Is the syntax (and semantics, for that matter) of "batch scripts" for sbatch formally documented anywhere?
(I'm looking for formal documentation, as opposed to examples.)
The DESCRIPTION section of the man page for sbatch begins with this paragraph:
sbatch submits a batch script to Slurm. The batch script may be given to sbatch through a file
name on the command line, or if no file name is specified, sbatch will read in a script from
standard input. The batch script may contain options preceded with "#SBATCH" before any exe-
cutable commands in the script.
That's about all I can find in the sbatch man page as to the syntax of a "batch script".
It says nothing, for example, about the fact that this script is required to begin with a shebang line. (One may infer this requirement, however, from the fact that all the examples in the EXAMPLES section meet it.)
It also says nothing of what interpreter one should put on the command line. Again, from the examples in the EXAMPLES section one may infer that /bin/sh is suitable, but one would have no reason to think that /bin/bash or /bin/zsh is also suitable (let alone, e.g., /bin/perl or /bin/python or /bin/ruby, etc.).
The documentation indeed only specifies 'batch script', which is to be understood as 'non-interactive script'.
Only if you try to submit a compiled program are you told about the shebang:
$ sbatch /usr/bin/time
sbatch: error: This does not look like a batch script. The first
sbatch: error: line must start with #! followed by the path to an interpreter.
sbatch: error: For instance: #!/bin/sh
But you can submit a script written in any language that supports # as comment symbol; the most common in that context are Bash, Python and Perl. You can also use for instance Lua but then you cannot incorporate the resource requirements in the script with #SBATCH directives.
Related
I know that source and . do the same thing, and I would be surprised to learn if the other pairs of commands in the title don't so the same thing (because I'm running bash as my shell, $SHELL [script] and bash [script] are equivalent, right??).
So what's the difference between the three methods of executing the script? I'm asking because I just learned that sourcing a script is NOT the exact same as executing it. In a way that I didn't find obvious from running my "experiments" and reading the man pages.
What are the other subtle differences that I couldn't find by blindly calling these functions on incredibly simple scripts that I've written? After reading the above-linked answer, I can strongly guess that the answer to my question will be quite a simple explanation, but in a way that I'd almost never fully discover by myself.
Here's the "experiment" I did:
$. myScript.sh
"This is the output to my script. I'd like to think it's original."
$source myScript.sh
"This is the output to my script. I'd like to think it's original."
$bash myScript.sh
"This is the output to my script. I'd like to think it's original."
$$SHELL myScript.sh
"This is the output to my script. I'd like to think it's original."
$./myScript.sh
"This is the output to my script. I'd like to think it's original."
$myScript.sh
"This is the output to my script. I'd like to think it's original."
. script and source script execute the contents of script in the current environment, i.e. without creating a subshell. On the upside this allows script to affect the current environment, for example changing environment variables or changing the current work directory. On the downside this allows script to affect the current environment, which is a potential security hazard.
bash script passes script to the bash interpreter to execute. Whatever shebang is given by script itself is ignored. ("Shebang" referring to the first line of script, which could e.g. read #!/bin/bash, or #!/usr/bin/perl, or #!/usr/bin/awk, to specify the interpreter to be used.)
$SHELL script passes script to whatever is your current shell interpreter to execute. That may, or may not, be bash. (The environment variable SHELL holds the name of your current shell interpreter. $SHELL, if running bash, is evaluated to /bin/bash, with the effect detailed in the previous paragraph.)
./script executes the contents of a file script in the current work directory. If there is no such file, an error is generated. The contents of $PATH have no effect on what happens.
script looks for a file script in the directories listed in $PATH, which may or may not include the current work directory. The first script found in this list of directories is executed, which may or may not be the one in your current work directory.
I know that source and . do the same thing, and I would be surprised to learn if the other pairs of commands in the title don't so the same thing (because I'm running bash as my shell, $SHELL [script] and bash [script] are equivalent, right??).
So what's the difference between the three methods of executing the script? I'm asking because I just learned that sourcing a script is NOT the exact same as executing it. In a way that I didn't find obvious from running my "experiments" and reading the man pages.
What are the other subtle differences that I couldn't find by blindly calling these functions on incredibly simple scripts that I've written? After reading the above-linked answer, I can strongly guess that the answer to my question will be quite a simple explanation, but in a way that I'd almost never fully discover by myself.
Here's the "experiment" I did:
$. myScript.sh
"This is the output to my script. I'd like to think it's original."
$source myScript.sh
"This is the output to my script. I'd like to think it's original."
$bash myScript.sh
"This is the output to my script. I'd like to think it's original."
$$SHELL myScript.sh
"This is the output to my script. I'd like to think it's original."
$./myScript.sh
"This is the output to my script. I'd like to think it's original."
$myScript.sh
"This is the output to my script. I'd like to think it's original."
. script and source script execute the contents of script in the current environment, i.e. without creating a subshell. On the upside this allows script to affect the current environment, for example changing environment variables or changing the current work directory. On the downside this allows script to affect the current environment, which is a potential security hazard.
bash script passes script to the bash interpreter to execute. Whatever shebang is given by script itself is ignored. ("Shebang" referring to the first line of script, which could e.g. read #!/bin/bash, or #!/usr/bin/perl, or #!/usr/bin/awk, to specify the interpreter to be used.)
$SHELL script passes script to whatever is your current shell interpreter to execute. That may, or may not, be bash. (The environment variable SHELL holds the name of your current shell interpreter. $SHELL, if running bash, is evaluated to /bin/bash, with the effect detailed in the previous paragraph.)
./script executes the contents of a file script in the current work directory. If there is no such file, an error is generated. The contents of $PATH have no effect on what happens.
script looks for a file script in the directories listed in $PATH, which may or may not include the current work directory. The first script found in this list of directories is executed, which may or may not be the one in your current work directory.
I know that source and . do the same thing, and I would be surprised to learn if the other pairs of commands in the title don't so the same thing (because I'm running bash as my shell, $SHELL [script] and bash [script] are equivalent, right??).
So what's the difference between the three methods of executing the script? I'm asking because I just learned that sourcing a script is NOT the exact same as executing it. In a way that I didn't find obvious from running my "experiments" and reading the man pages.
What are the other subtle differences that I couldn't find by blindly calling these functions on incredibly simple scripts that I've written? After reading the above-linked answer, I can strongly guess that the answer to my question will be quite a simple explanation, but in a way that I'd almost never fully discover by myself.
Here's the "experiment" I did:
$. myScript.sh
"This is the output to my script. I'd like to think it's original."
$source myScript.sh
"This is the output to my script. I'd like to think it's original."
$bash myScript.sh
"This is the output to my script. I'd like to think it's original."
$$SHELL myScript.sh
"This is the output to my script. I'd like to think it's original."
$./myScript.sh
"This is the output to my script. I'd like to think it's original."
$myScript.sh
"This is the output to my script. I'd like to think it's original."
. script and source script execute the contents of script in the current environment, i.e. without creating a subshell. On the upside this allows script to affect the current environment, for example changing environment variables or changing the current work directory. On the downside this allows script to affect the current environment, which is a potential security hazard.
bash script passes script to the bash interpreter to execute. Whatever shebang is given by script itself is ignored. ("Shebang" referring to the first line of script, which could e.g. read #!/bin/bash, or #!/usr/bin/perl, or #!/usr/bin/awk, to specify the interpreter to be used.)
$SHELL script passes script to whatever is your current shell interpreter to execute. That may, or may not, be bash. (The environment variable SHELL holds the name of your current shell interpreter. $SHELL, if running bash, is evaluated to /bin/bash, with the effect detailed in the previous paragraph.)
./script executes the contents of a file script in the current work directory. If there is no such file, an error is generated. The contents of $PATH have no effect on what happens.
script looks for a file script in the directories listed in $PATH, which may or may not include the current work directory. The first script found in this list of directories is executed, which may or may not be the one in your current work directory.
I infrequently have to write bash scripts for various unrelated purposes and while I usually have a good idea what commands I want in the script, I often have no idea what header to use or why I'm using one when I do find it. For example(s):
Standard shell script:
#!/bin/bash
Python:
#!/usr/bin/env python
Scripts seem to work fine without headers but if headers are the standard, there's a reason for them and they shouldn't be ignored. If it has an effect, then it's a valuable tool that could be used to accomplish more.
Minimally, I'd like to know what headers to use with MySQL scripts and what the headers do on Standard, Python, and MySQL scripts. Ideally, I'd like a generic list of headers or an understanding of how to create a header based on what program is being used.
How the Kernel Executes Things
Simplified (a bit), there are two ways the kernel in a POSIX system knows how to execute a program. One, if the program is in a binary format the kernel understands (such as ELF), the kernel can execute it "directly" (more detail out of scope). If the program is a text file starting with a shebang, such as
#!/usr/bin/somebinary -arg
or what-have-you, the kernel actually executes the command as if it had been directed to execute:
/usr/bin/somebinary -arg "$0"
where $0 here is the name of the script file you just tried to execute. (So you can immediately tell why so many scripting languages use # as a comment-starter – it means they don't have to treat the shebang as special.)
PATH and the env command
The kernel does not look at the PATH environment variable to determine which executable you're talking about, so if you are distributing a python script to systems that may have multiple versions of python installed, you can't guarantee that there will be a
#!/usr/bin/python
env, however, is POSIX, so you can count on it existing, and it will look up python in PATH. Thus,
#!/usr/bin/env python
will execute the script with the first python found in your PATH.
BASH, SH and Special Meanings for Invocation
Some programs have special semantics for how they're invoked. In particular, on many systems /bin/sh is a symlink to another shell, such as /bin/bash. While bash does not contain a perfectly POSIXLY_STRICT implementation of sh, when it is invoked as /bin/sh it is stricter than it would be if invoked as plain-old-bash.
MySQL and arg limitations
The shebang line can be length limited and technically, it can only support one argument, so mysql is a bit tricky – you can't expect to pass a username and database name to a mysql script.
#!/usr/bin/env mysql
use mydb;
select * from mytbl;
Will fail because the kernel will try mysql "$0". Even if you have your credentials in a .my.cnf file, mysql itself will try to treat "$0" as a database name. Likewise:
#!/usr/bin/mysql -e
use mydb;
select * from mytbl;
will fail because again, "$0" is not a table name (you hope).
There does not seem to be an appropriate syntax for directly executing a mysql script this way. Your best bet is to pipe the sql commands to mysql directly:
mysql < my_sql_commands
http://mywiki.wooledge.org/BashGuide/Practices#Choose_Your_Shell
When the first line of a script starts with #!, that's what's called a "shebang". When that script is run as an executable, the operating system uses that line to determine how to run the script -- that is to say, to find the program with which the script should be executed.
It's incorrect that "scripts work fine without headers" -- if you don't have a shebang line, you can't be invoked using the execve() call, which means that many (most?) programs won't be able to execute your script. Sometimes invocation from a shell will try to use that shell itself in the absence of a shebang, but you can't trust that to be the case.
(There's an exception to that -- if someone starts your script by running sh yourscript or bash yourscript, the shebang line isn't read at all, and the script they chose is used; however, running scripts this way is a bad practice, as the author typically knows better than the user what the correct interpreter is).
In short:
If you want to use modern features, and you want the user to be able to override the shell version in use by putting a different release of bash earlier in their path, use #!/usr/bin/env bash
If you want to use modern features and ensure that you always run with the system shell, use #!/bin/bash
If you're going to write your script to strictly conform with POSIX sh, use #!/bin/sh
There's not a limited list of shebang lines we can give you, since any native executable (non-script program) can be used as a script interpreter, and thus be placed in a shebang. If you created a file called myscript with #!/usr/bin/env yourprogram, gave it executable permissions, and ran ./myscript foo bar, this would result in /usr/bin/env yourprogram myscript foo bar being invoked; yourprogram would be run by /usr/bin/env (after a PATH lookup), and would be responsible for knowing what to do with myscript and its arguments.
For an extremely detailed history of shebang lines and how they work across systems both modern and ancient, see http://www.in-ulm.de/~mascheck/various/shebang/
I have made Bash scripts before and they all ran fine without #!/bin/bash at the beginning.
What's the point of putting it in? Would things be any different?
Also, how do you pronounce #? I know that ! is pronounced as "bang."
How is #! pronounced?
It's a convention so the *nix shell knows what kind of interpreter to run.
For example, older flavors of ATT defaulted to sh (the Bourne shell), while older versions of BSD defaulted to csh (the C shell).
Even today (where most systems run bash, the "Bourne Again Shell"), scripts can be in bash, python, perl, ruby, PHP, etc, etc. For example, you might see #!/bin/perl or #!/bin/perl5.
PS:
The exclamation mark (!) is affectionately called "bang". The shell comment symbol (#) is sometimes called "hash".
PPS:
Remember - under *nix, associating a suffix with a file type is merely a convention, not a "rule". An executable can be a binary program, any one of a million script types and other things as well. Hence the need for #!/bin/bash.
To be more precise the shebang #!, when it is the first two bytes of an executable (x mode) file, is interpreted by the execve(2) system call (which execute programs). But POSIX specification for execve don't mention the shebang.
It must be followed by a file path of an interpreter executable (which BTW could even be relative, but most often is absolute).
A nice trick (or perhaps not so nice one) to find an interpreter (e.g. python) in the user's $PATH is to use the env program (always at /usr/bin/env on all Linux) like e.g.
#!/usr/bin/env python
Any ELF executable can be an interpreter. You could even use #!/bin/cat or #!/bin/true if you wanted to! (but that would be often useless)
It's called a shebang. In unix-speak, # is called sharp (like in music) or hash (like hashtags on twitter), and ! is called bang. (You can actually reference your previous shell command with !!, called bang-bang). So when put together, you get haSH-BANG, or shebang.
The part after the #! tells Unix what program to use to run it. If it isn't specified, it will try with bash (or sh, or zsh, or whatever your $SHELL variable is) but if it's there it will use that program. Plus, # is a comment in most languages, so the line gets ignored in the subsequent execution.
Every distribution has a default shell. Bash is the default on the majority of the systems. If you happen to work on a system that has a different default shell, then the scripts might not work as intended if they are written specific for Bash.
Bash has evolved over the years taking code from ksh and sh.
Adding #!/bin/bash as the first line of your script, tells the OS to invoke the specified shell to execute the commands that follow in the script.
#! is often referred to as a "hash-bang", "she-bang" or "sha-bang".
The shebang is a directive to the loader to use the program which is specified after the #! as the interpreter for the file in question when you try to execute it. So, if you try to run a file called foo.sh which has #!/bin/bash at the top, the actual command that runs is /bin/bash foo.sh. This is a flexible way of using different interpreters for different programs. This is something implemented at the system level and the user level API is the shebang convention.
It's also worth knowing that the shebang is a magic number - a human readable one that identifies the file as a script for the given interpreter.
Your point about it "working" even without the shebang is only because the program in question is a shell script written for the same shell as the one you are using. For example, you could very well write a javascript file and then put a #! /usr/bin/js (or something similar) to have a javascript "Shell script".
The operating system takes default shell to run your shell script. so mentioning shell path at the beginning of script, you are asking the OS to use that particular shell. It is also useful for portability.
It is called a shebang. It consists of a number sign and an exclamation point character (#!), followed by the full path to the interpreter such as /bin/bash. All scripts under UNIX and Linux execute using the interpreter specified on a first line.
Bash standards for “Bourne-Again shell” is just one type of many available
shells in Linux.
A shell is a command line interpreter that accepts and runs commands.
Bash is often the default shell in most Linux distributions. This is why bash is
synonymous to shell.
The shell scripts often have almost the same syntaxes, but they also differ sometimes. For example, array index starts at 1 in Zsh instead of 0 in bash. A script
written for Zsh shell won’t work the same in bash if it has arrays.
To avoid unpleasant surprises, you should tell the interpreter that your shell script
is written for bash shell. How do you do that?
simply begin your bash script into #!/bin/bash
Also you will see some other parameters after #!/bin/bash,
for example
#!/bin/bash -v -x
read this to get more idea.
https://unix.stackexchange.com/questions/124272/what-do-the-arguments-v-and-x-mean-to-bash .
It can be useful to someone that uses a different system that does not have that library readily available. If that is not declared and you have some functions in your script that are not supported by that system, you should declare #/bin/bash. I've ran into this problem before at work and now I just include it as a practice.