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Please note that this page is under construction. We are documenting the 240-node cluster maya that will be available after Summer 2014. Currently, the 84-node cluster tara still operates independently, until it becomes part of maya at the end of Summer 2014. Please see the 2013 Resources Pages under the Resources tab for tara information.
Using scripts to manage a performance study

Introduction

Suppose you are conducting a parallel performance study using your code. Typically, you will want to observe its performance in solving several different problems, as you vary the numbers of nodes and processes per node in use. For each run of your program, you'll need a slightly different submission script. You'll also need to make sure your runs are neatly organized; perhaps each run has its own directory. Then it's necessary to run the study and collect the results into a table.

Managing a performance study can become tedious and also prone to error. On this page, we will show how to automate some repetitive tasks through shell scripting. These will include

The scripts on this page are written in Bash, but little knowledge of scripting should be required to get the example working. Based on your objectives and how your data is organized, the scripts shown here may not meet your specific needs. Hopefully they can be customized to your project, or at least give some ideas about what is possible.

Make sure you've read the tutorial for C programs first, to understand the basics of serial and parallel programming on maya.

Downloading the case study

For the remainder of this page, we will be using a case study to demonstrate the scripts. You can download it to maya using wget
[araim1@maya-usr1 ~]$ wget http://www.umbc.edu/hpcf/code/scripting-case-study/scripting-case-study.tar.gz
--2011-06-25 11:36:12--  http://www.umbc.edu/hpcf/code/scripting-case-study/scripting-case-study.tar.gz
Resolving www.umbc.edu... 130.85.12.11
Connecting to www.umbc.edu|130.85.12.11|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 3040 (3.0K) [application/x-tar]
Saving to: `scripting-case-study.tar.gz'

100%[======================================>] 3,040       --.-K/s   in 0s      

2011-06-25 11:36:12 (108 MB/s) - `scripting-case-study.tar.gz' saved [3040/3040]

[araim1@maya-usr1 ~]$
Then untar/unzip the file
[araim1@maya-usr1 ~]$ tar xvzf scripting-case-study.tar.gz
scripting-case-study/
scripting-case-study/studies/
scripting-case-study/studies/ppn.tex
scripting-case-study/studies/create-study.bash
scripting-case-study/studies/get-summary-table.bash
scripting-case-study/studies/get-ppn-table-latex.bash
scripting-case-study/studies/get-summary-table-latex.bash
scripting-case-study/studies/summary.tex
scripting-case-study/studies/summary.pdf
scripting-case-study/studies/get-ppn-table.bash
scripting-case-study/studies/ppn.pdf
scripting-case-study/src/
scripting-case-study/src/Makefile
scripting-case-study/src/utilities.c
scripting-case-study/src/utilities.h
scripting-case-study/src/report_time.c
[araim1@maya-usr1 ~]$ cd scripting-case-study/
[araim1@maya-usr1 scripting-case-study]$ ls
src  studies
[araim1@maya-usr1 scripting-case-study]$ 
Under the "src" directory we have an example C program, and inside the "studies" directory are some scripts we will demonstrate.

report_time program

Our performance study will be based on the report_time program, which we will now describe. The program will take a single command line argument, the "problem size" N. In a real application, this might represent a the number of grid points in a mesh for example. Our program will pretend that it took N / p seconds to run (where p is the number of MPI processes), and and write a file called "diag_time.dat" with this elapsed time in the following format
[araim1@maya-usr1 ~]$ cat diag_time.dat 
   00:02:03     0.03       2.06      123.45 % HH:MM:SS=hours=minutes=seconds
[araim1@maya-usr1 ~]$ 
Notice that there are four columns
  1. The time in HH:MM:SS format
  2. The time as a number of hours
  3. The time as a number of minutes
  4. The time as a number of seconds
We've found this file format with these four reported values to be useful. Of course, many other variations are possible.

In the interests of making a quick demonstration, the program does not actually take this long to run. It simply reports the time and exits. In a real performance study of course, your program will report an actual measured time.

We should also note that this program is a slight extension of hello_send_recv version 2 on the How to Compile page. This means that report_time is a full-fledged MPI program, although the requested processor cores are only used for sending a "hello" message.

Let's compile the program to get our executable

[araim1@maya-usr1 scripting-case-study]$ cd src/
[araim1@maya-usr1 src]$ ls
Makefile  report_time.c  utilities.c  utilities.h
[araim1@maya-usr1 src]$ make
mpicc -g -O3   -c utilities.c -o utilities.o
mpicc -g -O3    -c -o report_time.o report_time.c
mpicc -g -O3   utilities.o report_time.o -o report_time -lm 
[araim1@maya-usr1 src]$ ls
Makefile  report_time  report_time.c  report_time.o  utilities.c  utilities.h  utilities.o
[araim1@maya-usr1 src]$ 

Generating the study

Let's change to the "studies" directory
[araim1@maya-usr1 src]$ cd ../studies/
[araim1@maya-usr1 studies]$ 
Our goal will be to create the following directory structure
[araim1@maya-usr1 studies]$ ls study_*
study_n01024:
n001ppn1  n001ppn4  n002ppn1  n002ppn4  n004ppn1  n004ppn4  n008ppn1  n008ppn4  n016ppn1  n016ppn4  n032ppn1  n032ppn4
n001ppn2  n001ppn8  n002ppn2  n002ppn8  n004ppn2  n004ppn8  n008ppn2  n008ppn8  n016ppn2  n016ppn8  n032ppn2  n032ppn8

study_n02048:
n001ppn1  n001ppn4  n002ppn1  n002ppn4  n004ppn1  n004ppn4  n008ppn1  n008ppn4  n016ppn1  n016ppn4  n032ppn1  n032ppn4
n001ppn2  n001ppn8  n002ppn2  n002ppn8  n004ppn2  n004ppn8  n008ppn2  n008ppn8  n016ppn2  n016ppn8  n032ppn2  n032ppn8

study_n04096:
n001ppn1  n001ppn4  n002ppn1  n002ppn4  n004ppn1  n004ppn4  n008ppn1  n008ppn4  n016ppn1  n016ppn4  n032ppn1  n032ppn4
n001ppn2  n001ppn8  n002ppn2  n002ppn8  n004ppn2  n004ppn8  n008ppn2  n008ppn8  n016ppn2  n016ppn8  n032ppn2  n032ppn8
[araim1@maya-usr1 studies]$ 
The directory "study_n01024" represents problem size N = 1024, and so forth for study_n02048 and study_n04096. Within each study_nXXXXX directory we'll have many subdirectories of the form "nNNNppnY", which represent a run using NNN nodes, Y processes per node. Within each nNNNppnY, we'll place a batch script and a symlink to our executable (to avoid copying it many times)
[araim1@maya-usr1 studies]$ ls -l study_n01024/n002ppn4/
total 20
lrwxrwxrwx  1 araim1 pi_nagaraj   44 Jun 25 11:01 report_time -> /home/araim1/scripting-case-study/src/report_time
-rwxrwx---  1 araim1 pi_nagaraj  282 Jun 25 11:01 run.slurm
[araim1@maya-usr1 studies]$ 
The contents of the batch script should look something like this
[araim1@maya-usr1 studies]$ cat study_n01024/n002ppn4/run.slurm 
#!/bin/bash
#SBATCH --job-name=test_study
#SBATCH --output=slurm.out
#SBATCH --error=slurm.err
#SBATCH --partition=develop
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=4

srun ./report_time 1024
[araim1@maya-usr1 studies]$ 

To generate this structure, we can use the following script

#!/bin/bash

EXECUTABLE='/home/araim1/scripting-case-study/src/report_time'

# This function writes a SLURM script. We can call it with different parameter 
# settings to create different experiments
function write_script
{
    STUDY_NAME=$(printf 'study_n%05d' ${N})
    DIR_NAME=$(printf '%s/n%03dppn%d' ${STUDY_NAME} ${NODES} ${NPERNODE})

    if [ -d $DIR_NAME ] ; then
        echo "$DIR_NAME already exists, skipping..."
        return 0
    else
        echo "Creating job $DIR_NAME"
    fi

    mkdir -p $DIR_NAME

    cat << _EOF_ > ${DIR_NAME}/run.slurm
#!/bin/bash
#SBATCH --job-name=test_study
#SBATCH --output=slurm.out
#SBATCH --error=slurm.err
#SBATCH --partition=batch
#SBATCH --nodes=${NODES}
#SBATCH --ntasks-per-node=${NPERNODE}

srun ./report_time ${N}

_EOF_

    chmod 775 ${DIR_NAME}/run.slurm
    ln -s ${EXECUTABLE} ${DIR_NAME}/
}

# For each problem size, we'll run the experiment with 1, 2, 4, and 8 processors
# on 1, 2, 4, ..., 32 nodes
for N in 1024 2048 4096
do
    for NPERNODE in 1 2 4 8
    do
        for NODES in 1 2 4 8 16 32
        do
            write_script
        done
    done
done


Download: ../code/scripting-case-study/studies/create-study.bash
The function write_script is responsible for creating each single job directory, setting up the symlink to report_time, and creating the batch script. The loop at the bottom determines which combinations of N, number of nodes, and number of processes per node will be used in the study. Make a special note of the EXECUTABLE variable at the top, you will need to change the path to your report_time executable. Now we can simply run create-study.bash to get our directory structure
[araim1@maya-usr1 studies]$ ./create-study.bash 
Creating job study_n01024/n001ppn1
Creating job study_n01024/n002ppn1
Creating job study_n01024/n004ppn1
Creating job study_n01024/n008ppn1
Creating job study_n01024/n016ppn1
Creating job study_n01024/n032ppn1
Creating job study_n01024/n001ppn2
Creating job study_n01024/n002ppn2
Creating job study_n01024/n004ppn2
...
Creating job study_n04096/n008ppn8
Creating job study_n04096/n016ppn8
Creating job study_n04096/n032ppn8
[araim1@maya-usr1 studies]$ 

Running the study

We can submit many batch scripts at once with scripting. Here we will demonstrate a Bash "for" loop directly on the command prompt
[araim1@maya-usr1 studies]$ for i in study_n*/n*ppn*;
> do
> cd $i; sbatch run.slurm; cd ../../;
> done
Submitted batch job 64989
Submitted batch job 64990
Submitted batch job 64991
...
[araim1@maya-usr1 studies]$ 
For this example, our jobs require only a few seconds each, so there is no danger in submitting the whole performance study at once. However, for real programs with non-trivial run times, it's generally considered a bad user behavior to submit dozens of jobs at once. In these cases you should submit a "reasonable" number of jobs at once, and wait until those have finished to continue. This would be a good time to refer back to the usage policy, where a "reasonable" number of jobs is discussed.

This kind of loop can still be helpful in a real study, but make sure you're careful about which jobs you currently have in the batch system. A more careful selection can be accomplished in our loop by giving a more specific matching pattern such as "study_n*/n032ppn8", or by giving a listing such as the following

[araim1@maya-usr1 studies]$ for i in study_n01024/n032ppn8 study_n02048/n032ppn8 study_n04096/n032ppn8;
> do
> cd $i; sbatch run.slurm; cd ../../;
> done
Submitted batch job 64992
Submitted batch job 64993
Submitted batch job 64994
[araim1@maya-usr1 studies]$ 

Viewing a table of timings

Suppose we've run the test study above. We should now have a "diag_time.dat" file in each job directory.
[araim1@maya-usr1 studies]$ cat study_n01024/n001ppn1/diag_time.dat
   00:17:04     0.28      17.07     1024.00 % HH:MM:SS=hours=minutes=seconds
[araim1@maya-usr1 studies]$ 
Our goal is to create the following table
N = 1024
                           p=1         p=2         p=4         p=8        p=16        p=32  
1 process   per node  00:17:04    00:08:32    00:04:16    00:02:08    00:01:04    00:00:32  
2 processes per node  00:08:32    00:04:16    00:02:08    00:01:04    00:00:32    00:00:16  
4 processes per node  00:04:16    00:02:08    00:01:04    00:00:32    00:00:16    00:00:08  
8 processes per node  00:02:08    00:01:04    00:00:32    00:00:16    00:00:08    00:00:04  

N = 2048
                           p=1         p=2         p=4         p=8        p=16        p=32  
1 process   per node  00:34:08    00:17:04    00:08:32    00:04:16    00:02:08    00:01:04  
2 processes per node  00:17:04    00:08:32    00:04:16    00:02:08    00:01:04    00:00:32  
4 processes per node  00:08:32    00:04:16    00:02:08    00:01:04    00:00:32    00:00:16  
8 processes per node  00:04:16    00:02:08    00:01:04    00:00:32    00:00:16    00:00:08  

N = 4096
                           p=1         p=2         p=4         p=8        p=16        p=32  
1 process   per node  01:08:16    00:34:08    00:17:04    00:08:32    00:04:16    00:02:08  
2 processes per node  00:34:08    00:17:04    00:08:32    00:04:16    00:02:08    00:01:04  
4 processes per node  00:17:04    00:08:32    00:04:16    00:02:08    00:01:04    00:00:32  
8 processes per node  00:08:32    00:04:16    00:02:08    00:01:04    00:00:32    00:00:16  
To do this, we must first extract the appropriate column from each relevant diag_time.dat file. This can be accomplished using the gawk command
[araim1@maya-usr1 studies]$ cat study_n04096/n032ppn8/diag_time.dat
   00:00:16     0.00       0.27       16.00 % HH:MM:SS=hours=minutes=seconds
[araim1@maya-usr1 studies]$ gawk -F' ' '{ print $1 }' study_n04096/n032ppn8/diag_time.dat 
00:00:16
[araim1@maya-usr1 studies]$ gawk -F' ' '{ print $2 }' study_n04096/n032ppn8/diag_time.dat 
0.00
[araim1@maya-usr1 studies]$ gawk -F' ' '{ print $3 }' study_n04096/n032ppn8/diag_time.dat 
0.27
[araim1@maya-usr1 studies]$ gawk -F' ' '{ print $4 }' study_n04096/n032ppn8/diag_time.dat 
16.00
[araim1@maya-usr1 studies]$ 
We'll choose the first column for this demonstration, to display HH:MM:SS format. We can now create the table by iterating through each study, and extracting / printing the times in the right order, using careful formatting. The following script accomplishes this
#!/bin/bash

write_result()
{
    N=$1
    NODES=$2
    NPN=$3

    FILENAME=$(printf 'study_n%05d/n%03dppn%d/diag_time.dat' $N $NODES $NPN)
    if [ -f $FILENAME ] ; then
        RESULT=$(gawk -F' ' '{ print $1 }' $FILENAME 2>/dev/null)
        printf '  %8s  ' $RESULT
    else
        # If the file does not exist, write out a '---'
        printf '  %8s  ' '---'
    fi
}

write_header()
{
    printf '%20s' ''
    for i in $@
    {
         printf '%10s  ' $i
    }
    printf '\n'
}

for N in 1024 2048 4096
do
    echo "N = $N"

    write_header 'p=1' 'p=2' 'p=4' 'p=8' 'p=16' 'p=32'
    for NPERNODE in 1 2 4 8
    do
        if [ $NPERNODE -eq 1 ] ; then
            printf '%d process   per node' $NPERNODE
        else
            printf '%d processes per node' $NPERNODE
        fi

        for NODES in 1 2 4 8 16 32
        do
            write_result $N $NODES $NPERNODE
        done

        printf '\n'
    done

    printf '\n'
done


Download: ../code/scripting-case-study/studies/get-summary-table.bash
The function write_result executes our gawk script, but prints a "---" if the diag_time.dat file does not exist. The loop at the bottom ensures that the timings are printed in order, and with the correct formatting, so that we get our table. Running this script from within the "studies" directrory will yield the table.
[araim1@maya-usr1 studies]$ ./get-summary-table.bash 
N = 1024
                           p=1         p=2         p=4         p=8        p=16        p=32  
1 process   per node  00:17:04    00:08:32    00:04:16    00:02:08    00:01:04    00:00:32  
2 processes per node  00:08:32    00:04:16    00:02:08    00:01:04    00:00:32    00:00:16  
4 processes per node  00:04:16    00:02:08    00:01:04    00:00:32    00:00:16    00:00:08  
8 processes per node  00:02:08    00:01:04    00:00:32    00:00:16    00:00:08    00:00:04  

N = 2048
                           p=1         p=2         p=4         p=8        p=16        p=32  
1 process   per node  00:34:08    00:17:04    00:08:32    00:04:16    00:02:08    00:01:04  
2 processes per node  00:17:04    00:08:32    00:04:16    00:02:08    00:01:04    00:00:32  
4 processes per node  00:08:32    00:04:16    00:02:08    00:01:04    00:00:32    00:00:16  
8 processes per node  00:04:16    00:02:08    00:01:04    00:00:32    00:00:16    00:00:08  

N = 4096
                           p=1         p=2         p=4         p=8        p=16        p=32  
1 process   per node  01:08:16    00:34:08    00:17:04    00:08:32    00:04:16    00:02:08  
2 processes per node  00:34:08    00:17:04    00:08:32    00:04:16    00:02:08    00:01:04  
4 processes per node  00:17:04    00:08:32    00:04:16    00:02:08    00:01:04    00:00:32  
8 processes per node  00:08:32    00:04:16    00:02:08    00:01:04         ---         ---

[araim1@maya-usr1 studies]$ 
The last two cases of N = 4096 were not run in this example, to demonstrate the "---" feature.

Creating LaTeX tables

The script above can easily be modified to generate a LaTeX-ready table. That is, using "&" as the column separator and "\\" for newlines. It can be tedious to enter these manually, but it's easy to modify our script to include them. See the file get-summary-table-latex.bash in the tar.gz. Here is an example output
[araim1@maya-usr1 studies]$ ./get-summary-table-latex.bash 
N = 1024
                           p=1         p=2         p=4         p=8        p=16        p=32  
1 process   per node& 00:17:04  & 00:08:32  & 00:04:16  & 00:02:08  & 00:01:04  & 00:00:32  \\
2 processes per node& 00:08:32  & 00:04:16  & 00:02:08  & 00:01:04  & 00:00:32  & 00:00:16  \\
4 processes per node& 00:04:16  & 00:02:08  & 00:01:04  & 00:00:32  & 00:00:16  & 00:00:08  \\
8 processes per node& 00:02:08  & 00:01:04  & 00:00:32  & 00:00:16  & 00:00:08  & 00:00:04  \\

N = 2048
                           p=1         p=2         p=4         p=8        p=16        p=32  
1 process   per node& 00:34:08  & 00:17:04  & 00:08:32  & 00:04:16  & 00:02:08  & 00:01:04  \\
2 processes per node& 00:17:04  & 00:08:32  & 00:04:16  & 00:02:08  & 00:01:04  & 00:00:32  \\
4 processes per node& 00:08:32  & 00:04:16  & 00:02:08  & 00:01:04  & 00:00:32  & 00:00:16  \\
8 processes per node& 00:04:16  & 00:02:08  & 00:01:04  & 00:00:32  & 00:00:16  & 00:00:08  \\

N = 4096
                           p=1         p=2         p=4         p=8        p=16        p=32  
1 process   per node& 01:08:16  & 00:34:08  & 00:17:04  & 00:08:32  & 00:04:16  & 00:02:08  \\
2 processes per node& 00:34:08  & 00:17:04  & 00:08:32  & 00:04:16  & 00:02:08  & 00:01:04  \\
4 processes per node& 00:17:04  & 00:08:32  & 00:04:16  & 00:02:08  & 00:01:04  & 00:00:32  \\
8 processes per node& 00:08:32  & 00:04:16  & 00:02:08  & 00:01:04  &      ---  &      ---  \\

[araim1@maya-usr1 studies]$ 
We can easily convert this into a LaTeX table. See the file summary.tex included in the tar.gz.
[araim1@maya-usr1 studies]$ pdflatex summary.tex 
This is pdfeTeX, Version 3.141592-1.21a-2.2 (Web2C 7.5.4)
...
Output written on summary.pdf (1 page, 26486 bytes).
Transcript written on summary.log.
[araim1@maya-usr1 studies]$ 
This produces the output summary.pdf

It is often necessary to recreate these tables more than once when preparing a report. For example, after an initial draft we might realize that there is a bug, or maybe an opportunity for much better performance. We can create new LaTeX tables with minimal work now: simply rerun "get-summary-table-latex.bash" on the current output, and copy/paste the relevant lines into the tex file.

Timing tables by processes per node

Another commonly used table type is timing for 1, 2, 4, or 8 processes per node. For example:
Results for npn = 1
      p=1        p=2        p=4        p=8       p=16       p=32       p=64      p=128      p=256  
 00:17:04   00:08:32   00:04:16   00:02:08   00:01:04   00:00:32        ---        ---  
 00:34:08   00:17:04   00:08:32   00:04:16   00:02:08   00:01:04        ---        ---  
 01:08:16   00:34:08   00:17:04   00:08:32   00:04:16   00:02:08        ---        ---  

Results for npn = 2
      p=1        p=2        p=4        p=8       p=16       p=32       p=64      p=128      p=256  
 00:17:04   00:08:32   00:04:16   00:02:08   00:01:04   00:00:32   00:00:16        ---        ---  
 00:34:08   00:17:04   00:08:32   00:04:16   00:02:08   00:01:04   00:00:32        ---        ---  
 01:08:16   00:34:08   00:17:04   00:08:32   00:04:16   00:02:08   00:01:04        ---        ---  

Results for npn = 4
      p=1        p=2        p=4        p=8       p=16       p=32       p=64      p=128      p=256  
 00:17:04   00:08:32   00:04:16   00:02:08   00:01:04   00:00:32   00:00:16   00:00:08        ---  
 00:34:08   00:17:04   00:08:32   00:04:16   00:02:08   00:01:04   00:00:32   00:00:16        ---  
 01:08:16   00:34:08   00:17:04   00:08:32   00:04:16   00:02:08   00:01:04   00:00:32        ---  

Results for npn = 8
      p=1        p=2        p=4        p=8       p=16       p=32       p=64      p=128      p=256  
 00:17:04   00:08:32   00:04:16   00:02:08   00:01:04   00:00:32   00:00:16   00:00:08   00:00:04  
 00:34:08   00:17:04   00:08:32   00:04:16   00:02:08   00:01:04   00:00:32   00:00:16   00:00:08  
 01:08:16   00:34:08   00:17:04   00:08:32   00:04:16   00:02:08   00:01:04        ---        ---  

The scripts to generate these tables are very similar in nature to the ones from the previous sections. In the tar.gz file, see