178 lines
7.4 KiB
TeX
178 lines
7.4 KiB
TeX
The whole package, containing the models ``Planet Simulator'' and ``PUMA''
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along with the {\bf mo}del {\bf st}arter ``most''.
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The following subsection shows the commands to use for installation,
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assuming your downloadfile is named ```Most17.tgz´´´. For other
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formats like zip use unzip instead of tar.
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\section{Quick Installation}
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\begin{verbatim}
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tar -zxvf Most17.tgz
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cd Most17
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./configure.sh
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./most.x
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\end{verbatim}
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If your tar command doesn't support the ``-z'' option (e.g. on SOLARIS),
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type instead:
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\begin{verbatim}
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gunzip Most17.tgz
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tar -xvf Most17.tar
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cd Most17
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./configure.sh
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./most.x
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\end{verbatim}
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If this sequence of commands produces error messages,
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consult the FAQ (Frequently Asked Questions) and the README files
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in the Most17 directory. They are in plain text files that can be read with
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the more command or any other text editor.
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\section{Most17 directory }
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\begin{verbatim}
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home/Most17> ls -lg
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-rw-r--r-- 3730 FAQ <- Frequently Asked Questions
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-rw-r--r-- 7862 NEW_IN_VERSION_17 <- New in this version
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drwxr-xr-x 748 Plasim_RM_17 <- LaTeX source for RM
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drwxr-xr-x 612 Plasim_UG_17 <- LaTeX source for UG
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drwxr-xr-x 1122 Puma_UG_17 <- LaTeX source for UG
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-rw-r--r-- 718 README <- Read this first
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-rw-r--r-- 617 README.md <- File for download page
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-rw-r--r-- 1226 README_COUPLING_PLASIM_PUMA <- sic
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-rw-r--r-- 168 README_MAC_USER <- Notes for MAC user
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-rw-r--r-- 462 README_UBUNTU <- Notes for UBUNTU user
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-rw-r--r-- 698 README_WINDOWS_USER <- Notes for Windows user
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-rw-r--r-- 1548 cc_check.c <- Used by configure script
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-rwxr-xr-x 57 cleanplasim <- Empty run, bld and bin for PLASIM
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-rwxr-xr-x 51 cleanpuma <- Empty run, bld and bin for PUMA
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-rwxr-xr-x 48 cleansam <- Empty run, bld and bin for SAM
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-rwxr-xr-x 161 cmdpuma <- Build GUI-less PUMA
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-rwxr-xr-x 5611 configure.sh <- Configure script (for bash shell)
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-rw-r--r-- 308 csub.c <- Used by configure script
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-rw-r--r-- 234 f90check.f90 <- Used by configure script
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drwxr-xr-x 102 images <- Most images
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-rw-r--r-- 81 make_most <- Used by configure script
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-rw-r--r-- 154 makecheck <- Used by configure script
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-rw-r--r-- 108 makedebug <- Used by configure script
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-rw-r--r-- 84 makefile <- Makefile for building most.x
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-rw-r--r-- 113461 most.c <- C source code for most
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drwxr-xr-x 306 plasim <- Planet Simulator directory tree
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drwxr-xr-x 238 postprocessor <- Postprocessor source and docs
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drwxr-xr-x 306 puma <- PUMA directory tree
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drwxr-xr-x 510 sam <- SAM directory tree
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drwxr-xr-x 680 tools <- Some tools
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\end{verbatim}
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The directory structure must not be changed! Even empty directories must be
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kept as they are, because the Most program relies on their existence!
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For each model, currently ``Planet Simulator'', ``SAM'', and ``PUMA'', a directory exists
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(plasim or sam or puma) with the following subdirectories:
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\begin{verbatim}
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Most17/puma> ls -lg
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drwxr-xr-x 2 128 bin <- model executables
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drwxr-xr-x 2 1824 bld <- build directory
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drwxr-xr-x 2 280 dat <- initial and boundary data
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drwxr-xr-x 2 80 doc <- documentation, user's guide, reference manual
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drwxr-xr-x 2 928 run <- run directory
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drwxr-xr-x 2 1744 src <- source code
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\end{verbatim}
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After installation only ``dat'', ``doc'' and ``src'' contain files.
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All other directories are empty.
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``MoSt'' (the executable is named most.x) is used to define parameters,
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build the model, create a runscript and optional start the model.
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The directories of the model are used in the following manner:
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\section{Model build phase}
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Most writes an executable shell script to the ``bld'' directory
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and then executes it.
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First, it copies all necessary source files from ``src'' to ``bld''
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and modifies them according to the selected parameter configuration.
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Modification of source code is necessary for vertical and horizontal
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resolution changes, and when using more than one processor (parallel program
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execution). The original files in the ``src`` directory are not changed by MoSt.
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The program modules are then compiled and linked using the make command,
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also issued by MoSt. MoSt provides two different makefiles:
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one for the single CPU version and the other for the parallel version
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(using MPI, the Message Passing Interface).
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For Planet Simulator the resolution and CPU parameters are coded into the filename of the
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executable, in order that there are different names for different versions.
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E.g. the executable ``most\_plasim\_t21\_l10\_p2.x''
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is an executable compiled for a horizontal resolution of T21,
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a vertical resolution of 10 levels and 2 CPU's.
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PUMA and SAM use universal executables, that can be used for different
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resolutions, because they use dynamical array allocation at runtime.
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The executable is copied to the model's ``bin'' directory
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at the end of the build.
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Rebuilding may be forced by using the {clean\modir} command
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in the most directory.
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The build directory is not cleared after usage. The user may want
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to modify the makefile or the build script for his own purposes
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and start the building directly by executing the ``most\_\modir\_build''
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script.
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For permanent user modifications,
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the contents of the ``bld'' directory has to be copied elsewhere,
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because each usage of MoSt overwrites its contents.
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\section{Model run phase}
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After building the model with the selected configuration,
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MoSt writes or copies all the necessary files to the model's
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``run'' directory. These are the executable, initial and boundary data,
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namelist files containing the parameter, and finally the
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run script itself. Depending on the exit selected from MoSt,
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either ``Save \& Exit'' or ``Run \& Exit'', the run script is started
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from MoSt and takes control of the model run. A checkmark on
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GUI invokes the Graphical User Interface allowing the user to control
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and display variables during the run.
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Again, all the contents of the ``run'' directory are subject to change
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by the user. However, it is better to save the changed run setups
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in other user-created directories, because each usage of
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MoSt will overwrite the contents of the run directory.
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Alternatively, the user changed files could be renamed,
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because MoSt always generates files with names beginning with ``most\_''
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and leaves any other files untouched.
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\section{Running long simulations}
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For long simulations create a new directory on a file system
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that has enough free disk space to store the results.
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You can use the ``df'' command to check file systems.
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Hint 1: Do not use your home directory if there are file quotas.
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Your run may crash due to file quota being exceeded.
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Hint 2: If possible use a local disk for long runs.
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Network attached storage runs fine, but may slow down the model.
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Example:
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\begin{itemize}
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\item cd Most17
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\item ./most.x
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\item Select model and resolution
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\item Switch GUI off
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\item Switch Output on
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\item Edit number of years to run
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\item Click on ``Save \& Exit''
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\item Make a directory, e.g. mkdir /data/longsim
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\item cp {\modir/run/*} /data/longsim
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\item cd /data/longsim
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\item Edit the experiment name in most\_\modir\_run
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\item Edit the namelist files if necessary
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\item Start the simulation with most\_\modir\_run \&
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\end{itemize}
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