I am trying run a Fortran binary from within a Python script on a Mac. From the command line the Fortran binary works fine but when I run it with os.system or subprocess.open in Python then I get the following error:
dyld: Library not loaded: libimf.dylib
Referenced from: /Path/To/Binary
Reason: image not found
The Fortran binary is build with Intel Fortran. Any idea what goes wrong here?
EDIT:
I have these environmental variables set in my ~/.bash_profile which does not help:
export LD_LIBRARY_PATH="/opt/intel/compilers_and_libraries_2016.0.083/mac/compiler/lib"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/opt/intel/compilers_and_libraries_2016.1.111/mac/compiler/lib"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/opt/intel/compilers_and_libraries/mac/lib"
export DYLD_LIBRARY_PATH="/opt/intel/compilers_and_libraries_2016.0.083/mac/compiler/lib"
export DYLD_LIBRARY_PATH="$LD_LIBRARY_PATH:/opt/intel/compilers_and_libraries_2016.1.111/mac/compiler/lib"
export DYLD_LIBRARY_PATH="$LD_LIBRARY_PATH:/opt/intel/compilers_and_libraries/mac/lib"
I am running the python script from the terminal on my Mac. I tried printing from Python with
print os.environ['LD_LIBRARY_PATH']
print os.environ['DYLD_LIBRARY_PATH']
which both give the following error:
KeyError: 'DYLD_LIBRARY_PATH'
EDIT:
I tried running another binary with os.system in my Python code and that works fine.
I expect the problem is because there is no 'DYLD_LIBRARY_PATH' key in Python's os.environ dictionary; your profile setting of DYLD_LIBRARY_PATH seems fine, but Python isn't receiving it.
On my yosemite system, if I source the Intel-supplied compilervars.csh script to set DYLD_LIBRARY_PATH (resulting in a value of /opt/intel/compilers_and_libraries_2016.1.111/mac/compiler/lib:...) then the following succeeds for me
$ cat test.f90 && ifort test.f90 && python -c "import os; os.system('./a.out');"
print *, 'Hello World!'
end
Hello World!
(From bash you would presumably utilize the compilervars.sh script instead to do this.)
The problem is likely the new System Integrity Protection (SIP) built into Mac El Capitan. Basically, when you run a protected process, such as a python script, DYLD_LIBRARY_PATH is not passed to the script.
The best solution is recompiling your Fortran binaries in a manner that avoids the use of dynamic libraries. Alternatively, you can prevent this problem by disabling SIP (probably not recommended) as described here:
Macworld Article
You can find more information about this issue by searching "DYLD_LIBRARY_PATH SIP"
Related
Should I put the shebang in my Python scripts? In what form?
#!/usr/bin/env python
or
#!/usr/local/bin/python
Are these equally portable? Which form is used most?
Note: the tornado project uses the shebang. On the other hand the Django project doesn't.
The shebang line in any script determines the script's ability to be executed like a standalone executable without typing python beforehand in the terminal or when double clicking it in a file manager (when configured properly). It isn't necessary but generally put there so when someone sees the file opened in an editor, they immediately know what they're looking at. However, which shebang line you use is important.
Correct usage for (defaults to version 3.latest) Python 3 scripts is:
#!/usr/bin/env python3
Correct usage for (defaults to version 2.latest) Python 2 scripts is:
#!/usr/bin/env python2
The following should not be used (except for the rare case that you are writing code which is compatible with both Python 2.x and 3.x):
#!/usr/bin/env python
The reason for these recommendations, given in PEP 394, is that python can refer either to python2 or python3 on different systems.
Also, do not use:
#!/usr/local/bin/python
"python may be installed at /usr/bin/python or /bin/python in those
cases, the above #! will fail."
―"#!/usr/bin/env python" vs "#!/usr/local/bin/python"
It's really just a matter of taste. Adding the shebang means people can invoke the script directly if they want (assuming it's marked as executable); omitting it just means python has to be invoked manually.
The end result of running the program isn't affected either way; it's just options of the means.
Should I put the shebang in my Python scripts?
Put a shebang into a Python script to indicate:
this module can be run as a script
whether it can be run only on python2, python3 or is it Python 2/3 compatible
on POSIX, it is necessary if you want to run the script directly without invoking python executable explicitly
Are these equally portable? Which form is used most?
If you write a shebang manually then always use #!/usr/bin/env python unless you have a specific reason not to use it. This form is understood even on Windows (Python launcher).
Note: installed scripts should use a specific python executable e.g., /usr/bin/python or /home/me/.virtualenvs/project/bin/python. It is bad if some tool breaks if you activate a virtualenv in your shell. Luckily, the correct shebang is created automatically in most cases by setuptools or your distribution package tools (on Windows, setuptools can generate wrapper .exe scripts automatically).
In other words, if the script is in a source checkout then you will probably see #!/usr/bin/env python. If it is installed then the shebang is a path to a specific python executable such as #!/usr/local/bin/python (NOTE: you should not write the paths from the latter category manually).
To choose whether you should use python, python2, or python3 in the shebang, see PEP 394 - The "python" Command on Unix-Like Systems:
... python should be used in the shebang line only for scripts that are
source compatible with both Python 2 and 3.
in preparation for an eventual change in the default version of
Python, Python 2 only scripts should either be updated to be source
compatible with Python 3 or else to use python2 in the shebang line.
If you have more than one version of Python and the script needs to run under a specific version, the she-bang can ensure the right one is used when the script is executed directly, for example:
#!/usr/bin/python2.7
Note the script could still be run via a complete Python command line, or via import, in which case the she-bang is ignored. But for scripts run directly, this is a decent reason to use the she-bang.
#!/usr/bin/env python is generally the better approach, but this helps with special cases.
Usually it would be better to establish a Python virtual environment, in which case the generic #!/usr/bin/env python would identify the correct instance of Python for the virtualenv.
The purpose of shebang is for the script to recognize the interpreter type when you want to execute the script from the shell.
Mostly, and not always, you execute scripts by supplying the interpreter externally.
Example usage: python-x.x script.py
This will work even if you don't have a shebang declarator.
Why first one is more "portable" is because, /usr/bin/env contains your PATH declaration which accounts for all the destinations where your system executables reside.
NOTE: Tornado doesn't strictly use shebangs, and Django strictly doesn't. It varies with how you are executing your application's main function.
ALSO: It doesn't vary with Python.
You should add a shebang if the script is intended to be executable. You should also install the script with an installing software that modifies the shebang to something correct so it will work on the target platform. Examples of this is distutils and Distribute.
Sometimes, if the answer is not very clear (I mean you cannot decide if yes or no), then it does not matter too much, and you can ignore the problem until the answer is clear.
The #! only purpose is for launching the script. Django loads the sources on its own and uses them. It never needs to decide what interpreter should be used. This way, the #! actually makes no sense here.
Generally, if it is a module and cannot be used as a script, there is no need for using the #!. On the other hand, a module source often contains if __name__ == '__main__': ... with at least some trivial testing of the functionality. Then the #! makes sense again.
One good reason for using #! is when you use both Python 2 and Python 3 scripts -- they must be interpreted by different versions of Python. This way, you have to remember what python must be used when launching the script manually (without the #! inside). If you have a mixture of such scripts, it is a good idea to use the #! inside, make them executable, and launch them as executables (chmod ...).
When using MS-Windows, the #! had no sense -- until recently. Python 3.3 introduces a Windows Python Launcher (py.exe and pyw.exe) that reads the #! line, detects the installed versions of Python, and uses the correct or explicitly wanted version of Python. As the extension can be associated with a program, you can get similar behaviour in Windows as with execute flag in Unix-based systems.
When I installed Python 3.6.1 on Windows 7 recently, it also installed the Python Launcher for Windows, which is supposed to handle the shebang line. However, I found that the Python Launcher did not do this: the shebang line was ignored and Python 2.7.13 was always used (unless I executed the script using py -3).
To fix this, I had to edit the Windows registry key HKEY_LOCAL_MACHINE\SOFTWARE\Classes\Python.File\shell\open\command. This still had the value
"C:\Python27\python.exe" "%1" %*
from my earlier Python 2.7 installation. I modified this registry key value to
"C:\Windows\py.exe" "%1" %*
and the Python Launcher shebang line processing worked as described above.
Answer: Only if you plan to make it a command-line executable script.
Here is the procedure:
Start off by verifying the proper shebang string to use:
which python
Take the output from that and add it (with the shebang #!) in the first line.
On my system it responds like so:
$which python
/usr/bin/python
So your shebang will look like:
#!/usr/bin/python
After saving, it will still run as before since python will see that first line as a comment.
python filename.py
To make it a command, copy it to drop the .py extension.
cp filename.py filename
Tell the file system that this will be executable:
chmod +x filename
To test it, use:
./filename
Best practice is to move it somewhere in your $PATH so all you need to type is the filename itself.
sudo cp filename /usr/sbin
That way it will work everywhere (without the ./ before the filename)
If you have different modules installed and need to use a specific
python install, then shebang appears to be limited at first. However,
you can do tricks like the below to allow the shebang to be invoked
first as a shell script and then choose python. This is very flexible
imo:
#!/bin/sh
#
# Choose the python we need. Explanation:
# a) '''\' translates to \ in shell, and starts a python multi-line string
# b) "" strings are treated as string concat by python, shell ignores them
# c) "true" command ignores its arguments
# c) exit before the ending ''' so the shell reads no further
# d) reset set docstrings to ignore the multiline comment code
#
"true" '''\'
PREFERRED_PYTHON=/Library/Frameworks/Python.framework/Versions/2.7/bin/python
ALTERNATIVE_PYTHON=/Library/Frameworks/Python.framework/Versions/3.6/bin/python3
FALLBACK_PYTHON=python3
if [ -x $PREFERRED_PYTHON ]; then
echo Using preferred python $PREFERRED_PYTHON
exec $PREFERRED_PYTHON "$0" "$#"
elif [ -x $ALTERNATIVE_PYTHON ]; then
echo Using alternative python $ALTERNATIVE_PYTHON
exec $ALTERNATIVE_PYTHON "$0" "$#"
else
echo Using fallback python $FALLBACK_PYTHON
exec python3 "$0" "$#"
fi
exit 127
'''
__doc__ = """What this file does"""
print(__doc__)
import platform
print(platform.python_version())
Or better yet, perhaps, to facilitate code reuse across multiple python scripts:
#!/bin/bash
"true" '''\'; source $(cd $(dirname ${BASH_SOURCE[#]}) &>/dev/null && pwd)/select.sh; exec $CHOSEN_PYTHON "$0" "$#"; exit 127; '''
and then select.sh has:
PREFERRED_PYTHON=/Library/Frameworks/Python.framework/Versions/2.7/bin/python
ALTERNATIVE_PYTHON=/Library/Frameworks/Python.framework/Versions/3.6/bin/python3
FALLBACK_PYTHON=python3
if [ -x $PREFERRED_PYTHON ]; then
CHOSEN_PYTHON=$PREFERRED_PYTHON
elif [ -x $ALTERNATIVE_PYTHON ]; then
CHOSEN_PYTHON=$ALTERNATIVE_PYTHON
else
CHOSEN_PYTHON=$FALLBACK_PYTHON
fi
This is really a question about whether the path to the Python interpreter should be absolute or logical (/usr/bin/env) with respect to portability.
My view after thoroughly testing the behavior is that the logical path in the she-bang is the better of the two options.
Being a Linux Engineer, my goal is always to provide the most suitable, optimized hosts for my developer clients, so the issue of Python environments is something I really need a solid answer to. Encountering other answers on this and other Stack Overflow sites which talked about the issue in a general way without supporting proofs, I've performed some really granular testing & analysis on this very question on Unix.SE.
For files that are intended to be executable from the command-line, I would recommend
#! /usr/bin/env python3
Otherwise you don't need the shebang (though of course it doesn't harm).
If you use virtual environments like with pyenv it is better to write #!/usr/bin/env python
The pyenv setting will control which version of python and from which file location is started to run your script.
If your code is known to be version specific, it will help others to find why your script does not behave in their environment if you specify the expected version in the shebang.
If you want to make your file executable you must add shebang line to your scripts.
#!/usr/bin/env python3
is better option in the sense that this will not be dependent on specific distro of linux but could be used on almost all linux distro since it hunts for the python3 path from environment variables, which is different for different distros of linux.
whereas
#!/usr/local/bin/python3
would be a distro specific path for python3 and would not work if python3 is not found on this path, and could result in confusion and ambiguity for developer when migrating from one distro to another of linux.
Use first
which python
This will give the output as the location where my python interpreter (binary) is present.
This output could be any such as
/usr/bin/python
or
/bin/python
Now appropriately select the shebang line and use it.
To generalize we can use:
#!/usr/bin/env
or
#!/bin/env
I'm trying to build an Android kernel with make command. The script uses python2 to log errors in the print >> sys.stderr, line fashion. So instead of actual error output I get errors about incorrect python syntax.
I had an idea to delete python3, but I read that it could be harmful to the system as it comes bundled and many things might depend on it. Tried adding alias python=python2 at the end of the .bashrc file, rebooted the terminal, tested it with the line:
echo `python -c "print 'test'"` # prints 'test' correctly
But when I make, I still get the same errors, it somehow manages to use python3 anyways.
Where is my mistake?
You did not show your Makefile. The easiest thing is to define the absolute path of python on your system. You can get that by using the which command. Then, change python in Makefile to the absolute path that you found out using which python2.
Should I put the shebang in my Python scripts? In what form?
#!/usr/bin/env python
or
#!/usr/local/bin/python
Are these equally portable? Which form is used most?
Note: the tornado project uses the shebang. On the other hand the Django project doesn't.
The shebang line in any script determines the script's ability to be executed like a standalone executable without typing python beforehand in the terminal or when double clicking it in a file manager (when configured properly). It isn't necessary but generally put there so when someone sees the file opened in an editor, they immediately know what they're looking at. However, which shebang line you use is important.
Correct usage for (defaults to version 3.latest) Python 3 scripts is:
#!/usr/bin/env python3
Correct usage for (defaults to version 2.latest) Python 2 scripts is:
#!/usr/bin/env python2
The following should not be used (except for the rare case that you are writing code which is compatible with both Python 2.x and 3.x):
#!/usr/bin/env python
The reason for these recommendations, given in PEP 394, is that python can refer either to python2 or python3 on different systems.
Also, do not use:
#!/usr/local/bin/python
"python may be installed at /usr/bin/python or /bin/python in those
cases, the above #! will fail."
―"#!/usr/bin/env python" vs "#!/usr/local/bin/python"
It's really just a matter of taste. Adding the shebang means people can invoke the script directly if they want (assuming it's marked as executable); omitting it just means python has to be invoked manually.
The end result of running the program isn't affected either way; it's just options of the means.
Should I put the shebang in my Python scripts?
Put a shebang into a Python script to indicate:
this module can be run as a script
whether it can be run only on python2, python3 or is it Python 2/3 compatible
on POSIX, it is necessary if you want to run the script directly without invoking python executable explicitly
Are these equally portable? Which form is used most?
If you write a shebang manually then always use #!/usr/bin/env python unless you have a specific reason not to use it. This form is understood even on Windows (Python launcher).
Note: installed scripts should use a specific python executable e.g., /usr/bin/python or /home/me/.virtualenvs/project/bin/python. It is bad if some tool breaks if you activate a virtualenv in your shell. Luckily, the correct shebang is created automatically in most cases by setuptools or your distribution package tools (on Windows, setuptools can generate wrapper .exe scripts automatically).
In other words, if the script is in a source checkout then you will probably see #!/usr/bin/env python. If it is installed then the shebang is a path to a specific python executable such as #!/usr/local/bin/python (NOTE: you should not write the paths from the latter category manually).
To choose whether you should use python, python2, or python3 in the shebang, see PEP 394 - The "python" Command on Unix-Like Systems:
... python should be used in the shebang line only for scripts that are
source compatible with both Python 2 and 3.
in preparation for an eventual change in the default version of
Python, Python 2 only scripts should either be updated to be source
compatible with Python 3 or else to use python2 in the shebang line.
If you have more than one version of Python and the script needs to run under a specific version, the she-bang can ensure the right one is used when the script is executed directly, for example:
#!/usr/bin/python2.7
Note the script could still be run via a complete Python command line, or via import, in which case the she-bang is ignored. But for scripts run directly, this is a decent reason to use the she-bang.
#!/usr/bin/env python is generally the better approach, but this helps with special cases.
Usually it would be better to establish a Python virtual environment, in which case the generic #!/usr/bin/env python would identify the correct instance of Python for the virtualenv.
The purpose of shebang is for the script to recognize the interpreter type when you want to execute the script from the shell.
Mostly, and not always, you execute scripts by supplying the interpreter externally.
Example usage: python-x.x script.py
This will work even if you don't have a shebang declarator.
Why first one is more "portable" is because, /usr/bin/env contains your PATH declaration which accounts for all the destinations where your system executables reside.
NOTE: Tornado doesn't strictly use shebangs, and Django strictly doesn't. It varies with how you are executing your application's main function.
ALSO: It doesn't vary with Python.
You should add a shebang if the script is intended to be executable. You should also install the script with an installing software that modifies the shebang to something correct so it will work on the target platform. Examples of this is distutils and Distribute.
Sometimes, if the answer is not very clear (I mean you cannot decide if yes or no), then it does not matter too much, and you can ignore the problem until the answer is clear.
The #! only purpose is for launching the script. Django loads the sources on its own and uses them. It never needs to decide what interpreter should be used. This way, the #! actually makes no sense here.
Generally, if it is a module and cannot be used as a script, there is no need for using the #!. On the other hand, a module source often contains if __name__ == '__main__': ... with at least some trivial testing of the functionality. Then the #! makes sense again.
One good reason for using #! is when you use both Python 2 and Python 3 scripts -- they must be interpreted by different versions of Python. This way, you have to remember what python must be used when launching the script manually (without the #! inside). If you have a mixture of such scripts, it is a good idea to use the #! inside, make them executable, and launch them as executables (chmod ...).
When using MS-Windows, the #! had no sense -- until recently. Python 3.3 introduces a Windows Python Launcher (py.exe and pyw.exe) that reads the #! line, detects the installed versions of Python, and uses the correct or explicitly wanted version of Python. As the extension can be associated with a program, you can get similar behaviour in Windows as with execute flag in Unix-based systems.
When I installed Python 3.6.1 on Windows 7 recently, it also installed the Python Launcher for Windows, which is supposed to handle the shebang line. However, I found that the Python Launcher did not do this: the shebang line was ignored and Python 2.7.13 was always used (unless I executed the script using py -3).
To fix this, I had to edit the Windows registry key HKEY_LOCAL_MACHINE\SOFTWARE\Classes\Python.File\shell\open\command. This still had the value
"C:\Python27\python.exe" "%1" %*
from my earlier Python 2.7 installation. I modified this registry key value to
"C:\Windows\py.exe" "%1" %*
and the Python Launcher shebang line processing worked as described above.
Answer: Only if you plan to make it a command-line executable script.
Here is the procedure:
Start off by verifying the proper shebang string to use:
which python
Take the output from that and add it (with the shebang #!) in the first line.
On my system it responds like so:
$which python
/usr/bin/python
So your shebang will look like:
#!/usr/bin/python
After saving, it will still run as before since python will see that first line as a comment.
python filename.py
To make it a command, copy it to drop the .py extension.
cp filename.py filename
Tell the file system that this will be executable:
chmod +x filename
To test it, use:
./filename
Best practice is to move it somewhere in your $PATH so all you need to type is the filename itself.
sudo cp filename /usr/sbin
That way it will work everywhere (without the ./ before the filename)
If you have different modules installed and need to use a specific
python install, then shebang appears to be limited at first. However,
you can do tricks like the below to allow the shebang to be invoked
first as a shell script and then choose python. This is very flexible
imo:
#!/bin/sh
#
# Choose the python we need. Explanation:
# a) '''\' translates to \ in shell, and starts a python multi-line string
# b) "" strings are treated as string concat by python, shell ignores them
# c) "true" command ignores its arguments
# c) exit before the ending ''' so the shell reads no further
# d) reset set docstrings to ignore the multiline comment code
#
"true" '''\'
PREFERRED_PYTHON=/Library/Frameworks/Python.framework/Versions/2.7/bin/python
ALTERNATIVE_PYTHON=/Library/Frameworks/Python.framework/Versions/3.6/bin/python3
FALLBACK_PYTHON=python3
if [ -x $PREFERRED_PYTHON ]; then
echo Using preferred python $PREFERRED_PYTHON
exec $PREFERRED_PYTHON "$0" "$#"
elif [ -x $ALTERNATIVE_PYTHON ]; then
echo Using alternative python $ALTERNATIVE_PYTHON
exec $ALTERNATIVE_PYTHON "$0" "$#"
else
echo Using fallback python $FALLBACK_PYTHON
exec python3 "$0" "$#"
fi
exit 127
'''
__doc__ = """What this file does"""
print(__doc__)
import platform
print(platform.python_version())
Or better yet, perhaps, to facilitate code reuse across multiple python scripts:
#!/bin/bash
"true" '''\'; source $(cd $(dirname ${BASH_SOURCE[#]}) &>/dev/null && pwd)/select.sh; exec $CHOSEN_PYTHON "$0" "$#"; exit 127; '''
and then select.sh has:
PREFERRED_PYTHON=/Library/Frameworks/Python.framework/Versions/2.7/bin/python
ALTERNATIVE_PYTHON=/Library/Frameworks/Python.framework/Versions/3.6/bin/python3
FALLBACK_PYTHON=python3
if [ -x $PREFERRED_PYTHON ]; then
CHOSEN_PYTHON=$PREFERRED_PYTHON
elif [ -x $ALTERNATIVE_PYTHON ]; then
CHOSEN_PYTHON=$ALTERNATIVE_PYTHON
else
CHOSEN_PYTHON=$FALLBACK_PYTHON
fi
This is really a question about whether the path to the Python interpreter should be absolute or logical (/usr/bin/env) with respect to portability.
My view after thoroughly testing the behavior is that the logical path in the she-bang is the better of the two options.
Being a Linux Engineer, my goal is always to provide the most suitable, optimized hosts for my developer clients, so the issue of Python environments is something I really need a solid answer to. Encountering other answers on this and other Stack Overflow sites which talked about the issue in a general way without supporting proofs, I've performed some really granular testing & analysis on this very question on Unix.SE.
For files that are intended to be executable from the command-line, I would recommend
#! /usr/bin/env python3
Otherwise you don't need the shebang (though of course it doesn't harm).
If you use virtual environments like with pyenv it is better to write #!/usr/bin/env python
The pyenv setting will control which version of python and from which file location is started to run your script.
If your code is known to be version specific, it will help others to find why your script does not behave in their environment if you specify the expected version in the shebang.
If you want to make your file executable you must add shebang line to your scripts.
#!/usr/bin/env python3
is better option in the sense that this will not be dependent on specific distro of linux but could be used on almost all linux distro since it hunts for the python3 path from environment variables, which is different for different distros of linux.
whereas
#!/usr/local/bin/python3
would be a distro specific path for python3 and would not work if python3 is not found on this path, and could result in confusion and ambiguity for developer when migrating from one distro to another of linux.
Use first
which python
This will give the output as the location where my python interpreter (binary) is present.
This output could be any such as
/usr/bin/python
or
/bin/python
Now appropriately select the shebang line and use it.
To generalize we can use:
#!/usr/bin/env
or
#!/bin/env
I'm trying to run my Python script form the Terminal (I write the scripts in Sublime Text2 and I use a Mac osx). This is by no means my first time running one as such but I keep on getting this error that I have never seen before, nor do I understand it:
dyld: Library not loaded: #rpath/Python
Referenced from: /Users/ronaldoisabeast/Library/Enthought/Canopy_64bit/User/bin/python
Reason: image not found
The only two commands I wrote were:
dhcp-18-111-122-239:~ ronaldoisabeast$ cd Desktop/
dhcp-18-111-122-239:Desktop ronaldoisabeast$ python dicegame.py
export PATH=/usr/bin:$PATH
Putting that line in your ~/.bash_profile (and restarting your terminal) might fix your issue
I'm new to the site, and not an experienced programmer. I am trying to install a text aligner to my mac (leopard version 10.5.8). I have used the program before on other computers without difficulty. It requires the installation of XCode (done), SOX (done) and HTK (done). However, after navigating to the appropriate folder, I enter the command:
$ ./align.py [audio data folder]
and this error pops up:
Unknown option: -B
usage: /System/Library/Frameworks/Python.framework/Versions/2.5/Resources/Python.app/Contents/MacOS/Python [option] ... [-c cmd | -m mod | file | -] [arg] ...
Try `python -h' for more information.
So I type:
$ python -h
which gives me a list of options, including:
-B : don't write .py[co] files on import; also PYTHONDONTWRITEBYTECODE=x
Like I said, I'm pretty green to the world of programming, and so I'm not sure what to do with this information or how to fix the problem. I tried updating python, even though my previous version (2.5.1) should have worked. I now have 2.7.3 installed. Any advice would be much appreciated!!!
The first line of an executable script is called the "she-bang". It tells the shell which interpreter to use to run the following code.
The reason it was breaking by running ./align.py is because when you use that form, you tell it to execute using whatever is specified in that very first line:
#!/usr/local/bin/python
This says to use a python located specifically at this location. Usually you do not want an explicit path as it can cause problems (as it did for you) if that is not the appropriate python on your system. The better way, unless you have some specific needs, is to allow it to use whatever python your own environment resolves:
#!/usr/bin/env python
It worked when you ran: "python align.py", because now you are bypassing the shebang line, and calling your own python with the script as the first argument. This runs it directly.
I assume the first line of your script contains a shebang pointing at a wrong python and includes the -B flag.