Documents
CHPC Report 2007 (final).pdf
CHPCReport_2007.pdf
allocations

usage
fall2004.piusage.html
fall2004.userusage.html
fall2005.projusage.html
fall2005.userusage.html
fall2006.projusage.html
fall2006.userusage.html
fall2007.projusage.html
fall2007.userusage.html
icebox_qtd_by_project.html
qtd_by_pi_sierra.html
qtd_by_proj.html
qtd_by_user.html
qtd_by_user_sierra.html
qtd_bypi_sierra.html
spr2005.acctusage.html
spr2005.icebox_project.html
spr2005.piusage.html
spr2005.userusage.html
spr2006.projusage.html
spr2006.userusage.html
spr2007.projusage.html
spr2007.userusage.html
sum2004.piusage.html
sum2004.userusage.html
sum2005.projusage.html
sum2005.userusage.html
sum2006.projusage.html
sum2006.userusage.html
sum2007.projusage.html
sum2007.userusage.html
win2005.acctusage.html
win2005.piusage.html
win2005.userusage.html
win2006.projusage.html
win2006.userusage.html
win2007.projusage.html
win2007.userusage.html
win2008.projusage.html
win2008.userusage.html

forms

logos

logofiles
chpc-withtxt-ltbg-color-lg.jpg
chpc-withtxt-ltbg-color-mac.tif
chpc-withtxt-ltbg-color-med.jpg
chpc-withtxt-ltbg-color-pc.tif
chpc-withtxt-ltbg-color-sm.jpg
chpc-withtxt-ltbg-color.eps
chpc-withtxt-trans-col-lg.gif
chpc-withtxt-trans-col-med.gif
chpc-withtxt-trans-col-sm.gif
chpc_jira_heading.png
chpc_jira_heading.psd
chpc_logo_block.png
chpclogo1_wtxt.gif

manuals

faq

getting_started

hardware

software
C.html
Fortran.html
OpenBabel.html
PathscaleUserGuide.pdf
amber.html
atlas.html
autodock.html
blast.html
bmdp.html
cambridge.html
code
VT_ex.c
cblacs.h
ex1.c
ex2.c
ex3.c
ex4.c
ex5.f
ex_pvfs.c
g03_clusters.script
g03_icebox.script
g03_sierra.script
g98_icebox.script
g98_icebox2.script
g98_icebox3.script
g98_icebox_global.script
g98_icebox_local.script
g98_icebox_shmem.script
g98_sierra.script
gamess_arches.script
hello.c
mpiblast.script
nwchem_arches.script
nwchem_cluster.script
nwchem_icebox.script
nwchem_sierra.script
rn_eman.scr
rnamber_arches
rnamber_da_p
rnamber_ice
rnamber_ice_p
rnamber_mm_p
rnamber_sda_p
rndalton_arches_serial
rnfluent.script.txt
rng03
rng03_generic_web
rng03_newice_web
rng03_web_arches
rng03_web_icebox
rng03_web_sierra
rng98
rng98_generic_ice_test
rng98_generic_ice_web
rng98_generic_web
rnmolpro_arches_serial
rnnw_sierra_web
scalapk_ice.script
cxml.html
cyana.html
dalton.html
dock.html
ecce.html
g03.html
g98.html
gamess.html
grace.html
gv.html
hlm.html
index_topic.html
lisrel.html
mat_l.html
matlab.html
maui.html
molden.html
molpro.html
mpi-io.html
mpi.html
mpiblast.html
nag.html
nag_example.html
ncarg.html
nwchem.html
par_devel.html
pbs.html
petsc.html
prelis.html
rms.html
sas.html
scalapack.html
screen.html
splus.html
statit.html
sudaan.html
timing.html
totalview.html
uufs
vampir.html

user_guides

news

downtimes

2004

2005
20051229.02.html
20051216.01.html
20051209.01.html
20051206.01.html
20051130.01.html
20051108.01.html
20051103.01.html
20051102.01.html
20051012.01.html
20050914.01.html
20050727.01.html
20050714.01.html
20050623.01.html
20050510.01.html
20050507.01.html
20050502.01.html
20050420.01.html
20050409.01.html
20050331.01.html
20050323.01.html
20050320.02.html
20050316.01.html
20050302.01.html
20050225.01.html
20050224.01.html
20050223.02.html
20050127.01.html
20050112.01.html
20050108.01.html

2006

2007

2008

news_items

2004
20041212.01.html
20041211.01.html
20041210.03.html
20041210.02.html
20041210.01.html
20041209.01.html
20041206.01.html
20041201.01.html
20041123.02.html
20041123.01.html
20041117.02.html
20041117.01.html
20041112.03.html
20041112.02.html
20041112.01.html
20041111.01.html
20041110.02.html
20041110.01.html
20041029.01.html
20041025.01.html
20041019.01.html
20041018.02.html
20041018.01.html
20041008.01.html
20040924.01.html
20040917.01.html
20040910.01.html
20040903.01.html
20040827.01.html
20041212.01.html
20041211.01.html
20041210.01.html
20041209.01.html
20041206.01.html
20041203.01.html
20041112.01.html

2005
20061108.01.html
20060411.02.html
20051229.02.html
20051229.01.html
20051216.01.html
20051209.01.html
20051206.01.html
20051130.02.html
20051130.01.html
20051124.01.html
20051115.01.html
20051112.01.html
20051109.01.html
20051108.02.html
20051108.01.html
20051103.01.html
20051102.01.html
20051026.01.html
20051025.01.html
20051012.01.html
20050914.01.html
20050808.01.html
20050729.01.html
20050727.01.html
20050718.01.html
20050714.01.html
20050705.01.html
20050627.01.html
20050623.01.html
20050531.01.html
20050517.01.html
20050510.01.html
20050507.01.html
20050505.01.html
20050502.01.html
20050427.01.html
20050420.01.html
20050419.01.html
20050409.01.html
20050406.01.html
20050405.01.html
20050331.01.html
20050329.02.html
20050329.01.html
20050328.01.html
20050323.01.html
20050320.02.html
20050320.01.html
20050316.01.html
20050315.01.html
20050310.01.html
20050309.01.html
20050302.01.html
20050225.01.html
20050224.01.html
20050223.02.html
20050223.01.html
20050208.01.html
20050202.01.html
20050127.01.html
20050126.01.html
20050121.01.html
20050119.01.html
20050112.01.html
20050111.01.html
20050108.01.html
20050105.01.html
20051229.02.html
20051216.01.html
20051209.01.html
20051206.01.html
20051130.01.html
20051108.01.html
20051103.01.html
20051102.01.html
20051012.01.html
20050914.01.html
20050727.01.html
20050714.01.html
20050623.01.html
20050510.01.html
20050507.01.html
20050502.01.html
20050420.01.html
20050409.01.html
20050331.01.html
20050323.01.html
20050320.02.html
20050316.01.html
20050302.01.html
20050225.01.html
20050224.01.html
20050223.02.html
20050127.01.html
20050112.01.html
20050108.01.html

2006
20061121.01.html
20061003.01.html
20060829.01.html
20060811.01.html
20060802.01.html
20060801.01.html
20060713.01.html
20060712.01.html
20060706.01.html
20060411.01.html
20060323.02.html
20060323.01.html
20060308.01.html
20060303.01.html
20060228.01.html
20060215.01.html
20060101.01.html
20061121.01.html
20061003.01.html
20060829.01.html
20060811.01.html
20060801.01.html
20060712.01.html
20060706.01.html
20060323.02.html
20060323.01.html
20060308.01.html
20060303.01.html
20060215.01.html

2007
20070823.01.html
20070807.01.html
20070727.01.html
20070621.01.html
20070611.01.html
20070604.01.html
20070521.01.html
20070425.01.html
20070411.01.html
20070405.01.html
20070314.01.html
20070206.01.html
20070130.01.html
20070116.02.html
20070116.01.html
20070108.01.html
20071219.01.html
20071129.01.html
20070905.01.html
20070814.01.html
20070604.01.html
20070425.01.html
20070405.01.html
20070314.01.html
20070130.01.html
20070116.02.html

2008

newsletters

systemstatus

policies

presentations
CCpkg_chpc_spr08.pdf
Gaussian_chpc_spr08.pdf
IntroPar07.pdf
OverviewCHPCSpring2008.pdf
cs_email
index.cnt~.html
intro_mpi
IntroMPI05a.pdf
IntroMPI06.pdf
Slide1.GIF
Slide10.GIF
Slide11.GIF
Slide12.GIF
Slide13.GIF
Slide14.GIF
Slide15.GIF
Slide16.GIF
Slide17.GIF
Slide18.GIF
Slide19.GIF
Slide2.GIF
Slide20.GIF
Slide21.GIF
Slide22.GIF
Slide23.GIF
Slide24.GIF
Slide25.GIF
Slide26.GIF
Slide27.GIF
Slide28.GIF
Slide29.GIF
Slide3.GIF
Slide30.GIF
Slide31.GIF
Slide32.GIF
Slide4.GIF
Slide5.GIF
Slide6.GIF
Slide7.GIF
Slide8.GIF
Slide9.GIF

intro_omp
IntroOpenMP04.pdf
IntroOpenMP06.pdf
Slide1.GIF
Slide10.GIF
Slide11.GIF
Slide12.GIF
Slide13.GIF
Slide14.GIF
Slide15.GIF
Slide16.GIF
Slide17.GIF
Slide18.GIF
Slide19.GIF
Slide2.GIF
Slide20.GIF
Slide21.GIF
Slide22.GIF
Slide23.GIF
Slide24.GIF
Slide25.GIF
Slide26.GIF
Slide27.GIF
Slide28.GIF
Slide29.GIF
Slide3.GIF
Slide4.GIF
Slide5.GIF
Slide6.GIF
Slide7.GIF
Slide8.GIF
Slide9.GIF

mathlibs
MatLib05.pdf
MatLib06.pdf
Slide1.GIF
Slide10.GIF
Slide11.GIF
Slide12.GIF
Slide13.GIF
Slide14.GIF
Slide15.GIF
Slide16.GIF
Slide17.GIF
Slide18.GIF
Slide19.GIF
Slide2.GIF
Slide20.GIF
Slide21.GIF
Slide22.GIF
Slide23.GIF
Slide24.GIF
Slide25.GIF
Slide26.GIF
Slide27.GIF
Slide28.GIF
Slide3.GIF
Slide4.GIF
Slide5.GIF
Slide6.GIF
Slide7.GIF
Slide8.GIF
Slide9.GIF

mpi-io

mpi-omp

sc2004_arches

totalview
Slide1.GIF
Slide10.GIF
Slide11.GIF
Slide12.GIF
Slide13.GIF
Slide14.GIF
Slide15.GIF
Slide16.GIF
Slide17.GIF
Slide18.GIF
Slide19.GIF
Slide2.GIF
Slide20.GIF
Slide21.GIF
Slide22.GIF
Slide23.GIF
Slide24.GIF
Slide3.GIF
Slide4.GIF
Slide5.GIF
Slide6.GIF
Slide7.GIF
Slide8.GIF
Slide9.GIF
Totalview04.pdf
Totalview06.pdf

vampir
Slide1.GIF
Slide10.GIF
Slide11.GIF
Slide12.GIF
Slide13.GIF
Slide14.GIF
Slide15.GIF
Slide16.GIF
Slide17.GIF
Slide18.GIF
Slide19.GIF
Slide2.GIF
Slide20.GIF
Slide21.GIF
Slide22.GIF
Slide23.GIF
Slide24.GIF
Slide25.GIF
Slide26.GIF
Slide27.GIF
Slide28.GIF
Slide29.GIF
Slide3.GIF
Slide30.GIF
Slide4.GIF
Slide5.GIF
Slide6.GIF
Slide7.GIF
Slide8.GIF
Slide9.GIF
TAU06.pdf

research
CHPCBib.html
CHPCBibliography.20051228.pdf
CHPCBibliography.20060427.pdf
CHPCBibliography.20061004.pdf
CHPCBibliography.20070215.pdf
CHPCBibliography.20070323.pdf
CHPCBibliography.20070626.pdf
CHPCBibliography.20071025.pdf
CHPCBibliography.20080425.pdf
CHPCBibliography.pdf
EnNoteGuidedTour.pdf
adapt.pdf
gen-chpc.pdf
meteorology.pdf
posters.html
sanchez.pdf
victor.pdf
services.html
CHPC Documentation
CHPC Presentations
CHPC has developed a series of courses to help users make the most of the use of CHPC resources. We continue to add to and improve this series and present it every Fall-Winter. During Spring we present an abbreviated series of our most popular talks. We welcome suggestions for additional presentations.
If you'd like to view the slides from some of the presentations, you may click on the titles.
Next: Fall 2008
Last Presented: April 10th, 2008
by Julia Harrison
This presentation gives users new to CHPC, or interested in High Performance Computing an overview of the resources available at CHPC, and the policies and procedures to access these resources.
Topic covered will include:
- The platforms available
- Filesystems
- Access
- An overview of the batch system and policies
- Service Unit Allocations
Next Scheduled: Fall 2008
Last Presented: April 10th, 2008
by Martin Cuma
In this talk, we first discuss various parallel architectures and note which ones are represented at the CHPC, in particular, shared and distributed memory parallel computers. A very short introduction into two programming solutions for these machines, MPI and OpenMP, will then be given followed by instructions on how to compile, run, debug and profile parallel applications on the CHPC parallel computers. Although this talk is more directed towards those starting to explore parallel programming, more experienced users can gain from the second half of the talk, that will provide details on software development tools available at the CHPC.
Next Scheduled: Fall 2008
Last Presented: April 17, 2008
by Anita Orendt
This talk will focus on the computational chemistry software packages - Gaussian, Amber, NWChem, Molpro, Dalton, Babel, GaussView, ECCE - that are available on CHPC computer systems. The talk will be an overview of the packages and their capabilities, and will focus on details of how users can access the installations at CHPC.| This talk is the precursor for a second talk scheduled for next month that will focus on the use of Gaussian 98/03 and GaussView.
Next Scheduled: Fall 2008
Last Presented: April 24, 2008
by Anita Orendt
This presentation will focus on the use of Gaussian03 and Gaussview on the CHPC arches clusters. Batch scripts and input file formats will be discussed. Parallel scaling and timings with the different scratch options (TMP, MM, SERIAL, PARALLEL) will also be presented, along with a discussion of scratch needs of Gaussian03. Finally several demonstrations on the use of GaussView to build molecules, input structures, set up input files and to analyze output files will be presented.
Next Scheduled: Fall 2008
Last Presented: October 4th, 2007
by Martin Cuma
This course discusses introductory and selected intermediate topics in MPI programming. We base this presentation on two simple examples and explain the MPI parallel development of them. The first example encompasses MPI initialization and simple point to point communication (which takes place between two processes). The second example includes introduction to collective communication calls (where all active processes are involved) and options for effective data communication strategies, such as derived data types and packing the data. Some ideas on more advanced MPI programming options are discussed in the end of the talk.
Debugging with Totalview
PDF VersionNext Scheduled: Fall 2008
Last presented: October 18th, 2007
by Martin Cuma
This talk introduces Totalview, a debugger that has become a standard in the Unix code development comunity. After short introduction to its major features, we will present three examples, serial, parallel OpenMP and parallel MPI codes. Using these examples, we will show common and specific features for debugging these codes, as well as point out differences in using Totalview on different CHPC platforms.
Mathematical Libraries at CHPC
PDF VersionNext Scheduled: Fall 2008
Last Presented: October 25th, 2007
by Martin Cuma
In this talk we introduce the users to the mathematical libraries that are installed on the CHPC systems, which are designed to ease the programming and speed-up scientific applications. First, we will talk about BLAS, which is a standardized library of Basic Linear Algebra Subroutines, and present few examples. Then we briefly focus on other libraries that are in use, including freeware LAPACK, ScaLAPACK, PETSc and FFTW, and commercial NAG and custom libraries from Compaq.
Parallel performance analysis with TAU
PDF VersionNext Scheduled: Fall 2008
Last Presented: November 1s5, 2007
by Martin Cuma
TAU (Tuning and Analysis Utilities) is a profiling and tracing toolkit for performance analysis of parallel programs. In this talk, we will introduce TAU as a new and flexible tool for tracing of parallel programs on CHPC Arches clusters. We detail small changes necessary to turn on the tracing and then explain how to visualize the trace files in Vampir trace viewer. We will conclude with some specific examples and glimpse on other features that TAU provides.
Next Scheduled: Fall 2008
Last presented: December 6th, 2007
by Martin Cuma
This talk introduces OpenMP, an increasingly popular and relatively simple shared memory parallel programming model. Two parallelizing schemes, parallel do loops and parallel sections, were detailed using examples. Various clauses that allow user to modify the parallel execution were also presented, including sharing and privatizing of the variables, scheduling, synchronization and mutual exclusion of the parallel tasks. Finally, few hints were given on removing loop dependencies in order to obtain effective parallelization.
Statistical Resources at CHPC
Next: Fall 2008
Last Presented: September 6, 2007
by Byron Davis
This presentation gives users (and potential users) of CHPC's statistical resources an overview of the equipment and software presently available. Additionally a list of specialized statistical software will be presented that we've supported over the past 10 years or so.
Next scheduled:
by Martin Cuma
In this talk we explain how to perform fast parallel I/O operations on the CHPC computers. It should be beneficial for all users who are interested in speeding up their parallel applications via faster file operations. First, we describe in detail PVFS (Parallel Virtual File System), installed on arches. Then we go over several examples on how to perform parallel I/O on this file system, in particular, MPI-I/O extension to the MPI standard and native PVFS function calls. Subsequently we detail ways how to compile and run MPI-I/O applications on PVFS. We conclude the talk with an insight into some more advanced aspects of MPI-I/O.
Hybrid MPI-OpenMP Programming
Next Scheduled: based upon demand - please let us know if you'd be interested!
Last Presented: December 2nd, 2004, 1:30 p.m. INSCC
Auditorium
by Martin Cuma
In this talk we will introduce hybrid MPI-OpenMP programming model designed for distributed shared memory parallel (DSMP) computers. The new Arches metacluster is a representative of this family having two shared memory processors per node. OpenMP generally provides better performing alternative for parallelization inside a node and MPI is used for communication between the distributed processors. We will discuss cases when hybrid programming model is beneficial and provide examples of simple MPI-OpenMP codes on the dual processor nodes of the Icebox cluster.
Network Communication Tools: From Skype to Access Grid
Last Presented: April 20th, 1:30 p.m., INSCC Auditorium
by Jimmy Miklavcic
This presentation will look at the various Network Communication Tools available for use to researchers. It will look at the simplest tools such as Skype and at more sophisticated systems such as the Access Grid. Users will learn which tools will fit best into their communications needs and how CHPC can help you set up your own system or use the systems that we have available.


