Benchmarks and analysis of interconnection in HPC cluster

This software has folowing dependencies to compile it:

1. Requires
   1. C,C++ compilers: for example gcc,g++
   2. autoconf(2.69), automake(1.14)
   3. GnuMake
   4. NetCDF library with C aplication interface for it
2. For benchmarking requires:
   1. MPI-2 standard implementation: OpenMPI, IntelMPI and so one
3. For GUI requires:
   1. Qt version 4.5 but not Qt5. It requires qmake-qt4 tool.
   2. Qwt5, libqwt5-qt4
   3. OpenGL
   4. Support OpenMP in compiler and optionally OpenCL
4. For clustering requires
   1. NetCDF C++ interface.

To compile software you need to proceed folowing steps:

0. Install software dependencies.
1. Change directory to directory with sources. Then generate configure script by files configure.ac and macros from ac-macros directory. This step is performed by runnig make_configure.sh script.
2. Learn fitures and so one in configure file

     ./configure --help
   

3. Run ./configure, where show required components and prefix. For example:

       ./configure --prefix=$HOME/nt-2 --enable-qt-gui
   

4. Run make to compile necesossary components
5. Run make install to install all into the prefix directory. Please be carefully if prefix in configure was /usr or one of system catalogues. There is no correct uninstall script and you have to delete components manually.

There are some catalogues:

1. ac-macros - macros for configure
2. doc - supplementary documentation
3. share - supplementary tools and scripts
4. src/clustering - Clustering tools.
5. src/core - source files requires for many components.
6. src/network_test - benchmarking aplication
7. src/network_viewer_qt_v2 - tool for drawing results of benchmarking and it visual analyzis.
8. java - deprecated java GUI for vizualizing results.

Some information on principles of utilities organization can be found at this list of articles:

1. Gorelov A., Maysuradze A., Salnikov A. Delay structure mining in computing cluster // CEUR Workshop Proceedings. - Vol. 1482. - Aachen : M. Jeusfeld c/o Redaktion Sun SITE, Informatik V, RWTH Aachen Germany Germany, 2015. - P. 546-551.
2. Bannikov P.S., Salnikov A.N.. Retrieving topology of interconnections in computational cluster based on results of MPI benchmarks. Moscow University Computational Mathematics and Cybernetics. vol. 38, n. 2, pp. 73-82, 2014. DOI: 10.3103/S0278641914020022
3. Salnikov A.N., Andreev D.Yu, Lebedev R.D.. Toolkit for analyzing the communication environment characteristics of a computational cluster based on MPI standard functions. Moscow University Computational Mathematics and Cybernetics. vol. 36, n. 1, pp. 41-49, 2012. DOI: 10.3103/S0278641912010074
4. Alexey, S., Dmitry, A., and Roman, L. The analysis of cluster interconnect with the network_tests2 toolkit. In Recent Advances in the Message Passing Interface - 18th European MPI Users' Group Meeting, EuroMPI 2011, Santorini, Greece, September 18-21, 2011. Proceedings (Heidelberg, Germany, 2011), vol. 6960 of Lecture Notes in Computer Science, Heidelberg, Germany, pp. 160-169. DOI: 10.1007/978-3-642-24449-0_19
5. Salnikov Alexey N., Andreev Dmitry Y.. An MPI-Based System for Testing Multiprocessor and Cluster Communications. Lecture Notes in Computer Science. n. 5205, pp. 332-333, 2008. DOI: 10.1007/978-3-540-87475-1_48

You can learn how to easily (or not) deploy this tool on HPC clusters here.