A-INSTALL

#
# Version of PACKAGE MESONH "Open distribution"
#              PACK-MNH-V5-4-2
#              DATE : 03/04/2019
#              VERSION : MESONH MASDEV5_4 + BUG-2
#
#  MAP
#
#        0) TWO WAYS OF DOWNLOADING MESONH
#      I-A) DOWNLOAD VIA THE WEB MESONH HOME PAGE
#      I-B) DOWNLOAD VIA GIT ANONYMOUS 
#       II) CONFIGURING THE MESONH PACKAGE
#      III) COMPILING/INSTALLING THE MESONH PACKAGE ON YOUR LINUX COMPUTER 
#       IV) RUN SOME "SMALL KTEST" EXAMPLES
#        V) RECOMPILING YOUR 'OWN' SOURCES ONLY 
#       VI) COMPILING/INSTALLING MESONH ON GENCI & ECMWF & METEO COMPUTERS
#      VII) "SCANDOLLAR" = SCRIPTING YOUR OWN PROCEDURES 
#
#     VIII) TROUBLE-SHOOTING
#           a) Segmentation violation -> problem of "stack size" limit
#           b) Compiler bug with "ifort 10.0.xxx" 
#
#       IX) OPTIONAL COMPILATION
#           a) MNH_FOREFIRE for forefire runs ( external package needed )
#           b) MNH_RTTOV for optional radiative computation
#           c) MNH_ECRAD for optional compilation of new ECRAD radiative library from ECMWF
#           d) MNH_MEGAN for optional compilation of MEGAN 
#           e) cleaning previous compiled version
#
#
^L
#  0) TWO WAYS OF DOWNLOADING MESONH
#  =================================
#
#  MESONH sources and executables 
#  http://mesonh.aero.obs-mip.fr
#  are developed and maintained with the
#  Git tools ( https://git-scm.com/ )
#
#  There are two ways to download the package of
#  MESONH containing :
#    - sources 
#    - makefiles
#    - precompile exe 
#    - graphic tools
#    - basic examples
#
#  The first way is for VERY BASIC USER OF MESONH 
#  via a download of a "tar ball" in the WEB site of MESONH
#
#  The second way is for USER/DEVELOPER of MESONH
#  via the use of Git and an anonymous ssh connection to the Git repository of
#  the MESONH package 
# 
#
# REM: It is now strongly recommended, but not mandatory, 
#      for all users to use the Git solution, because:
#
#      * It's far more easy for us ( support team ) to give you some assistance
#        in case of trouble... as Git permits us to know exactly
#         what you have changed in the original PACKAGE
#
#      * It's much more easy for you to update to the last version...  
#        or at least see the change made for BUGFIX directly on our
#        installation.
#
#
#  Following, are presented the two mutually exclusive ways to get the MesoNH
#  package:
#
#
^L
# I-A) DOWNLOAD VIA THE WEB MESONH HOME PAGE
# ==========================================
#
# With your preferred web browser go to the MESONH WEB SITE
# 
#  http://mesonh.aero.obs-mip.fr/mesonh
#     ---> Download
#
# or directly
#
# http://mesonh.aero.obs-mip.fr/mesonh/dir_open/dir_MESONH/MNH-V5-4-2.tar.gz
#
# Then untar the file "PACK-MNH-V5-4-2.tar.gz" where you want to.
# For example, in your home directory:
#
 
cd ~
tar xvfz PACK-MNH-V5-4-2.tar.gz
      
#
#  Process now to the chapter to configure the MesoNH package.
#
# => II) CONFIGURING THE MESONH PACKAGE
#
^L
# I-B) DOWNLOAD VIA GIT ANONYMOUS
# ===============================
#
#    a) Prerequisites
#    ----------------
#
# In order to clone the Meso-NH git repository that contains sources, compiled
# libraries and binary tools, the git LFS extension is required to handle
# binary (or large) files. So before starting, be sure:
#
#  * to have git v1.8.2 or higher installed on your workstation. You can run
#    and check with:

git --version

#  * to install the git LFS extension (not included by default in the Git
#    package):
#    - get the linux git-lfs archive from the "Download v1.X.Y (Linux)" link on
#      the web page https://git-lfs.github.com/
#    - extract the archive and copy the git-lfs binary in your $HOME/bin (the
#      provided install.sh script doesn't need to be executed)
#    - from any directory, you can now execute:

git lfs install

#      that will set up some filters under the name "lfs" in the global Git
#      config file ($HOME/.gitconfig) 
#
#    b) Before cloning
#    -----------------
#
#  * Download the private key to access the anonymous Meso-NH Git server (read-
#    only access) by following the next link:
#

http://mesonh.aero.obs-mip.fr/mesonh54/GitSources?action=AttachFile&do=get&target=anongitmesonh.key

#
#    and save the file in your $HOME/.ssh/ directory.
#
#  * Change the access permissions of the key with:
#

chmod 600 $HOME/.ssh/anongitmesonh.key

#
#  * Copy/paste the following lines and add them in your $HOME/.ssh/config file
#    (create the file if it is missing):
#

Host anongit_mesonh
  User anongit
  IdentityFile ~/.ssh/anongitmesonh.key
  Hostname 195.83.22.22
  Port 22222

#
# Before cloning the repository, execute:
#

git config --global http.sslverify false

#
# This is necessary to disable the certificate checks because a self-signed
# certificate was used for the LFS server.
#
#    c) Cloning the Meso-NH Source repository on the developpement branch MNH-54-branch
#    ----------------------------------------------------------------------------------
#
# Finally you can clone the Meso-NH Git repository with the following command:
#

git lfs clone anongit@anongit_mesonh:/gitrepos/MNH-git_open_source-lfs.git -b MNH-54-branch MNH-V5-4-2

#
# that will create the MNH-V5-4-2 directory containing a clone (copy) of the
# Meso-NH package on the remote developpement branch MNH-54-branch
#
#
#   d) Checking out a given version of MESONH
#   -----------------------------------------
#
# Once the repository is cloned, it's better for you to checkout your own branch
# (by default, you are on HEAD of the MNH-54-branch development branch  ).
#
# To create your local branch corresponding to the V5-4-2 version, type:
#

cd MNH-V5-4-2
git checkout -b MYB-MNH-V5-4-2 PACK-MNH-V5-4-2

#
# MYB-MNH-V5-4-2 is the name of the local branch you created
# and
# PACK-MNH-V5-4-2 is the remote/origin tag on which it is based.
#
# The advantage of this way of downloading the package is that in the future
# you could check/update quickly differences with the new version of the
# package without having to download entirely the full package.
#
#  Suppose that a new version, for example "PACK-MNH-V5-4-2", is announced.
#
#  To see the differences with your working copy, do:
#

git fetch
git diff HEAD PACK-MNH-V5-4-2

#
#  To go to the new version, you can, for example, create a new local branch:
#

git checkout -b MYB-MNH-V5-4-2 PACK-MNH-V5-4-2

#
# At any time, you can also check for "uptodate" changes in the Git branch
# dedicated to the MNH54 version before the official release of the "bugN+1"
# bugfix version.
#

git fetch
git diff HEAD MNH-54-branch
  
#
# And, test this development (not yet official) version by going to this branch:
#

git checkout --track origin/MNH-54-branch
#
#    e) Cloning the Meso-NH Documentation repository
#
# In a similar fashion, you can clone the Meso-NH documentation Git repository
# with the following command:
#

git clone anongit@anongit_mesonh:/gitrepos/MNH-DOC.git

#
# that will create the MNH-DOC directory containing the latest LaTeX sources of
# the Meso-NH documentation.

#
#  Well, the use of git is not under the scope of this "INSTALL" document...
#
#   Now, go to the next chapter 
#
#   => II) CONFIGURING THE MESONH PACKAGE
#
#
^L
#
# II) CONFIGURING THE MESONH PACKAGE
# ==================================
#
#    For the installation process, you could now
#    use the "./configure" script like this 
#

cd ~/MNH-V5-4-2/src
./configure
. ../conf/profile_mesonh

#
#    this will create a configuration file "profile_mesonh" with
#    an extension reflecting the different "choices" made automatically
#    to match the computer on which you want to install MESONH
#   
#    WARNING :
#    =========
#    On GENCI & ECMWF & METEO/CNRM  computers, the './configure' is tuned to 
#    identify the computer on which the command is used
#    so the good compiler, MPI & netCDF libraries,... 
#    are automatically chosen
# 
#    /!\ This is not the case in your "own" personal Linux computer ...
#    So is up to you to set the ARCH variable correctly
#    ARCH     = Fortran compiler to use,
#    VER_MPI  = version of MPI to use ,
#    OPTLEVEL = 
#    etc ...
#    and all the other environnement variables. 
# 
#    Be default, for an unknown computer, you will have:
#
#   - the compiler choosen to be "gfortran" => ARCH=LXgfortran
#   - the MPI library to be the MPIVIDE  => VER_MPI=MPIVIDE
#     ( empty MPI library coming with MESONH package = no parallel run possible )
#   - the level of optimization for the compiler  => OPTLEVEL=DEBUG
#     (  for development purpose ,fast compilation & debugging )   
#       
#    SO IF NEEDED:
#    ============
#    you could change the default FLAG compiler/MPI/optlevel
#    like this, for example 

export ARCH=LXifort        # Use Intel "ifort" compiler on LX=linux Plateform 
export VER_MPI=MPIAUTO     # Use MPI with compiler wrapper 'mpif90', for computer having this wrapper installed 
export OPTLEVEL=O2         # Compile in O2, 4 times faster then DEBUG, but less error checks

./configure

#    and then source/load the new generate file

. ../conf/profile_mesonh.LXifort.MNH-V5-4-2.MPIAUTO.O2

#
#  REM: 
#  ====
#
#  - Options specific to compiling/architecture, like 'OPTLEVEL' are defined inside the "Rules.${ARCH}.mk" .
#
#  - Options specific to library like "mpi"="VER_MPI" or "cdf"="VER_CDF" are defined inside "Makefile.MESONH.mk"
#
#  - If needed, for adaptation to your requirements, look inside the files and changes options for your needs.
#  
#  - On PC-Linux, if needed, look at the "MesonhTEAM Wiki" to know how to compile the OpenMPI library with MESONH:
#
#    http://mesonh.aero.obs-mip.fr/teamwiki/MesonhTEAMFAQ/PC_Linux
#      --> Compilation of OPEN-MPI

^L
#   
# III) COMPILING/INSTALLING THE MESONH PACKAGE ON YOUR LINUX COMPUTER 
# ===================================================================
#
# go to the directory  "src"
#

cd  ~/MNH-V5-4-2/src

#
# if you have not already configured your MESONH environment
# either manually in your interactive session 
# or automatically through your .profile (or .bashrc), do:
#
# REM: use the configure file corresponding to your needs, cf. previous chapter 

. ../conf/profile_mesonh{use_the_good_version_here} 

#
# run the compilation by
#

(g)make

#
# The compilation will take about 20 minutes on modern PC-Linux ...
# 
# If you have a multi-processor machine you can speedup
# the compilation, for example on four cores, with:

(g)make -j 4

#
#
# The  object files "*.o"  &  main executables of the "MESONH PACKAGE" :
#
#  MESONH , PREP_IDEAL_CASE , PREP_REAL_CASE , etc ...
#
#  are compiled in one step and created in the directory
#
#    dir_obj-$(ARCH).../MASTER
#
# ( REM: the lib...a is only created and removed at the link phase;
#          this allows a parallel compilation of the sources ... ) 
#
# The exact name of this "dir_obj..." depends on the different environnement
# variables set by the "profile_mesonh...." which you have loaded before the compilation.
#
# This allows by loading different "profile_mesonh.." files to compile in the same
# source/installation directory different versions of MESONH , with different
# compilers, different versions of MPI, different USER sources...
#
#
# To install the new compiled program in the "$SRC_MESONH/exe"
# directory, after compilation, just run
#

make installmaster

#
# The executables with their full name, including $ARCH, compiler,
# MPI and level of optimization, will be linked in the "../exe" directory
# 
# REM: 
# ---
#      The "make installmaster" need to be done only one time by "version". 
#      If you only change/add source, you have to do "make" 

make
 
#
#  IV) RUN SOME "SMALL KTEST" EXAMPLES
#  ===================================
#
#  After compilation & installation, you could run
#  some basic "KTEST" examples from the "src" directory 
#  by running:

make examples 

# or by giving one of the "KTEST" names in 
#
# the list "001_2Drelief 002_3Drelief 003_KW78 004_Reunion 007_16janvier"

make 004_Reunion

#
#  EXAMPLES USING NCL
#  ===================
#
#  WITH 2 OPTIONS TO CONVERT FROM LFI TO NETCDF FORMAT
#  1: with extractdia
#  2: with lfi2cdf
#  Only for 2 KTEST : 004_Reunion and 007_16janvier
#

make ncl1_examples  # if using extractdia

#or

make ncl2_examples  # if using lfi2cdf

#
# Or by giving the KTEST name followed by _ncl1 or _ncl2
#

make 004_Reunion_ncl1

#or

make 004_Reunion_ncl2

^L
#
#  V) RECOMPILING YOUR OWN SOURCES ONLY 
#  ====================================
#
#  NOW YOU COULD GENERATE AND RECOMPILE YOUR OWN SOURCES ONLY
#  ( like BIBUSER in centralised MESONH version )
#
#  Suppose you want to create a "MY_MODIF" version ...
#
# Step-1 : prepare your source directory
# ---------------------------------------
#
# Put your own sources in a subdirectory of "${SRC_MESONH}/src" named 
#  
   
${SRC_MESONH}/src/MY_MODIF

#
#  All subdirectories in "MY_MODIF" will be scanned. So if you want,
#  you could make a subdirectory for each component of the MESONH
#  Package
#

cp .../mesonh.f90 MY_MODIF/MNH/.
cp .../isba.f90   MY_MODIF/SURFEX/.

#
#  /!\ WARNING :
#  -------------
#   - In this subdirectory, put only fortran source you want to compile !!!
#   Don't use it as a trash with old sources file like 'my_source.f90.old'
#   or 'tar' files 'mysource.tar' . 
#   - All 'spirituous' file will confuse the 'make' command.
#
#   
# Step-2 : configure/compiling with VER_USER=...
# ----------------------------------------------
# 
# - Logout of the current session to be sure to unset all the 
#   environnement variables loaded with the your 'master 'profile_mesonh'
#
# - Login again and:
#
#   - set the variable "VER_USER" with the name of your "USER VERSION",  
#   - set also the optional ARCH, VER_MPI... you want to use.
#  
# and run again the "./configure" command

#export ARCH=...
#export VER_MPI=...
export VER_USER=MY_MODIF
./configure

#
# this will regenerate the "profile-mesonh" file and a copy
# of this with the extent  "profile_mesonh...${VER_USER)..."
#
# as before load it & and compile with the command "make user"

. ../conf/profile_mesnh...${VER_USER}...

make user

# this will compile only your sources and the files depending on your sources
# and generate the new executables in your own directory
#
#   dir_obj-$(ARCH).../${VER_USER}
#
#
# WARNING : 
# ========
#  Before compiling your own sources be sure that these ones
#  are younger than the "*.o" files of the MASTER directory.
#  If any doubt, at any time use the command
#
#      touch *.f*
#
#     on your sources, and only on yours do that!!!
#
#
# Step-3 : running the examples 
# -----------------------------
#
#
# Now if the compilation is OK, you could test this new version with the "make examples".
#
# First, install the new binaries in the '${SRC_MESONH}/exe' with

make installuser

#   The "make installuser" needs to be done only one time by "version".

#
# And run the examples. Your version should appear in the name of the used executables.
#

make examples 

^L
#
#   VI) COMPILING/INSTALLING ON GENCI & ECMWF & METEO COMPUTERS
#   ===========================================================
#
#   After downloading "exactly" like on "any standalone PC" 
#   run the "./configure" command :
#

./configure

#
#  - If you do not have sufficient space in your "$HOME" directory,
#    install the whole package directly on the ${WORKDIR}
#
#   WARNING :
#   ======== 
#    - Think to do a backup of your installation 
#    - This space is no more "purged" but a "crash disk" could/will
#      probably occur !!!
# 

cd $WORKDIR
cd MNH-V5-4-2/src

./configure
 
#   
#   Due to limitation in time & memory on interactive connection 
#   then compile the MESONH PACKAGE in batch mode with the different "job_make_mesonh*" files
#   
#   at IDRIS :
#   ---------
#

#   - On ADA ( IBM/x3750 ) with :

llsubmit job_make_mesonh_IBM_ada

#
#
#   - On TURING (IBM BG/Q ) : 

llsubmit job_make_mesonh_BGQ

#
#
#   BACKUP : /!\ backup your work on "ergon"
#
#   
#   at CINES on JADE( SGI/ICE ) , OCCIGEN not tested yet  :
#   -------------------------------------------------------
# 
#   - install the PACKAGE in your "/store/${USER}" directory 
#   - you could compile in interactive mode
#
#    BACKUP : /!\ backup your work on "/data/${USER}"
# 


# 
#   at ECMWF on cca ( CRAY/XC30 ) :
#   ----------------------------
#
#   - to install MESONH go to your $PERM directory
#     if you need more disk space than allowed for 'standard' user 
#     Ask to Dominique Lucas, look this email :
#
#    http://mesonh.aero.obs-mip.fr/cgi-bin/mesonh_interne/mail2html.cgi?file=2009_09_24_15:31:54
#
#   - for the compilation use :

qsub job_make_mesonh_CRAY_cca

#
# REM : On CRAY computer cca , the default compiler is the CRAY one = crayftn .
#      I you have trouble with this one , you could compile with the Intel/ifort one .
#      Use the ifort one do :

export ARCH=LXifort
./configure

...

création du fichier -->  ../conf/profile_mesonh-LXifortI4-MNH-V5-4-2-MPICRAY-O2

# And for the compilation & example job , switch the ARCH variable to LXiort :

vi  job_make_mesonh_CRAY_cca(job_make_examples_CRAY_cca)

ARCH=LXifort
#ARCH=LXcray # this is the default one
. ../conf/profile_mesonh-${ARCH}I4-MNH-V5-4-2-MPICRAY-O2



#
#   EXAMPLES ON GENCI & ECMWF PLATFORMS
#   ====================================
#
#  - At IDRIS
#

# on ADA

llsubmit job_make_examples_IBM_ada

#on TURING

llsubmit job_make_examples_BGQ

#
#   - At CINES on JADE( SGI/ICE ) :
#
# load ".profile_mesonh..." & set the variables :
 
export MONORUN="mpirun -np 1"
export MPIRUN="mpirun -np 4 " 
  
# and run with 

make examples

#
#   - At ECMWF on cca
#

llsubmit  job_make_examples_CRAY_cca

#
# That's all for the basic INSTALLATION of the "MESONH PACKAGE"
#  

#
#  VII) "SCANDOLLAR" = SCRIPTING YOUR OWN PROCEDURES 
#  ====================================================

REM : not tested on 5-4-X version ...

# A small script 'scandollar' is in test in this version of MESONH.
# It will help you to build a complete chaining of an experiment. 
# The idea is to write some "template" scripts with '$VARIABLE' in the 
# Key point. Then 'scandollar' will parse this template files
# and generate the file with the variables evaluated ...
#
# First don't forget to load your "profile_mesonh..."
#
# So how it work  ...
#
#  Syntaxe 

export CONFEXP="YOUR_EXPERIMENT"
scandollar [list_directory]

# What is done :
#
#   for all (directory) in [liste directory]
#   go to this (directory)
#    - read the environnement variable in the user 'confdollar' file 
#    - read the default environnement variable for this 'machine' in ${CONF_DOLLAR}
#    - parse all the '*.ihm' file and put the transformed file 
#         (without extension in) in a new sub-directory '${CONFEXP}'
#
#  Without [list_directory] the current directory '.' is parsed . 
#
# As a demonstration the '16janvier Study Case' is build with this
# template script here :

$SRC_MESONH/MY_RUN/KTEST/007_16janvier_scandollar

#
# EXAMPLE :
# -------
#
# To parse only the first pgd step = directory '001_pgd1'

cd $SRC_MESONH/MY_RUN/KTEST/007_16janvier_scandollar/001_pgd1

export CONFEXP=512
scandollar

## OUTPUT ::

>#  read default config file :: --->  CONF_DOLLAR=/home/escj/DEV64/PACK-MNH-V5-4-2/conf/post/confdollar_aeropc_default
>#
>#  read    user config file :: --->  CONFIG=confdollar
>#
>#  processes file *.ihm and put them in ./512/ ::
>#          ---> run_prep_pgd_xyz.ihm =>  ./512/run_prep_pgd_xyz


#
# And to run this step 
#

cd $SRC_MESONH/MY_RUN/KTEST/007_16janvier_scandollar/001_pgd1/512
(qsub) run_prep_pgd_xyz # qsub on brodie 

# To parse all these steps 

cd $SRC_MESONH/MY_RUN/KTEST/007_16janvier_scandollar/
scandollar 0*

## OUTPUT ::
>#
>#  read default config file :: --->  CONF_DOLLAR=/home/escj/DEV64/PACK-MNH-V5-4-2/conf/post/confdollar_aeropc_default
>#
>#  read    user config file :: --->  CONFIG=confdollar
>#
>#  processes file *.ihm and put them in 001_pgd1/512/ ::
>#          ---> run_prep_pgd_xyz.ihm =>  001_pgd1/512/run_prep_pgd_xyz
...
>#  read    user config file :: --->  CONFIG=confdollar
>#
>#  processes file *.ihm and put them in 008_run2/512/ ::
>#          ---> run_mesonh_xyz.ihm =>  008_run2/512/run_mesonh_xyz
>#
...
>#  read    user config file :: --->  CONFIG=confdollar
>#
>#  processes file *.ihm and put them in 011_diaprog/512/ ::
>#          ---> run_diaprog.ihm =>  011_diaprog/512/run_diaprog


#
# The chaining of the differents steps is control by the "RMSHELL" variable .
# To inhibit put a "#" in it , eather in your current shell
# or in the 'confdollar' file .

export RMSHELL="#"

#
# Some 'predefine' variables are set in the '${CONF_DOLLAR}' default files
#   --> One file is defined by know-computer . 
#
#   Are included files for 'brodie' , 'vargas' , ( babel beta-test ) , 'c1a' , 'jade' & 'aeropc*' ( = default for unknown host )

export  CONF_DOLLAR=${SRC_MESONH}/conf/post/confdollar_aeropc_default

#
#   You could define your own default file and use it by setting
#   in your shell the  'CONF_DOLLAR' variable 
#   ( By default './configure' will set it for you in the profile_mesonh file ) 


#
#  ON GENCI PLATEFORM 
#  ------------------
# 
#  You will find my "own" personal installation of MESONH 
#  in the next directory . If you need only to run MESONH
#  without recompiliong new sources for MESONH, you could :
#
#  - source/load my own "profile_mesonh" without modification
# 
#  - and copy the scripts examples  with 

cp -R  007_16janvier_scandollar /.../your_directory
  
#

# 
# You could also copy only the differents "*/512"  sub-directory
# if you don't when ti use the "scandollar" script  .
#
# 
#   You will the need to change only information corresponding 
#   the location to your own path directory for the input/ouput data .
#  
#   So
#
#  - At IDRIS :
#    ==========
#
#  On Brodie
#  ---------
#
# use this "profile_mesonh" :

.  /home/rech/mnh/rmnh007/DEV/MNH-V5-4-2/conf/profile_mesonh-SX8-MNH-V5-4-2-MPIAUTO-O4

# And the examples are here ( link to my $WORKDIR in actually )  

/home/rech/mnh/rmnh007/DEV/MNH-V5-4-2/MY_RUN/KTEST/007_16janvier_scandollar

#
#  On vargas
#  ---------
#  use this "profile_mesonh" :

. /workgpfs/rech/mnh/rmnh007/DEV/MNH-V5-4-2/conf/profile_mesonh-AIX64-MNH-V5-4-2-MPIAUTO-O2

# and examples here :

/workgpfs/rech/mnh/rmnh007/DEV/MNH-V5-4-2/MY_RUN/KTEST/007_16janvier_scandollar

# 
#  - At CINES on JADE :
#    =================
#
# use 

. /work/escobar/DEV/MNH-V5-4-2/conf/profile_mesonh-LXifort-MNH-V5-4-2-MPIICE-O2

# and the exemples

/work/escobar/DEV/MNH-V5-4-2/MY_RUN/KTEST/007_16janvier_scandollar

#
#  - At ECMWF on cxa :
#    ===============
#
# use

. /c1a/ms_perm/au5/MNH-V5-4-2/conf/profile_mesonh-AIX64-MNH-V5-4-2-MPIAUTO-O2

# and the examples

/c1a/ms_perm/au5/MNH-V5-4-2/MY_RUN/KTEST/007_16janvier_scandollar


#
#  Good luck!!!
#

#
# VIII) TROUBLE-SHOOTING
# ======================
#
#
# a) "Segmentation violation" -> problem of "stack size" limit
# ------------------------------------------------------------
#
#  When running the examples coming with the MESONH package, if you obtain
#  a "segmentation violation" error it is probably a problem with
#  the "stack size" limit on your Linux computer ...
#
#  Check this limit with the command

ulimit -s

#  The limit is given in Kbytes and is often 8192 KB
#
#  ---> this mean only 8Mbytes for array in stack memory
#
#  It's a very low walue !!!
#
#  We recommend you to put it to "unlimited" in your
#  ".bashrc" or ".profile" like this

ulimit -s unlimited


#
# b) Compiler BUG with "ifort 10.0.xxx" 
# -------------------------------------
#
#   Some routines do not compile with
#   the version "10.0.XXX" of "ifort" ( at least until 10.0.023 )
#
#    Solution ---> Upgrade to ifort "10.1.015"
#
#   The ifort "10.1.008" has also some bug in the generation
#   of optimized 'vectorized SSE' code resulting in unpredictable
#   "Flaoting Point" error
#
#    Solution ---> compile the routine with problem with '-O1' option
#                  or upgrade to at least "10.1.015" version
#   
#
#
# IX) OPTIONAL COMPILATION
===========================
# a) MNH_FOREFIRE for forefire runs ( external package needed )
# -------------------------------------------------------------
#
#  If you want to use coupled(inline) run with FOREFIRE and MESONH
#  you could compile the interfaced/coupling routine by activating
#  this variable before any compilation

export MNH_FOREFIRE=1.0

# and then the configure 

./configure

#
# after this compile as usually
#

make
etc ...

#
# The FOREFIRE API package himself must be compiled independently from MesoNH
# The git repository is here https://github.com/forefireAPI/firefront/tree/2014.01
# it could be cloned by

git clone -b 2014.01 https://github.com/forefireAPI/firefront.git

# it depend on netcdf and scons for is compilation
# the "libForeFIre.so" generate must by referenced in the LD_LIBRARY_PATH
# or move/linked to the 'exe' directory of MesoNH
#    

# see d) for cleaning previously version if needed

# b) MNH_RTTOV for optional radiative computation
# --------------------------------------
#
# The RTTOV package was not included into the open source version of Meso-NH
# because it needs a licence agrement.
#
# ----------------------------------
# OPTION 1: Use version 11.3 of RTTOV 
# -----------------------------------
# Download the RTTOV package rttov113.tar.gz by following the instructions given on http://nwpsaf.eu/site/software/rttov/
#
# Install the RTTOV package rttov113.tar.gz
cd MNH.../src/LIB
mkdir RTTOV-11.3
cd RTTOV-11.3
tar xvfz rttov113.tar.gz
cd src
make ARCH=ifort        # Use Intel "ifort" compiler; other options: gfortran, NAG, pgf90, IBM
#
# And then for the compilation, run the 'configure' script preceded with the setting of the MNH_RTTOV variable:
#

cd MNH.../src/
export MNH_RTTOV=1
export VER_RTTOV=11.3
./configure

etc ...

# ----------------------------------
# OPTION 2: Use version 8.7 of RTTOV 
# ----------------------------------
# For already(old) licencied MesoNH users (MNH-4-X version with research licence see here: http://mesonh.aero.obs-mip.fr/mesonh410/UserInformation)
#
# the package could be reloaded in this way  
#
# - With cvs access
#

cd MNH.../src/LIB
cvs up -rPACK-MNH-V4-10-3 -d -P RTTOV

#
# - With WEB access (with WEB login/pass as usually) the RTTOV package could also be retrieve in tarball with wget like this:
#

cd MNH.../src/LIB
wget --http-user=USER  --http-password=PASS 'http://mesonh.aero.obs-mip.fr/cgi-bin/mesonh_interne/viewcvs.cgi/MNH-VX-Y-Z/src/LIB/RTTOV/?view=tar&pathrev=PACK-MNH-V4-10-3' -O RTTOV.tar.gz
tar xvfz RTTOV.tar.gz

# /!\ don't forget the ''.  Otherwise, this will not work!

#
# And then for the compilation, run the 'configure' script preceded with the setting of the MNH_RTTOV variable:
#

cd MNH.../src/
export MNH_RTTOV=1
export VER_RTTOV=8.7
./configure

etc ...

# c) MNH_ECRAD for optional compilation of new ECRAD radiative library from ECMWF