source: lmdz_wrf/trunk/tools/documentation/install.html @ 1531

Last change on this file since 1531 was 1442, checked in by lfita, 8 years ago

Adding more information about `python-netcdf4'
File size: 4.0 KB
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1<HTML>
2  <HEAD>
3    <META HTTP-EQUIV="Content-Type" CONTENT="text/html; CHARSET=utf-8"/>
4    <LINK REL="stylesheet" TYPE="text/css" HREF="PyNCplot.css"/>
5  </HEAD>
6
7  <!--BODY STYLE="color:rgb(240,240,240);font-size:1em;"-->
8  <BODY CLASS="genintro"> 
9    <H1>Installation guide</H1>
10    A step-by-step instructions to follow in order to install all the required packages and tools. <BR>
11
12    Example of installation in a Debian 8 as root:
13    <OL>
14      <LI>as root</LI>
15      <DIV CLASS="codetxt">$ su</DIV>
16      <LI>install subversion, version control packaes</LI>
17      <DIV CLASS="codetxt"># apt-get install subversion</DIV>
18      <LI>install GIT, different paradigm version control</LI>
19      <DIV CLASS="codetxt"># apt-get install git</DIV>
20
21      <LI>get python and its necessary applications</LI>
22      <DIV CLASS="codetxt"># apt-get install python python-scipy python-numpy cython cython-dbg</DIV>
23
24      <LI>get netcdf libraries tools and applications (cdo and nco are also installed maybe not required...)</LI>
25      <DIV CLASS="codetxt"># apt-get install netcdf-bin netcdf-dbg libnetcdf-dev netcdf-doc ncview cdo nco</DIV>
26
27      <LI>get hdf5</LI>
28      <DIV CLASS="codetxt"># apt-get install libhdf5-dev</DIV>
29
30      <LI>install matplotlib and basemap in order to plot and drow maps</LI>
31      <DIV CLASS="codetxt"># apt-get install python-matplotlib python-matplotlib-data python-matplotlib-doc python-mpltoolkits.basemap python-mpltoolkits.basemap-data</DIV>
32
33      <LI>install system tools (Scripts use L<SUP>A</SUP>T<SUB>E</SUB>X interface for titles and labels)</LI>
34      <DIV CLASS="codetxt"># apt-get install dvipng</DIV>
35
36      <LI>install netcdf4, python API interface to netCDF files</LI>
37        <OL>
38          <LI> Some new linux distributions (at least Debian >8) provide the netcdf4 API in the package systems:</LI>
39            <DIV CLASS="codetxt"># apt-get install python-netcdf4</DIV>
40          <LI> Otherwise, it can be manually done. Be careful with interferencies with anaconda (some issues on mixture of netcdf libraries have been detected).
41          <UL>
42            <LI>Following <A CLASS="la" HREF="https://github.com/Unidata/netcdf4-python"  TARGET="_blank">https://github.com/Unidata/netcdf4-python</A>)</LI>
43            <DIV CLASS="codetxt"># git clone https://github.com/Unidata/netcdf4-python.git<BR>
44              cd netcdf4-python/</DIV>
45            <LI>Editing `setup.cfg' to add/change some values (there are installation issues if `nc-config' is used along installation)</LI>
46            <PRE><CODE>
47use_ncconfig=False
48netCDF4_dir = /usr/local
49HDF5_dir = /usr/local
50HDF5_libdir = /usr/lib/x86_64-linux-gnu/hdf5/serial
51HDF5_INCDIR = /usr/include/hdf5/serial
52</CODE></PRE>
53            <DIV CLASS="codetxt">
54# python setup.py build >& run_pysetup.log<BR>
55# python setup.py install >& run_pyinstall.log</DIV>
56          </UL>
57        </OL>
58      <LI>Getting the scripts, no need to be root:</LI>
59        <DIV CLASS="codetxt"># exit<BR>
60      $ cd $HOME <BR>
61      $ svn co http://svn.lmd.jussieu.fr/LMDZ_WRF/trunk/tools PyNCplot</DIV>
62     <LI>Now all the scripts are held in ${HOME}/PyNCplot. It might be desirable to set an environment variable to make life easier:
63      <DIV CLASS="codetxt">$ export pyHOME=${HOME}/PyNCplot</DIV>
64      <LI>Finally one need to compile the Fortran modules using the same python to run the scripts. This is done using a standard `Makefile' and the tool <A CLASS="la" HREF="https://docs.scipy.org/doc/numpy-dev/f2py/" TARGET="_blank">f2py</A> to link Fortran compiled codes to python. There are different versions for different LMD/IPSL and French HPC machines. For a standard linux 64-bits machine (debain 7) there is one example as `Makefile.foudre'. Follow the instructions there in after linking the appropriated file:</LI>
65      <DIV CLASS="codetxt">
66      $ ln -s Makefile.[machine].[compiler] ./Makefile
67      </DIV>
68      At the end one should have:
69      <PRE><CODE>
70      module_ForDiag.so
71      module_ForInt.so
72      </CODE></PRE>
73
74      </OL>
75
76  </BODY>
77</HTML>
78
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