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| − | [[Image:Sharcnet_logo.jpg|center]]
| + | __NOTOC__ |
| − | <center><big>'''Help Wiki'''</big></center>
| + | {| style="border-spacing: 8px;" |
| | | | |
| − | ---- | + | | valign="top" style="cellpadding:1em; padding:1em; border:3px solid #0645ad; background-color:#87cefa; border-radius:7px"| |
| | + | == New to SHARCNET == |
| | | | |
| | + | * [[Getting an Account with SHARCNET | Getting an Account]] |
| | + | * [[Attending SHARCNET Webinars]] |
| | + | * [[Dedicated Resources | NRAC & Dedicated Resources]] |
| | + | * [https://docs.computecanada.ca/wiki/Compute_Canada_Documentation Compute Canada Documentation] |
| | | | |
| − | __TOC__
| + | | valign="top" style="cellpadding:1em; padding:1em; border:3px solid #0645ad; background-color:#f6e8e8; border-radius:7px"| |
| | | | |
| | + | == Tutorials == |
| | | | |
| − | == General Help ==
| + | * [[LINUX_SHELL | LINUX & SHELL]] |
| − | * [[Knowledge Base]] (an expanded FAQ) | + | * [[HPC_PROGRAMMING | Serial & Parallel Programming]] |
| | + | * [[Online Seminars#Online Seminars (recordings)|Online General Interests Seminar Series]] |
| | + | * [https://www.sharcnet.ca/help/index.php/Summer_Schools SHARCNET Summer Schools] |
| | + | * [https://goo.gl/HXAdC6 '''SHARCNET on YouTube'''] |
| | + | |- |
| | + | | valign="top" width="50%" style="padding:1em; border:3px solid #0645ad; background-color:#fafad2; border-radius:7px" | |
| | | | |
| − | == SHARCNET == | + | == Software == |
| − | === Introductory Material ===
| + | * [https://docs.computecanada.ca/wiki/Utiliser_des_modules/en Modules] |
| − | * [[Attending SHARCNET Webinars]] (online reference) | + | * [https://docs.computecanada.ca/wiki/Available_software Available Software ] |
| − | * [[Getting Started with SHARCNET]] (online reference) | + | |
| | | | |
| − | === User Environment === | + | | valign="top" style="padding:1em; border:3px solid #0645ad; background-color:#e8f6e8; border-radius:7px" | |
| − | * [[Hardware/System Resources]] (online reference of all documented systems)
| + | |
| − | * [[SSH|SSH (Secure Shell)]] (self-directed tutorial)
| + | |
| − | * [[Configuring your software environment with Modules]]
| + | |
| − | * [[Choosing A Password]] (self-directed tutorial)
| + | |
| − | * [[Linux and vi Editor Fundamentals]] (self-directed tutorial/online reference)
| + | |
| − | ** [[vi and vim configuration]]
| + | |
| − | * [[Getting Started with Compiling Code on SHARCNET]] (self-directed tutorial)
| + | |
| − | * [[SHARCNET Software Development Environment]] (self-directed tutorial)
| + | |
| − | * [[Signal Handling and Checkpointing]] (self-directed tutorial)
| + | |
| − | * [[Managing a Large Number of Jobs]]
| + | |
| − | * [[Using Subversion|Revision control with Subversion]] (self-directed tutorial)
| + | |
| − | * [[Git|Revision control with Git]]
| + | |
| − | * [[Locally installed software]] (software build documentation)
| + | |
| − | * [[Make utility and makefiles]]
| + | |
| | | | |
| − | == Programming == | + | == Hardware == |
| − | === General Parallel Programming ===
| + | *[https://docs.computecanada.ca/wiki/Graham Graham - SHARCNET's main cluster] |
| − | * [[Media:Overview_of_HPC.pdf|Overview of HPC]] (slides) | + | *[[Dusky|Dusky]] - smaller cluster incorporating older hardware |
| − | * [[Media:Parallel_Computing_Models.pdf|Parallel Computing Models]] (slides)
| + | |} |
| − | * [[Media:Parallel_Software_Design.pdf|Parallel Software Design]] (slides)
| + | |
| − | * [http://www.mcs.anl.gov/~itf/dbpp/ Designing and Building Parallel Programs] (online book and references)
| + | |
| − | * [[Reviews of Selected Development Stage Languages]] (niche and/or development-stage languages and runtime platforms)
| + | |
| − | | + | |
| − | ===MPI===
| + | |
| − | * [[Getting Started with MPI]] (self-directed tutorial)
| + | |
| − | * [http://www.mcs.anl.gov/research/projects/mpi/ MPI Standard] (online reference)
| + | |
| − | * [http://www.mpi-forum.org/ MPI Forum] (online reference)
| + | |
| − | * [http://www.netlib.org/utk/papers/mpi-book/mpi-book.html MPI: The complete Reference (Snir, et al.)] (online book)
| + | |
| − | * [[Parallel Java: Using MPJ Express on SHARCNET]] (installation/usage instructions)
| + | |
| − | ===Serial Processing===
| + | |
| − | * [[Media:Automating_Tasks_Using_bash.pdf|Automating Tasks Using bash]] (slides: overview/examples)
| + | |
| − | * [[Automating Tasks Using bash]] (self-directed tutorial - under construction)
| + | |
| − | * [[Throughput Computing|Serial Farming / Throughput Computing]] (self-directed tutorial)
| + | |
| − | | + | |
| − | ===Shared Memory (SMP)===
| + | |
| − | * [[OpenMP]] (self-directed tutorial)
| + | |
| − | * [[Media:Introduction_to_POSIX_Threads.pdf|Introduction to POSIX Threads]] (slides: introduction/usage)
| + | |
| − | * [http://randu.org/tutorials/threads/ Pthreads Tutorial] (online tutorial)
| + | |
| − | * [http://cs.pub.ro/~apc/2003/resources/pthreads/uguide/document.htm Pthreads API] (online reference)
| + | |
| − | * [http://software.intel.com/en-us/articles/intel-guide-for-developing-multithreaded-applications/ Intel Guide for Developing Multithreaded Applications] (online reference)
| + | |
| − | | + | |
| − | ===Accelerators===
| + | |
| − | * [[Media:Programming_the_Cell_Multiprocessor.pdf|Programming the Cell Multiprocessor]] (slides: introduction/usage)
| + | |
| − | * [[GPU Accelerated Computing| GPGPU / GPU Accelerated Computing]] (self-directed tutorial)
| + | |
| − | * [[FPGA Accelerated Computing]] (self-directed tutorial)
| + | |
| − | * ''Articles of Interest''
| + | |
| − | ** [http://babrodtk.at.ifi.uio.no/files/publications/brodtkorb_etal_star_heterocomp_final.pdf State-of-the-art in heterogeneous computing] <i>Scientific Programming 18 (2010) 1–33 DOI 10.3233/SPR-2009-0296</i> (comprehensive 33-page article)
| + | |
| − | ** [http://portal.acm.org/citation.cfm?id=1816021&coll=GUIDE&dl=GUIDE&CFID=11111111&CFTOKEN=2222222&ret=1 Debunking the 100X GPU vs. CPU Myth: An Evaluation of Throughput Computing on CPU and GPU] <i>ACM SIGARCH Computer Architecture News 2010 </i> (comparison of different computing kernels, including optimization and performance, on the GPU and CPU, as well as '''accurate''' benchmarks)
| + | |
| − | | + | |
| − | === Performance Analysis / Debugging ===
| + | |
| − | * [[Common Bugs and Debugging with gdb]] (self-directed tutorial)
| + | |
| − | * [[Parallel Debugging with DDT]] (tutorial)
| + | |
| − | * [[Measuring Parallel Scaling Performance]] (tutorial)
| + | |
| − | * [[Analyzing I/O Performance]]
| + | |
| − | * [[Monitoring Jobs]]
| + | |
| − | | + | |
| − | ===Language Specific Resources===
| + | |
| − | * [[Using MATLAB]] (self-directed tutorial)
| + | |
| − | * [[Media:Fortran_Signal_Handling.pdf|Fortran Signal Handling]] (article)
| + | |
| − | * [[Media:Contrasting_MATLAB_and_Fortran.pdf|Contrasting MATLAB and Fortran]] (slides)
| + | |
| − | * [[Media:Frontiers_of_HPC_Unified_Parallel_C.pdf|Unified Parallel C (UPC)]] (slides: overview/usage/examples)
| + | |
| − | * [[Using R and MPI]]
| + | |
| − | * [[Using CRAY POINTERS in a FORTRAN 90 PROGRAM]]
| + | |
| − | * [[Reading from c BINARY_FILES generated by a fortran program]]
| + | |
| − | | + | |
| − | ===Numerical Methods===
| + | |
| − | * [[Solving Systems of Sparse Linear Equations ]] (self-directed tutorial)
| + | |
| − | * [[Analytical Computation]] (self-directed tutorial)
| + | |
| − | * [[RUNGE-KUTTA Tutorial]] (self-directed tutorial)
| + | |
| − | * [[BLACS (Basic Linear Algebra Communication Subprograms) Examples]]
| + | |
| − | * [[LAPACK and ScaLAPACK Examples]]
| + | |
| − | * [[INTERPRETERS vs COMPILERS]]
| + | |
| − | * [[NAG LAPACK "extras" library]]
| + | |
| − | * [[EIGENVALUES OF NON-SYMMETRIC MATRICES]]
| + | |
| − | * [[KRONECKER PRODUCT (ScaLAPACK,OCTAVE,F90)]]
| + | |
| − | * [[Eigenproblem solved with PETSc_SLEPc]]
| + | |
| − | * [[Complete FFTW Examples in C F90 OCTAVE and PETSc]]
| + | |
| − | * [[Advanced SBVP Example in C, F90, OCTAVE and PETSc]]
| + | |
| − | * [[Media:Parallel_Numerical_Solution_of_PDEs_with_Message_Passing.pdf|Parallel Numerical Solution of PDEs with Message Passing]] (article/tutorial)
| + | |
| − | | + | |
| − | == Domain Portals ==
| + | |
| − | * [[Astrophysics]]
| + | |
| − | * [[Bioinformatics]]
| + | |
| − | * [[Digital Humanities]]
| + | |
| − | * [[HPC Services for Industry]]
| + | |
| − | * [[Chemistry, Biochemistry and Biophysics]]
| + | |
| − | * [[Gaussian on SHARCNET systems]]
| + | |
| − | | + | |
| − | == Visualization ==
| + | |
| − | * [[Remote Graphical Connections]] (Using graphical programs remotely)
| + | |
| − | * Visualization of 2D and 3D datasets with [[ParaView]]
| + | |
| − | * [[Visualization Workstations]]
| + | |
| − | | + | |
| − | == AccessGrid ==
| + | |
| − | * [[How To Use]]
| + | |
| − | * [[Presentations]]
| + | |
| − | * [[Common Problems]]
| + | |
| − | * [[AccessGrid on your Desktop]]
| + | |
| − | == Seminar Archive ==
| + | |
| − | * [[Online Seminars#Online Seminars (recordings)|Online Seminars]] (recordings of recent online seminars)
| + | |
| − | * [[Online Seminars#Recorded Talks|Recorded Talks]] (live talks recorded by SHARCNET)
| + | |
| − | * [[Summer School 2010 "Preschool" talks]]
| + | |
| − | | + | |
| − | == Wiki Help ==
| + | |
| − | * [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
| + | |
| − | * [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
| + | |
| − | * [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
| + | |
| − | | + | |
| − | == SOFTWARE PACKAGES USAGE ==
| + | |
| − | === LAPACK ===
| + | |
| − | ''' Solve Linear System Ax=b'''
| + | |
| − | | + | |
| − | As an example of using LAPACK let's consider the following '''identity ''' of linear equations of order 6:
| + | |
| − | : <math>\mathbf
| + | |
| − | | + | |
| − | \begin{bmatrix}
| + | |
| − | 3.0 &-1. & 0.0 & 0.0 & 0.0 & 1.0 \\
| + | |
| − | -1. & 3.0 &-1. & 0.0 & 1.0 & 0.0 \\
| + | |
| − | 0.0 & -1. & 3.0 & 0.0 & 0.0 & 0.0 \\
| + | |
| − | 0.0 & 0.0 & 0.0 & 3.0 & -1. & 0.0 \\
| + | |
| − | 0.0 & 1.0 & 0.0 & -1. & 3.0 &-1. \\
| + | |
| − | 1.0 & 0.0 & 0.0 & 0.0 & -1. & 3.0
| + | |
| − | \end{bmatrix}
| + | |
| − | \begin{bmatrix}
| + | |
| − | 1.0 \\
| + | |
| − | 2.0 \\
| + | |
| − | 3.0 \\
| + | |
| − | 4.0 \\
| + | |
| − | 5.0 \\
| + | |
| − | 6.0 \\
| + | |
| − | \end{bmatrix}
| + | |
| − | =
| + | |
| − | \begin{bmatrix}
| + | |
| − | 7.0 \\
| + | |
| − | 7.0 \\
| + | |
| − | 7.0 \\
| + | |
| − | 7.0 \\
| + | |
| − | 7.0 \\
| + | |
| − | 14.0 \\
| + | |
| − | \end{bmatrix}
| + | |
| − | </math>
| + | |
| − | | + | |
| − | If we write the above '''identity''' with following symbols:
| + | |
| − | :'''Ax''' = '''b'''
| + | |
| − | and assume that '''x''' is unknown, then we can try to solve for '''x''' using some LAPACK subroutine.
| + | |
| − | Here is how we proceed:
| + | |
| − | * Find out what LAPACK subroutine solves the system of linear equations:
| + | |
| − | ::'''Ax''' = '''b'''
| + | |
| − | :(subroutine '''dgesv''' is what we need).
| + | |
| − | *Write a fortran program which defines '''A''', '''b''' and calls dgesv to solve for '''x'''
| + | |
| − | ! file_name = solve.f90
| + | |
| − |
| + | |
| − | program solve_N6
| + | |
| − | !
| + | |
| − | ! This program solves Ax=B using LAPACK subroutine dgesv
| + | |
| − | ! A is a double precision 6 by 6 matrix defined in the program.
| + | |
| − | ! B is a double precision vector of length 6 also defined in the program.
| + | |
| − | !
| + | |
| − | implicit none
| + | |
| − | integer info, N, nrhs, lda, ldb
| + | |
| − | parameter (N=6, nrhs=1, lda=N, ldb=N)
| + | |
| − | double precision A(N,N), B(ldb,nrhs)
| + | |
| − | integer indx(N)
| + | |
| − |
| + | |
| − | integer i, j
| + | |
| − | !
| + | |
| − | ! Defined matrix A:
| + | |
| − |
| + | |
| − | data A / 3. , -1. , 0. , 0. , 0. , 1. , &
| + | |
| − | & -1. , 3. , -1. , 0. , 1. , 0. , &
| + | |
| − | & 0. , -1. , 3. , 0. , 0. , 0. , &
| + | |
| − | & 0. , 0. , 0. , 3. , -1. , 0. , &
| + | |
| − | & 0. , 1. , 0. , -1. , 3. , -1. , &
| + | |
| − | & 1. , 0. , 0. , 0. , -1. , 3. /
| + | |
| − |
| + | |
| − |
| + | |
| − | data B / 7. , 7. , 7. , 7. , 7. , 14. /
| + | |
| − | !
| + | |
| − | print *,"N = ", N
| + | |
| − | print *,"A = "
| + | |
| − | print *,A
| + | |
| − | print *,"B = "
| + | |
| − | print *,B
| + | |
| − | print *," "
| + | |
| − |
| + | |
| − | call dgesv( N, nrhs, A, lda, indx, B, ldb, info )
| + | |
| − | !
| + | |
| − | ! Parameters of dgesv
| + | |
| − | !
| + | |
| − | ! N is the matrix size, N >= 1 . (input)
| + | |
| − | !
| + | |
| − | ! nhrs is the number of Right Sides to be solved
| + | |
| − | ! --here 1 (input)
| + | |
| − | !
| + | |
| − | ! A is the matrix in Ax = B, overwritten on output by
| + | |
| − | ! L and U -- where L*U = A (rows permuted)
| + | |
| − | ! A is double precision N by N , but with leading
| + | |
| − | ! dimension lda >= N .
| + | |
| − | ! A is input, but is different on output (in/out) .
| + | |
| − | !
| + | |
| − | ! lda is the leading dimension of A. lda >= N .
| + | |
| − | !
| + | |
| − | ! indx , integer array dimension N, indx(i)
| + | |
| − | ! was interchanged with the ith row of A. (output)
| + | |
| − | !
| + | |
| − | ! B , double precision array of dimension (ldb,nhrs)
| + | |
| − | ! On input it is the right hand side(s) B, on output
| + | |
| − | ! it is the solution vector(s) x. (in/out)
| + | |
| − | !
| + | |
| − | ! info integer, output info = 0 indicates a successful exit
| + | |
| − | ! info <= -i, the ith argument was illegal.
| + | |
| − | ! info = i means u(i,i) was zero so factorization
| + | |
| − | ! not completed.
| + | |
| − | !
| + | |
| − | print *,"X = "
| + | |
| − | print *,B
| + | |
| − |
| + | |
| − | stop
| + | |
| − | end
| + | |
| − | | + | |
| − | *Write a makefile named '''Makefile''' to compile, link, and submit a job to the batch system
| + | |
| − | : Make sure to include the ACML library for intel by issuing the command:
| + | |
| − | module load acml/ifort/4.4.0
| + | |
| − | before using the makefile '''Makefile''':
| + | |
| − | | + | |
| − | # file_name = Makefile
| + | |
| − | # Makefile for solve.f90
| + | |
| − |
| + | |
| − | ROOTDIR = $(shell pwd)
| + | |
| − |
| + | |
| − | SRC = solve.f90
| + | |
| − | OBJ = $(SRC:.f90=.o)
| + | |
| − |
| + | |
| − | LIBS = $(LDFLAGS) -lacml
| + | |
| − |
| + | |
| − | TARGET = solve_exec
| + | |
| − |
| + | |
| − | OUTPUTFILE=FORTRAN_LAPACK_SOLVE
| + | |
| − |
| + | |
| − | all: $(TARGET)
| + | |
| − |
| + | |
| − | $(TARGET): $(OBJ)
| + | |
| − | $(FC) -o $@ $(CPPFLAGS) $(OBJ) $(LIBS)
| + | |
| − |
| + | |
| − | $(OBJ): ${SRC}
| + | |
| − | $(FC) $(FFLAGS) -c ${SRC}
| + | |
| − |
| + | |
| − | help:; @echo " "
| + | |
| − | @echo "USAGE: "
| + | |
| − | @echo "make help To get this listing"
| + | |
| − | @echo "make To compile the FORTRAN LAPACK program in current environment"
| + | |
| − | @echo "make subjob To submit the executable to a batch queue using sqsub"
| + | |
| − | @echo "make clean Remove *.o and executable files"
| + | |
| − | @echo "make list List the compilers in current environment"
| + | |
| − | @echo " "
| + | |
| − |
| + | |
| − | list:
| + | |
| − | @echo
| + | |
| − | @echo "ROOTDIR: $(ROOTDIR)"
| + | |
| − | @echo "FC Compiler: $(FC)"
| + | |
| − | @echo "FFLAGS: $(FFLAGS)"
| + | |
| − | @echo "LDFLAGS: $(LDFLAGS)"
| + | |
| − | @echo "OUTPUT FILE: $(OUTPUTFILE)"
| + | |
| − | @echo " "
| + | |
| − | @echo "LD_LIBRARY_PATH: " $(LD_LIBRARY_PATH)
| + | |
| − |
| + | |
| − | clean:
| + | |
| − | @echo "Removing *.o and executable files"
| + | |
| − | rm -rf *.o $(TARGET)
| + | |
| − |
| + | |
| − | subjob:;
| + | |
| − | rm -rf $(OUTPUTFILE)
| + | |
| − | sqsub -t -r 1h --mpp=2.0G -o ${CLU}_$(OUTPUTFILE) -n 1 ./$(TARGET)
| + | |
| − | | + | |
| − | For more details on the '''identity''' of linear equations of any order N, see:
| + | |
| − | | + | |
| − | https://www.sharcnet.ca/help/index.php/Solving_Systems_of_Sparse_Linear_Equations
| + | |
| − | | + | |
| − | Also, you can find more information on '''modules''' and '''make utility and makefiles''' in the following two references:
| + | |
| − | | + | |
| − | https://www.sharcnet.ca/help/index.php/Configuring_your_software_environment_with_Modules
| + | |
| − | | + | |
| − | https://www.sharcnet.ca/help/index.php/Make_utility_and_makefiles
| + | |
| − | | + | |
| − | === ScaLAPACK ===
| + | |
| − | === PETSc_SLEPc ===
| + | |
| − | === R ===
| + | |