I have a shell script that expects three variable names when run on my system, in the following way:
run.csh VarName1 VarName2 VarName3
where the variable names are combined in the script to a string referring to the name of the data file on which the script operates.
However, when I try to run it on the PBS system, using:
qsub run.csh VarName1 VarName2 VarName3
I'm getting an error related to the syntax of the command.
My question: how can I properly run the script with the 3 variable names given as inputs?
Related
In matlab I can change to another shell by the bang (!) Notation.
Example:
I enter a conda Environment in MATLAB by the following command:
!cmd '"%windir%\System32\cmd.exe" /K ""C:\Program Files\Anaconda3\Scripts\activate_<conda-env-name>.bat" "C:\Program Files\Anaconda3""'
My MATLAB Command window then Displays following:
(<conda-env-name>) U:\some_starting_path>
Now, is there a way to send commands to this newly entered shell in a programmatic way, so that that command is evaluated in that very shell's syntax and not as a MATLAB-command?
For example, how can I write code that will execute a Python command without needing to enter it manually into the command line?
Not using the ! command or system(). Those are "one and done" functions.
But you can use Java's java.lang.Process API from within Matlab to control and interact with an ongoing process.
function control_another_process
pb = java.lang.ProcessBuilder(["myCommand", "myArg1", "myArg2"]);
proc = pb.start; % now proc is a java.lang.Process object
stdin = proc.getOutputStream; % Here's how you send commands to the process
stdout = proc.getInputStream; % And here's how you get its output
stderr = proc.getErrorStream;
% ... now do stuff with the process ...
end
You can use this with a shell, with python, or any other command.
Here's a Matlab class that wraps up the Java code to make it convenient to work with in Matlab: https://github.com/apjanke/janklab/blob/master/Mcode/classes/%2Bjl/%2Butil/Process.m
Let's consider the following perl script:
#!/usr/bin/perl
system("C:/Program Files (x86)/Microsoft Visual Studio/2017/Enterprise/Common7/Tools/VsDevCmd.bat");
system("msbuild");
The batch file invoked with the first system call is supposed to set up some environment variables so that the msbuild executable in the second system call can be found.
When I run this perl script I get the following error:
'msbuild' is not recognized as an internal or external command,
operable program or batch file.
So it looks like the environment variables set in the batch file are not made available to the context of the perl script. What can I do to make this work?
Note 1
Running first the batch file from a console window and then running msbuild works fine. So the batch file works as expected and msbuild is actually available.
Note 2
My real-world perl script is much longer. This example here is a massive simplification which allows to reproduce the problem. So I cannot easily replace the perl script with a batch file, for example.
Note 3
The funny thing is: I've been using this perl script for one or two years without any problems. Then suddenly it stopped working.
Your process has an associated environment which contains things like the search path.
When a sub-process starts, the new process has a new, separate, environment which starts as a copy of the parent process's environment.
Any process (including sub-processes) can change their own environment. They cannot, however, change their parent's process's environment.
Running system() creates a new environment.
So when you call system() to set up your environment, it starts a new sub-process with a new environment. Your batch program then changes this new environment. But then the sub-process exits and its environment ceases to exist - taking all of the changes with it.
You need to run the batch file in a parent process, before running your Perl program.
I have tried running a script in the MATLAB command line and it says
>> run(ex1)
Undefined function or variable 'ex1'.
>> run(exp1.m)
Undefined variable "exp1" or function "exp1.m".
You're using run wrong. You need to encapsulate the script name as a string:
>> run('ex1.m');
You'll need to make sure that your working directory is set to where the script is located, because the above way to call run assumes local referencing.
Please read the documentation on run in the future: http://www.mathworks.com/help/matlab/ref/run.html
However, you can just type in ex1 in the command prompt and it'll still work... as long as you're in the working directory of where the script is run, and ensuring that you don't have any variables in your workspace that have the same name as the script file:
>> ex1
I run the Lua script using command line:
scipt.lua arg
But when I want to print the value arg1 in script:
print(arg[1])
Result is nil.
When I try to run it like:
lua script.lua arg
It returns not recognized command for windows.
What I am doing wrong? How can I get parameters from command line?
I don't see any problem with your example. Since you are able to run this command, but do not get any arguments passed, it's possible that whatever script registered the association, didn't use the syntax for passing arguments. You can find the registered association and check the command to make sure it includes %* to pass all the parameters to the script.
You can find where the executable is by using where lua.exe command and then call that executable directly from the command line to see if it works.
I have a series of perl scripts that I want to run one after another on a unix system. What type of file would this be / could I reference it as in documentation? BASH, BATCH, Shell Script File?
Any help would be appreciated.
Simply put the commands you would use to run them manually in a file (say, perlScripts.sh):
#!/bin/sh
perl script1.pl
perl script2.pl
perl script3.pl
Then from the command line:
$ sh perlScripts.sh
Consider using Perl itself to run all of the scripts. If the scripts don't take command line arguments, you can simply use:
do 'script1.pl';
do 'script2.pl';
etc.
do 'file_name' basically copies the file's code into the current script and executes it. It gives each file its own scope, however, so variables won't clash.
This approach is more efficient, because it starts only one instance of the Perl interpreter. It will also avoid repeated loading of modules.
If you do need to pass arguments or capture the output, you can still do it in a Perl file with backquotes or system:
my $output = `script3.pl file1.txt`; #If the output is needed.
system("script3.pl","file1.txt"); #If the output is not needed.
This is similar to using a shell script. However, it is cross-platform compatible. It means your scripts only rely on Perl being present, and no other external programs. And it allows you to easily add functionality to the calling script.