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No Linux Fedora esolher entre 3 principais grupos de pacotes:
+
No Linux Fedora escolher entre 3 principais grupos de pacotes:
 
;Office and Productivity: provides the OpenOffice.org, the Planner project management application, graphical tools such as the GIMP, and multimedia applications.  
 
;Office and Productivity: provides the OpenOffice.org, the Planner project management application, graphical tools such as the GIMP, and multimedia applications.  
 
;Software Development:    provides the necessary tools to compile software on your Fedora system.  
 
;Software Development:    provides the necessary tools to compile software on your Fedora system.  
 
;Web server:              provides the Apache Web server.
 
;Web server:              provides the Apache Web server.
 +
 +
;;[http://fedoraproject.org/wiki/Fedora_13_Alpha_release_notes Fedora 13 Alpha release notes]
  
 
==Core Network Services==
 
==Core Network Services==
Linha 17: Linha 19:
 
Some automated processes use the email service to send reports and messages to the system administrator. By default, the email, logging, and printing services do not accept connections from other systems. Fedora installs the NFS sharing, HTTP, and VNC components without enabling those services.
 
Some automated processes use the email service to send reports and messages to the system administrator. By default, the email, logging, and printing services do not accept connections from other systems. Fedora installs the NFS sharing, HTTP, and VNC components without enabling those services.
 
You may configure your Fedora system after installation to offer email, file sharing, logging, printing and remote desktop access services. The SSH service is enabled by default. You may use NFS to access files on other systems without enabling the NFS sharing service.
 
You may configure your Fedora system after installation to offer email, file sharing, logging, printing and remote desktop access services. The SSH service is enabled by default. You may use NFS to access files on other systems without enabling the NFS sharing service.
 +
 +
==User level MPI==
 +
A rethink of MPI software management has been made in Fedora and relevant packaging guidelines have been adopted for Fedora 13.
 +
 +
Instead of the system-wide alternatives system, support for MPI compilers and runtimes is now managed at userlevel in Fedora with environment modules. The compilers, runtimes and any software compiled against them are installed in separate directories outside the $PATH. Now, for example, it is possible to run program A in one terminal session with Open MPI and program B with MPICH2 in another session. For this reason no default MPI runtime is set by default.
 +
 +
To load support for Open MPI on Fedora 13 x86_64 run $ module load openmpi-x86_64 and for MPICH2 $ module load mpich2-x86_64. If you want e.g. Open MPI support to be automatically available in your sessions, add the command above to your shell config.
  
 
==Slave Nodes==
 
==Slave Nodes==
Linha 22: Linha 31:
 
Going with my example node names and IP addresses, this is what I chose during setup:
 
Going with my example node names and IP addresses, this is what I chose during setup:
  
−
  Workstation  
+
  Workstation
−
  auto partition  
+
  auto partition
−
  remove all partitions on system  
+
  remove all partitions on system
−
  use LILO as the boot loader  
+
  use LILO as the boot loader
−
  put boot loader on the MBR  
+
  put boot loader on the MBR
−
  host name wolf01  
+
  host name wolf01
−
  ip address 192.168.0.101  
+
  ip address 192.168.0.101
 
  add the user "wolf"
 
  add the user "wolf"
−
  same password as on all other nodes  
+
  same password as on all other nodes
 
  NO firewall
 
  NO firewall
  
 
The ONLY package installed: '''network servers'''. Un-select all other packages.
 
The ONLY package installed: '''network servers'''. Un-select all other packages.
 +
* Applications/Editions/emacs
 +
* Applications/Eng Scientific
 +
* Servers/DNS Name (nao)
 +
* Servers/Server Configurations tools (nao)
 +
* Servers/Windows File System (nao)
 +
 +
==Pacotes usados em WestGrid (exemplo)==
 +
#  Software on Computational Resources
 +
##  UNIX Environment
 +
### bash,tcsh,sh,csh,ksh
 +
#  Files and Data
 +
### emacs - GNU version of this common text editor
 +
### nedit - a graphical editor recommended for PC users, but requires X Windows.
 +
### pico - A simple non-graphical text editor with on-screen reminders for commonly-used commands.
 +
### vim - an enhanced version of vi
 +
#  Programming
 +
##  Fortran
 +
### f77 is wrapper script for $FC, $F77,defaulting to ifort
 +
### f90 is wrapper script for $FC, $F90,defaulting to ifort
 +
### f77 is wrapper script for $FC, $F95,defaulting to ifort
 +
### Intel 11.1 (ifort, f77,f90,f95)
 +
### GNU 4.3.2 (gfortran)
 +
### Open64 4.2.2.1 (openf90, openf95)
 +
### f77 links to g77
 +
### GNU 4.3.2 (gfortran)
 +
### GNU 3.4.6 (g77)
 +
### Portland Group 7.0-2 (pgf77, pgf90)
 +
### Intel 9.1 (ifort)
 +
### Absoft 8.2 (f90)
 +
##  C
 +
### Intel 11.1 (icc,cc)
 +
### GNU 4.3.2 (gcc)
 +
### Open64 4.2.2.1 (opencc)
 +
##  C++
 +
### GNU 4.4.0 gcc
 +
### Intel 11.1 (c++, icpc)
 +
### GNU 4.3.2 (g++)
 +
### Open64 4.2.2.1 (openCC)
 +
## Java
 +
## Perl
 +
## Python
 +
##  Utilities
 +
### CMake - Cross platform software build system
 +
### filepp - Generic file preprocessor
 +
### ftnchek - FORTRAN 77 syntax checker
 +
### Jam - Make replacement for C/C++ projects. See: www.perforce.com/jam/jam.html
 +
##  Debuggers
 +
### cvd - CASEVision/ProDev Workshop (graphical) debugger /usr/sbin/cvd
 +
### dbx - Common UNIX debugger
 +
### ddd - Graphical front end to other debuggers
 +
### gdb - GNU debugger
 +
### idb - Intel debugger
 +
### ladebug - Debugger for HP systems Supports parallel debugging
 +
### pgdbg - Portland Group graphical debugger
 +
### totalview - Etnus Totalview commercial graphical debugger
 +
##  Libraries
 +
### Boost - An eclectic collection of C++ libraries. See www.boost.org for more information.
 +
### GNU libgomp - GNU implementation of the OpenMP Application Programming Interface (API). See gcc.gnu.org/onlinedocs/libgomp/ for more information.
 +
### STLport - An implementation of the Standard Template Library. See www.stlport.org for more information.
 +
##  Version Control
 +
### Subversion - An open source alternative to CVS for managing files for large development projects. The Subversion client, svn, is provided to give access to repositories outside of WestGrid. See http://subversion.tigris.org/ for more information.
 +
#  Mathematical Libraries and Applications
 +
##  Comprehensive Libraries
 +
### ESSL - IBM Engineering and Scientific Subroutine Library.
 +
### GSL - GNU Scientific Library.
 +
### MKL - Intel Math Kernel Library.
 +
### SCSL - Scientific Computing Software Library.
 +
##  Differential Equation Solvers
 +
### PETSc - Toolkit for parallel solution of differential equations.
 +
##  Fourier Transforms
 +
### FFTW - A widely-used FFT implementation.
 +
##  Linear Algebra (See also MATLAB below.)
 +
### BLAS - Basic Linear Algebra Subprograms.
 +
### LAPACK - Linear algebra subroutine package.
 +
### PIM - Parallel Iterative Methods.
 +
### ScaLAPACK - Scalable LAPACK.
 +
### WSMP - Watson Sparse Matrix Package.
 +
##  Mesh Partitioning
 +
### METIS - Mesh and graph partitioning.
 +
##  Statistics
 +
### R - Software environment and language for statistical data analysis.
 +
# Graphics
 +
## Animation
 +
### mencoder (MPEG encoding) mplayer (video player)
 +
##  Charting
 +
### Grace/Xmgrace - GUI-based x-y plotting for thesis and publication-quality graphs. Also includes data transformations and curve fitting.
 +
### Gnuplot - Command-driven x-y plotting program, generally of lower quality than xmgrace, but offering some 3D features.
 +
##  Geographic data handling
 +
### GMT - Generic Mapping Tools - Script-driven package of utilities for gridding and contouring geographic and Cartesian data sets, with support for many map projections. Vector plots, surface plots and other types of graphics are supported.
 +
### NCAR Graphics - Libraries and utilities for contour maps, vector and streamline plots, X-Y graphs, map databases and other visualization tools developed for the support of meteorological applications but with a broad range of applications in other disciplines.
 +
### VISAT - An image processing and data analysis program for remotely sensed data. VISAT is part of the BEAM toolkit mentioned below
 +
##  Image format handling
 +
### libjpeg - Independent JPEG Group JPEG compression library and image file conversion programs, djpeg and cjpeg.
 +
### libtiff - TIFF (Tagged Image File Format) image library.
 +
### Netpbm - Image conversion utilities and library.
 +
### pdflib - PDF file handling library ("PDFlib-Lite" for non-commercial use)
 +
### zlib - Data compression library.
 +
##  OpenGL-related
 +
### Vendor's OpenGL
 +
### Mesa
 +
### GLUT
 +
# Chemistry and Biochemistry Applications
 +
## Electronic structure calculations and molecular dynamics
 +
### ABINIT - a DFT-based package for electronic structure and other properties of molecules and periodic solids. It also includes options for molecular dynamics. Basic usage instructions are given here .
 +
### AMBER - Suite of programs for molecular dynamics and other molecular simulations. Licensing restrictions and basic usage instructions are given here.
 +
### CPMD - Software for ab initio molecular dynamics. Users should be aware of the license requirements.
 +
### DL_POLY - A suite of programs for molecular dynamics. Licensing restrictions and basic usage instructions are given here .
 +
### GAMESS - A general ab initio quantum chemistry package. Basic WestGrid usage instructions and licensing restrictions are given here
 +
### Gaussian - A suite of programs for semi-empirical and ab initio molecular orbital calculations. Licensing restrictions and basic usage instructions are given here .
 +
### GROMACS - A suite of programs for molecular dynamics calculations. Instructions for using GROMACS on WestGrid systems are given here
 +
### LAMMPS - Classic molecular dynamics simulator
 +
### Molden - A pre- and post-processing program for molecular and electronic structure. See the Molden and Molden OpenGL developer's site for more information.
 +
### NAMD - A molecular dynamics simulator for large biomolecular systems. License restrictions and basic job submission instructions are given here . Note: NAMD is also available on Tantalus
 +
### Quantum ESPRESSO - A suite of programs for electronic structure and materials modelling. Basic usage instructions are given here .
 +
### SIESTA - An electronic structure and ab-initio quantum-mechanical molecular dynamics package. Note SIESTA is available only for approved license holders. Register here then write to support@westgrid.ca to request access.
 +
### VASP - An ab-initio quantum-mechanical molecular dynamics package based on pseudopotentials and a plane wave basis set. Note VASP is available only for approved license holders. For more information about access, see here .
 +
### YAeHMOP - Yet Another extended Huckel Molecular Orbital Package
 +
##  Sequence Analysis
 +
### BLAST+ - Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. See the BLAST site for more information.
 +
### ARB - Sequence database handling and phylogenic analysis.
 +
### NEURON - An environment for simulating neurons and networks of neurons. See the NEURON site for more information.
 +
# Other Applications
 +
##  Electromagnetics
 +
### Lumerical FDTD Solutions - Package employing finite-difference time-domain techniques primarily for electromagnetic propagation problems. Basic usage instructions are available here .
 +
##  General Purpose Numerical
 +
### MATLAB
 +
### Octave - A general purpose numerical package that is largely compatible with MATLAB
 +
##  Geophysics
 +
### Seplib - A seismic data processing package from the Stanford Exploration Project (SEP) .
 +
### Seismic Un*x - An open source collection of software for seismic processing and research. Some brief usage notes on the WestGrid installation are here .
 +
##  Satellite Data Analysis
 +
### BEAM - a toolbox for viewing and analyzing remotely-sensed data, such as from earth-orbiting satellites. Included is VISAT, an image processing and data analysis program, command-line data processing tools and a JAVA API for extending the toolbox.
  
 
==Veja também==
 
==Veja também==
 
* http://distrowatch.com/table.php?distribution=fedora
 
* http://distrowatch.com/table.php?distribution=fedora
 
* https://admin.fedoraproject.org/pkgdb/collections/?_csrf_token=51f23d5508608cb3aa6821bcfb51e2758a634902
 
* https://admin.fedoraproject.org/pkgdb/collections/?_csrf_token=51f23d5508608cb3aa6821bcfb51e2758a634902
 +
* http://www.westgrid.ca/support/software

Edição atual tal como às 15h05min de 8 de junho de 2010

No Linux Fedora escolher entre 3 principais grupos de pacotes:

Office and Productivity
provides the OpenOffice.org, the Planner project management application, graphical tools such as the GIMP, and multimedia applications.
Software Development
provides the necessary tools to compile software on your Fedora system.
Web server
provides the Apache Web server.
Fedora 13 Alpha release notes

Core Network Services

All Fedora installations include the following network services:

  • centralized logging through syslog
  • email through SMTP (Simple Mail Transfer Protocol)
  • network file sharing through NFS (Network File System)
  • remote access through SSH (Secure SHell)
  • resource advertising through mDNS (multicast DNS)

The default installation also provides:

  • network file transfer through HTTP (HyperText Transfer Protocol)
  • printing through CUPS (Common UNIX Printing System)
  • remote desktop access through VNC (Virtual Network Computing)

Some automated processes use the email service to send reports and messages to the system administrator. By default, the email, logging, and printing services do not accept connections from other systems. Fedora installs the NFS sharing, HTTP, and VNC components without enabling those services. You may configure your Fedora system after installation to offer email, file sharing, logging, printing and remote desktop access services. The SSH service is enabled by default. You may use NFS to access files on other systems without enabling the NFS sharing service.

User level MPI

A rethink of MPI software management has been made in Fedora and relevant packaging guidelines have been adopted for Fedora 13.

Instead of the system-wide alternatives system, support for MPI compilers and runtimes is now managed at userlevel in Fedora with environment modules. The compilers, runtimes and any software compiled against them are installed in separate directories outside the $PATH. Now, for example, it is possible to run program A in one terminal session with Open MPI and program B with MPICH2 in another session. For this reason no default MPI runtime is set by default.

To load support for Open MPI on Fedora 13 x86_64 run $ module load openmpi-x86_64 and for MPICH2 $ module load mpich2-x86_64. If you want e.g. Open MPI support to be automatically available in your sessions, add the command above to your shell config.

Slave Nodes

Going with my example node names and IP addresses, this is what I chose during setup: 

Workstation
auto partition
remove all partitions on system
use LILO as the boot loader
put boot loader on the MBR
host name wolf01
ip address 192.168.0.101
add the user "wolf"
same password as on all other nodes
NO firewall

The ONLY package installed: network servers. Un-select all other packages.

  • Applications/Editions/emacs
  • Applications/Eng Scientific
  • Servers/DNS Name (nao)
  • Servers/Server Configurations tools (nao)
  • Servers/Windows File System (nao)

Pacotes usados em WestGrid (exemplo)

  1. Software on Computational Resources
    1. UNIX Environment
      1. bash,tcsh,sh,csh,ksh
  2. Files and Data
      1. emacs - GNU version of this common text editor
      2. nedit - a graphical editor recommended for PC users, but requires X Windows.
      3. pico - A simple non-graphical text editor with on-screen reminders for commonly-used commands.
      4. vim - an enhanced version of vi
  3. Programming
    1. Fortran
      1. f77 is wrapper script for $FC, $F77,defaulting to ifort
      2. f90 is wrapper script for $FC, $F90,defaulting to ifort
      3. f77 is wrapper script for $FC, $F95,defaulting to ifort
      4. Intel 11.1 (ifort, f77,f90,f95)
      5. GNU 4.3.2 (gfortran)
      6. Open64 4.2.2.1 (openf90, openf95)
      7. f77 links to g77
      8. GNU 4.3.2 (gfortran)
      9. GNU 3.4.6 (g77)
      10. Portland Group 7.0-2 (pgf77, pgf90)
      11. Intel 9.1 (ifort)
      12. Absoft 8.2 (f90)
    2. C
      1. Intel 11.1 (icc,cc)
      2. GNU 4.3.2 (gcc)
      3. Open64 4.2.2.1 (opencc)
    3. C++
      1. GNU 4.4.0 gcc
      2. Intel 11.1 (c++, icpc)
      3. GNU 4.3.2 (g++)
      4. Open64 4.2.2.1 (openCC)
    4. Java
    5. Perl
    6. Python
    7. Utilities
      1. CMake - Cross platform software build system
      2. filepp - Generic file preprocessor
      3. ftnchek - FORTRAN 77 syntax checker
      4. Jam - Make replacement for C/C++ projects. See: www.perforce.com/jam/jam.html
    8. Debuggers
      1. cvd - CASEVision/ProDev Workshop (graphical) debugger /usr/sbin/cvd
      2. dbx - Common UNIX debugger
      3. ddd - Graphical front end to other debuggers
      4. gdb - GNU debugger
      5. idb - Intel debugger
      6. ladebug - Debugger for HP systems Supports parallel debugging
      7. pgdbg - Portland Group graphical debugger
      8. totalview - Etnus Totalview commercial graphical debugger
    9. Libraries
      1. Boost - An eclectic collection of C++ libraries. See www.boost.org for more information.
      2. GNU libgomp - GNU implementation of the OpenMP Application Programming Interface (API). See gcc.gnu.org/onlinedocs/libgomp/ for more information.
      3. STLport - An implementation of the Standard Template Library. See www.stlport.org for more information.
    10. Version Control
      1. Subversion - An open source alternative to CVS for managing files for large development projects. The Subversion client, svn, is provided to give access to repositories outside of WestGrid. See http://subversion.tigris.org/ for more information.
  4. Mathematical Libraries and Applications
    1. Comprehensive Libraries
      1. ESSL - IBM Engineering and Scientific Subroutine Library.
      2. GSL - GNU Scientific Library.
      3. MKL - Intel Math Kernel Library.
      4. SCSL - Scientific Computing Software Library.
    2. Differential Equation Solvers
      1. PETSc - Toolkit for parallel solution of differential equations.
    3. Fourier Transforms
      1. FFTW - A widely-used FFT implementation.
    4. Linear Algebra (See also MATLAB below.)
      1. BLAS - Basic Linear Algebra Subprograms.
      2. LAPACK - Linear algebra subroutine package.
      3. PIM - Parallel Iterative Methods.
      4. ScaLAPACK - Scalable LAPACK.
      5. WSMP - Watson Sparse Matrix Package.
    5. Mesh Partitioning
      1. METIS - Mesh and graph partitioning.
    6. Statistics
      1. R - Software environment and language for statistical data analysis.
  5. Graphics
    1. Animation
      1. mencoder (MPEG encoding) mplayer (video player)
    2. Charting
      1. Grace/Xmgrace - GUI-based x-y plotting for thesis and publication-quality graphs. Also includes data transformations and curve fitting.
      2. Gnuplot - Command-driven x-y plotting program, generally of lower quality than xmgrace, but offering some 3D features.
    3. Geographic data handling
      1. GMT - Generic Mapping Tools - Script-driven package of utilities for gridding and contouring geographic and Cartesian data sets, with support for many map projections. Vector plots, surface plots and other types of graphics are supported.
      2. NCAR Graphics - Libraries and utilities for contour maps, vector and streamline plots, X-Y graphs, map databases and other visualization tools developed for the support of meteorological applications but with a broad range of applications in other disciplines.
      3. VISAT - An image processing and data analysis program for remotely sensed data. VISAT is part of the BEAM toolkit mentioned below
    4. Image format handling
      1. libjpeg - Independent JPEG Group JPEG compression library and image file conversion programs, djpeg and cjpeg.
      2. libtiff - TIFF (Tagged Image File Format) image library.
      3. Netpbm - Image conversion utilities and library.
      4. pdflib - PDF file handling library ("PDFlib-Lite" for non-commercial use)
      5. zlib - Data compression library.
    5. OpenGL-related
      1. Vendor's OpenGL
      2. Mesa
      3. GLUT
  6. Chemistry and Biochemistry Applications
    1. Electronic structure calculations and molecular dynamics
      1. ABINIT - a DFT-based package for electronic structure and other properties of molecules and periodic solids. It also includes options for molecular dynamics. Basic usage instructions are given here .
      2. AMBER - Suite of programs for molecular dynamics and other molecular simulations. Licensing restrictions and basic usage instructions are given here.
      3. CPMD - Software for ab initio molecular dynamics. Users should be aware of the license requirements.
      4. DL_POLY - A suite of programs for molecular dynamics. Licensing restrictions and basic usage instructions are given here .
      5. GAMESS - A general ab initio quantum chemistry package. Basic WestGrid usage instructions and licensing restrictions are given here
      6. Gaussian - A suite of programs for semi-empirical and ab initio molecular orbital calculations. Licensing restrictions and basic usage instructions are given here .
      7. GROMACS - A suite of programs for molecular dynamics calculations. Instructions for using GROMACS on WestGrid systems are given here
      8. LAMMPS - Classic molecular dynamics simulator
      9. Molden - A pre- and post-processing program for molecular and electronic structure. See the Molden and Molden OpenGL developer's site for more information.
      10. NAMD - A molecular dynamics simulator for large biomolecular systems. License restrictions and basic job submission instructions are given here . Note: NAMD is also available on Tantalus
      11. Quantum ESPRESSO - A suite of programs for electronic structure and materials modelling. Basic usage instructions are given here .
      12. SIESTA - An electronic structure and ab-initio quantum-mechanical molecular dynamics package. Note SIESTA is available only for approved license holders. Register here then write to support@westgrid.ca to request access.
      13. VASP - An ab-initio quantum-mechanical molecular dynamics package based on pseudopotentials and a plane wave basis set. Note VASP is available only for approved license holders. For more information about access, see here .
      14. YAeHMOP - Yet Another extended Huckel Molecular Orbital Package
    2. Sequence Analysis
      1. BLAST+ - Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. See the BLAST site for more information.
      2. ARB - Sequence database handling and phylogenic analysis.
      3. NEURON - An environment for simulating neurons and networks of neurons. See the NEURON site for more information.
  7. Other Applications
    1. Electromagnetics
      1. Lumerical FDTD Solutions - Package employing finite-difference time-domain techniques primarily for electromagnetic propagation problems. Basic usage instructions are available here .
    2. General Purpose Numerical
      1. MATLAB
      2. Octave - A general purpose numerical package that is largely compatible with MATLAB
    3. Geophysics
      1. Seplib - A seismic data processing package from the Stanford Exploration Project (SEP) .
      2. Seismic Un*x - An open source collection of software for seismic processing and research. Some brief usage notes on the WestGrid installation are here .
    4. Satellite Data Analysis
      1. BEAM - a toolbox for viewing and analyzing remotely-sensed data, such as from earth-orbiting satellites. Included is VISAT, an image processing and data analysis program, command-line data processing tools and a JAVA API for extending the toolbox.

Veja também

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