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Swift for the Cloud

Modes of operation

  1. Static mode: You define your cluster ahead of swift runs.

  2. Dynamic mode: Cloud resources provisioned dynamically.

Swift installation

Prerequisites: Java 1.7 Ant Python 2.7 The following steps

# Install swift-trunk from git
https://github.com/swift-lang/swift-k.git
# Extract package
tar xfz swift-0.95-RC6.tar.gz
# Add swift to the PATH environment variable
export PATH=$PATH:/path/to/swift-0.95-RC6/bin

Get the swift-on-cloud repository

Clone the repository from github

git clone https://github.com/yadudoc/swift-on-cloud.git
cd swift-on-cloud

Or, download the zip file from github and unpack.

# Download
wget https://github.com/yadudoc/swift-on-cloud/archive/master.zip
unzip master.zip
mv swift-on-cloud-master swift-on-cloud
cd swift-on-cloud

Run the swift-cloud-tutorial from the cloud

To run the tutorial on Google Compute Engine (GCE), follow the instructions here:
https://github.com/yadudoc/swift-on-cloud/tree/master/compute-engine
or, follow instructions for GCE, in the compute-engine folder of the swift-on-cloud repository. Once your instances are running, connect to the headnode. Everthing that you require for the swift-cloud-tutorial is already set up for you on the headnode.

Simple "science applications" for the workflow tutorial

This tutorial is based on two intentionally trivial example programs, simulation.sh and stats.sh, (implemented as bash shell scripts) that serve as easy-to-understand proxies for real science applications. These "programs" behave as follows.

simulate.sh

The simulation.sh script serves as a trivial proxy for any more complex scientific simulation application. It generates and prints a set of one or more random integers in the range [0-2^62) as controlled by its command line arguments, which are:

$ ./app/simulate.sh --help
./app/simulate.sh: usage:
    -b|--bias       offset bias: add this integer to all results [0]
    -B|--biasfile   file of integer biases to add to results [none]
    -l|--log        generate a log in stderr if not null [y]
    -n|--nvalues    print this many values per simulation [1]
    -r|--range      range (limit) of generated results [100]
    -s|--seed       use this integer [0..32767] as a seed [none]
    -S|--seedfile   use this file (containing integer seeds [0..32767]) one per line [none]
    -t|--timesteps  number of simulated "timesteps" in seconds (determines runtime) [1]
    -x|--scale      scale the results by this integer [1]
    -h|-?|?|--help  print this help
$

All of thess arguments are optional, with default values indicated above as [n].

With no arguments, simulate.sh prints 1 number in the range of 1-100. Otherwise it generates n numbers of the form (R*scale)+bias where R is a random integer. By default it logs information about its execution environment to stderr. Here’s some examples of its usage:

$ simulate.sh 2>log
       5
$ head -4 log

Called as: /home/wilde/swift/tut/CIC_2013-08-09/app/simulate.sh:
Start time: Thu Aug 22 12:40:24 CDT 2013
Running on node: login01.osgconnect.net

$ simulate.sh -n 4 -r 1000000 2>log
  239454
  386702
   13849
  873526

$ simulate.sh -n 3 -r 1000000 -x 100 2>log
 6643700
62182300
 5230600

$ simulate.sh -n 2 -r 1000 -x 1000 2>log
  565000
  636000

$ time simulate.sh -n 2 -r 1000 -x 1000 -t 3 2>log
  336000
  320000
real    0m3.012s
user    0m0.005s
sys     0m0.006s

stats.sh

The stats.sh script serves as a trivial model of an "analysis" program. It reads N files each containing M integers and simply prints the\ average of all those numbers to stdout. Similarly to simulate.sh it logs environmental information to the stderr.

$ ls f*
f1  f2  f3  f4

$ cat f*
25
60
40
75

$ stats.sh f* 2>log
50

Basic of the Swift language with local execution

A Summary of Swift in a nutshell

  • Swift scripts are text files ending in .swift The swift command runs on any host, and executes these scripts. swift is a Java application, which you can install almost anywhere. On Linux, just unpack the distribution tar file and add its bin/ directory to your PATH.

  • Swift scripts run ordinary applications, just like shell scripts do. Swift makes it easy to run these applications on parallel and remote computers (from laptops to supercomputers). If you can ssh to the system, Swift can likely run applications there.

  • The details of where to run applications and how to get files back and forth are described in configuration files separate from your program. Swift speaks ssh, PBS, Condor, SLURM, LSF, SGE, Cobalt, and Globus to run applications, and scp, http, ftp, and GridFTP to move data.

  • The Swift language has 5 main data types: boolean, int, string, float, and file. Collections of these are dynamic, sparse arrays of arbitrary dimension and structures of scalars and/or arrays defined by the type declaration.

  • Swift file variables are "mapped" to external files. Swift sends files to and from remote systems for you automatically.

  • Swift variables are "single assignment": once you set them you can’t change them (in a given block of code). This makes Swift a natural, "parallel data flow" language. This programming model keeps your workflow scripts simple and easy to write and understand.

  • Swift lets you define functions to "wrap" application programs, and to cleanly structure more complex scripts. Swift app functions take files and parameters as inputs and return files as outputs.

  • A compact set of built-in functions for string and file manipulation, type conversions, high level IO, etc. is provided. Swift’s equivalent of printf() is tracef(), with limited and slightly different format codes.

  • Swift’s foreach {} statement is the main parallel workhorse of the language, and executes all iterations of the loop concurrently. The actual number of parallel tasks executed is based on available resources and settable "throttles".

  • In fact, Swift conceptually executes all the statements, expressions and function calls in your program in parallel, based on data flow. These are similarly throttled based on available resources and settings.

  • Swift also has if and switch statements for conditional execution. These are seldom needed in simple workflows but they enable very dynamic workflow patterns to be specified.

We’ll see many of these points in action in the examples below. Lets get started!

Part 1: Run a single application under Swift

The first swift script, p1.swift, runs simulate.sh to generate a single random number. It writes the number to a file.

p1 workflow
p1.swift
sys::[cat ../part01/p1.swift]

To run this script, run the following command:

$ cd part01
$ swift p1.swift
Swift 0.94.1 RC2 swift-r6895 cog-r3765

RunID: 20130827-1413-oa6fdib2
Progress:  time: Tue, 27 Aug 2013 14:13:33 -0500
Final status: Tue, 27 Aug 2013 14:13:33 -0500  Finished successfully:1
$ cat sim.out
      84
$ swift p1.swift
$ cat sim.out
      36

To cleanup the directory and remove all outputs (including the log files and directories that Swift generates), run the cleanup script which is located in the tutorial PATH:

$ cleanup
Note
 You’ll also find two Swift configuration files in each partNN directory of this tutorial. These specify the environment-specific details of where to find application programs (file apps) and where to run them (file sites.xml). These files will be explained in more detail in parts 4-6, and can be ignored for now.

Part 2: Running an ensemble of many apps in parallel with a "foreach" loop

The p2.swift script introduces the foreach parallel iteration construct to run many concurrent simulations.

part02
p2.swift
sys::[cat ../part02/p2.swift]

The script also shows an example of naming the output files of an ensemble run. In this case, the output files will be named output/sim_N.out.

In part 2, we also update the apps file. Instead of using shell script (simulate.sh), we use the equivalent python version (simulate.py). The new apps file now looks like this:

sys::[cat ../part02/apps]

Swift does not need to know anything about the language an application is written in. The application can be written in Perl, Python, Java, Fortran, or any other language.

To run the script and view the output:

$ cd ../part02
$ swift p2.swift
$ ls output
sim_0.out  sim_1.out  sim_2.out  sim_3.out  sim_4.out  sim_5.out  sim_6.out  sim_7.out  sim_8.out  sim_9.out
$ more output/*
::::::::::::::
output/sim_0.out
::::::::::::::
      44
::::::::::::::
output/sim_1.out
::::::::::::::
      55
...
::::::::::::::
output/sim_9.out
::::::::::::::
      82

Part 3: Analyzing results of a parallel ensemble

After all the parallel simulations in an ensemble run have completed, its typically necessary to gather and analyze their results with some kind of post-processing analysis program or script. p3.swift introduces such a postprocessing step. In this case, the files created by all of the parallel runs of simulation.sh will be averaged by by the trivial "analysis application" stats.sh:

part03
p3.swift
sys::[cat ../part03/p3.swift]

To run:

$ cd part03
$ swift p3.swift

Note that in p3.swift we expose more of the capabilities of the simulate.sh application to the simulation() app function:

app (file o) simulation (int sim_steps, int sim_range, int sim_values)
{
  simulate "--timesteps" sim_steps "--range" sim_range "--nvalues" sim_values stdout=filename(o);
}

p3.swift also shows how to fetch application-specific values from the swift command line in a Swift script using arg() which accepts a keyword-style argument and its default value:

int nsim   = toInt(arg("nsim","10"));
int steps  = toInt(arg("steps","1"));
int range  = toInt(arg("range","100"));
int values = toInt(arg("values","5"));

Now we can specify that more runs should be performed and that each should run for more timesteps, and produce more that one value each, within a specified range, using command line arguments placed after the Swift script name in the form -parameterName=value:

$ swift p3.swift -nsim=3 -steps=10 -values=4 -range=1000000

Swift 0.94.1 RC2 swift-r6895 cog-r3765

RunID: 20130827-1439-s3vvo809
Progress:  time: Tue, 27 Aug 2013 14:39:42 -0500
Progress:  time: Tue, 27 Aug 2013 14:39:53 -0500  Active:2  Stage out:1
Final status: Tue, 27 Aug 2013 14:39:53 -0500  Finished successfully:4

$ ls output/
average.out  sim_0.out  sim_1.out  sim_2.out
$ more output/*
::::::::::::::
output/average.out
::::::::::::::
651368
::::::::::::::
output/sim_0.out
::::::::::::::
  735700
  886206
  997391
  982970
::::::::::::::
output/sim_1.out
::::::::::::::
  260071
  264195
  869198
  933537
::::::::::::::
output/sim_2.out
::::::::::::::
  201806
  213540
  527576
  944233

Now try running (-nsim=) 100 simulations of (-steps=) 1 second each:

$ swift p3.swift -nsim=100 -steps=1
Swift 0.94.1 RC2 swift-r6895 cog-r3765

RunID: 20130827-1444-rq809ts6
Progress:  time: Tue, 27 Aug 2013 14:44:55 -0500
Progress:  time: Tue, 27 Aug 2013 14:44:56 -0500  Selecting site:79  Active:20  Stage out:1
Progress:  time: Tue, 27 Aug 2013 14:44:58 -0500  Selecting site:58  Active:20  Stage out:1  Finished successfully:21
Progress:  time: Tue, 27 Aug 2013 14:44:59 -0500  Selecting site:37  Active:20  Stage out:1  Finished successfully:42
Progress:  time: Tue, 27 Aug 2013 14:45:00 -0500  Selecting site:16  Active:20  Stage out:1  Finished successfully:63
Progress:  time: Tue, 27 Aug 2013 14:45:02 -0500  Active:15  Stage out:1  Finished successfully:84
Progress:  time: Tue, 27 Aug 2013 14:45:03 -0500  Finished successfully:101
Final status: Tue, 27 Aug 2013 14:45:03 -0500  Finished successfully:101

We can see from Swift’s "progress" status that the tutorial’s default swift.properties parameters for local execution allow Swift to run up to 20 application invocations concurrently on the login node. We’ll look at this in more detail in the next sections where we execute applications on the site’s compute nodes.

Running applications on compute nodes with Swift

Part 4: Running a parallel ensemble on compute nodes

p4.swift will run our mock "simulation" applications on compute nodes. The script is similar to as p3.swift, but specifies that each simulation app invocation should additionally return the log file which the application writes to stderr.

Now when you run swift p4.swift you’ll see that two types output files will placed in the output/ directory: sim_N.out and sim_N.log. The log files provide data on the runtime environment of each app invocation. For example:

$ cat output/sim_0.log

Called as: simulate.sh: --timesteps 1 --range 100 --nvalues 5

Start time: Tue Oct 22 14:54:11 CDT 2013
Running as user: uid=5116(davidk) gid=311(collab) groups=311(collab),104(fuse),1349(swift),45053(swat)
Running on node: stomp
Node IP address: 140.221.9.237

Simulation parameters:

bias=0
biasfile=none
initseed=none
log=yes
paramfile=none
range=100
scale=1
seedfile=none
timesteps=1
output width=8

Environment:

EDITOR=vim
HOME=/homes/davidk
JAVA_HOME=/nfs/proj-davidk/jdk1.7.0_01
LANG=C
....

Performing larger Swift runs

To test with larger runs, there are two changes that are required. The first is a change to the command line arguments. The example below will run 1000 simulations with each simulation taking 5 seconds.

$ swift p6.swift -steps=5 -nsim=1000

Part 5: Controlling the compute-node pools where applications run

This section is under development.

Part 6: Specifying more complex workflow patterns

p6.swift expands the workflow pattern of p4.swift to add additional stages to the workflow. Here, we generate a dynamic seed value that will be used by all of the simulations, and for each simulation, we run an pre-processing application to generate a unique "bias file". This pattern is shown below, followed by the Swift script.

part06
p6.swift
sys::[cat ../part06/p6.swift]

Note that the workflow is based on data flow dependencies: each simulation depends on the seed value, calculated in this statement:

seedfile = genseed(1);

and on the bias file, computed and then consumed in these two dependent statements:

  biasfile = genbias(1000, 20, simulate_script);
  (simout,simlog) = simulation(steps, range, biasfile, 1000000, values, simulate_script, seedfile);

To run:

$ cd ../part06
$ swift p6.swift

The default parameters result in the following execution log:

$ swift p6.swift
Swift 0.94.1 RC2 swift-r6895 cog-r3765

RunID: 20130827-1917-jvs4gqm5
Progress:  time: Tue, 27 Aug 2013 19:17:56 -0500

*** Script parameters: nsim=10 range=100 num values=10

Progress:  time: Tue, 27 Aug 2013 19:17:57 -0500  Stage in:1  Submitted:10
Generated seed=382537
Progress:  time: Tue, 27 Aug 2013 19:17:59 -0500  Active:9  Stage out:1  Finished successfully:11
Final status: Tue, 27 Aug 2013 19:18:00 -0500  Finished successfully:22

which produces the following output:

$ ls -lrt output
total 264
-rw-r--r-- 1 p01532 61532     9 Aug 27 19:17 seed.dat
-rw-r--r-- 1 p01532 61532   180 Aug 27 19:17 bias_9.dat
-rw-r--r-- 1 p01532 61532   180 Aug 27 19:17 bias_8.dat
-rw-r--r-- 1 p01532 61532   180 Aug 27 19:17 bias_7.dat
-rw-r--r-- 1 p01532 61532   180 Aug 27 19:17 bias_6.dat
-rw-r--r-- 1 p01532 61532   180 Aug 27 19:17 bias_5.dat
-rw-r--r-- 1 p01532 61532   180 Aug 27 19:17 bias_4.dat
-rw-r--r-- 1 p01532 61532   180 Aug 27 19:17 bias_3.dat
-rw-r--r-- 1 p01532 61532   180 Aug 27 19:17 bias_2.dat
-rw-r--r-- 1 p01532 61532   180 Aug 27 19:17 bias_1.dat
-rw-r--r-- 1 p01532 61532   180 Aug 27 19:17 bias_0.dat
-rw-r--r-- 1 p01532 61532    90 Aug 27 19:17 sim_9.out
-rw-r--r-- 1 p01532 61532 14897 Aug 27 19:17 sim_9.log
-rw-r--r-- 1 p01532 61532 14897 Aug 27 19:17 sim_8.log
-rw-r--r-- 1 p01532 61532    90 Aug 27 19:17 sim_7.out
-rw-r--r-- 1 p01532 61532    90 Aug 27 19:17 sim_6.out
-rw-r--r-- 1 p01532 61532 14897 Aug 27 19:17 sim_6.log
-rw-r--r-- 1 p01532 61532    90 Aug 27 19:17 sim_5.out
-rw-r--r-- 1 p01532 61532 14897 Aug 27 19:17 sim_5.log
-rw-r--r-- 1 p01532 61532    90 Aug 27 19:17 sim_4.out
-rw-r--r-- 1 p01532 61532 14897 Aug 27 19:17 sim_4.log
-rw-r--r-- 1 p01532 61532 14897 Aug 27 19:17 sim_1.log
-rw-r--r-- 1 p01532 61532    90 Aug 27 19:18 sim_8.out
-rw-r--r-- 1 p01532 61532 14897 Aug 27 19:18 sim_7.log
-rw-r--r-- 1 p01532 61532    90 Aug 27 19:18 sim_3.out
-rw-r--r-- 1 p01532 61532 14897 Aug 27 19:18 sim_3.log
-rw-r--r-- 1 p01532 61532    90 Aug 27 19:18 sim_2.out
-rw-r--r-- 1 p01532 61532 14898 Aug 27 19:18 sim_2.log
-rw-r--r-- 1 p01532 61532    90 Aug 27 19:18 sim_1.out
-rw-r--r-- 1 p01532 61532    90 Aug 27 19:18 sim_0.out
-rw-r--r-- 1 p01532 61532 14897 Aug 27 19:18 sim_0.log
-rw-r--r-- 1 p01532 61532     9 Aug 27 19:18 average.out
-rw-r--r-- 1 p01532 61532 14675 Aug 27 19:18 average.log

Each sim_N.out file is the sum of its bias file plus newly "simulated" random output scaled by 1,000,000:

$ cat output/bias_0.dat
     302
     489
      81
     582
     664
     290
     839
     258
     506
     310
     293
     508
      88
     261
     453
     187
      26
     198
     402
     555

$ cat output/sim_0.out
64000302
38000489
32000081
12000582
46000664
36000290
35000839
22000258
49000506
75000310

We produce 20 values in each bias file. Simulations of less than that number of values ignore the unneeded number, while simualtions of more than 20 will use the last bias number for all remoaining values past 20. As an exercise, adjust the code to produce the same number of bias values as is needed for each simulation. As a further exercise, modify the script to generate a unique seed value for each simulation, which is a common practice in ensemble computations.

Tips for Specific Resources

Open Science Data Cloud

  1. When you start instances on OSDC, use the standard Ubuntu image.

  2. Ensure that your SSH key is added to the instance for password login.

  3. Swift should run on the OSDC headnode.

  4. You can use the following command within coaster-service.conf to automatically populate WORKER_HOSTS with the IP addresses of all active instances you have running.

export WORKER_HOSTS=$( nova list | grep ACTIVE | sed -e 's/^.*private=//' -e 's/ .*//' |sed ':a;N;$!ba;s/\n/ /g' )