask run which can be used to start up your flask application and this command will use the value set within your FLASK_APP environment variable when it attempts to start your flask server. So the reason why your python3 -m flask run command works is because you're telling your operating system's install of python to run the flask run command as a script, which is how this command is intended to be invoked.
For reference:
-m mod : run library module as a script (terminates option list)
Additionally, python attempts to resolve modules from it's sys.path environment variable and it looks in the following order of directories to resolve the requested module:
The current directory where the script has been invoked. This is why you can always import modules contained in the same directory as one another.
The value of your PYTHONPATH environment variable
The standard library directory on your path
Lastly, the site packages directory, i.e. your third party packages like flask
Now the reason your flask run command didn't initially work is because python couldn't find flask within any of the four locations listed above. However, once you gave the -m python knew to look in your site-packages directory for flask and was able to find said module.
For reference you can see where python is looking to resolve modules by printing out the sys.path variable to the console:
import sys
print(sys.path)
Ok so that answers the first part of your first question, now as for the second part of your first question:
"If I run sudo apt install python3-flask, will I get two installations of flask?"
Yes, this would install flask globally on your system and I would highly advise against this as you can mess up your system pretty badly if you're not careful. So how do I avoid messing with my system level python configurations?
Virtualenv to the rescue, Virtual environments allow you to have a sandboxed area to play around with libraries. With the worst case scenario being you blow them away and start fresh if you screwed something up, without affecting your Operating System's install of python. You should have a one to one relationship between each python project and virtual environment. If you use virtualenv I highly suggest looking into Virtualenvwrapper which wraps virtualenv with easier to remember commands. Although I think all the cool kids are using pipenv now so you may want to look into that as well, I will leave that decision up to you. What's nice is once you've activated your virtual environment and are developing you can just use flask run since your virtual environment will be on your python path.
As for your second question: "Can the two commands be combined into one command without using environment variable?"
No you would still need to set the FLASK_APP environment variable to use flask run since it looks for the value of that environment variable to start your flask server. Perhaps you could try something like:
FLASK_APP=hello.py flask run
on the command line and see if that helps you, but you're still setting the FLASK_APP environment variable. Alternatively, you could just start the entry file for your flask server directly, with a:
python hello.py
I know that was a lot, but hopefully that helps clarify things for you!
I have an account to a computing cluster that uses Scientific Linux. Of course I only have user access. I'm working with python and I need to run python scripts, so I need to import some python modules. Since I don't have root access, I installed a local python copy on my $HOME with all the required modules. When I run the scripts on my account (hosting node), they run correctly. But in order to submit jobs to the computing queues (to process on much faster machines), I need to submit a bash script that has a line that executes the scripts. The computing cluster uses SunGrid Engine. However when I submit the bash script, I get an error that the modules I installed can't be found! I can't figure out what is wrong. I hope if you can help.
You could simply call your python program from the bash script with something like: PYTHONPATH=$HOME/lib/python /path/to/my/python my_python_script
I don't know how SunGrid works, but if it uses a different user than yours, you'll need global read access to your $HOME. Or at least to the python libraries.
First, whether or not this solution works for you depends heavily on how the cluster is set up. That said, the general solution to your problem is below. If the compute cluster has access to the same files as you do in your home directory, I see no reason why this would not work.
You need to be using a virtualenv. Install your software inside that virtualenv along with any additional python packages you need. Then in your batch bash script, provide the full path to the python interpreter within that virtualenv.
Note: to install python packages inside your virtualenv, you need to use the pip instance that is in your virtualenv, not the system pip.
Example:
$ virtualenv foo
$ cd foo
$ ./bin/pip install numpy
Then in your bash script:
/path/to/foo/bin/python /path/to/your/script.py
Have you tried to add these in your python code:
import sys
sys.path.append("..")
from myOtherPackage import myPythonFile
This works very well for my code when I run it on Cluster and I wanted to call my "myPythonFile" from other package "myOtherPackage"