Example Jobs

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GCC 4.9.2

The default GCC for CentOS 6 is 4.4.7 which will be used when running your jobs. Please see this section regarding the use of GCC 4.9.2.

C example

The Problem and the Code

Consider the following simple, well-suited job for a cluster: comparison of independent Monte Carlo calculations of π. The following C-program implements random sampling of points withing a square bounding a circle. (The probability of landing inside the circle can be shown to be π/4)

#include <stdio.h>
#include <stdlib.h>
#include <time.h>

int main(int argc, char *argv[])
{
   int i,N,incirc=0;
   double x,y,circrad2;

   sscanf(argv[1], "%d", &N);         // get iteration number from input
   srand(time(NULL));                 // seed random number generator

   circrad2=1.0*RAND_MAX; 
   circrad2*=circrad2;                // Define radius squared

   for(i=0;i<N;i++){
      x=1.0*rand(); y=1.0*rand();     // get rand. point and
      incirc += (x*x+y*y) < circrad2; // check if inside circle
   }

   printf("pi=%.12f\n",4.0*incirc/N); // display probability
   return 0;
}

Compiling this program (that we may save as calcpi.c)

gcc calcpi.c -o calcpi

yields an executable calcpi that is ready for submission.

Preparation for Job Submission

To prepare the job execution space and inform Condor of the appropriate run environment, create a job description file (e.g. calcpi.condor)

Executable  = calcpi
Requirements = ParallelSchedulingGroup == "stats group"
+AccountingGroup = "group_statistics_testjob.username"
Universe   = vanilla
output     = calcpi$(Process).out
error      = calcpi$(Process).err
Log        = calcpi.log
Arguments  = 100000000
should_transfer_files = YES
when_to_transfer_output = ON_EXIT
Queue 50

The last line specifies that 50 instances should be scheduled on the cluster. The description file specifies the executable and the arguments passed to it during execution. (In this case we are requesting that all instances iterate 10e9 times in the program's sampling loop.) The requirement field insists that the job stay on the Statistics Cluster. (All statistics nodes are labeled with "stats group" in their Condor ClassAds) Output and error files are targets for standard out and standard error streams respectively. The log file is used by Condor to record in real time the progress in job processing. Note that this setup labels output files by process number to prevent a job instance from overwritting files belonging to another. The current values imply that all files are to be found in the same directory as the description file.

Note that this example uses the Accounting Group "group_statistics_testjob" with the user's username appended at the end. If running a default, standard job, do not include this line. For more explanation, please see this page on Job Policy.

The universe variable specifies the condor runtime environment. For the purposes of these independent jobs, the simplest "vanilla" universe suffices. In a more complicated parallel task, with checkpointing and migration, MPI calls etc., more advanced run-time environments are employed, often requiring specilized linking of the binaries. The lines specifying transfer settings are important to avoid any assumptions about accessibility over nfs. They should be included whether or not any output files (aside from standard output and error) are necessary.

Job Submission and Management

While logged in on stats, the job is submitted with:

condor_submit calcpi.condor

The cluster can be queried before or after submission to check its availability. Two very versatile commands exist for this purpose: condor_status and condor_q. The former returns the status of the nodes (broken down by virtual machines that can each handle a job instance.) The latter command shows the job queue including the individual instances of every job and the submission status (e.g. idling, busy etc.) Using condor_q a few seconds after submission shows:

-- Submitter: stat31.phys.uconn.edu : <192.168.1.41:44831> : stat31.phys.uconn.edu
 ID      OWNER            SUBMITTED     RUN_TIME ST PRI SIZE CMD
  33.3   prod            1/30 15:37   0+00:00:02 R  0   9.8  calcpi 100000000
  33.4   prod            1/30 15:37   0+00:00:00 R  0   9.8  calcpi 100000000
  33.5   prod            1/30 15:37   0+00:00:00 R  0   9.8  calcpi 100000000
  33.6   prod            1/30 15:37   0+00:00:00 R  0   9.8  calcpi 100000000
  33.7   prod            1/30 15:37   0+00:00:00 R  0   9.8  calcpi 100000000
  33.8   prod            1/30 15:37   0+00:00:00 R  0   9.8  calcpi 100000000

6 jobs; 0 idle, 6 running, 0 held

By this time, only 6 jobs are left on the cluster, all with status 'R' - running. Various statistics are given including a job ID number. This handle is useful if intervention is required like manual removal of frozen job instances from the cluster. Now, comparing the results (e.g. with command cat calcpi*.out) shows

...
pi=3.141215440000
pi=3.141447360000
pi=3.141418120000
pi=3.141797520000
...

R example

The Problem and the Code

Consider the following simple, well-suited job for a cluster: independent Monte Carlo calculations of π. The following R-program implements random sampling of points withing a square bounding a circle. (The probability of landing inside the circle can be shown to be π/4)

#!/home/statsadmin/R/bin/Rscript

# Prepare: collect command line arguments,
# set iteration number and a unique seed
args <- commandArgs()
set.seed(Sys.time())
n <- as.numeric(args[length(args)-1])

# Collect n samples
x <- runif(n)
y <- runif(n)

# Compute and output the value of pi
pihat <- sum(x * x + y * y < 1) / n * 4
pihat
write(pihat, args[length(args)])
proc.time()

Let us save this script as calcpi.R. Note the very important first line of this script. Without it, executing the script would require a command like Rscript calcpi.R Specifying the location of the interpreter in the first line after '#!' and adding the permission to execute this script with a command:

chmod a+x calcpi.R

greatly simplifies the handling of this program - especially useful for submission to the cluster.

Preparation for Job Submission

To prepare the job execution space and inform Condor of the appropriate run environment, create a job description file (e.g. Rcalcpi.condor)

executable = calcpi.R
universe = vanilla
Requirements = ParallelSchedulingGroup == "stats group"
+AccountingGroup = "group_statistics_testjob.username"

should_transfer_files = YES
when_to_transfer_output = ON_EXIT

arguments = 10000000 pihat-$(Process).dat
output    = pi-$(Process).Rout
error     = pi-$(Process).err
log       = pi.log

Queue 50

The last line specifies that 50 instances should be scheduled on the cluster. The description file specifies the executable, an independent process universe called "vanilla" and a requirement that the job should be confined on the Statistics Cluster. Next, the important "transfer files" parameters specify that any necessay input files (not relevant here) should be transfered to the execution nodes and all files generated by the program should be transfered back to the launch directory. (These avoid any assumptions about directory accessibility over nfs.)

The arguments to be passed to the executable are just what the script expects: iteration number and output file name. The output, error and log file parameters represent the stdout, stderr and Condor job log target files respectively. Note the unique labeling of these files according to the associated process with the $(Process) place holder.

Job Submission and Management

The job is submitted with:

condor_submit Rcalcpi.condor

The cluster can be queried before or after submission to check its availability. Two very versatile commands exist for this purpose: condor_status and condor_q. The former returns the status of the nodes (broken down by virtual machines that can each handle a job instance.) The latter command shows the job queue including the individual instances of every job and the submission status (e.g. idling, busy etc.) Using condor_q some time after submission shows:

-- Submitter: stat31.phys.uconn.edu : <192.168.1.41:44831> : stat31.phys.uconn.edu
 ID      OWNER            SUBMITTED     RUN_TIME ST PRI SIZE CMD
   7.0   stattestusr     3/25 15:03   0+00:00:00 R  0   9.8  calcpi.R 10000000
   7.6   stattestusr     3/25 15:03   0+00:00:04 R  0   9.8  calcpi.R 10000000
   7.10  stattestusr     3/25 15:03   0+00:00:00 R  0   9.8  calcpi.R 10000000
   7.28  stattestusr     3/25 15:03   0+00:00:00 R  0   9.8  calcpi.R 10000000
   7.45  stattestusr     3/25 15:03   0+00:00:00 R  0   9.8  calcpi.R 10000000
   7.49  stattestusr     3/25 15:03   0+00:00:00 R  0   9.8  calcpi.R 10000000

6 jobs; 0 idle, 6 running, 0 held

By this time, only 6 jobs are left on the cluster, all with status 'R' - running. Various statistics are given including a job ID number. This handle is useful if intervention is required like manual removal of frozen job instances from the cluster. A command condor_rm 7.28 would remove just that instance, whereas condor_rm 7 will remove this entire job. Now, comparing the results (e.g. with command cat pihat-*.dat) shows

...
3.141672
3.141129
3.14101
3.142149
3.141273
...

Matlab example

The Problem and Code

Matlab can be run in batch mode (i.e. non-interactive mode) on the cluster. No graphics can be used when running on the cluster. The following example demonstrates a simple Matlab example which saves the output to be opened later in Matlab interactively.

File: Matlab_example.m

% A linear regression example file to be executed

x = 0:0.01:1;
y = 1+2*x+2*x.^2+randn(1,length(x));

P = polyfit(x,y,2);

filename = 'regression.mat';
save(filename)

Preparation for Job Submission

To prepare the job execution space and inform Condor of the appropriate run environment, create a job description file (e.g. matlab.condor)

executable = /bin/bash
universe = vanilla
Requirements = ParallelSchedulingGroup == "stats group"
+AccountingGroup = "group_statistics_testjob.username"
initialdir = /path/to/your/jobs/directory
transfer_input_files = Matlab_example.m, runMatlab
should_transfer_files = YES
when_to_transfer_output = ON_EXIT
on_exit_remove = (ExitCode =?= 0)
transfer_output_remaps = "regression.mat = /path/to/your/jobs/directory/regression-$(Process).mat"
request_cpus = 1

arguments = runMatlab
output    = matlab-$(Process).out
error     = matlab-$(Process).err
log       = matlab-$(Process).log

Queue 50

In this example the initial directory was specified. This allows the user to submit the job from any directory and Condor will find all appropriate files within initialdir. To prevent the script from overwriting the outputs the option transfer_output_remaps can be used. This tells Condor how to transfer the file and in this case there is the $(Process) number to distinguish each output file. Another addition here is running the code through a bash script. An example script is as follows:

#!/bin/sh

exe="matlab"
nodesktop="-nodesktop"
nosplash="-nosplash"
file="< Matlab_example.m"

command=( "$exe" "$nodesktop" "$nosplash" "$file" )

"${command[@]}"

The runMatlab script needs to have executable permissions for the user, group, and other (i.e. chmod +x runMatlab)

Job Submission and Management

The job is submitted with:

condor_submit matlab.condor

The cluster can be queried before or after submission to check its availability. Two very versatile commands exist for this purpose: condor_status and condor_q. The former returns the status of the nodes (broken down by virtual machines that can each handle a job instance.) The latter command shows the job queue including the individual instances of every job and the submission status (e.g. idling, busy etc.) Using condor_q some time after submission shows:

-- Submitter: stat31.phys.uconn.edu : <192.168.1.41:44831> : stat31.phys.uconn.edu
 ID      OWNER            SUBMITTED     RUN_TIME ST PRI SIZE CMD
   7.0   stattestusr     3/25 15:03   0+00:00:00 R  0   9.8   /bin/bash runMatlab
   7.6   stattestusr     3/25 15:03   0+00:00:04 R  0   9.8   /bin/bash runMatlab
   7.10  stattestusr     3/25 15:03   0+00:00:00 R  0   9.8   /bin/bash runMatlab
   7.28  stattestusr     3/25 15:03   0+00:00:00 R  0   9.8   /bin/bash runMatlab
   7.45  stattestusr     3/25 15:03   0+00:00:00 R  0   9.8   /bin/bash runMatlab
   7.49  stattestusr     3/25 15:03   0+00:00:00 R  0   9.8   /bin/bash runMatlab

6 jobs; 0 idle, 6 running, 0 held

By this time, only 6 jobs are left on the cluster, all with status 'R' - running. Various statistics are given including a job ID number. This handle is useful if intervention is required like manual removal of frozen job instances from the cluster. A command condor_rm 7.28 would remove just that instance, whereas condor_rm 7 will remove this entire job.

Acknowledgement

Examples provided by Igor Senderovich, Alex Barnes, Yang Liu