Loop through files of remote server

I'm using matlab to perform simulations on a cluster, where the jobs are submitted from a local machine through matlab to the cluster.

A sample submission script might look like this:

%%Get handle to the job scheduler
sched = findResource();

%%Create a job
job = createJob(sched, 'FileDependencies', {'Analysis.m'});

%%Create the tasks
filelist=dir('/dir1/dir2/')
for tidx = 1:length(filelist)
   tasks(tidx) = createTask(job,@Analysis, 1, {tidx}); 
end

%%Submit the job
submit(job)

I'm now trying to obtain and loop through some files on the cluster and run a script on the files, say, Analysis.m

How would I do this to get a file list on the cluster and not on the local machine from which the job-scheduling, and then pass each file to the Analysis.m one at a time?

Answer 1

[Edric Ellis]

Perhaps a PARFOR loop on the cluster would be simplest. Something like this:

     function x = doStuff
     % list the files on the cluster
     d = dir( '/path/on/cluster/*.dat' );

     % loop over the files - this will spread the work
     % among the workers
     parfor ii = 1:numel( d )
       x(ii) = someFcn( d(ii).name );
     end

Then, you need to submit 'doStuff' as a matlabpool job to the cluster, something like this:

     job = createMatlabpoolJob( sched, 'MaximumNumberOfWorkers', 4 );
     createTask( job, @doStuff, 1, ... );

Or, in this situation, you can even use the BATCH command to submit the job

     job = batch( @doStuff, 1, {}, 'Matlabpool', 4 );

[CP]

Sorry, I'm new to this part of matlab so I'm a bit confused. I don't think I'm supposed to run stuff from the cluster, I think I can only do it locally and submit the work there via the various commands to create jobs. In that case, wouldn't the line: d=dir() try to get directory listings from the local machine?

[CP]

Oh never mind, I didn't notice that the top part was a separate function. I'll give it a shot.

[CP]

Ok my attempt is below. It seems one of the workers exited and the local matlab showed the following message:

"Field reference for multiple structure elements that is followed by more reference blocks is an error"

There are no structures in the PrevTargAnalyze.m that is called, so any idea on what is causing the message? (the dir command is probably the only structure I see).

%%%%%%%%%%%%%%%%%%%%%%%%

%%----startJobs.m-----%%

%%%%%%%%%%%%%%%%%%%%%%%%

sched = findResource();

nlabs = 4;

job = createMatlabPoolJob(sched, 'FileDependencies', {'doJobs.m','PrevTargAnalyze.m'}, 'MinimumNumberOfWorkers', nlabs, 'MaximumNumberOfWorkers', nlabs);

task = createTask(job, @doJobs,1,{});

submit(job)

waitForState(job, 'finished')

if ~isempty(task.ErrorMessage)

disp(task.ErrorMessage)

else

y = getAllOutputArguments(job)

end

%%%%%%%%%%%%%%%%%%%%%%%

%%-----doJobs.m------%%

%%%%%%%%%%%%%%%%%%%%%%%

function x = doJobs

dirlist=dir('/scratch/harry/SpatialWM/delay/');

for idxd = 1:length(dirlist)

%grab current target neuron upper and lower range from directory

name

[i j]=strread(dirlist.name(idxd), '%s %s', 'delimiter', '-');

%Set slice time to analyze

sliceTime=2500;

filedir=['/scratch/harry/SpatialWM/delay/' dirlist.name(idxd)];

filelist = dir([filedir '*.dat']);

parfor idxf = 1:length(filelist)

PrevTargAnalyze(['/scratch/harry/SpatialWM/delay/' dirlist(idxd).name '/' filelist(idxf).name],i,j,sliceTime);

end

end

[CP]

Ok I managed to fix everything and got this to work. There's only one issue with it, in that it is limited to 16 workers (server setting) per job. How can I split this into several jobs using this method?

Answer 2

[Walter Roberson]

You have dirlist.name(idxd) but that should be dirlist(idxd).name

[CP]

Thanks, I then got the message Output argument "x" not assigned, and fixed that by changing function x = doJobs to function doJobs() and now I'm getting "Too many output arguments." This is extremely hard to debug without line numbers, is there some way I can retrieve those, as I don't want to be spamming the forum for every little trivial error.

[CP]

I also tried reverting back to:

function x = dojobs

and adding an output to PrevTargAnalyze function as well, and then doing x = PrevTargAnalyze inside the parfor, and it still complains that x is not assigned =/