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External tools
Table of contents
1. 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 computing machine (except forge).
The common account configuration files allow you to access the proper version of the tools (e.g. module load).
1.1. Forge
The forge.ipsl.jussieu.fr machine is a forge trac
- Welcome page of the User guide as TracWiki and its attached documents
- Source code archives with the svn server
- Problem tracker (tickets)
1.2. Remote and secure connections
- ssh and associated commands (scp, rsync, protocol svn+ssh)
1.3. Shell
- bash : recommended for interactive mode --- You can read 2016 IPSL documentation on Bash here
- ksh : used in batch scripts
- awk gnu ([g]awk)
- make gnu ([g]make)
1.4. Version control
- Official website: subversion
- Basic command: svn
- Online subversion manual: http://svnbook.red-bean.com/index.en.html
You can read some 2016 IPSL slides on svn here
1.5. C++ compilers
1.6. Fortran compilers
To learn how to use Fortran, IDRIS training: http://www.idris.fr/formations/fortran/
Some Fortran compilers :
1.7. FORTRAN libraries
- NetCDF4 parallel
- HDF5 parallel
- MPI/OpenMP
1.8. Generating executables
Default for compiling the models: FCM.
1.9. Batch manager
- slurm and slurm ccc_*
- torque-maui
- LoadLeveler
1.10. Mail program
- mail[x]
1.11. NetCDF tools
You can read 2016 IPSL documentation on nco / cdo / netcdf here
2. Tools for analyze and visualization of NetCDF files
You can read 2016 IPSL documentation on ferret here
3. A few tips for further reading
3.1. Unix
Google "Unix Tutorial" is a good starting point.
- Unix introduction -- You can read 2016 IPSL documentation on Unix 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
3.2. Text editors
3.2.1. Emacs
- Official website: http://www.gnu.org/software/emacs/ -- You can find a list of emacs commands here
3.2.2. vi and vim
- vim documentation : http://www.vim.org/docs.php -- You can read 2016 IPSL documentation on vi / vim here
3.3. Programming and scripting languages
3.3.1. 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/
You can read 2016 IPSL documentation on Python here
4. BootCamp IPSL presentations - documentations - hands on sessions
{24 of march 2016}
- Unix 20160324_unix.pdf
- vi 20160324_vi.pdf
- emacs 20160324_emacs_commands.pdf
- shell bash 20160324_bash.pdf TP test.bash
- netcdf 20160324_netcdf.pdf
- cdo - nco 20160324_cdo_nco.pdf
- Ferret 20160324_ferret.pdf
- python 20160324_python.pdf TP fibonacci.py plotting_topo.py reading_nc.py
- svn 20160324_svn.pdf
All the HandsOn (TP and netcdf files) were available on IDRIS (Ergon) and TGCC (Curie) : $(ccc_home --cccwork -u igcmg)/TRAINING/MODIPSL_HandsOn_20181127/ -- there were not update to new computers centers
Attachments (24)
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bash.pdf
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added by acosce 8 years ago.
pdf cours bash bootcamp 24 mars
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cdo_nco.pdf
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added by acosce 8 years ago.
pdf cours cdo_nco bootcamp 24 mars
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emacs_commands.pdf
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added by acosce 8 years ago.
pdf liste commandes emacs bootcamp 24 mars
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ferret.pdf
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added by acosce 8 years ago.
pdf cours ferret bootcamp 24 mars
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netcdf.pdf
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added by acosce 8 years ago.
pdf cours netcdf bootcamp 24 mars
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python.pdf
(269.7 KB) -
added by acosce 8 years ago.
pdf cours python bootcamp 24 mars
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svn.pdf
(189.7 KB) -
added by acosce 8 years ago.
pdf cours svn bootcamp 24 mars
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unix.pdf
(309.9 KB) -
added by acosce 8 years ago.
pdf cours unix bootcamp 24 mars
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vi.pdf
(294.3 KB) -
added by acosce 8 years ago.
pdf cours vi bootcamp 24 mars
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fibonacci.py
(798 bytes) -
added by acosce 8 years ago.
fichier TP python fibonacci Bootcamp 24 mars 2016
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plotting_topo.py
(1.1 KB) -
added by acosce 8 years ago.
fichier TP python plotting_topo Bootcamp 24 mars 2016
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reading_nc.py
(458 bytes) -
added by acosce 8 years ago.
fichier TP python reading_nc Bootcamp 24 mars 2016
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test.bash
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added by acosce 8 years ago.
fichier TP bash BootCamp? 24 mars 2016
- 20160324_bootcamp_pdf.tar (2.4 MB) - added by acosce 8 years ago.
- bash.2.pdf (216.5 KB) - added by acosce 8 years ago.
- 20160324_bash.pdf (216.5 KB) - added by acosce 8 years ago.
- 20160324_cdo_nco.pdf (410.6 KB) - added by acosce 8 years ago.
- 20160324_emacs_commands.pdf (21.1 KB) - added by acosce 8 years ago.
- 20160324_ferret.pdf (499.9 KB) - added by acosce 8 years ago.
- 20160324_netcdf.pdf (279.2 KB) - added by acosce 8 years ago.
- 20160324_python.pdf (291.7 KB) - added by acosce 8 years ago.
- 20160324_svn.pdf (189.7 KB) - added by acosce 8 years ago.
- 20160324_unix.pdf (309.9 KB) - added by acosce 8 years ago.
- 20160324_vi.pdf (294.3 KB) - added by acosce 8 years ago.