Error: Unexpected MATLAB operator on Cluster

Hi Everyone,

I'm very new to matlab programming language.

I have a directory "example_first" in which there are few matlab scripts and some input files on which I want to run the functions given in matlab scripts.

example_first
   ├──input.score
   ├──input.param
   ├──input.expr
   ├──shortmain.m
   ├──input.m
   ├──dist.m

I'm using linux terminal and on cluster (workload manager is Slurm) I created a shell script like below to submit the job.

#!/bin/bash
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=4G
#SBATCH --time=05:59:59
cd /home/documents/example_first
ml MATLAB/r2016a
matlab -nodisplay -nosplash -nojvm -r "run shortmain.m"
matlab -r 'shortmain(/home/documents/example_first/input.expr, /home/documents/example_first/input.score, /home/documents/example_first/input.param, Trans)'

Submitted the job like this:

sbatch test.sh

In the slurm.out file I see like following:

MATLAB is selecting SOFTWARE OPENGL rendering.
Opening log file:  /home/java.log.41769

                            < M A T L A B (R) >
                  Copyright 1984-2016 The MathWorks, Inc.
                   R2016a (9.0.0.341360) 64-bit (glnxa64)
                             February 11, 2016

 
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
 

        Academic License

 shortmain(/home/documents/example_first/input.expr, /home/documents/example_first/input.score, /home/documents/example_first/input.param, Trans)
              |
Error: Unexpected MATLAB operator.

Can anyone please help me how to resolve this error. This is the first time I'm using matlab.

Any help is appreciated. thanq.

[lu wang]

My guess is that it might related to how you pass the variables to your function inside the batch.

what is the Trans in your last function variable?

your code:

matlab -nodisplay -nosplash -nojvm -r "run shortmain.m"

matlab -r 'shortmain(/home/documents/example_first/input.expr, /home/documents/example_first/input.score, /home/documents/example_first/input.param, Trans)'

try this :

matlab -nodisplay -nosplash -nojvm -r "shortmain"

and put the path inside your shortmain.m by:

addpath('/home/documents/example_first/')

open and load the input.score, input.param inside the shortmain.m

hope this helps

Lu

[venkat K]

sorry, basically "shortmain.m" is matlab script in which shortmain function is given. I want to execute this shortmain function on the input.expr, input.score, input.param files. "Trans" is a name I should mention which is related to files, without this the function wont work.

Should I try the way you mentioned above?

Answer 1

[Walter Roberson]

matlab -r 'shortmain(''/home/documents/example_first/input.expr'', ''/home/documents/example_first/input.score'', ''/home/documents/example_first/input.param'', ''Trans'')'

or

matlab -r 'shortmain("/home/documents/example_first/input.expr", "/home/documents/example_first/input.score", "/home/documents/example_first/input.param", "Trans")'

or

matlab -r "shortmain('/home/documents/example_first/input.expr', '/home/documents/example_first/input.score', '/home/documents/example_first/input.param', 'Trans')"

[venkat K]

I tried this way already. I got the below error:

Error: The input character is not valid in MATLAB statements or expressions.

[Edric Ellis]

That error is because in R2016a, the double-quote character isn't valid. It can be tricky to get the quotes completely correct in these situations - but in this case, you could try to take advantage of MATLAB's command-dual syntax, and do something like

matlab -r "shortmain /home/documents/example_first/input.expr /home/documents/example_first/input.score /home/documents/example_first/input.param Trans"

[Walter Roberson]

Good point about R2016a and quotes.

My first and third should have worked in R2016a though.

[venkat K]

Wowww thanks a lot Edric Ellis. You are absolutely right and worked without any error. Thanks a lot again.

[venkat K]

Yes Walter Roberson, first and third of yours also worked for me. Yesterday, I tried the second and didn't try the other. Thanks a lot.