How to run Matlab batch script and save the results











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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?










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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?










    share|improve this question


























      up vote
      2
      down vote

      favorite
      1









      up vote
      2
      down vote

      favorite
      1






      1





      #!/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?










      share|improve this question















      #!/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






      share|improve this question















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      edited Nov 9 at 6:21









      Compo

      15.3k3926




      15.3k3926










      asked Nov 9 at 3:39









      vera_kkk

      113




      113
























          1 Answer
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          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).






          share|improve this answer























          • 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











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          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).






          share|improve this answer























          • 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















          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).






          share|improve this answer























          • 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













          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).






          share|improve this answer














          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).







          share|improve this answer














          share|improve this answer



          share|improve this answer








          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


















          • 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


















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