Cpre584 - User contributions [en]

Team Challenger

2013-03-12T23:23:32Z

Carterp: /* References */

== Team Members ==

* Xinying Wang
* Qilin Li
* Zhong Hu

== References ==
* [http://i.cs.hku.hk/~alse/hkubrg/projects/idba/ IDBA - A Practical Iterative de Bruijn Graph De Novo Assembler]

== Wiki Contributions ==

* Xinying Wang
:* week 1
::* Convey vector personalities offer OpenMP-like programming approach with FPGA accelerating. [http://www.fpl2012.org/Presentations/W4B2.pdf]
::* Weekly presentation slides [[Media:week1slides.pptx]]
:* week 2
::* A Sparse Matrix Personality for the Convey HC-1 [http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=5771239&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D5771239]
:* week 3
::* Translate verilog version adder file to vhdl code.
::* Discuss the implementation of QR application on convey system
::* Cordic Algorithm Implementations on FPGA [http://cutler.eecs.berkeley.edu/classes/ee225c/Papers/cordic.pdf]
:* week 4
::* Convey computing with bioinformatics applications [http://hpcsociety.org/Resources/Documents/121212Kirby-CONVEY-SHPCP_121212.pdf]
:* week 5
::* Tutorial for COREGEN [http://homepages.cae.wisc.edu/~ece554/website/Xilinx/Coregen_user_guide.pdf]
* Qilin Li
:* week 1
::* Introduction to Compilers for Convey [http://www.conveycomputer.com/files/3913/5085/4426/Compiler_Data_Sheet.pdf]
::* GPGPU Programming on example of CUDA [http://panoramix.ift.uni.wroc.pl/~maq/cuda/prezentacja-cuda-eng.pdf]
::* Parallel Programming in CUDA C [http://developer.download.nvidia.com/books/cuda-by-example/cuda-by-example-sample.pdf]
:* week 2
::* [http://www.cs.colby.edu/maxwell/courses/tutorials/maketutor/ A Simple Makefile Tutorial]
:* week 3
::* [http://newbiedoc.sourceforge.net/text_editing/vim.html#MODES-CL A Simple VIM Tutorial]
:* week 4
::* [[Media:ConveySystemAdministrationGuide.pdf | Convey System Administration Guide]]
* Zhong Hu
::* CUDA Global Memory Usage & Strategy. [http://developer.download.nvidia.com/CUDA/training/cuda_webinars_GlobalMemory.pdf]
::* CUDA C++ code samples.[http://docs.nvidia.com/cuda/cuda-samples/index.html]
:* make-up for week 2
::* QR ecomposition on GPUs[http://dl.acm.org/citation.cfm?id=1513904]
::* Introduction to Householder algorithm in QR decomposition application[http://math.fullerton.edu/mathews/n2003/householdermod.html]
:* make-up for week 3
::* CUDA Memory Model[https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=7&cad=rja&ved=0CEoQFjAG&url=https%3A%2F%2Fhub.vscse.org%2Fsite%2Fresources%2F2010%2F06%2F00048%2FCUDA_04.pdf&ei=_dwZUY73NKji2gWqo4GYDQ&usg=AFQjCNGgxpCFWYepx6v32fTHNyRI1pOOtA&sig2=6TW0elRmtCKW3i_fAqAT_g&bvm=bv.42261806,d.b2I]
::* CUBLAS Library Usage Reference[https://www.docs.nvidia.com/cuda/pdf/CUDA_CUBLAS_Users_Guide.pdf]
:* week 4
::* system Verilog tutorial[http://www.asic-world.com/systemverilog/tutorial.html]
:* week 5
::* most commonly used CUDA wiki website[https://developer.nvidia.com/category/zone/cuda-zone]
::* Nvidia GPU versions and corresponding compute capability[http://en.wikipedia.org/wiki/CUDA#Version_features_and_specifications]
::* methods to check CUDA memory constraints in terms of different GPU versions[http://3dgep.com/?p=1913]
:* week 6
::* open source software lists for genome alignment and assembly[http://seqanswers.com/wiki/Software/list].

Team Challenger

2013-03-12T23:21:39Z

Carterp:

== Team Members ==

* Xinying Wang
* Qilin Li
* Zhong Hu

== References ==

== Wiki Contributions ==

* Xinying Wang
:* week 1
::* Convey vector personalities offer OpenMP-like programming approach with FPGA accelerating. [http://www.fpl2012.org/Presentations/W4B2.pdf]
::* Weekly presentation slides [[Media:week1slides.pptx]]
:* week 2
::* A Sparse Matrix Personality for the Convey HC-1 [http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=5771239&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D5771239]
:* week 3
::* Translate verilog version adder file to vhdl code.
::* Discuss the implementation of QR application on convey system
::* Cordic Algorithm Implementations on FPGA [http://cutler.eecs.berkeley.edu/classes/ee225c/Papers/cordic.pdf]
:* week 4
::* Convey computing with bioinformatics applications [http://hpcsociety.org/Resources/Documents/121212Kirby-CONVEY-SHPCP_121212.pdf]
:* week 5
::* Tutorial for COREGEN [http://homepages.cae.wisc.edu/~ece554/website/Xilinx/Coregen_user_guide.pdf]
* Qilin Li
:* week 1
::* Introduction to Compilers for Convey [http://www.conveycomputer.com/files/3913/5085/4426/Compiler_Data_Sheet.pdf]
::* GPGPU Programming on example of CUDA [http://panoramix.ift.uni.wroc.pl/~maq/cuda/prezentacja-cuda-eng.pdf]
::* Parallel Programming in CUDA C [http://developer.download.nvidia.com/books/cuda-by-example/cuda-by-example-sample.pdf]
:* week 2
::* [http://www.cs.colby.edu/maxwell/courses/tutorials/maketutor/ A Simple Makefile Tutorial]
:* week 3
::* [http://newbiedoc.sourceforge.net/text_editing/vim.html#MODES-CL A Simple VIM Tutorial]
:* week 4
::* [[Media:ConveySystemAdministrationGuide.pdf | Convey System Administration Guide]]
* Zhong Hu
::* CUDA Global Memory Usage & Strategy. [http://developer.download.nvidia.com/CUDA/training/cuda_webinars_GlobalMemory.pdf]
::* CUDA C++ code samples.[http://docs.nvidia.com/cuda/cuda-samples/index.html]
:* make-up for week 2
::* QR ecomposition on GPUs[http://dl.acm.org/citation.cfm?id=1513904]
::* Introduction to Householder algorithm in QR decomposition application[http://math.fullerton.edu/mathews/n2003/householdermod.html]
:* make-up for week 3
::* CUDA Memory Model[https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=7&cad=rja&ved=0CEoQFjAG&url=https%3A%2F%2Fhub.vscse.org%2Fsite%2Fresources%2F2010%2F06%2F00048%2FCUDA_04.pdf&ei=_dwZUY73NKji2gWqo4GYDQ&usg=AFQjCNGgxpCFWYepx6v32fTHNyRI1pOOtA&sig2=6TW0elRmtCKW3i_fAqAT_g&bvm=bv.42261806,d.b2I]
::* CUBLAS Library Usage Reference[https://www.docs.nvidia.com/cuda/pdf/CUDA_CUBLAS_Users_Guide.pdf]
:* week 4
::* system Verilog tutorial[http://www.asic-world.com/systemverilog/tutorial.html]
:* week 5
::* most commonly used CUDA wiki website[https://developer.nvidia.com/category/zone/cuda-zone]
::* Nvidia GPU versions and corresponding compute capability[http://en.wikipedia.org/wiki/CUDA#Version_features_and_specifications]
::* methods to check CUDA memory constraints in terms of different GPU versions[http://3dgep.com/?p=1913]
:* week 6
::* open source software lists for genome alignment and assembly[http://seqanswers.com/wiki/Software/list].

Team Cyc05

2013-02-12T22:03:47Z

Carterp: /* PengQing */

{| border="1" cellpadding="5" cellspacing="0" align="right"
|+'''Team Cyc05'''
|-
| align="center" width="200px" | [[Image:Cy.jpg]]
|-
! style="background:#CD1014;" | Cyc05 Team Logo
|-
|-
| colspan="2" align="center" |
{| border="0"
|+''Team Members''
|-
| Osama G. Attia (ogamal)
|-
| Tyler Johnson (tyler07)
|-
| PengQing Xie (carterp)
|}
|}

== Team Members ==
* Osama G. Attia
* Tyler Johnson
* PengQing Xie

== Weekly Presentations ==
*Week 1 - [[Media:Cyc05_-_Presentation_01.pdf | Presentation Slides Week 1]]
*Week 2 - [[Media:Cyc05_Week_2.pdf | Presentation Slides Week 2]]
*Week 3 - [[Media:Cyc05_week3_presentation.pdf‎ | Presentation Slides Week 3]]

== Wiki Contributions ==
=== Tyler ===
*Week 1
**[[Useful Modelsim Commands]]
**[[Media:Modelsim_pe_user_10.0d.pdf | Modelsim Users Guide]]
*Week2
** [[Media:Connect_Remotely_Via_VPN.pdf | Guide to Remote Connecting]]
*Week3
**[[Adding VHDL Files to a Project]] Additions and alterations
**Hosted the scripts for Kevinss tutorial and provided a link for it
**Modified the landing page to Kevni't tutorial to have the pdf, and a link to the scripts
**Modified [[Tutorial: Creating a Custom Bitfile]], some details were unclear and/or left out about using your newly built bitfile

=== Osama ===
*Week 1: Creating Team Cyc05 page.
*Week 2:
**Updating [[Connecting to convey-1.ece.iastate.edu]] with usage policy
**Adding [[Frequently Asked Questions]] page
* Week 3:
**Updating the [[Frequently Asked Questions]] page
**Adding and maintaining the [[Using the Memory Controller Interface]] page
* Week 4:
**[[Media:Vhd2v isnt.txt|Python script to generate instantiation code of VHDL module in Verilog]]
**[[Media:Convey_mc_ports.txt|Python script to generate the MC interface signals in VHDL]]
**[[Media:convey_mc_ports_vhdl.txt|MC interface signals]] in VHDL
**Adding more stuff to the [[Frequently Asked Questions]] page

=== PengQing ===
*Week 1:
**[http://sn0v.wordpress.com/2012/12/07/installing-cuda-5-on-ubuntu-12-04/ Installing CUDA on Ubuntu]
**[http://graphics.stanford.edu/~mhouston/public_talks/R520-mhouston.pdf General Purpose Computation on GPUs (GPGPU)]
*Week 2:
**[http://vol.verilog.com/VOL/main.htm Verilog self-study online course]
*Week 3:
**[http://www.ece.msstate.edu/~reese/EE4743/lectures/verilog_intro_2002/verilog_intro_2002.pdf Verilog vs. VHDL]
*Week 4:
**[http://www.vogella.com/articles/Git/article.html git tutorial]

Team Cyc05

2013-02-12T21:35:49Z

Carterp: /* PengQing */

Main Page

2013-02-06T23:15:53Z

Carterp: /* Helpful Guides */

== Articles ==
=== Convey HC-1 Tutorials ===
* [[Connecting to convey-1.ece.iastate.edu]]
* [[Convey environment setup|Setting Up Environment Variables on Convey's HC-1]]
* [[Convey PDK Tutorial]]
* [[Using the Memory Controller Interface]]
* [[Running the Vector Adder Example Application]]

* [[Analyze the Simpleton Basic App]]
* [[Tutorial: Creating a Custom Bitfile | Create a Custom Bitfile]]
* [[Using a Custom Bitfile in C Code]]
* [[Adding VHDL Files to a Project]]
* [[The Verilog Hardware Interface for CAE]]
* [[Using ISE's Core Generator to build FIFOs and other IP cores]]
* [[Running Different Bitfiles on each AE | Projects with Multiple Bitfiles]]
* [[Using the Write-Complete Interface]]
* [[Using the Timing Analyzer]]

* [[Using SPAT]]
* [[Using GPROF]]
* [[Convey vector example | Example of Loop Unrolling using FPGA]]
* [[Sobel Algorithm | Speeding up Sobel Algorithm]]
* [[Frequently Asked Questions]]

== Reference Manuals ==
=== Convey ===
* [[Media:ConveyPDKReferenceManual.pdf | Convey PDK Reference Manual (.pdf)]] (updated to V5.2; April 2012)
* [[Media:ConveyProgrammersGuide.pdf | Convey Programmers Guide (.pdf)]] (updated to V1.8; November 2010)
* [[Media:ConveyReferenceManual.pdf | Convey Reference Manual (.pdf)]]
* [[Media:ConveySpatUsersGuide.pdf | Convey SPAT (Simulator Performance Analysis Tool) Guide]]
* [[Media:Convey PDK Training.pdf | Convey PDK (.pdf)]]
* [[Media:Convey Overview.pdf | Convey Overview (.pdf)]]

The newet version of these documents are available at [http://www.conveysupport.com/help/?page_id=112 Convey's Support Site]

=== CUDA ===
* [[Media:CUDA_C_Programming_Guide.pdf | CUDA_C_Programming_Guide (.pdf)]]
* [[Media:CUDA_C_Best_Practices_Guide.pdf | CUDA_C_Best_Practices_Guide(.pdf)]]
* [[Media:CUDA_Memory.pdf | CUDA_Memory (.pdf)]]

==Links==
* [http://www.asic-world.com www.asic-world.com] - Great Tutorials for those Learning HDLs
* [http://memocode.irisa.fr MemoCODE 2012]
** [[Media:2012-memocode-contest.pdf | MemoCODE Contest.pdf]]
** [http://memocode.irisa.fr/2012/2012-memocode-contest.tar.gz Reference Implementation]
** [ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/human_g1k_v37.fasta.gz Human Reference Genome (human_g1k_v37.fasta.gz)]
** [ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/data/NA06985/sequence_read/ERR050082.filt.fastq.gz Example Reads (ERR050082.filt.fastq.gz)]
** [http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA06985/sequence_read/ERR050082.filt.fastq.gz Example Reads (Alternative Link) (ERR050082.filt.fastq.gz)]

* [[2010 Main Page | CprE 584 2010 Wiki Main Page]]
* [http://class.ee.iastate.edu/cpre583/ CprE 583 Website]
* [http://class.ece.iastate.edu/cpre584/ CprE 584 Website]

=== Other Articles ===
* [[Assignment|Assignments]]
* [[A quick start on CUDA]]

== Helpful Guides ==
* [http://www.c7t-hdl.com/Docs/C7T_AN05_Customized_WaveView_ModelSim_ISE.pdf Modelsim and ISE]
* [http://www.fpga.com.cn/hdl/training/verilog%20reference%20guide.pdf The Verilog Golden Reference]
* [http://courseware.ee.calpoly.edu/~bmealy/shock_awe_vhdl_adobe.pdf "The Shock and Awe" VHDL Tutorial]
* [http://www.ece.msstate.edu/~reese/EE4743/lectures/verilog_intro_2002/verilog_intro_2002.pdf Verilog vs. VHDL]
* [http://esd.cs.ucr.edu/labs/tutorial/ VHDL Simple Code Examples]
* [http://www.seas.upenn.edu/~ese171/vhdl/vhdl_primer.html VHDL Primer]
* [http://www.kxcad.net/electronic_Xilinx_guide/mergedProjects/xsim/html/xs_p_ml_instantiation.htm Using VHDL components in Verilog]
* [[Media:Modelsim_pe_user_10.0d.pdf | Modelsim Users Guide]]
* [[Useful Modelsim Commands]]
* [http://sn0v.wordpress.com/2012/12/07/installing-cuda-5-on-ubuntu-12-04/ Installing CUDA on Ubuntu]
* [http://graphics.stanford.edu/~mhouston/public_talks/R520-mhouston.pdf General Purpose Computation on GPUs (GPGPU)]
* Convey vector personalities offer OpenMP-like programming approach with FPGA accelerating. [http://www.fpl2012.org/Presentations/W4B2.pdf]
* [[Media:Connect_Remotely_Via_VPN.pdf | Guide to Remote Connecting]]

== Readings for Memocode 2012 ==
*[[Media:Brief_Bioinform-2010-Li-473-83.pdf|A survey on algorithms for sequencing]]
*[[Media:Gb-2009-10-3-r25.pdf|Burrows-Wheeler indexing]]

== Spring 2012 Teams ==
* [[Team Gryffindor]]
* [[Team Slytherin]]
* [[Team 142857]]
== Spring 2013 Teams ==
* [[Team Cyc05]]
* [[Team Challenger]]
* [[Team Blitz]]

Team Cyc05

2013-02-06T23:13:22Z

Carterp: /* PengQing */

{| border="1" cellpadding="5" cellspacing="0" align="right"
|+'''Team Cyc05'''
|-
| align="center" width="200px" | [[Image:Cy.jpg]]
|-
! style="background:#CD1014;" | Cyc05 Team Logo
|-
|-
| colspan="2" align="center" |
{| border="0"
|+''Team Members''
|-
| Osama G. Attia (ogamal)
|-
| Tyler Johnson (tyler07)
|-
| PengQing Xie (carterp)
|}
|}

== Team Members ==
* Osama G. Attia
* Tyler Johnson
* PengQing Xie

== Weekly Presentations ==
*Week 1 - [[Media:Cyc05_-_Presentation_01.pdf | Presentation Slides Week 1]]
*Week 2 - [[Media:Cyc05_Week_2.pdf | Presentation Slides Week 2]]
*Week 3 - [[Media:Cyc05_week3_presentation.pdf‎ | Presentation Slides Week 3]]

== Wiki Contributions ==
=== Tyler ===
*Week 1
**[[Useful Modelsim Commands]]
**[[Media:Modelsim_pe_user_10.0d.pdf | Modelsim Users Guide]]
*Week2
** [[Media:Connect_Remotely_Via_VPN.pdf | Guide to Remote Connecting]]
*Week3
**[[Adding VHDL Files to a Project]] Additions and alterations
**Hosted the scripts for Kevinss tutorial and provided a link for it
**Modified the landing page to Kevni't tutorial to have the pdf, and a link to the scripts
**Modified [[Tutorial: Creating a Custom Bitfile]], some details were unclear and/or left out about using your newly built bitfile

=== Osama ===
*Week 1: Creating Team Cyc05 page.
*Week 2:
**Updating [[Connecting to convey-1.ece.iastate.edu]] with usage policy.
**Adding [[Frequently Asked Questions]] page.
* Week 3:
**Updating the [[Frequently Asked Questions]] page.
**Adding and maintaining the [[Using the Memory Controller Interface]] page.

=== PengQing ===
*Week 1:
**[http://sn0v.wordpress.com/2012/12/07/installing-cuda-5-on-ubuntu-12-04/ Installing CUDA on Ubuntu]
**[http://graphics.stanford.edu/~mhouston/public_talks/R520-mhouston.pdf General Purpose Computation on GPUs (GPGPU)]
*Week 2:
**[http://vol.verilog.com/VOL/main.htm Verilog self-study online course]
*Week 3:
**[http://www.ece.msstate.edu/~reese/EE4743/lectures/verilog_intro_2002/verilog_intro_2002.pdf Verilog vs. VHDL]

Team Cyc05

2013-02-06T23:13:13Z

Carterp: /* PengQing */

{| border="1" cellpadding="5" cellspacing="0" align="right"
|+'''Team Cyc05'''
|-
| align="center" width="200px" | [[Image:Cy.jpg]]
|-
! style="background:#CD1014;" | Cyc05 Team Logo
|-
|-
| colspan="2" align="center" |
{| border="0"
|+''Team Members''
|-
| Osama G. Attia (ogamal)
|-
| Tyler Johnson (tyler07)
|-
| PengQing Xie (carterp)
|}
|}

== Team Members ==
* Osama G. Attia
* Tyler Johnson
* PengQing Xie

== Weekly Presentations ==
*Week 1 - [[Media:Cyc05_-_Presentation_01.pdf | Presentation Slides Week 1]]
*Week 2 - [[Media:Cyc05_Week_2.pdf | Presentation Slides Week 2]]
*Week 3 - [[Media:Cyc05_week3_presentation.pdf‎ | Presentation Slides Week 3]]

== Wiki Contributions ==
=== Tyler ===
*Week 1
**[[Useful Modelsim Commands]]
**[[Media:Modelsim_pe_user_10.0d.pdf | Modelsim Users Guide]]
*Week2
** [[Media:Connect_Remotely_Via_VPN.pdf | Guide to Remote Connecting]]
*Week3
**[[Adding VHDL Files to a Project]] Additions and alterations
**Hosted the scripts for Kevinss tutorial and provided a link for it
**Modified the landing page to Kevni't tutorial to have the pdf, and a link to the scripts
**Modified [[Tutorial: Creating a Custom Bitfile]], some details were unclear and/or left out about using your newly built bitfile

=== Osama ===
*Week 1: Creating Team Cyc05 page.
*Week 2:
**Updating [[Connecting to convey-1.ece.iastate.edu]] with usage policy.
**Adding [[Frequently Asked Questions]] page.
* Week 3:
**Updating the [[Frequently Asked Questions]] page.
**Adding and maintaining the [[Using the Memory Controller Interface]] page.

=== PengQing ===
*Week 1:
**[http://sn0v.wordpress.com/2012/12/07/installing-cuda-5-on-ubuntu-12-04/ Installing CUDA on Ubuntu]
**[http://graphics.stanford.edu/~mhouston/public_talks/R520-mhouston.pdf General Purpose Computation on GPUs (GPGPU)]
*Week 2:
**[http://vol.verilog.com/VOL/main.htm Verilog self-study online course]
*Week 3:
***[http://www.ece.msstate.edu/~reese/EE4743/lectures/verilog_intro_2002/verilog_intro_2002.pdf Verilog vs. VHDL]

Team Cyc05

2013-02-05T22:58:57Z

Carterp: /* Wiki Contributions */

{| border="1" cellpadding="5" cellspacing="0" align="right"
|+'''Team Cyc05'''
|-
| align="center" width="200px" | [[Image:Cy.jpg]]
|-
! style="background:#CD1014;" | Cyc05 Team Logo
|-
|-
| colspan="2" align="center" |
{| border="0"
|+''Team Members''
|-
| Osama G. Attia (ogamal)
|-
| Tyler Johnson (tyler07)
|-
| PengQing Xie (carterp)
|}
|}

== Team Members ==
* Osama G. Attia
* Tyler Johnson
* PengQing Xie

== Weekly Presentations ==
*Week 1 - [[Media:Cyc05_-_Presentation_01.pdf | Presentation Slides Week 1]]
*Week 2 - [[Media:Cyc05_Week_2.pdf | Presentation Slides Week 2]]

== Wiki Contributions ==
*Tyler
**Week 1
***[[Useful Modelsim Commands]]
***[[Media:Modelsim_pe_user_10.0d.pdf | Modelsim Users Guide]]
**Week2
*** [[Media:Connect_Remotely_Via_VPN.pdf | Guide to Remote Connecting]]
**Week3
***[[Adding VHDL Files to a Project]] Additions and alterations
***Hosted the scripts for Kevinss tutorial and provided a link for it
***Modified the landing page to Kevni't tutorial to have the pdf, and a link to the scripts
***Modified [[Tutorial: Creating a Custom Bitfile]], some details were unclear and/or left out about using your newly built bitfile
*Osama
**Week 1: Creating Team Cyc05 page.
**Week 2:
***Updating [[Connecting to convey-1.ece.iastate.edu]] with usage policy
***Adding [[Frequently Asked Questions]] page

*PengQing
**Week 1:
***[http://sn0v.wordpress.com/2012/12/07/installing-cuda-5-on-ubuntu-12-04/ Installing CUDA on Ubuntu]
***[http://graphics.stanford.edu/~mhouston/public_talks/R520-mhouston.pdf General Purpose Computation on GPUs (GPGPU)]
**Week 2:
***[http://vol.verilog.com/VOL/main.htm Verilog self-study online course]
**Week 3:
***[http://www.ece.msstate.edu/~reese/EE4743/lectures/verilog_intro_2002/verilog_intro_2002.pdf Verilog vs. VHDL]

Team Cyc05

2013-02-05T22:56:29Z

Carterp: /* Wiki Contributions */

{| border="1" cellpadding="5" cellspacing="0" align="right"
|+'''Team Cyc05'''
|-
| align="center" width="200px" | [[Image:Cy.jpg]]
|-
! style="background:#CD1014;" | Cyc05 Team Logo
|-
|-
| colspan="2" align="center" |
{| border="0"
|+''Team Members''
|-
| Osama G. Attia (ogamal)
|-
| Tyler Johnson (tyler07)
|-
| PengQing Xie (carterp)
|}
|}

== Team Members ==
* Osama G. Attia
* Tyler Johnson
* PengQing Xie

== Weekly Presentations ==
*Week 1 - [[Media:Cyc05_-_Presentation_01.pdf | Presentation Slides Week 1]]
*Week 2 - [[Media:Cyc05_Week_2.pdf | Presentation Slides Week 2]]

== Wiki Contributions ==
*Tyler
**Week 1
***[[Useful Modelsim Commands]]
***[[Media:Modelsim_pe_user_10.0d.pdf | Modelsim Users Guide]]
**Week2
*** [[Media:Connect_Remotely_Via_VPN.pdf | Guide to Remote Connecting]]
**Week3
***[[Adding VHDL Files to a Project]] Additions and alterations
***Hosted the scripts for Kevinss tutorial and provided a link for it
***Modified the landing page to Kevni't tutorial to have the pdf, and a link to the scripts
***Modified [[Tutorial: Creating a Custom Bitfile]], some details were unclear and/or left out about using your newly built bitfile
*Osama
**Week 1: Creating Team Cyc05 page.
**Week 2:
***Updating [[Connecting to convey-1.ece.iastate.edu]] with usage policy
***Adding [[Frequently Asked Questions]] page

*PengQing
**Week 1:
***[http://sn0v.wordpress.com/2012/12/07/installing-cuda-5-on-ubuntu-12-04/ Installing CUDA on Ubuntu]
***[http://graphics.stanford.edu/~mhouston/public_talks/R520-mhouston.pdf General Purpose Computation on GPUs (GPGPU)]
**Week 2:
***
**Week 3:
***[http://www.ece.msstate.edu/~reese/EE4743/lectures/verilog_intro_2002/verilog_intro_2002.pdf Verilog vs. VHDL]

Team Cyc05

2013-02-05T22:55:53Z

Carterp: /* Wiki Contributions */

{| border="1" cellpadding="5" cellspacing="0" align="right"
|+'''Team Cyc05'''
|-
| align="center" width="200px" | [[Image:Cy.jpg]]
|-
! style="background:#CD1014;" | Cyc05 Team Logo
|-
|-
| colspan="2" align="center" |
{| border="0"
|+''Team Members''
|-
| Osama G. Attia (ogamal)
|-
| Tyler Johnson (tyler07)
|-
| PengQing Xie (carterp)
|}
|}

== Team Members ==
* Osama G. Attia
* Tyler Johnson
* PengQing Xie

== Weekly Presentations ==
*Week 1 - [[Media:Cyc05_-_Presentation_01.pdf | Presentation Slides Week 1]]
*Week 2 - [[Media:Cyc05_Week_2.pdf | Presentation Slides Week 2]]

== Wiki Contributions ==
*Tyler
**Week 1
***[[Useful Modelsim Commands]]
***[[Media:Modelsim_pe_user_10.0d.pdf | Modelsim Users Guide]]
**Week2
*** [[Media:Connect_Remotely_Via_VPN.pdf | Guide to Remote Connecting]]
**Week3
***[[Adding VHDL Files to a Project]] Additions and alterations
***Hosted the scripts for Kevinss tutorial and provided a link for it
***Modified the landing page to Kevni't tutorial to have the pdf, and a link to the scripts
***Modified [[Tutorial: Creating a Custom Bitfile]], some details were unclear and/or left out about using your newly built bitfile
*Osama
**Week 1: Creating Team Cyc05 page.
**Week 2:
***Updating [[Connecting to convey-1.ece.iastate.edu]] with usage policy
***Adding [[Frequently Asked Questions]] page

*PengQing
**Week 1:
***[http://sn0v.wordpress.com/2012/12/07/installing-cuda-5-on-ubuntu-12-04/ Installing CUDA on Ubuntu]
***[http://graphics.stanford.edu/~mhouston/public_talks/R520-mhouston.pdf General Purpose Computation on GPUs (GPGPU)]
**Week 2:
***
**Week 3:
***[http://www.ece.msstate.edu/~reese/EE4743/lectures/verilog_intro_2002/verilog_intro_2002.pdf]

Team Cyc05

2013-02-05T22:55:29Z

Carterp: /* Wiki Contributions */

{| border="1" cellpadding="5" cellspacing="0" align="right"
|+'''Team Cyc05'''
|-
| align="center" width="200px" | [[Image:Cy.jpg]]
|-
! style="background:#CD1014;" | Cyc05 Team Logo
|-
|-
| colspan="2" align="center" |
{| border="0"
|+''Team Members''
|-
| Osama G. Attia (ogamal)
|-
| Tyler Johnson (tyler07)
|-
| PengQing Xie (carterp)
|}
|}

== Team Members ==
* Osama G. Attia
* Tyler Johnson
* PengQing Xie

== Weekly Presentations ==
*Week 1 - [[Media:Cyc05_-_Presentation_01.pdf | Presentation Slides Week 1]]
*Week 2 - [[Media:Cyc05_Week_2.pdf | Presentation Slides Week 2]]

== Wiki Contributions ==
*Tyler
**Week 1
***[[Useful Modelsim Commands]]
***[[Media:Modelsim_pe_user_10.0d.pdf | Modelsim Users Guide]]
**Week2
*** [[Media:Connect_Remotely_Via_VPN.pdf | Guide to Remote Connecting]]
**Week3
***[[Adding VHDL Files to a Project]] Additions and alterations
***Hosted the scripts for Kevinss tutorial and provided a link for it
***Modified the landing page to Kevni't tutorial to have the pdf, and a link to the scripts
***Modified [[Tutorial: Creating a Custom Bitfile]], some details were unclear and/or left out about using your newly built bitfile
*Osama
**Week 1: Creating Team Cyc05 page.
**Week 2:
***Updating [[Connecting to convey-1.ece.iastate.edu]] with usage policy
***Adding [[Frequently Asked Questions]] page

*PengQing
**Week 1:
***[http://sn0v.wordpress.com/2012/12/07/installing-cuda-5-on-ubuntu-12-04/ Installing CUDA on Ubuntu]
***[http://graphics.stanford.edu/~mhouston/public_talks/R520-mhouston.pdf General Purpose Computation on GPUs (GPGPU)]
**Week 2:
***
**Week 3:http://www.ece.msstate.edu/~reese/EE4743/lectures/verilog_intro_2002/verilog_intro_2002.pdf
***

Team Cyc05

2013-02-05T22:27:04Z

Carterp: /* Wiki Contributions */

Team Cyc05

2013-02-05T22:26:31Z

Carterp: /* Wiki Contributions */

Main Page

2013-01-22T04:11:14Z

Carterp: /* Helpful Guides */

== Articles ==
=== Convey HC-1 Tutorials ===
* [[Connecting to convey-1.ece.iastate.edu]]
* [[Convey environment setup|Setting Up Environment Variables on Convey's HC-1]]
* [[Running the Vector Adder Example Application]]
* Convey pdk tutorial: [[image:ConveyTutorial1.pdf]] (uses newCnyProject script)
* [[Analyze the Simpleton Basic App]]
* [[Tutorial: Creating a Custom Bitfile | Create a Custom Bitfile]]
* [[Using a Custom Bitfile in C Code]]
* [[Adding VHDL Files to a Project]]
* [[The Verilog Hardware Interface for CAE]]
* [[Using ISE's Core Generator to build FIFOs and other IP cores]]
* [[Running Different Bitfiles on each AE | Projects with Multiple Bitfiles]]
* [[Using the Write-Complete Interface]]
* [[Using the Timing Analyzer]]

* [[Using SPAT]]
* [[Using GPROF]]
* [[Convey vector example | Example of Loop Unrolling using FPGA]]
* [[Sobel Algorithm | Speeding up Sobel Algorithm]]

== Reference Manuals ==
=== Convey ===
* [[Media:ConveyPDKReferenceManual.pdf | Convey PDK Reference Manual (.pdf)]] (updated to V5.2; April 2012)
* [[Media:ConveyProgrammersGuide.pdf | Convey Programmers Guide (.pdf)]] (updated to V1.8; November 2010)
* [[Media:ConveyReferenceManual.pdf | Convey Reference Manual (.pdf)]]
* [[Media:ConveySpatUsersGuide.pdf | Convey SPAT (Simulator Performance Analysis Tool) Guide]]
* [[Media:Convey PDK Training.pdf | Convey PDK (.pdf)]]
* [[Media:Convey Overview.pdf | Convey Overview (.pdf)]]

The newet version of these documents are available at [http://www.conveysupport.com/help/?page_id=112 Convey's Support Site]

=== CUDA ===
* [[Media:CUDA_C_Programming_Guide.pdf | CUDA_C_Programming_Guide (.pdf)]]
* [[Media:CUDA_C_Best_Practices_Guide.pdf | CUDA_C_Best_Practices_Guide(.pdf)]]
* [[Media:CUDA_Memory.pdf | CUDA_Memory (.pdf)]]

==Links==
* [http://www.asic-world.com www.asic-world.com] - Great Tutorials for those Learning HDLs
* [http://memocode.irisa.fr MemoCODE 2012]
** [[Media:2012-memocode-contest.pdf | MemoCODE Contest.pdf]]
** [http://memocode.irisa.fr/2012/2012-memocode-contest.tar.gz Reference Implementation]
** [ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/human_g1k_v37.fasta.gz Human Reference Genome (human_g1k_v37.fasta.gz)]
** [ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/data/NA06985/sequence_read/ERR050082.filt.fastq.gz Example Reads (ERR050082.filt.fastq.gz)]
** [http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA06985/sequence_read/ERR050082.filt.fastq.gz Example Reads (Alternative Link) (ERR050082.filt.fastq.gz)]

* [[2010 Main Page | CprE 584 2010 Wiki Main Page]]
* [http://class.ee.iastate.edu/cpre583/ CprE 583 Website]
* [http://class.ece.iastate.edu/cpre584/ CprE 584 Website]

=== Other Articles ===
* [[Assignment|Assignments]]
* [[A quick start on CUDA]]

== Helpful Guides ==
* [http://www.c7t-hdl.com/Docs/C7T_AN05_Customized_WaveView_ModelSim_ISE.pdf Modelsim and ISE]
* [http://www.fpga.com.cn/hdl/training/verilog%20reference%20guide.pdf The Verilog Golden Reference]
* [http://courseware.ee.calpoly.edu/~bmealy/shock_awe_vhdl_adobe.pdf "The Shock and Awe" VHDL Tutorial]
* [http://esd.cs.ucr.edu/labs/tutorial/ VHDL Simple Code Examples]
* [http://www.seas.upenn.edu/~ese171/vhdl/vhdl_primer.html VHDL Primer]
* [http://www.kxcad.net/electronic_Xilinx_guide/mergedProjects/xsim/html/xs_p_ml_instantiation.htm Using VHDL components in Verilog]
* [[Media:Modelsim_pe_user_10.0d.pdf | Modelsim Users Guide]]
* [[Useful Modelsim Commands]]
* [http://sn0v.wordpress.com/2012/12/07/installing-cuda-5-on-ubuntu-12-04/ Installing CUDA on Ubuntu]
* [http://graphics.stanford.edu/~mhouston/public_talks/R520-mhouston.pdf General Purpose Computation on GPUs (GPGPU)]

== Readings for Memocode 2012 ==
*[[Media:Brief_Bioinform-2010-Li-473-83.pdf|A survey on algorithms for sequencing]]
*[[Media:Gb-2009-10-3-r25.pdf|Burrows-Wheeler indexing]]

== Spring 2012 Teams ==
* [[Team Gryffindor]]
* [[Team Slytherin]]
* [[Team 142857]]
== Spring 2013 Teams ==
* [[Team Cyc05]]
* [[Team Challenger]]
* [[Team Blitz]]

Team Cyc05

2013-01-22T04:05:03Z

Carterp: /* Wiki Contributions */

Team Cyc05

2013-01-22T03:57:30Z

Carterp: /* Wiki Contributions */

Main Page

2013-01-22T03:56:44Z

Carterp: /* Helpful Guides */

== Articles ==
=== Convey HC-1 Tutorials ===
* [[Connecting to convey-1.ece.iastate.edu]]
* [[Convey environment setup|Setting Up Environment Variables on Convey's HC-1]]
* [[Running the Vector Adder Example Application]]
* Convey pdk tutorial: [[image:ConveyTutorial1.pdf]] (uses newCnyProject script)
* [[Analyze the Simpleton Basic App]]
* [[Tutorial: Creating a Custom Bitfile | Create a Custom Bitfile]]
* [[Using a Custom Bitfile in C Code]]
* [[Adding VHDL Files to a Project]]
* [[The Verilog Hardware Interface for CAE]]
* [[Using ISE's Core Generator to build FIFOs and other IP cores]]
* [[Running Different Bitfiles on each AE | Projects with Multiple Bitfiles]]
* [[Using the Write-Complete Interface]]
* [[Using the Timing Analyzer]]

* [[Using SPAT]]
* [[Using GPROF]]
* [[Convey vector example | Example of Loop Unrolling using FPGA]]
* [[Sobel Algorithm | Speeding up Sobel Algorithm]]

== Reference Manuals ==
=== Convey ===
* [[Media:ConveyPDKReferenceManual.pdf | Convey PDK Reference Manual (.pdf)]] (updated to V5.2; April 2012)
* [[Media:ConveyProgrammersGuide.pdf | Convey Programmers Guide (.pdf)]] (updated to V1.8; November 2010)
* [[Media:ConveyReferenceManual.pdf | Convey Reference Manual (.pdf)]]
* [[Media:ConveySpatUsersGuide.pdf | Convey SPAT (Simulator Performance Analysis Tool) Guide]]
* [[Media:Convey PDK Training.pdf | Convey PDK (.pdf)]]
* [[Media:Convey Overview.pdf | Convey Overview (.pdf)]]

The newet version of these documents are available at [http://www.conveysupport.com/help/?page_id=112 Convey's Support Site]

=== CUDA ===
* [[Media:CUDA_C_Programming_Guide.pdf | CUDA_C_Programming_Guide (.pdf)]]
* [[Media:CUDA_C_Best_Practices_Guide.pdf | CUDA_C_Best_Practices_Guide(.pdf)]]
* [[Media:CUDA_Memory.pdf | CUDA_Memory (.pdf)]]

==Links==
* [http://www.asic-world.com www.asic-world.com] - Great Tutorials for those Learning HDLs
* [http://memocode.irisa.fr MemoCODE 2012]
** [[Media:2012-memocode-contest.pdf | MemoCODE Contest.pdf]]
** [http://memocode.irisa.fr/2012/2012-memocode-contest.tar.gz Reference Implementation]
** [ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/human_g1k_v37.fasta.gz Human Reference Genome (human_g1k_v37.fasta.gz)]
** [ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/data/NA06985/sequence_read/ERR050082.filt.fastq.gz Example Reads (ERR050082.filt.fastq.gz)]
** [http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA06985/sequence_read/ERR050082.filt.fastq.gz Example Reads (Alternative Link) (ERR050082.filt.fastq.gz)]

* [[2010 Main Page | CprE 584 2010 Wiki Main Page]]
* [http://class.ee.iastate.edu/cpre583/ CprE 583 Website]
* [http://class.ece.iastate.edu/cpre584/ CprE 584 Website]

=== Other Articles ===
* [[Assignment|Assignments]]
* [[A quick start on CUDA]]

== Helpful Guides ==
* [http://www.c7t-hdl.com/Docs/C7T_AN05_Customized_WaveView_ModelSim_ISE.pdf Modelsim and ISE]
* [http://www.fpga.com.cn/hdl/training/verilog%20reference%20guide.pdf The Verilog Golden Reference]
* [http://courseware.ee.calpoly.edu/~bmealy/shock_awe_vhdl_adobe.pdf "The Shock and Awe" VHDL Tutorial]
* [http://esd.cs.ucr.edu/labs/tutorial/ VHDL Simple Code Examples]
* [http://www.seas.upenn.edu/~ese171/vhdl/vhdl_primer.html VHDL Primer]
* [http://www.kxcad.net/electronic_Xilinx_guide/mergedProjects/xsim/html/xs_p_ml_instantiation.htm Using VHDL components in Verilog]
* [[Media:Modelsim_pe_user_10.0d.pdf | Modelsim Users Guide]]
* [[Useful Modelsim Commands]]
* [http://sn0v.wordpress.com/2012/12/07/installing-cuda-5-on-ubuntu-12-04/ Installing CUDA on Ubuntu]

== Readings for Memocode 2012 ==
*[[Media:Brief_Bioinform-2010-Li-473-83.pdf|A survey on algorithms for sequencing]]
*[[Media:Gb-2009-10-3-r25.pdf|Burrows-Wheeler indexing]]

== Spring 2012 Teams ==
* [[Team Gryffindor]]
* [[Team Slytherin]]
* [[Team 142857]]
== Spring 2013 Teams ==
* [[Team Cyc05]]
* [[Team Challenger]]
* [[Team Blitz]]

Main Page

2013-01-22T03:55:56Z

Carterp: /* Helpful Guides */

== Articles ==
=== Convey HC-1 Tutorials ===
* [[Connecting to convey-1.ece.iastate.edu]]
* [[Convey environment setup|Setting Up Environment Variables on Convey's HC-1]]
* [[Running the Vector Adder Example Application]]
* Convey pdk tutorial: [[image:ConveyTutorial1.pdf]] (uses newCnyProject script)
* [[Analyze the Simpleton Basic App]]
* [[Tutorial: Creating a Custom Bitfile | Create a Custom Bitfile]]
* [[Using a Custom Bitfile in C Code]]
* [[Adding VHDL Files to a Project]]
* [[The Verilog Hardware Interface for CAE]]
* [[Using ISE's Core Generator to build FIFOs and other IP cores]]
* [[Running Different Bitfiles on each AE | Projects with Multiple Bitfiles]]
* [[Using the Write-Complete Interface]]
* [[Using the Timing Analyzer]]

* [[Using SPAT]]
* [[Using GPROF]]
* [[Convey vector example | Example of Loop Unrolling using FPGA]]
* [[Sobel Algorithm | Speeding up Sobel Algorithm]]

== Reference Manuals ==
=== Convey ===
* [[Media:ConveyPDKReferenceManual.pdf | Convey PDK Reference Manual (.pdf)]] (updated to V5.2; April 2012)
* [[Media:ConveyProgrammersGuide.pdf | Convey Programmers Guide (.pdf)]] (updated to V1.8; November 2010)
* [[Media:ConveyReferenceManual.pdf | Convey Reference Manual (.pdf)]]
* [[Media:ConveySpatUsersGuide.pdf | Convey SPAT (Simulator Performance Analysis Tool) Guide]]
* [[Media:Convey PDK Training.pdf | Convey PDK (.pdf)]]
* [[Media:Convey Overview.pdf | Convey Overview (.pdf)]]

The newet version of these documents are available at [http://www.conveysupport.com/help/?page_id=112 Convey's Support Site]

=== CUDA ===
* [[Media:CUDA_C_Programming_Guide.pdf | CUDA_C_Programming_Guide (.pdf)]]
* [[Media:CUDA_C_Best_Practices_Guide.pdf | CUDA_C_Best_Practices_Guide(.pdf)]]
* [[Media:CUDA_Memory.pdf | CUDA_Memory (.pdf)]]

==Links==
* [http://www.asic-world.com www.asic-world.com] - Great Tutorials for those Learning HDLs
* [http://memocode.irisa.fr MemoCODE 2012]
** [[Media:2012-memocode-contest.pdf | MemoCODE Contest.pdf]]
** [http://memocode.irisa.fr/2012/2012-memocode-contest.tar.gz Reference Implementation]
** [ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/human_g1k_v37.fasta.gz Human Reference Genome (human_g1k_v37.fasta.gz)]
** [ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/data/NA06985/sequence_read/ERR050082.filt.fastq.gz Example Reads (ERR050082.filt.fastq.gz)]
** [http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA06985/sequence_read/ERR050082.filt.fastq.gz Example Reads (Alternative Link) (ERR050082.filt.fastq.gz)]

* [[2010 Main Page | CprE 584 2010 Wiki Main Page]]
* [http://class.ee.iastate.edu/cpre583/ CprE 583 Website]
* [http://class.ece.iastate.edu/cpre584/ CprE 584 Website]

=== Other Articles ===
* [[Assignment|Assignments]]
* [[A quick start on CUDA]]

== Helpful Guides ==
* [http://www.c7t-hdl.com/Docs/C7T_AN05_Customized_WaveView_ModelSim_ISE.pdf Modelsim and ISE]
* [http://www.fpga.com.cn/hdl/training/verilog%20reference%20guide.pdf The Verilog Golden Reference]
* [http://courseware.ee.calpoly.edu/~bmealy/shock_awe_vhdl_adobe.pdf "The Shock and Awe" VHDL Tutorial]
* [http://esd.cs.ucr.edu/labs/tutorial/ VHDL Simple Code Examples]
* [http://www.seas.upenn.edu/~ese171/vhdl/vhdl_primer.html VHDL Primer]
* [http://www.kxcad.net/electronic_Xilinx_guide/mergedProjects/xsim/html/xs_p_ml_instantiation.htm Using VHDL components in Verilog]
* [[Media:Modelsim_pe_user_10.0d.pdf | Modelsim Users Guide]]
* [[Useful Modelsim Commands]]
* [http://sn0v.wordpress.com/2012/12/07/installing-cuda-5-on-ubuntu-12-04/ Installing CUDA 5 on Ubuntu 12.04]

== Readings for Memocode 2012 ==
*[[Media:Brief_Bioinform-2010-Li-473-83.pdf|A survey on algorithms for sequencing]]
*[[Media:Gb-2009-10-3-r25.pdf|Burrows-Wheeler indexing]]

== Spring 2012 Teams ==
* [[Team Gryffindor]]
* [[Team Slytherin]]
* [[Team 142857]]
== Spring 2013 Teams ==
* [[Team Cyc05]]
* [[Team Challenger]]
* [[Team Blitz]]