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:
- [Contents] pCEE618-01 xCEE618-01
- History of parallel computing
- Top 500 supercomputer in the world
- Remote login and text editors
- Linux/Unix commands
- [HW] CEE618-SP13-HW01 + Frenkel + How-to-Use-the-vi-Editor
- [Additional Reading Assignments]
- Uri Alon, How to choose a good scientific problem, Molecular Cell, 2009 (35) 726 (to be discussed in the next class).
- NanoTextEditor (optional for one who has hard time to learn how to use vim editor).
- [Contents] pCEE618-01 xCEE618-01
- [01/28/2013] Languages and utilities
- [Contents] pCEE618-lecture-02 xCEE618-lecture-02
- FORTRAN 77/90 to 2003: module and object-oriented programming
- “Make” utility
- [HW] CEE618-SP13-HW02
- [Mandatory Reading Assignments]
- Guide to FORTRAN 2003 Programming (PDF), Chapter 1 & 2 (p. 1-75)
- Practice codes: p. 27, 34-35, 53, 57, and 64.
- [Contents] pCEE618-lecture-02 xCEE618-lecture-02
- [01/25/2013] Serial examples
- [Contents] pCEE618-SP13-03 xCEE618-SP13-03
- Partial differential equation
- Linear Algebra
- Eigen values and eigen vectors
- Queueing systm (PBS)
- [Homework] CEE618-SP13-HW03
- [Notes] Separation of Variables (typo-corrected) and EigenSystem
- [References]
- [Contents] pCEE618-SP13-03 xCEE618-SP13-03
- [02/01/2013] Message Passing Interface (MPI): basics (1)
- [Content] pCEE618-SP13-04 xCEE618-SP13-04
- Initialize and Finalize
- Broadcast and Reduce
- [Homework] CEE618-SP13-HW04
- [Reading Assignment]
- Uri Alon, How to choose a good scientific problem, Molecular Cell, 2009 (35) 726
- Gropp et al. Using MPI, p. 21-26 Gropp-book-pi-cal
- [Content] pCEE618-SP13-04 xCEE618-SP13-04
- [02/08/2013] Message Passing Interface (MPI): basics (2)
- [Contents] pCEE618-SP13-05 xCEE618-SP13-05
- Send
- Receive
- Scatter
- Gather
- [Homework] CEE618-SP13-HW05
- [Contents] pCEE618-SP13-05 xCEE618-SP13-05
- [02/15/2013] OpenMP vs. MPI
- [Contents] pCEE618-SP13-06 xCEE618-SP13-06
- Review of pi-calculation using MPI
- Extension to OpenMP OpenMP_and_MPI_for_Dummies
- Comparative analysis of MPI and OpenMP
- [Homework] CEE618-SP13-HW06b
- [Contents] pCEE618-SP13-06 xCEE618-SP13-06
- [02/22/2013] OpenMP and MPI more (Announcement)
- [Content] pCEE618-SP13-07 xCEE618-SP13-07
- Parallel Computing Terms
- OpenMP (cont’d)
- Matrix Multiplication
- [Midterm] CEE618-SP13-MT1-rev
- [Content] pCEE618-SP13-07 xCEE618-SP13-07
- [03/01/2013] PuTTY, Profiling, and ScaLapck
- [Contents] pCEE618-SP13-08 xCEE618-SP13-08
- Profiling: GNU gprof (gprof_LU3dlapack & gprof_LU3dlapack_graph) and Intel vTune
- ssh-key login using PuTTY: PuTTY-Filezilla
- Parallel matrix multiplication using pdgemm (pdgemm) of Scalapack (pmm_result)
- (Parallel linear system solving)
- [Homework] CEE618-SP13-HW08
- [Contents] pCEE618-SP13-08 xCEE618-SP13-08
- [03/08/2013] OpenFOAM – computational fluid dynamics (CFD): basics CEE618-SP13-09
- [Contents] Cavity-Paraview
- Mesh generation: cubic, cubicsym_geo, cubicsym_msh
- gmsh manual
- gmsh tutorial
- gmsh-cavity-tutorial (for homework)
- OpenFOAM: p, U, boundary, controlDict, cavity (PBS)
- Paraview
- Video Tutorial: Gmsh+OpenFOAM+Paraview
- Mesh generation: cubic, cubicsym_geo, cubicsym_msh
- HW09: CEE618-SP13-HW09
- [Contents] Cavity-Paraview
- [03/15/2013] OpenFOAM – Cavity flow (2) pCEE618-SP13-10 (revised), xCEE618-SP13-10
- [Activity] Visiting cluster room (fractal_cluster_Information)
- [Contents]
- Mesh generation
- File specification
- Parallel runs
- HW10: CEE618-SP13-HW10 (revised) Flow in non-cubic cavity
- [03/22/2013] OpenFOAM: pipe flow and fire simulation pCEE618-SP13-11
- Navier-Stokes Equation (NS eq Tables)
- Channels
- fireFoam
- 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)
- Parallel particle dynamics in aqueous systems: in confined spaces and fluid flow
- Visualization of particle motion: static images
- HW: CEE618-SP13-HW12short use data of force (force444FT) and coordinates (coord444) of 4 by 4 by 4 array.
- Reading:
- [04/12/2013] Random Number Generation CEE618-SP13-13 xCEE618-SP13-13
- Contents
- Uniform deviates: RanNumGen.xls
- Normal (Gaussian) Deviates
- Basics of network security:
- Services (services)
- iptables (iptables_4_security)
- Reading Assignments
- Labwork:
- ssh-keygen using PuTTy + login fractal
- generate normally distributed random numbers using Excel file
- HW: work on your final projects
- Contents
- [04/19/2013] Supplementary Topics and Final Tips
- Files: pCEE618-SP13-14 and s6ppCEE618-SP13-14
- Scalapack revisited (BandedMat_pdgesv_8by8)
- OpenFOAM
- qsub revisted – dependent job handling: first, second, and depJobSub
- [04/26/2013] Final exam – Students’ term project presentation/report
- Announcement for final projects
- Format
- Presentation: 10 min. per student, maximum 10-12 slides
- Outline
- Title page
- Introduction and problem statement
- Approach: methodology, conditions, and assumptions
- Results and discussion + Broad impacts and future reusability
- Conclusion
- Media: Students are encouraged to bring a USB stick with all files and individual laptop for hardware compatibility.
- Outline
- Report: 5-7 pages, 12 fonts, 1.5 spacing, 2 inch margin at every side
- Outline: similar to that of Presentation + references
- Presentation: 10 min. per student, maximum 10-12 slides
- Submission
- Email oral presentation file (.ppt) and final report (.doc)
- Students can use Google Documents and Presentation.
- Submission should be anytime before the class starts.
Important dates:
- [03/29/2013] Good Friday
- [05/01/2013] Wednesday, Last Day of Instruction