----------------------------------------------------------------------
SDAP - SEQUOIA Data Assimilation Platform
A SIROCCO community code
(GNU GPL) P. De Mey 1999-2017 all versions
----------------------------------------------------------------------
LICENSING INFORMATION
----------------------------------------------------------------------
The latest SDAP code for UnixTM and Linux is available from the
repository of the project's web page http://sequoia-dap.sourceforge.net.
The present document, and the SDAP system components in their present
and future versions are distributed under the GNU General Public
License (GPL). Do not remove the following notice:
**** COPYRIGHT NOTICE -- DO NOT DISSOCIATE FROM SOFTWARE ****
** SDAP Copyright 1999-2017 Pierre De Mey demey-redir@neyak.org
**
** SDAP is free software; you can redistribute it and/or
** modify it under the terms of the GNU General Public License
** as published by the Free Software Foundation; either version 2
** of the License, or (at your option) any later version.
**
** This program is distributed in the hope that it will be useful,
** but WITHOUT ANY WARRANTY; without even the implied warranty of
** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
** GNU General Public License for more details.
**
** You should have received a copy of the GNU General Public License
** along with this program; if not, write to the Free Software
** Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
** MA 02110-1301, USA.
----------------------------------------------------------------------
CODE REPOSITORY
----------------------------------------------------------------------
The SDAP project main page is http://sequoia-dap.sourceforge.net/.
The code can be downloaded from there by means of an SVN client.
An experimental public clone repository (not always up-to-date) is
https://https://github.com/pdemey/sequoia-dap-code/ .
----------------------------------------------------------------------
DOCUMENTATION
----------------------------------------------------------------------
The code license is in 'gpl.htm'.
The documentation is in 'etc/doc/'.
A regularly updated Users Guide is in 'etc/doc/sdap-users-guide.html'.
A not so regularly updated Manual is in 'etc/doc/sdap-manual.pdf'.
The Release Notes are a bit further down.
A list of targets for the Makefile is included near the beginning of
the main Makefile.
----------------------------------------------------------------------
GETTING STARTED
----------------------------------------------------------------------
Download and install the current build:
(1) open an account on Sourceforge
(2) svn checkout svn://svn.code.sf.net/p/sequoia-dap/code/ sdap
(3) 'cd sdap'
(4) 'make newconfig' and select a configuration
(5) edit 'sdap.conf' and review the default choices
(6) 'make'
It is recommended to do 'svn update' from time to time. If you open an
account on the Sourceforge page and subscribe to sequoia-dap, you will
receive e-mail announcements of all commits. You can then decide to
update your local copy after important commits of bug fixes.
You might also get SDAP from tarballs, although this distribution
method is deprecated:
(1) unpack the SDAP-tree tarball (tar xzf SDAP-tree-verXXX.tgz)
(2) move the other *.tgz packages in the components/ directory
(3) 'make unpackall'
(4-6) follow steps (4-6) above.
The Users Guide is in 'etc/doc/sdap-users-guide.html'.
You can open a ticket on Sourceforge for any special requests or bug
reports.
----------------------------------------------------------------------
A SHORT MEMO ON SDAP DIRECTORIES
----------------------------------------------------------------------
In the configuration file 'sdap.conf', used for compilation:
SRCDIR Directory where the SDAP Makefile is launched
BINDIR Directory where SDAP creates executables
In the launch script 'launch.sh', used for execution:
LAUNCH_DIR Directory where 'launch.sh' is launched
ROOT_EXE_DIR General root directory for SDAP execution
JOB_EXE_DIR Root directory for this job execution (under ROOT_EXE_DIR)
MEMBER_EXE_DIR Execution directory for this member (under JOB_EXE_DIR)
SDAP_BIN_DIR Directory where the SDAP executable resides (=BINDIR above)
SDAP_BIN_NAME Name of the SDAP executable (=name of kernel, usually)
----------------------------------------------------------------------
RELEASE NOTES
----------------------------------------------------------------------
::::1.5::::
Current working version. Jointly developed by Pierre De Mey and
Malek Ghantous under AMICO project funding. Developers for the
scrumcat tool are PDM, Marios Kailas and Vassilis Vervatis.
MAIN OBJECTIVES OF THIS VERSION:
- a first implementation of the SDAP/NEMO interface
- a better SDAP/BELUGA-S.26 interfacing, with optional correction of the
open boundaries
- adherence to AMICO specifications
- adherence to more modern coding rules
- a generally consolidated code and documentation
- bug fixes.
WHAT HAS CHANGED:
- Many things done but not documented here for lack of time
- Sampling rate modification/decimation mechanism for input data
- NetCDF data loader
- Standardized ocean data types (physics/bgc/air-sea interface)
- A new ulib has been created for the 'scrumcat' tool (CMEMS/SCRUM) including
a partial implementation of a NEMO interface
- Run modes: free, assim, pseudo
- A new ulib has been created for S.26
- The code name is now 'SDAP' for 'SEQUOIA Data Assimilation Platform'
-- this is reflected everywhere, e.g. the configuration file is now
'sdap.conf' (was 'sequoia.conf')
- The format of the 'sdap.conf' file is different -- when upgrading from a
previous 'sequoia.conf': (1) choose a configuration in etc/conf/ and copy
the chosen 'sdap.conf' to the root directory, and (2) adapt that file to
match your previous 'sequoia.conf' settings
- The 'sdap.conf' file is not versioned any more -- therefore user
customizations are kept
- The documentation has been upgraded and homogenized
- Everything has been translated to free-format .F90 and tested
- Many improvements and several bug fixes
- The former shak and sap components have been moved to a unique SDAP library
- The etc/ directory contains the configuration files, the documentation, and
ancillary files
- The etc/conf directory contains configuration files for several configurations
-- new configurations can be added and versioned as needed
- The WORKDIR macro in sdap.conf and AK_WD variable in launch.sh had similar
names while meaning different things; WORKDIR has been renamed BINDIR, i.e.,
the directory where the SDAP Makefile creates its executables
- The directory names in 'sdap.conf' and 'launch.sh' have been changed so that
they are much easier to understand and more consistent. A short memo on
directories has been added to this README file.
WHAT WILL CHANGE:
- More changes pending
WHAT DOES NOT CHANGE:
- The user experience is almost identical to the previous versions
Code repository: https://sourceforge.net/p/sequoia-dap/code/HEAD/tree/branches/1.5/
::::1.4::::
Merged evolutions of the 1.2 branch with SEQUOIA/SYMPHONIE coupler and
some "experimental" elements from the 1.3 branch.
Added handling of pseudo-observations and modified the command line
accordingly.
Added MPI support via the ASEYA library.
Code repository: https://sourceforge.net/p/sequoia-dap/code/HEAD/tree/branches/1.4/
::::1.2.3::::
This version handles the selection of the SEQUOIA working directory.
Code repository: none (available by special request)
::::1.2.2::::
Changed behavior of the 'make install' target and added standalone
installer for /bin/bash (if available).
Code repository: none (available by special request)
::::1.2.1::::
The OLA subsystem has been reorganized.
The main Makefile now makes modules for the User Library as well. Therefore
the ULIB must be able to 'make modules'.
Code repository: https://sourceforge.net/p/sequoia-dap/code/HEAD/tree/branches/1.2.1sirocco1/
::::1.2::::
Initial release with Ensemble-based DA.
This is compatible only with versions 1.2 of the components since the
main Makefile has been modified to make all MODULEs first (except for the
ulibs). However a version 1.0 tree should be able to make everything for
1.2 components.
'make' without arguments makes 'config cleanall modules libs launcher',
i.e. all you want to make usually.
'make install' unpacks any existing tarballs in place in the components
repository. Clearly this is a start and we need to make further steps
towards automatic installation in the future.
A few changes in sequoia.conf:
- The options for g95 have been added.
- The new template is meant to be more error-proof (it should be harder
to link a kernel with a ulib made for another kernel).
- Default parameter file for the BELUGA kernel added.
Code repository: none (available by special request)
::::1.0::::
A few changes in sequoia.conf:
- The macro SHAK has been added. It should point to the kernel shared
library.
- The macro AKERN-TEST has been removed. The kernel tests can be made
by specifying the corresponding package under the ULIB macro. The Makefile
has been changed accordingly.
The Makefile and the test files (test-*.prm) have been updated.
Code repository: none (available by special request)
::::0.98::::
- There are a few changes in sequoia.conf. In particular only the NAMES
of components should now be given (no path). Also the work directory can
now be specified. It can be located outside the SEQUOIA directory hierarchy
(e.g. on the disk where the model is run, which can be different from the
disk where sources reside).
- In this version the launcher (executable) is 'made' in ULIB, not in SAP
anymore. One given ULIB can 'make' several launchers. As a consequence
the variable LAUNCHER has been added in sequoia.conf and must be set.
This version of sequoia-tree is therefore incompatible with pre-0.98
versions of the components. It is the first version to be compatible
with the new sofa kernel.
- 'make cleanall' now 'makes clean' everywhere but does not do
'make unlink' anymore.
::::0.97::::
- cosmetic changes
::::0.92::::
- make config now updates links
::::0.91::::
::::0.90::::
Initial release. Not all functions implemented.
Compilation order: akern, sap, ulib, then the launcher. This is a bit
complicated and may be simplified in the future.
