How to run Matlab batch script and save the results
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2
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#!/bin/bash
###########################
#
#PBS -l nodes=1:ppn=12
#PBS -l walltime=00:30:00
XXXXXXXXXx and below is my script details about running matlab
I want to save the results from the trial.m however it does not work.
export JOBID=`echo "${PBS_JOBID}" | cut -d'.' -f1`
cd ${PBS_O_WORKDIR}
module load matlab/R2017b
matlab
trial.m
My script name: trial.m
How to save the results from trial.m to my environment?
In my trial.m matlab file, I have the following codes to display my results, does this work? betas and values are two vector of numbers
disp(betas);
disp(values);
save('parameters.mat','betas','values');
In addition, trial.m needs to call external functions that I saved in the same file, can it call automatically?
bash matlab sh
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up vote
2
down vote
favorite
#!/bin/bash
###########################
#
#PBS -l nodes=1:ppn=12
#PBS -l walltime=00:30:00
XXXXXXXXXx and below is my script details about running matlab
I want to save the results from the trial.m however it does not work.
export JOBID=`echo "${PBS_JOBID}" | cut -d'.' -f1`
cd ${PBS_O_WORKDIR}
module load matlab/R2017b
matlab
trial.m
My script name: trial.m
How to save the results from trial.m to my environment?
In my trial.m matlab file, I have the following codes to display my results, does this work? betas and values are two vector of numbers
disp(betas);
disp(values);
save('parameters.mat','betas','values');
In addition, trial.m needs to call external functions that I saved in the same file, can it call automatically?
bash matlab sh
add a comment |
up vote
2
down vote
favorite
up vote
2
down vote
favorite
#!/bin/bash
###########################
#
#PBS -l nodes=1:ppn=12
#PBS -l walltime=00:30:00
XXXXXXXXXx and below is my script details about running matlab
I want to save the results from the trial.m however it does not work.
export JOBID=`echo "${PBS_JOBID}" | cut -d'.' -f1`
cd ${PBS_O_WORKDIR}
module load matlab/R2017b
matlab
trial.m
My script name: trial.m
How to save the results from trial.m to my environment?
In my trial.m matlab file, I have the following codes to display my results, does this work? betas and values are two vector of numbers
disp(betas);
disp(values);
save('parameters.mat','betas','values');
In addition, trial.m needs to call external functions that I saved in the same file, can it call automatically?
bash matlab sh
#!/bin/bash
###########################
#
#PBS -l nodes=1:ppn=12
#PBS -l walltime=00:30:00
XXXXXXXXXx and below is my script details about running matlab
I want to save the results from the trial.m however it does not work.
export JOBID=`echo "${PBS_JOBID}" | cut -d'.' -f1`
cd ${PBS_O_WORKDIR}
module load matlab/R2017b
matlab
trial.m
My script name: trial.m
How to save the results from trial.m to my environment?
In my trial.m matlab file, I have the following codes to display my results, does this work? betas and values are two vector of numbers
disp(betas);
disp(values);
save('parameters.mat','betas','values');
In addition, trial.m needs to call external functions that I saved in the same file, can it call automatically?
bash matlab sh
bash matlab sh
edited Nov 9 at 6:21
Compo
15.3k3926
15.3k3926
asked Nov 9 at 3:39
vera_kkk
113
113
add a comment |
add a comment |
1 Answer
1
active
oldest
votes
up vote
4
down vote
Invoke MATLAB and execute trial.m
via the following command:
matlab -r trial -logfile logfile.log -nodisplay -nosplash
Make sure trial.m
exits MATLAB when it finishes, to continue executing any post-processing steps. You should also suppress the MATLAB GUI and Splash screens since the script is running non-interactively. Also make sure that trial.m
forces MATLAB to exit by using the exit
command.
Save the results of trial.m
to the environment by calling the save
function to create a .MAT file.
NOTE: To access the file using other software, save in CSV format by calling csvwrite.
csvwrite('betas.csv',betas);
csvwrite('values.csv',values);
MATLAB Alternative to Bash
Alternatively you could use MATLAB's parrallel computing toolbox to submit the job. In this case you no longer need the bash script. However, you would need to modify your MATLAB files to handle the job submission to the cluster (here).
do I need to add commands in matlab.m file indicating that I am running batch job through the cluster? I saw that R has similar function in script.pbs file R CMD BATCH indicating running batch job
– vera_kkk
Nov 22 at 18:17
@vera_kkk, see my edits. I hope they answer your question about what is needed to be done to prepare your job for submission.
– Azim
Nov 23 at 20:34
add a comment |
1 Answer
1
active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
up vote
4
down vote
Invoke MATLAB and execute trial.m
via the following command:
matlab -r trial -logfile logfile.log -nodisplay -nosplash
Make sure trial.m
exits MATLAB when it finishes, to continue executing any post-processing steps. You should also suppress the MATLAB GUI and Splash screens since the script is running non-interactively. Also make sure that trial.m
forces MATLAB to exit by using the exit
command.
Save the results of trial.m
to the environment by calling the save
function to create a .MAT file.
NOTE: To access the file using other software, save in CSV format by calling csvwrite.
csvwrite('betas.csv',betas);
csvwrite('values.csv',values);
MATLAB Alternative to Bash
Alternatively you could use MATLAB's parrallel computing toolbox to submit the job. In this case you no longer need the bash script. However, you would need to modify your MATLAB files to handle the job submission to the cluster (here).
do I need to add commands in matlab.m file indicating that I am running batch job through the cluster? I saw that R has similar function in script.pbs file R CMD BATCH indicating running batch job
– vera_kkk
Nov 22 at 18:17
@vera_kkk, see my edits. I hope they answer your question about what is needed to be done to prepare your job for submission.
– Azim
Nov 23 at 20:34
add a comment |
up vote
4
down vote
Invoke MATLAB and execute trial.m
via the following command:
matlab -r trial -logfile logfile.log -nodisplay -nosplash
Make sure trial.m
exits MATLAB when it finishes, to continue executing any post-processing steps. You should also suppress the MATLAB GUI and Splash screens since the script is running non-interactively. Also make sure that trial.m
forces MATLAB to exit by using the exit
command.
Save the results of trial.m
to the environment by calling the save
function to create a .MAT file.
NOTE: To access the file using other software, save in CSV format by calling csvwrite.
csvwrite('betas.csv',betas);
csvwrite('values.csv',values);
MATLAB Alternative to Bash
Alternatively you could use MATLAB's parrallel computing toolbox to submit the job. In this case you no longer need the bash script. However, you would need to modify your MATLAB files to handle the job submission to the cluster (here).
do I need to add commands in matlab.m file indicating that I am running batch job through the cluster? I saw that R has similar function in script.pbs file R CMD BATCH indicating running batch job
– vera_kkk
Nov 22 at 18:17
@vera_kkk, see my edits. I hope they answer your question about what is needed to be done to prepare your job for submission.
– Azim
Nov 23 at 20:34
add a comment |
up vote
4
down vote
up vote
4
down vote
Invoke MATLAB and execute trial.m
via the following command:
matlab -r trial -logfile logfile.log -nodisplay -nosplash
Make sure trial.m
exits MATLAB when it finishes, to continue executing any post-processing steps. You should also suppress the MATLAB GUI and Splash screens since the script is running non-interactively. Also make sure that trial.m
forces MATLAB to exit by using the exit
command.
Save the results of trial.m
to the environment by calling the save
function to create a .MAT file.
NOTE: To access the file using other software, save in CSV format by calling csvwrite.
csvwrite('betas.csv',betas);
csvwrite('values.csv',values);
MATLAB Alternative to Bash
Alternatively you could use MATLAB's parrallel computing toolbox to submit the job. In this case you no longer need the bash script. However, you would need to modify your MATLAB files to handle the job submission to the cluster (here).
Invoke MATLAB and execute trial.m
via the following command:
matlab -r trial -logfile logfile.log -nodisplay -nosplash
Make sure trial.m
exits MATLAB when it finishes, to continue executing any post-processing steps. You should also suppress the MATLAB GUI and Splash screens since the script is running non-interactively. Also make sure that trial.m
forces MATLAB to exit by using the exit
command.
Save the results of trial.m
to the environment by calling the save
function to create a .MAT file.
NOTE: To access the file using other software, save in CSV format by calling csvwrite.
csvwrite('betas.csv',betas);
csvwrite('values.csv',values);
MATLAB Alternative to Bash
Alternatively you could use MATLAB's parrallel computing toolbox to submit the job. In this case you no longer need the bash script. However, you would need to modify your MATLAB files to handle the job submission to the cluster (here).
edited Nov 23 at 20:34
answered Nov 9 at 6:35
Azim
6,48063257
6,48063257
do I need to add commands in matlab.m file indicating that I am running batch job through the cluster? I saw that R has similar function in script.pbs file R CMD BATCH indicating running batch job
– vera_kkk
Nov 22 at 18:17
@vera_kkk, see my edits. I hope they answer your question about what is needed to be done to prepare your job for submission.
– Azim
Nov 23 at 20:34
add a comment |
do I need to add commands in matlab.m file indicating that I am running batch job through the cluster? I saw that R has similar function in script.pbs file R CMD BATCH indicating running batch job
– vera_kkk
Nov 22 at 18:17
@vera_kkk, see my edits. I hope they answer your question about what is needed to be done to prepare your job for submission.
– Azim
Nov 23 at 20:34
do I need to add commands in matlab.m file indicating that I am running batch job through the cluster? I saw that R has similar function in script.pbs file R CMD BATCH indicating running batch job
– vera_kkk
Nov 22 at 18:17
do I need to add commands in matlab.m file indicating that I am running batch job through the cluster? I saw that R has similar function in script.pbs file R CMD BATCH indicating running batch job
– vera_kkk
Nov 22 at 18:17
@vera_kkk, see my edits. I hope they answer your question about what is needed to be done to prepare your job for submission.
– Azim
Nov 23 at 20:34
@vera_kkk, see my edits. I hope they answer your question about what is needed to be done to prepare your job for submission.
– Azim
Nov 23 at 20:34
add a comment |
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