DA-MDS

Deterministic Annealing Multidimensional Scaling (DA-MDS) is a high performance implementation of the WDA-SMACOF algorithm.

Success Stories

• Million Sequence Clustering at http://salsahpc.indiana.edu/millionseq/
• The Fungi Phylogenetic Project at http://salsafungiphy.blogspot.com/

Prerequisites

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1. Operating System

• SPDIAL is extensively tested and known to work on,
  • Red Hat Enterprise Linux Server release 6.7 (Santiago)
  • Red Hat Enterprise Linux Server release 5.10 (Tikanga)
  • Ubuntu 12.04.3 LTS
  • Ubuntu 12.10
• This may work in Windows systems depending on the ability to setup OpenMPI properly, however, this has not been tested and we recommend choosing a Linux based operating system instead.

2. Java

• Download Oracle JDK 8 from http://www.oracle.com/technetwork/java/javase/downloads/index.html
• Extract the archive to a folder named jdk1.8.0
• Set the following environment variables.

  JAVA_HOME=<path-to-jdk1.8.0-directory>
  PATH=$JAVA_HOME/bin:$PATH
  export JAVA_HOME PATH

3. Apache Maven

• Download latest Maven release from http://maven.apache.org/download.cgi
• Extract it to some folder and set the following environment variables.

  MVN_HOME=<path-to-Maven-folder>
  $PATH=$MVN_HOME/bin:$PATH
  export MVN_HOME PATH

5. OpenMPI

• We recommend using OpenMPI 1.10.1 although it work with the previous 1.8 versions. Note, if using a version other than 1.10.1 please remember to set Maven dependency appropriately in the pom.xml.

• Download OpenMPI 1.10.1 from http://www.open-mpi.org/software/ompi/v1.10/downloads/openmpi-1.10.1.tar.gz

• Extract the archive to a folder named openmpi-1.10.1

• Also create a directory named build in some location. We will use this to install OpenMPI

• Set the following environment variables

  BUILD=<path-to-build-directory>
  OMPI_1101=<path-to-openmpi-1.10.1-directory>
  PATH=$BUILD/bin:$PATH
  LD_LIBRARY_PATH=$BUILD/lib:$LD_LIBRARY_PATH
  export BUILD OMPI_1101 PATH LD_LIBRARY_PATH

• The instructions to build OpenMPI depend on the platform. Therefore, we highly recommend looking into the $OMPI_1101/INSTALL file. Platform specific build files are available in $OMPI_1101/contrib/platform directory.
• In general, please specify --prefix=$BUILD and --enable-mpi-java as arguments to configure script. If Infiniband is available (highly recommended) specify --with-verbs=<path-to-verbs-installation>. Usually, the path to verbs installation is /usr. In summary, the following commands will build OpenMPI for a Linux system.

  cd $OMPI_1101
  ./configure --prefix=$BUILD --enable-mpi-java
  make;make install

• If everything goes well mpirun --version will show mpirun (Open MPI) 1.10.1. Execute the following command to instal $OMPI_1101/ompi/mpi/java/java/mpi.jar as a Maven artifact.

  mvn install:install-file -DcreateChecksum=true -Dpackaging=jar -Dfile=$OMPI_1101/ompi/mpi/java/java/mpi.jar -DgroupId=ompi -DartifactId=ompijavabinding -Dversion=1.10.1

• Few examples are available in $OMPI_1101/examples. Please use mpijavac with other parameters similar to javac command to compile OpenMPI Java programs. Once compiled mpirun [options] java -cp <classpath> class-name arguments command with proper values set as arguments will run the MPI Java program.

Building DA-MDS

• Check all prerequisites are satisfied before building DA-MDS
• Clone this git repository from git@github.com:DSC-SPIDAL/damds.git Let's call this directory damdshome
• Once above two steps are completed, building DA-MDS requires only one command, mvn install, issued within damdshome.

Note : If you have not built https://github.com/DSC-SPIDAL/common library locally please follow the following instructions

Please follow the following instructions to build this project with maven This is needed because of an SSL certificate issue with a dependency maven repo

execute the following commands from the root directory of the repo

keytool -import -file ./resources/ricecert/cs.rice.edu.cer -keystore /tmp/riceKeyStore

You can change the name of the key store and the path to it if you prefer to. This command will first ask for a password, provide any password of your choosing with at least 6 characters then it will show the following

Trust this certificate? [no]: 

type "y" and then press enter. Now the cert has been properly installed. Next use the following command to compile the code

mvn -Djavax.net.ssl.trustStore=/tmp/riceKeyStore clean install

Running DA-MDS

The following shell script may be used with necessary modifications to run the program.

#!/bin/bash

# Java classpath. This should include paths to damds dependent jar files and the damds-1.0.jar
# The dependent jar files may be obtained by running mvn dependency:build-classpath command within damdshome
cp=<classpath>

# Obtain working directory
wd=`pwd`
# Character x as a variable
x='x'

# A text file listing available nodes
hosts=<path-to-hostfile>
# Number of nodes
nodes=<num-nodes>
# Number of cores per node
cpn=8

# Options for Java runtime
jopts="-Xms64M -Xmx64M"

# Number of threads to use within one dapwc process
tpn=<threads-per-process>
# Number of processes per node
ppn=<processes-per-node>
# Total parallelism expressed as a pattern TxPxN
# where T is number of threads per process, P is processes per node, and N is total nodes
pat=$tpn$x$ppn$x$nodes

# Number of computing units assigned per process, assuming $cpn is divisible by $ppn
bw=$(($cpn/$ppn))

mmaps=1
# Directory to memory map. Ideally, set this to where tmpfs is in Linux
mmapdir=/dev/shm/$USER

echo "Running $pat on `date`" >> status.txt
# Invoke MPI to run dapwc
mpirun --report-bindings --mca btl ^tcp --hostfile $hostfile --map-by ppr:$ppn:node:PE=$bw --rank-by core -np $(($nodes*$ppn)) java $jopts -cp $cp edu.indiana.soic.spidal.damds.Program -c config$pat.properties -n $nodes -t $tpn -mmaps $mmaps -mmapdir $mmapdir | tee $pat/mds-out.txt
echo "Finished $pat on `date`" >> status.txt

The arguments listed in the mpirun command fall into three categories.

• OpenMPI Runtime Parameters
  • --report-bindings requests OpenMPI runtime to output how processes are mapped to processing elements (cores) in the allocated nodes.
  • --mca btl ^tcp instructs to disable tcp, which is useful when running on Infiniband.
  • --hostfile indicates the file listing available nodes. Each node has to be a in a separate line.
  • --map-by ppr:$ppn:node:PE=$bw controls process mapping and binding. This is a topic on its own right, but the specific values in this example requests processes to be mapped by node while binding each to bw number of processing elements. A good set of slides on this topic is available at http://www.slideshare.net/jsquyres/open-mpi-explorations-in-process-affinity-eurompi13-presentation
  • -np $(($nodes*$ppn)) determines the total number of processes to run and in this case it is equal to nodes*ppn
• Java Runtime Parameters
  • $jopts in this case lists initial and maximum heap sizes for a JVM instance.
  • -cp indicates paths to find required classes where each entry is separated by a : (in Linux)
• Program (dapwc) Parameters
  • -c points to the configuration file. This is a Java properties files listing values for each parameter that damds requires. Details on these parameters will follow in a later section.
  • -n indicates the total number of nodes
  • -t denotes the number of threads to use within one instance of damds
  • -mmaps is the number of memory maps to use. Set this to 1 for the best performance
  • -mmapdir points to the directory where memory maps should be created. Ideally, it should point to tmpfs directory in Linux

Configuring damds

The following table summarizes the parameters used in dapwc.

Parameter	Description	Default Value	Type
DistanceMatrixFile	Path of the pairwise distance file.	n/a	String
WeightMatrixFile	Path of the pairwise weight matrix file or the simple linear weights text file.	n/a	String
LabelDataFile	Path of the points' labels file.	n/a	String
InitialPoints File	Path of the initial points file.	n/a	String
PointsFile	Path of the output points file.	n/a	String
TimingFile	Path of the output timing information.	n/a	String
SummaryFile	Path of the output summary file.	n/a	String
NumberDataPoints	Total number of data points.	n/a	Integer
TargetDimension	Target dimension of the output points.	3	Integer
DistanceTransform	Raise distances to the power of DistanceTransform.	1.0	Double
Threshold	Stress threshold.	0.000001	Double
Alpha	Cooling factor.	0.95	Double
TminFactor	The minimum temperature factor.	0.5	Double
StressIterations	The maximum number of stress loops to run.	10000	Integer
CGIterations	The maximum number of conjugate gradient loops	20	Integer
IsSammon	The flag to determine if sammon distances should be used	false	Boolean
BlockSize	The block size to use in block matrix multiplication	64	Integer
IsBigEndian	The flat to indicate the endianness of the binary distance file.	false	Boolean
IsMemoryMapped	The flag to indicate if memory mapped files should be used to load data.	true	Boolean
TransformationFunction	The path of the jar file containing additional distance transformations.	null	String
WeightTransformationFunction	The path of the jar file containing additional weight transformations.	null	String
Repetitions	The number of repetitions (see below).	1	Integer
MaxTempLoops	The maximum number of temperature loops (see below).	0	Integer
IsSimpleWeights	The flag to indicate if weights are read from a simple linear file.	false	Boolean

Repetitions is a quick way to test large data sizes using a smaller original distances and weights files. For example with a NxN data set and a Repetitions=2, DA-MDS will do a 2Nx2N run. It does so by tiling the NxN matrix 4 times (2 horizontally and 2 vertically).

MaxTempLoops allows to test the program for performance without running for full convergence by allowing it to run only the specified number of temperature loops. Setting this to 0 will disable it and will do the full run.

Acknowledgement

We like to express our sincere gratitude to Prof. Vivek Sarkar and his team at Rice University for giving us access and continuous support for the HJ library. We are also thankful to FutureSystems project and its support team for their support with HPC systems. Also, we thank Intel for their support of the Juliet cluster system that we used to test DA-MDS. Last but not least OpenMPI community deserves equal recognition for their valuable support.

We also like to thank the following companies for providing us Open Source licences for their profiler software.

• ej-technologies the creator of JProfiler (http://www.ej-technologies.com/products/jprofiler/overview.html)

• YourKit supports open source projects with its full-featured Java Profiler. YourKit, LLC is the creator of YourKit Java Profiler and YourKit .NET Profiler, innovative and intelligent tools for profiling Java and .NET applications