GNU compiliers

• GNU compiler online documentation: http://gcc.gnu.org/onlinedocs/

HPC

• The Art of HPC, Texbooks by Victor Eijkhout of TACC: The Art of HPC

• HPC training material by ORNL: https://www.olcf.ornl.gov/for-users/training/training-archive/

• HPC tutorials by NCSA https://www.citutor.org/login.php

• HPC carpentry https://hpc-carpentry.github.io

R

SLURM Job Submission with R, Python, Bash

R (Programming Language)

How to run R programs on taki

How to useRon the Bioinformatics cluster

High-Performance and Parallel Computing with R

Quick Intro to Parallel Computing in R

Parallel Processing in R

How-to go parallel in R - basics + tips

Parallel Computing: Introduction to MPI

MPI Tutorial for R (Rmpi)

Rmpi Tutorial 2: Sending Data

MPI programming

• MPI Home pages: http://www-unix.mcs.anl.gov/mpi/

• Free MPI implementation useful for testing: http://www.open-mpi.org/software/ompi/v1.2/

• An MPI tutorial: http://www-unix.mcs.anl.gov/mpi/tutorial/gropp/talk.html

• MPI: The Complete Reference. Snir, Otto, Huss-Lederman, Walker and Dongarra. MIT Press. ISBN 0 262 69184 1

• MPI: The Complete Reference, volume 2. Gropp et al. MIT Press. ISBN 0262571234

• Using MPI. Gropp, Lusk, Skjellum. MIT Press. ISBN 0 262 57104 8

OpenMP programming

• Parallel Programming in OpenMP. Chandra, Kohr, Menon, Dagum, Maydan, McDonald. Morgan Kaufmann. ISBN: 1558606718

Parallel programming

• Practical Parallel Programming. Gregory V. Wilson. MIT Press. ISBN 0 262 23186 7

• Designing and Building Parallel Programs. Ian Foster. Addison-Wesley. ISBN 0 201 57594 9 http://www.mcs.anl.gov/dbpp/

• Parallel Computing Works! Roy D. Williams, Paul C. Messina (Editor), Geoffrey Fox (Editor), Mark Fox Morgan Kaufmann Publishers; ISBN: 1558602534

• Parallel programming with MPI. Peter S. Pancheco. The complete set of C and Fortran example programs for this book are available at http://www.cs.usfca.edu/mpi

Programming languages

• Fortran 90/95 Explained. Metcalf and Reid. Oxford Science Publications. ISBN 0 19 851888 9

• Fortran 90 Programming. Ellis, Philips, Lahey. Addison-Wesley. ISBN 0-201-54446-6

• Programmers Guide to Fortran90. Brainerd, Goldberg, Adams. Unicomp. ISBN 0-07-000248-7

• The High-Performance Fortran Handbook. Koelbel, Loveman, Schreiber, Steele, Zosel. ISBN 0-262-11185-3 / 0-262-61094-9

• Parallel Programming using C++. G.V.Wilson and P Lu. MIT Press. ISBN 0 262 73118 5

Programming skills

• Debugging and Performance Tuning for Parallel Computing Systems, Simmons et al.

• Foundations of Parallel Programming, A Machine-independent Approach, Lewis.