Introduction to ACENET Accelerating Discovery with Computational Research May, 2015

Transcription

1 Introduction to ACENET Accelerating Discovery with Computational Research May, 2015

2 What is ACENET?

3 What is ACENET? Shared regional resource for... high-performance computing (HPC) remote collaboration visualization Hardware, software, and personnel

4 Mandate We facilitate research, education and innovation in Atlantic Canada by providing Advanced Research Computing resources and expertise. Accelerate discovery in Atlantic Canada

5 Consortium

6 History Began in CFI funding $25 million Similar organizations developed in other regions. The four regions have come together with a national umbrella organization called Compute Canada. Compute Canada operates as a federated model; ACENET is Compute Canada s regional partner in Atlantic Canada. Compute Canada helps to: better allocate scarce funding dollars; provide researchers with seamless access to infrastructure and resources nationally; and enable the advanced computing community to have a single, strong voice in the national forum.

7 Computing Resources Available A wide array of High Performance Computing and storage systems Big Data and Data Analytics tools and environments Leading edge GPU computing systems Highspeed, secure file transfer with the Globus Portal Extensive software library GenAP computing platform to access and use genomic datasets Compute Canada s Cloud computing and environment Data storage and back-up systems that provide stability and security options over your desktop Desktop and mobile videoconferencing Collaboration rooms at all ACENET partner institutions to deliver and view large videoconferences. Immersive 3D Visualization Data Cave at Saint Mary s University

8 ACENET Expertise Available Determining computing resources needed Designing, optimizing and troubleshooting computer code Customizing tools In-depth collaboration where needed Group and individual training from novice to advanced Accessible and responsive support staff Installing, managing and maintaining advanced research computing equipment Access to Digital Humanities expertise Access to 3D Visualization expertise

9 ? What is Advanced Research Computing

10 High Performance Computing (HPC) Supercomputing Computationally Intensive Data Mining BIG DATA Cloud Parallel Computing High Performance Data Analysis (HPDA) Data Intensive Simulation & Analysis Data Intensive

11 Answer: Any computing that is too big for a desktop.

12 What is High Performance Computing Many CPUs working on one problem Many serial jobs running at once; or Many CPUs working in close coordination. Communication between CPUs is key! Advantages Faster results Larger problems or more detailed simulations Principal tool: Computer cluster

13 ACENET Computers Four clusters 7000 CPU cores 20 TB RAM 500 TB disk storage Plus tape Plus software Remember: Shared resources! Hundreds of users aggregated numbers

14 What is a Cluster? Internet Dynamic Resource Manager scheduler "Grid Engine" "head node" cl001 cl002 cl003 cl cl999 storage storage storage

15 How Do I Get an Account? Go to No, you don t have to pay any money. Just tell us once a year about the great research you re doing so the taxpayers can be convinced to continue funding this resource.

16 How Do I Get Connected? Logging in: ssh Secure Shell Moving Data Around: sftp Secure File Transfer Protocol Scp Secure Copy Both provided with Mac OS X or Linux ssh -X [email protected] sftp [email protected] Windows? apple Try MobaXterm or PuTTY and WinSCP. Just google for them

17 Command-Line Interface

18 Applications Molecular Gaussian Gromacs Q-Chem VASP NAMD Math&CS Sage GAP DiVinE... Astro Engineering ANSYS Fluent CFX OpenFOAM Earth &Ocean CDO NCO GMT... Bio AbySS Bowtie rapsearch2 MrBayes Migrate-n WebMO VMD StarLab IRAF PhyML PLINK Software requests to:

19 Software Development Languages Compiler Parallel Libraries Tools C/C++ Fortran Suites GCC APIs Open MPI LAPACK FFTW TotalView dbx, gdb Perl Intel OpenMP GSL Valgrind Python PGI... ACML make R netcdf cvs, svn Java... HDF Boost git Software requests to: [email protected]

20 Data Analysis R Rmpi Octave Matlab* *Distributed Computing Server Python Numpy SciPy Sage pympi pylab matplotlib Software requests to: [email protected]

21 Available Compilers At ACENET C, C++, and Fortran Portland Group (PGI) version 8 pgcc, pgcc, pgf77, pgf90, pgf95 GNU suite versions 3 and 4 gcc, g++, gcc4, g++4, gfortran, g77 Intel Compiler Suite XE 2011 icc, icpc, ifort SunStudio version 12 cc, CC, f77, f90, f95 See

22 Environment Modules $ module list Currently Loaded Modulefiles: 1) pgi/ ) totalview/ ) openmpi/pgi/1.2.9 $ gcc -version gcc (GCC) $ module avail gcc gcc/4.4.3(default) gcc/4.6.4 gcc/4.8.0 $ module load gcc $ gcc --version gcc (GCC) changed! $ module unload gcc

23 MPI OpenMPI is default implementation Use modules to vary the underlying compiler, e.g. $ module unload openmpi $ module load gcc openmpi/gcc See

24 Parallel Job Processing $ cat jobscript #$ -cwd #$ -j yes #$ -l h_rt=48:00:00 #$ -l h_vmem=2g #$ -pe ompi* 32 module purge module load gcc openmpi/gcc mpirun./application Notice that process count and host list is passed automatically from Grid Engine to Open MPI.

25 Where To Go For Help Online: gcc help man gcc ACEnet wiki support: Please supply as much info as possible

26 What Cluster Should I Use? It doesn't matter, ONE ACCOUNT IS GOOD EVERYWHERE Multiple serial jobs? Shared memory parallel? MPI? Terabytes of storage? Some software has only local license Fit in anywhere Fundy best; Glooscap good Mahone, Placentia best; Fundy good Probably Glooscap e.g. Matlab DCS & Gaussian only at Placentia See for availability, or contact your Computational Research Consultant