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# Important tools used in the IPSL climate modeling framework #

The following tools are used for all steps from setup to post processing. They must be available on the [wiki:DocBenv computing machine] (except [#Forge forge]).

The [wiki:DocBenvEcommonfiles common] account configuration files allow you to access the proper version of the tools (e.g. {{{module load}}}).

## Forge ##

The forge.ipsl.jussieu.fr machine is a forge [http://www.edgewall.org/ trac]
 * Welcome page of the [wiki:Doc User guide] as TracWiki and its attached documents
 * Source code archives with the [http://subversion.tigris.org/ svn] server 
 * Problem tracker (tickets)

## Remote and secure connections ##
 * {{{ssh}}} and associated commands ({{{scp}}}, {{{rsync}}}, protocol {{{svn+ssh}}})

## Shell ##
 * bash : recommended for interactive mode   --- You can read IPSL documentation on Bash [https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/DocKexterntools#BootCampIPSLpresentations-documentations-handsonsessions here]
 * ksh : used in batch scripts
 * awk gnu ({{{[g]awk}}})
 * make gnu ({{{[g]make}}})
 
## Version control ##

 * Official website: [http://subversion.apache.org/ subversion] 
 * Basic command: [wiki:DocKexterntoolsAsvnbasic svn]
 * Online subversion manual: http://svnbook.red-bean.com/index.en.html

You can read some IPSL slides on svn [https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/DocKexterntools#BootCampIPSLpresentations-documentations-handsonsessions here]

## C++ compilers ##

## Fortran compilers ##
To learn how to use Fortran, see e.g. 
 * Michel Olagnon's Fortran 90 List: http://www.ifremer.fr/ditigo/molagnon/fortran90/engfaq.html
 * IDRIS training (the latest is available in English only): http://www.idris.fr/data/cours/lang/fortran/choix_doc.html

Some Fortran compilers :
  * Portland 
  * Intel 
  * NAG
  * gfortran 
  * g95

## FORTRAN libraries ##
 * [http://www.unidata.ucar.edu/software/netcdf/ NetCDF4 parallel]
 * [http://www.hdfgroup.org/HDF5/doc/fortran/index.html HDF5 parallel] 
 * MPI/OpenMP

## Generating executables ##
Default for [wiki:Doc/Compile compiling] the models: [https://www.metoffice.gov.uk/research/weather/weather-science-it/fcm FCM].

## Batch manager ##
 * slurm and slurm {{{ccc_*}}}
 * torque-maui
 * !LoadLeveler

## Mail program ##
 * mail[x]

## NetCDF tools ##
 * [http://nco.sourceforge.net/ nco]
 * [https://code.zmaw.de/projects/cdo cdo]
 
You can read IPSL documentation on nco / cdo / netcdf [https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/DocKexterntools#BootCampIPSLpresentations-documentations-handsonsessions here]

# Tools for analyze and visualization of NetCDF files #

 * [http://ferret.wrc.noaa.gov/ ferret]
 * [http://www.ncl.ucar.edu/ NCL]
 * [http://meteora.ucsd.edu/~pierce/ncview_home_page.html ncview]
 * [http://www.exelisvis.com/language/en-US/ProductsServices/IDL.aspx IDL]
 * [http://forge.ipsl.jussieu.fr/saxo/ SAXO]

You can read IPSL documentation on ferre [https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/DocKexterntools#BootCampIPSLpresentations-documentations-handsonsessions here]

# A few tips for further reading #

## Unix ##
 Google "Unix Tutorial" is a good starting point.
 * Unix introduction -- You can read an IPSL documentation on Unix [https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/DocKexterntools#BootCampIPSLpresentations-documentations-handsonsessions here]
 * Linux Documentation: http://www.tldp.org/guides.html
   * Advanced Bash-Scripting guide. Mendel Cooper : http://tldp.org/LDP/abs/html/
   * Bash guide for beginners.Machtelt Garrels http://tille.garrels.be/training/bash/
 * Portable shell programming : http://www.gnu.org/software/autoconf/manual/autoconf.html#Portable-Shell

## Text editors ##
### Emacs ###
 * Official website: http://www.gnu.org/software/emacs/    -- You can find a list of emacs commands [https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/DocKexterntools#BootCampIPSLpresentations-documentations-handsonsessions here]
### vi and vim ###
 * vim documentation : http://www.vim.org/docs.php   -- You can read an IPSL documentation on vi / vim [https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/DocKexterntools#BootCampIPSLpresentations-documentations-handsonsessions here]



## Programming and scripting languages ##
### Python ###
 * Python and CDAT tips: http://www.johnny-lin.com/cdat_tips/
 * Python and memory management:
  * problem http://www.evanjones.ca/python-memory.html
  * mailing list archive: http://mail.python.org/pipermail/python-list/
  * model validation tool: http://motherlode.ucar.edu:8080/thredds/cdmValidate.html
 
You can read an IPSL documentation on Python [https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/DocKexterntools#BootCampIPSLpresentations-documentations-handsonsessions here]

# !BootCamp IPSL presentations - documentations - hands on sessions # 
{24 of march 2016}
 * Unix [attachment:20160324_unix.pdf] 
 * vi [attachment:20160324_vi.pdf]
 * emacs  [attachment:20160324_emacs_commands.pdf]
 * shell bash [attachment:20160324_bash.pdf] TP [attachment:test.bash]
 * netcdf [attachment:20160324_netcdf.pdf]
 * cdo - nco [attachment:20160324_cdo_nco.pdf]
 * ferret [attachment:20160324_ferret.pdf]
 * python [attachment:20160324_python.pdf] TP [attachment:fibonacci.py] [attachment:plotting_topo.py] [attachment:reading_nc.py]
 * svn [attachment:20160324_svn.pdf]

All the !HandsOn (TP and netcdf files) are available on IDRIS (Ergon) and TGCC (Curie) : ${PATH_IPSL_account}/TRAINING/BOOTCAMP_HandsOn_20160324