[Condor-users] anyone with experience with matlab

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I have been trying to set up condor with matlab for quite a while. I have simplified my matlab code that I am trying to run and am still having difficulty get the results. It seems as if Condor is returning results before matlab has a chance to finish completing the tasks. I am using the matlab distributed computing engine but am just asking for help from anyone that is familiar with matlab. I am going to paste my code below and was wondering if someone could take a look at it and see if there seems to be any glaring mistakes that my team and I can not figure out.

First, I have a m file named trial.m. this is the code that I want to run and get results from.

function trial()

jm = findResource('scheduler','configuration', 'generic');

set(jm,'configuration','generic');

job1 = createJob(jm);

createTask(job1, @sum, 1, {[1 1]});

createTask(job1, @sum, 1, {[2 2]});

createTask(job1, @sum, 1, {[3 3]});

createTask(job1, @sum, 1, {[4 4]});

submit(job1);

waitForState(job1, 'finished', 60)

results = getAllOutputArguments(job1)

Next, is my submit function through matlab

function submitfcn(scheduler, job, props, extraCondorSubmitArgs) %#ok Not using job

%SUBMITFCN Submit a Matlab job to a Condor scheduler

% See also workerDecodeFunc.

% Assign the relevant values to environment variables, starting

% with identifying the decode function to be run by the worker:

decodeFcn = 'workerDecodeFunc';

if nargin < 4

extraCondorSubmitArgs = '';

end

% Ask the workers to print debug messages by default by setting MDCE_DEBUG to

% true.

jobEnvVars = {'MDCE_DECODE_FUNCTION',decodeFcn, ...

...%' MDCE_STORAGE_LOCATION',props.StorageLocation, ...

' MDCE_STORAGE_CONSTRUCTOR',props.StorageConstructor, ...

' MDCE_JOB_LOCATION',props.JobLocation, ...

' MDCE_DEBUG','true'};

taskEnvVars = cell(1, numel(props.TaskLocations));

for i = 1:numel(props.TaskLocations)

taskEnvVars{i} = {'MDCE_TASK_LOCATION', props.TaskLocations{i}};

end

if isempty(scheduler.ClusterMatlabRoot)

warning('distcomp:condor:NoClusterMatlabRoot', ...

['The scheduler''s ClusterMatlabRoot property is empty.\n', ...

'Using matlabroot instead.']);

clusterMatlabRoot = matlabroot;

else

clusterMatlabRoot = scheduler.ClusterMatlabRoot;

end

matlabScript = fullfile(clusterMatlabRoot, 'bin', 'matlab');

% ... Do we need the following ??? ...

if ispc

matlabScript = [matlabScript, '.bat'];

end

matlabArgs = strrep(scheduler.matlabCommandToRun, 'matlab ', '');

% Determine where to save the standard output, standard error and the

% Condor log.

logFiles = cell(1, props.NumberOfTasks);

outFiles = cell(1, props.NumberOfTasks);

errFiles = cell(1, props.NumberOfTasks);

for i = 1:props.NumberOfTasks

taskLoc = fullfile(scheduler.DataLocation, props.TaskLocations{i});

logFiles{i} = [taskLoc, '.log'];

outFiles{i} = [taskLoc, '.out'];

errFiles{i} = [taskLoc, '.err'];

end

% Create one condor submit file for all the tasks.

script = createCondorSubmitScript(matlabScript, matlabArgs, ...

jobEnvVars, taskEnvVars, ...

errFiles, outFiles, logFiles);

% Submit a Condor job that executes all the tasks:

...%[pathstr, name, ext, versn] = fileparts(script);

...% script2 = name;

% Execute the submit command on the remote host.

%copyfile(script, '.')

condorSubmitCommand = ['condor_submit ', script, ' ', extraCondorSubmitArgs];

[s, w] = system(condorSubmitCommand);

% Leave behind the necessary debugging information if the submission failed.

if s ~= 0

warning('distcomp:condor:SubmitFailed', ...

['Call to condor_submit failed with the following message:\n\n', ...

' %s\n\n', ...

'The submit command used was:\n\n %s\n\n', ...

'Not deleting the submission file %s.'], ...

w, condorSubmitCommand, script2);

else

% Display the Condor job number:

disp(w);

% Clean up:

delete(script);

% delete(script2);

end

function filename = createCondorSubmitScript(matlabScript, matlabArgs, jobEnvVars, taskEnvVars, errFiles, outFiles, logFiles)

%Create a Condor submit script that forwards the correct environment variables

%and executes Matlab.

% We assume that the decode function has been put on the path of the MATLAB

% workers, e.g. by putting it into $MATLABROOT/toolbox/local.

% Double all backslashes so fprintf prints out a single backslash.

matlabScript = strrep(matlabScript, '\', '\\');

matlabArgs = strrep(matlabArgs, '\', '\\');

jobEnvVars = strrep(jobEnvVars, '\', '\\');

for i = 1:numel(taskEnvVars)

taskEnvVars{i} = strrep(taskEnvVars{i}, '\', '\\');

end

outFiles = strrep(outFiles, '\', '\\');

errFiles = strrep(errFiles, '\', '\\');

logFiles = strrep(logFiles, '\', '\\');

condorHeader = [ 'Universe = vanilla\n', ...

'Executable = condor_exec.bat \n',... %s\n', ...

'Transfer_Executable = true\n', ...

'Requirements = (machine == "condor01.integrity-apps.com")\n'

];

taskString = ['Arguments = %s\n', ...

'Environment = "%s"\n', ...

...%'input = matlab_metadata.mat \n', ...

'Error = %s\n', ...

'Output = %s\n', ...

'Log = %s\n', ...

'should_transfer_files = YES \n',...

'transfer_input_files = matlab_metadata.mat, job1.in.mat, job1.common.mat, job1.state.mat, job1.out.mat \n', ...

'when_to_transfer_output = ON_EXIT \n',...

'notify_user = jrichardson@xxxxxxxxxxxxxxxxxx \n',...

'Queue\n\n'];

filename = tempname;

fid = fopen(filename, 'wt');

fprintf(fid, condorHeader, matlabScript);

for i = 1:numel(taskEnvVars)

% Create a cell-array of all the environment variables we want to set

% for the current task, and transform it into a string for the Condor

% script.

envString = createCondorEnvString({jobEnvVars{:}, taskEnvVars{i}{:}});

% Append a clause to the Condor script to queue the current task.

fprintf(fid, taskString, matlabArgs, envString, errFiles{i}, outFiles{i}, logFiles{i});

end

fclose(fid);

function envString = createCondorEnvString(envVars)

%envStr = createCondorEnvString(envVars)

% envVars should be a cell arra of even length. The even entries are

% the environment variables, the odd entries are their values.

% In Condor, environment variables are specified in UNIX as

% Environment = var1=val1;var2=val2;...varn=valn

% and on Windows, the separator is '|' instead of ';', i.e. the format is

% Environment = var1=val1|var2=val2|...varn=valn

if ispc

envSep = ' ';

else

envSep = ';';

end

envString = '';

for i = 1:2:numel(envVars)

envString = [envString, envVars{i}, '=', envVars{i + 1}, envSep];

end

Now is my executable that is being passed through condor. There might be a problem here. It calls worker.bat that starts matlab.bat which starts matlab. My argument is worker.bat

@echo off

IF EXIST "C:\MATLAB_DISTRIBUTED\R2007a\bin\" (SET DRIVELETTER=C)

SET DL=%DRIVELETTER%:\MATLAB_DISTRIBUTED\R2007a\bin\

IF EXIST "G:\MATLAB_DISTRIBUTED\R2007a\bin\" (SET DRIVELETTER=G)

SET DL=%DRIVELETTER%:\MATLAB_DISTRIBUTED\R2007a\bin\

echo %DL%

echo %DRIVELETTER% "is the DRIVELETTER "

SET TEMP=%_CONDOR_SCRATCH_DIR%

SET

%DL%%1

SET

Any suggestions will be greatly appreciated. Currently, I receive a message saying that the job is completed while tasks are still running and I get a result of an empty 4 x 0 array

Josh Richardson

Integrity Applications Incorporated Intern (IAI)

703-378-8672 ext 632

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[Condor-users] anyone with experience with matlab