-----Original
Message-----
From:
condor-users-bounces@xxxxxxxxxxx [mailto:condor-users-bounces@xxxxxxxxxxx]
On Behalf Of Richardson,
Joshua
Sent: Thursday,
August 02, 2007 13:32
To:
Condor-Users Mail
List
Subject: [Condor-users] anyone with
experience with matlab
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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