Amber Cluster Benchmark

A process to submit an amber job to a cluster for a range of Processors.
The metrics are gathered to record the results in ns/day to see the scaling metrics.

Requirements:

• R software = R is needed to generate the png graph of the results. Obtained from https://www.r-project.org/

• Amber software = Amber is purchased from http://ambermd.org

• A web server that has User_dir enabled for Apache. This allows users to have a website at http://web-server/~username that is located at /home/username/public_html.

• Torque PBS queue server is assumed for job creation.

Step 1: clone the repository with git.

% git clone https://github.com/hamhpc/amber_cluster_benchmark.git
% cd amber_cluster_benchmark

Step 2: edit the configuration.

Edit the run_tests.sh script to make sure that it will operate in your environment. 
% vi run_tests.sh

Step 2a: add your input files.

You can add your input files into the etc directory of the amber_cluster_benchmark directory. 
Be sure to update the names of the files in the step 2 (above).

Step 3: run the tests.

% ./run_tests.sh                

 This will submit a bunch of jobs to the queue. It's a sequence of NPROC's from 2 up to the max. 
 You can specify the NCPUS in the run_test.sh script. The jobs will take some time. 
 The large ones will complete first and the last to complete is the 2 CPU. 
 It usually finishes in under 1.5 hours which is what the walltime is set for the job runs. 

Step 4: compile the results.

After all the jobs are run and off the queue you'll need to gather the results and create the web page and graph. 

% cd ~/amber_cluster_bechmark/results_Jan-06-2017-15:27    (note it'll have the date of when you ran these tests)   
% ./make_web.sh

This will run the R script to generate the graph called make_graph.R. 
It'll also build the results in your public_html directory. 

From the head node webserver access: 

http://<head_node_server>/~<YOUR USERNAME>/amber_cluster_benchmark/index.html

Step 5 (optional): Get GPU results.

After building the cluster page and graph now it's time to run the gpu tests and have that image added to the index.html. 

% cd ~/amber_cluster_benchmark/
% ./gpu_tests.sh

This will run the gpu tests. Make sure to edit the gpu_tests.sh script to suit your environment. 

Step 6 (optional): compile the GPU results.

After all the jobs are run and off the queue you'll need to gather the results and create the GPU graph. 

% cd ~/amber_cluster_bechmark/results_gpu-Jan-06-2017-15:27    (note it'll have the date of when you ran these tests) 

Before making the graph, edit the results file (results-gpu.csv) and change the hosts to reflect the short_hostname:#.
This is so the graph will look and fit better in the image. 
Change gpunode.domain.edu/1 to gpunode:1 to represent the second card on that host. 

Now build the graph image by running: 

% ./make_web.sh

This will run the R script to generate the graph called make_graph.R. 
It'll also build the results in your public_html directory. 

From the head node webserver access: 

http://<head_node_server>/~<YOUR USERNAME>/amber_cluster_benchmark/index.html

You should now see the GPU graph on the page in addition to the previous cluster test.