Sponsored Content
Full Discussion: qsub and Matlab
Top Forums UNIX for Dummies Questions & Answers qsub and Matlab Post 302141901 by laether on Tuesday 23rd of October 2007 09:41:28 AM
Old 10-23-2007
Question qsub and Matlab

I am trying to run a Matlab function, file.m, with qsub. Here is a portion of my .sge file:

echo Starting to run Matlab
matlab -nojvm -nodesktop -r "file('${inputfile}');exit;"
echo finished running Matlab

The last two lines of the Matlab function are:

disp('finished');
exit

So my problem is this: The Matlab function runs fine, I haven't checked to see if it saves the .mat file, but the input file is what it should be, and it displays "finished" in the .o output file, and there are no errors. But I think that after it exits Matlab, UNIX doesn't know that it's finished because the "echo finished running Matlab" in the .sge file does not happen. It gets hung up after the "exit;" and stays in the "r" state when I qstat.

Does anyone have an idea of why this happens and how to fix it?

I can tell you that if I type in the "matlab -nojvm ..." line at the command line in my terminal, it runs fine, no errors, and exits Matlab like it should, and saves the .mat file.

What I don't want is to have to write a Matlab script...the codes right now are nice and compact and I have to pass an input file to the function. I could write a new UNIX script and just put the input file loop in the function and run it at the command line without qsub, but I've written this sge script and I'd like to see it work if it can.

Thanks.
 

10 More Discussions You Might Find Interesting

1. UNIX for Advanced & Expert Users

Problem Running qsub multiple jobs

Hello, I have a perl script that takes in one file of input and outputs to a file. I would like to run this script on several input files, and I would like to run it with qsub, something like this: Input files: FileListDssp.txt.numaa FileListDssp.txt.numab FileListDssp.txt.numac etc.. ... (1 Reply)
Discussion started by: InfoSeeker
1 Replies

2. Shell Programming and Scripting

qsub

Hey all, I have a binary file, named "exe1" that receives a parameter. (I don't have its source code). Executing "exe1" results in creating 3 output files. I have a bash script that runs "exe1". I want to enter "exe1" to cluster queue (using subq command) But i want to do it more than... (1 Reply)
Discussion started by: elad2109
1 Replies

3. UNIX for Dummies Questions & Answers

Help with Weighted Regression in Matlab

I need to weight the regression I am performing on a data file. I am not using all the numbers in the file. Here are my variables: Y = data(,1) X has the same bracketed first term, and the second term is I have eight different weights I want to give, one weight corresponding to two different... (0 Replies)
Discussion started by: kssteig
0 Replies

4. Shell Programming and Scripting

qsub in a bash script?

I was just wondering if it is permissible to qsub from a bash script as follows: #! /bin/sh echo "altering .txt in dir $DIR with retokenize.py" for f in $DIR/txt/*.txt; do echo $f; /l2/nlp/i2b2/retokenize.py < $f > ${f//.txt/.tok}; done echo "altering .tok in dir $DIR with awk... (0 Replies)
Discussion started by: kcgb20
0 Replies

5. UNIX for Dummies Questions & Answers

Qsub and printf

Hello, I have some issue with qsub and the standard output : I launch a script that "echoes" the string "abc" and then executes a C program in which I print informations with the printf function ; the .o file contains "abc" but not the information displayed by printf. I also tried... (0 Replies)
Discussion started by: Shaderw
0 Replies

6. UNIX for Advanced & Expert Users

Collecting job id from qsub command

Hello. Hopefully this is the right forum, did a search and found some similar questions here. I'm trying to find out if there is a way to get the job id while submitting a job using qsub. I want to monitor the list of active jobs using qstat and when my jobid is no longer on the active list, I... (3 Replies)
Discussion started by: aeoleon88
3 Replies

7. UNIX for Dummies Questions & Answers

qsub equivalent of bsub command

"bsub -o /dev/null -P something -q normal -a optimize -n 1 -R \"rusage\ span\\" -J GUISETUP_${PID} \"dc_shell-t -f .dc_script_$job_index.tcl -output_log_file .dc_shell_$job_index.log \"" Can anybody please tell me the qsub equivalent for this command? ---------- Post updated at 06:48 AM... (0 Replies)
Discussion started by: chaudhary3031
0 Replies

8. UNIX for Advanced & Expert Users

Submitting multiple qsub jobs

Hi all, Today, I want to ask how to submit multiple qsub jobs. I want to submit 100 .sh files for the simulations. The name of files is run_001.sh, run_002.sh, run_003.sh, ..... ..... run_100.sh Submitting each file manually are time-consuming, hence, I want to make another .sh file... (11 Replies)
Discussion started by: syg3434
11 Replies

9. Shell Programming and Scripting

Qsub + job array + while read; do; done

Linux Server Hi! just some help... I'm using a "Sun Grid Engine" with "qsub" In one hand I have this code while read -r H; do echo ${H}; done < list The number of the lines in the list file is 100. On the other hand I want to create a job array with the option -t echo... (3 Replies)
Discussion started by: echo manolis
3 Replies

10. Shell Programming and Scripting

Submit a qsub script SGE

Hello, I'm working on a SGE cluster and trying to echo the variables passed to the qsub command. My script is as follows #!/bin/bash #$ -V #$ -cwd #$ -pe make 10 if ; then echo "Variable is not set" else echo "Variable says: $StatedUserName" fi and I run the... (1 Reply)
Discussion started by: nans
1 Replies
SCRIPT(1)						    BSD General Commands Manual 						 SCRIPT(1)

NAME
script -- make typescript of terminal session SYNOPSIS
script [-adfkpqr] [-F pipe] [-t time] [file [command ...]] DESCRIPTION
The script utility makes a typescript of everything printed on your terminal. It is useful for students who need a hardcopy record of an interactive session as proof of an assignment, as the typescript file can be printed out later with lpr(1). If the argument file is given, script saves all dialogue in file. If no file name is given, the typescript is saved in the file typescript. If the argument command is given, script will run the specified command with an optional argument vector instead of an interactive shell. The following options are available: -a Append the output to file or typescript, retaining the prior contents. -d When playing back a session with the -p flag, do not sleep between records when playing back a timestamped session. -F pipe Immediately flush output after each write. This will allow a user to create a named pipe using mkfifo(1) and another user may watch the live session using a utility like cat(1). -f Create file.filemon or typescript.filemon using filemon(4). -k Log keys sent to the program as well as output. -p Play back a session recorded with the -r flag in real time. -q Run in quiet mode, omit the start, stop and command status messages. -r Record a session with input, output, and timestamping. -t time Specify the interval at which the script output file will be flushed to disk, in seconds. A value of 0 causes script to flush after every character I/O event. The default interval is 30 seconds. The script ends when the forked shell (or command) exits (a control-D to exit the Bourne shell (sh(1)), and exit, logout or control-D (if ignoreeof is not set) for the C-shell, csh(1)). Certain interactive commands, such as vi(1), create garbage in the typescript file. The script utility works best with commands that do not manipulate the screen. The results are meant to emulate a hardcopy terminal, not an addressable one. ENVIRONMENT
The following environment variables are utilized by script: SCRIPT The SCRIPT environment variable is added to the sub-shell. If SCRIPT already existed in the users environment, its value is overwrit- ten within the sub-shell. The value of SCRIPT is the name of the typescript file. SHELL If the variable SHELL exists, the shell forked by script will be that shell. If SHELL is not set, the Bourne shell is assumed. (Most shells set this variable automatically). SEE ALSO
csh(1), filemon(4) (for the history mechanism). HISTORY
The script command appeared in 3.0BSD. The -d, -p and -r options first appeared in NetBSD 2.0 and were ported to FreeBSD 9.2. BUGS
The script utility places everything in the log file, including linefeeds and backspaces. This is not what the naive user expects. It is not possible to specify a command without also naming the script file because of argument parsing compatibility issues. When running in -k mode, echo cancelling is far from ideal. The slave terminal mode is checked for ECHO mode to check when to avoid manual echo logging. This does not work when the terminal is in a raw mode where the program being run is doing manual echo. If script reads zero bytes from the terminal, it switches to a mode when it only attempts to read once a second until there is data to read. This prevents script from spinning on zero-byte reads, but might cause a 1-second delay in processing of user input. BSD
December 4, 2013 BSD
All times are GMT -4. The time now is 06:44 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy