CEE618S13

In spring semester 2013, CEE 618 “Parallel Computing for Engineers” will be offered.
This page will be kept updated until this course is finished.

Discussion forum for CEE618S13

Classroom POST 214 Don Kim lab
Date and Time: Friday, 9:30 am – 12:30 pm
CEE course schedule for Spring 2013
CEE618_Syllabus-2013S

Weekly Schedule

[01/11/2013] Introduction to parallel computing:
1. [Contents] pCEE618-01 xCEE618-01
  1. History of parallel computing
  2. Top 500 supercomputer in the world
  3. Remote login and text editors
  4. Linux/Unix commands
2. [HW] CEE618-SP13-HW01 + Frenkel + How-to-Use-the-vi-Editor
3. [Additional Reading Assignments]
  1. Uri Alon, How to choose a good scientific problem, Molecular Cell, 2009 (35) 726 (to be discussed in the next class).
  2. NanoTextEditor (optional for one who has hard time to learn how to use vim editor).
[01/28/2013] Languages and utilities
1. [Contents] pCEE618-lecture-02 xCEE618-lecture-02
  1. FORTRAN 77/90 to 2003: module and object-oriented programming
  2. “Make” utility
2. [HW] CEE618-SP13-HW02
3. [Mandatory Reading Assignments]
  1. Guide to FORTRAN 2003 Programming (PDF), Chapter 1 & 2 (p. 1-75)
  2. Practice codes: p. 27, 34-35, 53, 57, and 64.
[01/25/2013] Serial examples
1. [Contents] pCEE618-SP13-03 xCEE618-SP13-03
  1. Partial differential equation
  2. Linear Algebra
  3. Eigen values and eigen vectors
  4. Queueing systm (PBS)
2. [Homework] CEE618-SP13-HW03
3. [Notes] Separation of Variables (typo-corrected) and EigenSystem
4. [References]
  1. Example Programs by NAG (previously LINPACK)
  2. LAPACAK Quick Reference Guide to the Driver Routines
[02/01/2013] Message Passing Interface (MPI): basics (1)
1. [Content] pCEE618-SP13-04 xCEE618-SP13-04
  1. Initialize and Finalize
  2. Broadcast and Reduce
2. [Homework] CEE618-SP13-HW04
3. [Reading Assignment]
  1. Uri Alon, How to choose a good scientific problem, Molecular Cell, 2009 (35) 726
  2. Gropp et al. Using MPI, p. 21-26 Gropp-book-pi-cal
[02/08/2013] Message Passing Interface (MPI): basics (2)
1. [Contents] pCEE618-SP13-05 xCEE618-SP13-05
  1. Send
  2. Receive
  3. Scatter
  4. Gather
2. [Homework] CEE618-SP13-HW05
[02/15/2013] OpenMP vs. MPI
1. [Contents] pCEE618-SP13-06 xCEE618-SP13-06
  1. Review of pi-calculation using MPI
  2. Extension to OpenMP OpenMP_and_MPI_for_Dummies
  3. Comparative analysis of MPI and OpenMP
2. [Homework] CEE618-SP13-HW06b
[02/22/2013] OpenMP and MPI more (Announcement)
1. [Content] pCEE618-SP13-07 xCEE618-SP13-07
  1. Parallel Computing Terms
  2. OpenMP (cont’d)
  3. Matrix Multiplication
2. [Midterm] CEE618-SP13-MT1-rev
[03/01/2013] PuTTY, Profiling, and ScaLapck
1. [Contents] pCEE618-SP13-08 xCEE618-SP13-08
  1. Profiling: GNU gprof (gprof_LU3dlapack & gprof_LU3dlapack_graph) and Intel vTune
  2. ssh-key login using PuTTY: PuTTY-Filezilla
  3. Parallel matrix multiplication using pdgemm (pdgemm) of Scalapack (pmm_result)
  4. (Parallel linear system solving)
2. [Homework] CEE618-SP13-HW08
[03/08/2013] OpenFOAM – computational fluid dynamics (CFD): basics CEE618-SP13-09
1. [Contents] Cavity-Paraview
  1. Mesh generation: cubic, cubicsym_geo, cubicsym_msh
    1. gmsh manual
    2. gmsh tutorial
    3. gmsh-cavity-tutorial (for homework)
  2. OpenFOAM: p, U, boundary, controlDict, cavity (PBS)
  3. Paraview
  4. Video Tutorial: Gmsh+OpenFOAM+Paraview
2. HW09: CEE618-SP13-HW09
[03/15/2013] OpenFOAM – Cavity flow (2) pCEE618-SP13-10 (revised), xCEE618-SP13-10
1. [Activity] Visiting cluster room (fractal_cluster_Information)
2. [Contents]
  1. Mesh generation
  2. File specification
  3. Parallel runs
3. HW10: CEE618-SP13-HW10 (revised) Flow in non-cubic cavity
[03/22/2013] OpenFOAM: pipe flow and fire simulation pCEE618-SP13-11
1. Navier-Stokes Equation (NS eq Tables)
2. Channels
  1. Rectangular duct
  2. Cylinder
3. fireFoam
4. HW11: CEE618-SP13-HW11
[03/29/2013] Spring break: no class
[04/05/2013] Dissipative Hydrodynamics (DHD) pCEE618-SP13-12 (s4ppCEE618-SP13-12, s6ppCEE618-SP13-12)
1. Parallel particle dynamics in aqueous systems: in confined spaces and fluid flow
2. Visualization of particle motion: static images
3. HW: CEE618-SP13-HW12short use data of force (force444FT) and coordinates (coord444) of 4 by 4 by 4 array.
4. Reading:
  1. Hassonjee, Q., Ganatos, P., & Pfeffer, R. (1988). J. Fluid Mech., 197, 1–37. PDF
  2. Albert S. Kim, Chemistry Letters, 41 (10) (2012) 1128-1130. PDF
[04/12/2013] Random Number Generation CEE618-SP13-13 xCEE618-SP13-13
1. Contents
  1. Uniform deviates: RanNumGen.xls
  2. Normal (Gaussian) Deviates
2. Basics of network security:
  1. Services (services)
  2. iptables (iptables_4_security)
3. Reading Assignments
4. Labwork:
  1. ssh-keygen using PuTTy + login fractal
  2. generate normally distributed random numbers using Excel file
5. HW: work on your final projects
[04/19/2013] Supplementary Topics and Final Tips
1. Files: pCEE618-SP13-14 and s6ppCEE618-SP13-14
2. Scalapack revisited (BandedMat_pdgesv_8by8)
3. OpenFOAM
  1. Mixed: Convective Diffusion using icoFoam and scalarTransportFoam (PDF and HTML)
  2. Parallel OpenFOAM revisited
4. qsub revisted – dependent job handling: first, second, and depJobSub
[04/26/2013] Final exam – Students’ term project presentation/report
1. Announcement for final projects
2. Format
  1. Presentation: 10 min. per student, maximum 10-12 slides
    1. Outline
      1. Title page
      2. Introduction and problem statement
      3. Approach: methodology, conditions, and assumptions
      4. Results and discussion + Broad impacts and future reusability
      5. Conclusion
    2. Media: Students are encouraged to bring a USB stick with all files and individual laptop for hardware compatibility.
  2. Report: 5-7 pages, 12 fonts, 1.5 spacing, 2 inch margin at every side
    1. Outline: similar to that of Presentation + references
3. Submission
  1. Email oral presentation file (.ppt) and final report (.doc)
  2. Students can use Google Documents and Presentation.
  3. Submission should be anytime before the class starts.