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Introduction to ACENET Accelerating Discovery with Computational Research May, 2015


Academic year: 2021

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Introduction to ACENET

Accelerating Discovery with Computational Research May, 2015


What is ACENET?

Shared regional resource for...

high-performance computing (HPC)

… remote collaboration

… visualization



We facilitate







Atlantic Canada by providing Advanced Research

Computing resources and expertise.



Began in 2003.

CFI funding $25 million – 2006. 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.


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.


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


What is




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






Any computing that is too big for a



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!



Faster results


Larger problems or more detailed simulations


ACENET Computers

Four clusters

7000 CPU cores


500 TB disk storage

Plus tape

Plus software

Remember: Shared resources!

Hundreds of users




What is a Cluster?

storage storage storage cl004 cl003 ... cl002 cl999 cl001 "head node" Dynamic Resource Manager


"Grid Engine"



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.


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 username@mahone.ace-net.ca sftp username@placentia.ace-net.ca


Try MobaXterm or PuTTY and WinSCP. Just google for them




Software requests to:


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


Software Development


Tools TotalView dbx, gdb Valgrind make cvs, svn git ... Languages C/C++ Fortran Perl Python R Java ... Parallel APIs Open MPI OpenMP ... Libraries LAPACK FFTW GSL ACML netCDF HDF Boost ... Compiler Suites GCC Intel PGI …


Data Analysis



Numpy SciPy Sage pyMPI pylab matplotlib





*Distributed Computing Server


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


Environment Modules

$ module list

Currently Loaded Modulefiles:

1) pgi/8.0-6 3) totalview/8.8.0-2

2) openmpi/pgi/1.2.9

$ gcc –-version

gcc (GCC) 3.4.6 ...

$ module avail gcc

gcc/4.4.3(default) gcc/4.6.4 gcc/4.8.0

$ module load gcc

$ gcc --version

gcc (GCC) 4.4.3 ... ←


$ module unload gcc



OpenMPI is default implementation

Use modules to vary the underlying compiler, e.g.

$ module unload openmpi

$ module load gcc openmpi/gcc


Parallel Job Processing

Notice that process count and host list is passed automatically from Grid Engine to Open MPI.

$ 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


Where To Go For Help


•  gcc –help •  man gcc

ACEnet wiki

•  http://acceleratediscovery.ca/wiki/ACEnet

Email support:

•  support@ace-net.ca

•  Please supply as much info as possible


What Cluster Should I Use?

It doesn't matter,


Multiple serial jobs?

Shared memory parallel?


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 www.acceleratediscovery.ca/wiki/Software for availability, or contact your Computational Research Consultant


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