NHP-pRF/Analysis_code/LISA/Prep/pRF_CreateParallel4LISA_worker_ephys.m

function pRF_CreateParallel4LISA_worker_ephys(...
    parallel_fun, joblist, parallel_fun_dir, job_name)

% This function serves to create parallel Jobs for a given script
% to parallalise it for a given list of jobs.
%
% Therefore, it creates executable sh-scripts, which execute each single
% job, as well as one script which passes all the single job scripts to
% the cluster computer. (LISA @ SurfSara).
%
% This version requsts 600MB free on the host machine. If your job does not
% require free memory (also matlab already needs quite a bit), use
% create_parallel_nomem.m.
%
% IMPORTANT: The function runs on linux: all pathes must be linux style
%
% PARAMETERS
%   parallel_fun: name of the function (e.g. 'example_function', NOT
%               'example_script.m', 'example_function()', etc.). This
%               function must take exactly 1 argument as input. For an
%               example, see parallel_example_fun.m;
%
%   joblist: a structure with information on what jobs to create, with how
%               many parallel processes, and how to split volumes in
%               slice-chunks
%
%   parallel_fun_dir: path to parallel_fun, will be used to add to the
%               matlab path on the remote machines
%
% OPTIONAL
%   job_name: string to identify your job. Subdirectories with this name will
%       be created inside the specified batch directory and the log
%       directory, so that multiple jobs can be executed at the same time.
%       If no jobname is given, the name of prallel_fun together with the
%       current date and time will be used as job name.

%% basic input checks -----------------------------------------------------
% check if parallel_fun ends with .m or ()
if length(parallel_fun) >= 2 && (strcmp(parallel_fun(end-1:end), '.m') || ...
        strcmp(parallel_fun(end-1:end), '()'))
    parallel_fun = parallel_fun(1:end-2);
end

%% set parameters ---------------------------------------------------------
% default name for jobs
if ~exist('job_name', 'var')
    job_name = [parallel_fun '_' datestr(now, 'yyyymmddTHHMMSS')];
end

% project_dir on LISA
project_dir = '/home/pcklink/PRF'; % must be the ABSOLUTE path
% log dir on LISA
log_file_dir = [project_dir '/Logs/']; % add jobname
% set local log folder
log_file_dir_local = [pwd '/Logs/']; % add jobname
% job files will be locally written to:
cd ..
batch_dir = fullfile(pwd, 'Jobs', ['JOBS_' job_name]); % add jobname

%% location of scripts ----------------------------------------------------
% set location of execute_matlab_process.sh
execute_matlab_process_sh = ['$TMPDIR/PRF/BashScripts/'...
    'pRF_run_analyzePRF_LISA_ephys.sh']; % must be ABSOLUTE path

%% PROCESSING STARTS FROM HERE (no more parameters to check) ==============
%% create batch & log folder ----------------------------------------------
disp('Creating batch & log folders')
[success, message] = mkdir(batch_dir);
if ~success
    error(['Could not create directory for batch_dir: ' message])
end

if ispc
    error('Windows will not work due to path definitions. Run on Linux')
else
    [success, message] = mkdir(log_file_dir_local);
    if ~success
        error(['Could not create directory for log_file_dir_local: ' message])
    end
end

%% Check if main batch files already exists -------------------------------
% set initial behaviour, if you want to overwrite sh-files which are there
overwrite_file = 'ask';
disp('Creating batch files')

% check if main sh-file to start all jobs exists
filename_all = sprintf(['send_all_prf-fitting_jobs_' joblist.monkey '.sh']);
fullfilename_all = [batch_dir '/' filename_all];
if exist(fullfilename_all, 'file')
    disp(' ')
    disp(['File ' fullfilename_all ' already exist.'])
    overwrite_file = input('Should it be overwritten? [y, n, a (all)]: ', 's');
    if ~(strcmpi(overwrite_file, 'y') || strcmpi(overwrite_file, 'a'))
        error(['File ' filename_all ' already exists and should not be '...
            'overwritten. Solve problem and start again.'])
    end
    delete(fullfilename_all)
end

%% Create the batch files -------------------------------------------------
% The main batch file handles passing the single job batch files to the
display(['Creating main batch file: ' fullfilename_all])
fid_commit_all = fopen(fullfilename_all, 'w');

% ensure that the right shell is used !#/bin/sh
fprintf(fid_commit_all, '#!/bin/bash\n');
% add comment that THIS file submits the stuff to condor
fprintf(fid_commit_all, '#\n');
fprintf(fid_commit_all, ['# This bash-script submits all jobs to the server, '...
    'instead of running them locally.\n']);
fprintf(fid_commit_all, ['# If you want to submit only some jobs to the server,'...
    'simply add a "#" in front of \n' ...
    '#the ones you like to ommit and execute the script then.\n']);
fprintf(fid_commit_all, '#\n');
fprintf(fid_commit_all, '\nmkdir -p $HOME/PRF/Logs/slurm\n');
fprintf(fid_commit_all, 'cd $HOME/PRF/Logs/slurm\n');
fprintf(fid_commit_all, 'chmod +x $HOME/PRF/Code/Jobs/*\n\n');

% create all single job batchfiles, and add for each a call in the main
% batch file
for job_ind = 1:length(joblist.sessinc)
    for job_ind2 = 1:length(joblist.instances)
        %% create batchfile for current job -------------------------------
        % create/overwrite file
        filename = sprintf('run_job_Ses-%s_%s_%s_%s.sh', joblist.sessions{...
            joblist.sessinc(job_ind),1},num2str(job_ind2),job_name,joblist.monkey);
        fullfilename = [batch_dir '/' filename];
        
        disp(['Creating Batch file for Job ' num2str(job_ind) '_' num2str(job_ind2) ': ' fullfilename])
        if exist(fullfilename, 'file')
            if ~strcmpi(overwrite_file, 'a')
                disp(' ')
                disp(['File ' fullfilename ' already exist.'])
                overwrite_file = input('Should it be overwritten? [y, n, a (all)]: ', 's');
                if ~(strcmpi(overwrite_file, 'y') || strcmpi(overwrite_file, 'a'))
                    error(['File ' filename ' already exists and should not be '...
                        'overwritten. Solve problem and start again.'])
                end
            end
            delete(fullfilename)
        end
        
        % open single subject file
        fid_single = fopen(fullfilename , 'w');
 
        % ==== SLURM ====
        % ensure that the right shell is used !#/bin/bash
        fprintf(fid_single, '#!/bin/bash\n');
        % SLURM definitions
        fprintf(fid_single, '#SBATCH -N 1 --ntasks-per-node=16\n');
        fprintf(fid_single, '#SBATCH -t 05:00:00\n');
        fprintf(fid_single, '#SBATCH --mail-type=END\n');
        fprintf(fid_single, '#SBATCH --mail-user=p.c.klink@gmail.com\n');
        fprintf(fid_single, '\n');
        
        fprintf(fid_single, 'source ~/.bash_profile\n'); 
        fprintf(fid_single, 'source ~/.bashrc\n');
        fprintf(fid_single, 'umask u+rwx,g+rwx\n\n');

        % information
        fprintf(fid_single, 'echo job id $SLURM_JOBID\n');
        fprintf(fid_single, 'echo job name $SLURM_JOB_NAME\n');
        fprintf(fid_single, 'echo submitted by $SLURM_JOB_ACCOUNT\n');
        fprintf(fid_single, 'echo from $SLURM_SUBMIT_DIR\n');
        fprintf(fid_single, 'echo the allocated nodes are: $SLURM_JOB_NODELIST\n');
        
        % SLURM requirements
        fprintf(fid_single, '\nmodule load pre2019\n');

        
        % add a comment what this script does
        jobnameline = ['\n# INFO: ' job_name '_' joblist.sessions{...
            joblist.sessinc(job_ind),1} '_' ...
            joblist.instances{job_ind2} '\n'];
        try
            fprintf(fid_single, jobnameline);
        catch ME
            disp(ME);
        end
        
        fprintf(fid_single, '\n');
        
        fprintf(fid_single,'mkdir -p $TMPDIR/PRF\n');
        fprintf(fid_single,'mkdir -p $TMPDIR/PRF/Logs/\n');
%         fprintf(fid_single,['cp -r $HOME/PRF/Data/' joblist.type '/' joblist.monkey '/' ...
%             joblist.sessions{joblist.sessinc(job_ind),1} '* $TMPDIR/PRF\n']);
        fprintf(fid_single, 'cp -r $HOME/PRF/Code/* $TMPDIR/PRF\n');
        fprintf(fid_single,'cd $TMPDIR/PRF\n\n');
        fprintf(fid_single,['chmod +x ' execute_matlab_process_sh '\n\n']);
        % exec parfun (Monkey,Session,Slices,HRF,numWorkers,modeltype,cv)
        line = sprintf('%s \\\n\t%s %s %s %s [%s] \\\n\t%s %s %s %s %s \\\n\t', ...
            execute_matlab_process_sh, parallel_fun, ...
            joblist.monkey, joblist.sessions{joblist.sessinc(job_ind),1}, ...
            joblist.instances{job_ind2},...
            num2str(joblist.sessions{joblist.sessinc(job_ind),2}),...
            joblist.modeltype,...
            num2str(joblist.xvalmode),...
            joblist.resfld,...
            log_file_dir, parallel_fun_dir);
        logline= ['$TMPDIR/PRF/Logs/Log_' joblist.monkey '_'  ...
            joblist.sessions{joblist.sessinc(job_ind),1} '_' ...
            joblist.instances{job_ind2} '_' ...
            joblist.modeltype ...
            '_xval' num2str(joblist.xvalmode) '.txt'];
        fprintf(fid_single, '%s %s %s\n\n', line, '|& tee', logline);
        fprintf(fid_single,['cp ' logline ' $HOME/PRF/Logs/\n']);
        
        % finally: pass exit status of execute_matlab_process.sh to LISA
        fprintf(fid_single, 'exit $?\n');
        fclose(fid_single);
        
        disp(['Adding ' fullfilename ' to original batch file.']);
        
        fullfilename2 = ['$HOME/PRF/Code/Jobs/' filename];
        line = sprintf('%s %s', 'sbatch ', fullfilename2);
        fprintf(fid_commit_all, '%s\n', line);       
    end
    fprintf(fid_commit_all, '\n');
end
fclose(fid_commit_all);
system(['chmod +x ' fullfilename_all]);
end