I am trying to run an Abaqus-python script file from another python script executed in Spyder (python 3.7, windows 10).
If I run the following command in CMD
abaqus cae -noGUI model.py
the code executes as expected. However, if I try to run cp = subprocess.run('abaqus cae -noGUI model.py',shell=True)
I don't get any output. Below is what is returned in cp.
Notes:
The Abaqus-python file I am trying to run is in the same folder as the python script I have.
I have tried various sp.call, sp.run, os.systems in different string and list formats.
"C:\Abaqus\Commands" and "C:\SIMULIA\Commands" are both in my PATH environment variable.
I think the -noGUI call is important to the problem. I can't seem to find others on SO with this issue.
After a fair amount of digging, I think the issue is that the PATH for my python install is done thought Anaconda so I have a different path this vs CMD. I fixed this by adding the full Abaqus location to the command. See below.
subprocess.call(r'C:\SIMULIA\Commands\abaqus job=Job-1 ask_delete=OFF interactive', shell=True)
I am not sure what your problem is due to, but note that Abaqus scripting is based on python 2.7, therefore you might need to downgrade it
Related
I have the following problem: I wrote a bash script for data analysis that works perfectly fine when I run it from the terminal. To further automate the process I wanted to use a python script that runs the bash script (using subprocess.call), changes the working directory, and reruns the script (and so on). This also worked fine when I did it on my MacBook. However, I need to do the analysis on a Linux machine and here the problem occurred. Again, running the script from the terminal worked fine but once I tried doing this with my python script it fails to find the relevant functions for the analysis. The functions are stored inside the anaconda3/bin folder.
(Python does not even find other functions like "pip")
Of course, I could add the path to all the functions in the bash script but this seems very inefficient to me. So my question is: is there any better way of telling python where to look for the functions? And can you maybe explain to me why running the script from the terminal works but not when I use subprocess.call?
Here is the python script:
import subprocess
import os
path_list = ["Path1",
"Path2"
]
for path in path_list:
os.chdir(path)
subprocess.call("Users/.../bash_script", shell=True)
I'm just posting my series of comments as an answer since I think this at least constitutes a reasonable answer for anyone running into a similar issue (your question could definitely be common enough to index from search engine results).
Issue:
...running the script from the terminal worked fine but once I tried doing this with my python script it fails to find the relevant functions for the analysis
In general, you can troubleshoot this kind of problem with:
import subprocess
subprocess.call('echo $PATH', shell=True)
If the directory that contains the relevant binaries/scripts/etc. is not in the output, then you are facing a PATH issue in the shell created by subprocess.call.
The exact problem as confirmed by the OP in comments is that anaconda3/bin is not part of your PATH. Your script works in a regular terminal session because of the Anaconda initialization function that gets added to your .bashrc when installing.
Part of an answer that is very helpful here: Python - Activate conda env through shell script
The problem with your script, though, lies in the fact that the .bashrc is not sourced by the subshell that runs shell scripts (see this answer for more info). This means that even though your non-login interactive shell sees the conda commands, your non-interactive script subshells won't - no matter how many times you call conda init.
Solution 1: Manually use the Anaconda sourcing function in your script
As the OP mentioned in the comments, their workaround was to use the initialization function added to their .bashrc in the script they are trying to run. Although this perhaps feels like not a great solution, this is a "good enough" workaround. Unfortunately I don't use Anaconda on Linux so I don't have an exact snippet of what this looks like. See the next section for a possibly "cleaner" solution.
Solution 2: Use bash -i to run your script
As mentioned in the same answer linked above, you might be able to use:
bash -i Users/.../bash_script
This will tell bash to run in interactive mode, which then properly sources your .bashrc file when creating the shell. As a result, Anaconda and related functions should work properly.
Solution 3: Manually add anaconda3/bin to PATH
You can check out this answer to decide if this is something you want to do. Keep in mind they are speaking about a Windows OS but most of the same applies to Linux.
When you add the directory to your PATH, you are specifically telling your system to always look in that directory for commands when executing by name, e.g. ping or which. This can have unexpected behavior if you have conflicts (e.g. a command is found with the same name in /usr/bin and .../anaconda3/bin), and as such Anaconda does not add its bin folder to your PATH by default.
This is not necessarily "dangerous" per se, it's just not an ideal solution for most people. However, you are the boss of your own system. If you decide this works for your particular workflow, you can just add the export to your script:
export PATH="path/to/anaconda3/bin:$PATH"
This will set the PATH for use in the current shell and sub-processes.
Solution 4: Manually source the conda script (possibly outdated)
As mentioned in this answer, you can also opt to manually source the conda.sh script (keep in mind your conda.sh might be in another directory):
source /opt/anaconda/etc/profile.d/conda.sh
This will essentially run that shell script and add the included functionality to the current shell (e.g the one spawned by subprocess.call).
Keep in mind this answer is quite a bit older (~2013) and may not apply anymore, depending how much conda has changed over the years.
Notes
As I mentioned in the comments, you may want to post some related questions on https://unix.stackexchange.com/. You have an interesting configuration challenge that may be better suited for answers specifically pertaining to Linux, since your issue is sourcing directly from Linux shell behavior.
I have spent hours looking into this issue without any success.
I've looked at various SO discussions and none seem to solve my problem so out of pure frustration here is my question...
I'm trying to launch a script within a windows batch file. The problem is that when I do the script fails because it can not find some of the modules used.
After various attempts I have found that the batch file aspect, at this stage, seems to be irrelevant.
So, ignoring batch files for a minute, If I run the script like this
pipenv run python myscript.py
It works. If I run the following it doesnt
path-to-env\Scripts\activate
python myscript.py
It returns an error ModuleNotFoundError: No module named 'xxx'
It activates the venv OK, but something is not right as it cant find code used in script
Within my IDE (Visual Code) everything works OK
I do have quite a complicated directory structure but given that both the IDE and "pipenv run python myscript.py" work as expected it must be due to something else.
Any ideas or pointers on where I need to be looking? I'm afraid my understanding of pipenv isnt up to solving this ;)
EDIT
In my attempts to solve this I had added the line PYTHONPATH=. to my .env file. This seems to be responsible for allowing this line to work:
pipenv run python myscript.py
If I remove it, then the above ALSO generates the ModuleNotFoundError
OK so after trying lots of various combinations I did finally manage to get this to work.
Although I have no idea why this solution works and others didnt..
It requires two batch files.
One to launch the python script which will contain a line like this
python myscript.py
And another to create the env via pipenv and then call the first batch file
It will have a line like this
pipenv run \path\to\first\batchfile.bat
This combination works and can be successfully called from the Windows Task Scheduler
I am new to python and wanted to make a simple script that acted like the ls command in a mac/linux terminal but for cmd in windows. The code itself works and if I run the script using python ls_script.py in my cmd it works fine. However, I want to make it so that I can run it in any active directory by just typing in ls in my cmd. I made an environment variable in cmd called ls that has a value of python ....\ls_script.py, which assumed would work since if i were to type that exact thing in manually, it works. However, when I just type in ls, it gives the following error:
"'ls' is not recognized as an internal or external command, operable program, or batch file."
I don't think your problem has anything to do with python, considering that the python script does what you want. The problem is getting the environment variable to work, right?
I believe this question has the answer you're looking for:
How to create ls in windows command prompt?
In short, it looks to me like the way to achieve what you wanted was to not use environment variables, but to create a batch file instead.
although I have been using python a long time very easily in a Linux environment, I have tremendous trouble to even install it correctly in a windows environment. I hope this is a question to be asked here, as it is not directly a programming question.
Especially, I have the following problems:
When on the command line, python is not a recognized command. Do I have to set the Windows path manually myself? If so, how to do that?
When starting a python script, should this be done with python.exe or pythonw.exe? What is the difference?
I also tried to install ipython several times, it never got installed (even after following the starting ipythonenter link description here thread.
When starting a script with python.exe, a window pops up and closes immediately. I saw some hints in putting in a readline command, which is of no help if there is a syntax error in the script. So how to be able to keep the window open, or how to run the command on the cmd.exe?
Thank you for any help on these items.
Alex
1) Look here: www.computerhope.com/issues/ch000549.htm
2) It has already been answered, always try to use search before asking question:
pythonw.exe or python.exe?
4) When using cmd.exe just navigate to your script folder using dir for changing directories and C:,D:,etc. for changing drives. Then run script by typing just the script name. When installed correctly, Python automatically launches .py scripts with python, so you don't have to write 'python' before script name. When run in cmd, window will stay open. If you want it to stay open even when launching script with double-click, use function waiting for user input, see here How to keep a Python script output window open?
You might want to use Python3.3, there is a new launcher for Python scripts in it. By that, you can start Python scripts with py <scriptname> which has the benefit of being installed in your path (C:\Windows\system32) and you can use a shebang to tell whether the script is for Python2 or Python3.
Also
In addition to the launcher, the Windows installer now includes an
option to add the newly installed Python to the system PATH
(contributed by Brian Curtin in issue 3561).
I'm trying to learn python but have some problem running source files from power shell. When I type 'python' it opens up and I can type python commands directly in the shell. I think this is called interactive mode. But when I try to run/execute a source file I get an error message: It sayys: Syntax error: invalid syntax.
I use 'python myfile.py' when I try to execute the script.
If I run the same file from IDLE it works just fine. Ana idea what I'm doing wrong?
Here is myfile.py. I'm running python 2.7
# filename: myfile.py
while True:
s = raw_input('Enter something: ')
if s == 'Quit':
break
print 'Lenght of the string is', len(s)
print 'Done'
You might have more than one version of Python installed and the version IDLE is using is newer. To see what version of python you have you can type >python -V at a command line. If that version looks appropriate then you might need the full path to the file as the second parameter. E.g >python C:\myfile.py.
If you installed Python correctly there is always a chance that just typing the name of the script will run it with python. E.g. >myfile.py
I always find that adding C:\Python27 to the %PATH% variable and .PY to the %PATHEXT% variable makes running scripts easier. In this case just >myfile should work.
Edit after Update:
Typing just >python with no parameters opens python in 'interactive mode' which is different from the batch or scripting mode that your script is intended for. If executed with arguments the first argument is taken as the file path and further arguments are passed to the script in the sys.argv list.
You will need to put the full path of the Python executable within the command line in order for it to work. You could check and ensure that your python exe is included in your Path among your system variables.
Disclaimer: I don't know PowerShell, but I do know cmd.exe.
I don't know why python myfile.py doesn't work, but assuming that PowerShell bears at least some similarity to cmd.exe, the following should probably work: myfile.py. That's right, just enter the name of the Python script and hit enter.
If you started by typing "python" in powershell you will need to get out of that script.
If you are in python type:
quit()
then type
python myfile.py
This should work if your python is installed correctly.
Try to type this in Powershell:
$env:path="$env:Path;C:\Python33
After this, command
python yourfile.py
should work.
This my sound silly, especially coming from a beginner.
Just save the file on your desktop. Open up powershell and drag the file directly into powershell and it opens. kind of tedious but it works