common

SPIDAL libraries depend on the common project in DSC-SPIDAL github. We need to build it first.

 git clone https://github.com/DSC-SPIDAL/common.git
 cd common
 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 SSL cert has been properly installed. Next use the following command to compile the code

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

DA-MDS

DA-MDS is the deterministic annealing implementation of Multidimensional Scaling algorithm. The project can be built from the source.

 git clone https://github.com/DSC-SPIDAL/damds.git
 cd damds
 mvn install

After building it will create a Jar file inside the target directory.

Usually people run MDS using a cluster manager such as slurm. We have provided a sample script in bin directory that can be used to run the program on a single machine.

Run example - local machine

DA-MDS is configured using a configuration file. A sample configuration file with two input files for distance and weight matrices can be found in examples/input folder.

Lets run this sample using the damds.sh file found in bin directory.

 cd bin
 ./damds.sh ../examples/input/config.properties 1 4 

The first argument to the script is the location of configuration file. Second argument is the number of nodes. In our case it is 1 as we run on local machine. The third argument is the number of processes. In this case we are using 4 processes.

After the program finished executing, the output will be in a file called damds-points.txt inside the bin directory.

You can upload this file to WebPlotViz using the following link to visualize the data. Note: you may need to register in WebPlotViz before you can upload the files.

https://spidal-gw.dsc.soic.indiana.edu/dashboard

Run example - slurm cluster

You can use the damds_slurm.sh found in bin directory to run the program in a slurm HPC cluster. In this example we assume that you have built damds in a shared file system where every node can access the data files with the same file path.

 cd bin
 ./damds_slurm.sh ../examples/input/config.properties 4 

The above command will run the example using 4 nodes.

DAPWC

Deterministic Annealing Pairwise Clustering (dapwc) is a scalable and parallel clustering program that operate on non vector space

 git clone https://github.com/DSC-SPIDAL/dapwc.git
 cd dapwc
 mvn install

After building it will create a Jar file inside the target directory.