- Timestamp:
- 2019-01-22T17:31:57+01:00 (5 years ago)
- Location:
- NEMO/trunk
- Files:
-
- 2 edited
Legend:
- Unmodified
- Added
- Removed
-
NEMO/trunk/INSTALL.rst
r10279 r10557 6 6 :local: 7 7 8 Dependencies 9 ============ 10 11 | The NEMO source code is written in Fortran 95 and part of its dependencies are already included (``./ext``): 12 AGRIF preprocessing program "conv", FCM build system and IOIPSL library for outputs. 13 | And some Perl 5, Fortran compiler (ifort, gfortran, pgfortran, ...), MPI library (Open MPI or MPICH) 14 15 But The following dependencies should be from the official repositories of your Linux distribution but 16 you will probably have to compile them from source for enabling parallel I/O support. 17 18 - `HDF5`_ (C library) 19 - `NetCDF`_ (C and Fortran libraries) 20 21 Extract the source code 22 ======================= 23 24 Download the source code 25 ------------------------ 8 Prerequisites 9 ============= 10 11 - The NEMO source code is written in Fortran 95 and some of its prerequisite 12 tools and libraries are already included in the (``./ext``) subdirectory. These 13 include: the AGRIF preprocessing program "conv"; the FCM build system and the 14 IOIPSL library for parts of the output. 15 | 16 - Other requirements that your system needs to provide include: a Perl 5 interpreter; a modern 17 Fortran compiler (ifort, gfortran, pgfortran, ...) and (in most cases) a MPI library 18 (e.g. OpenMPI or MPICH). The latter is not strictly essential since it is possible 19 to compile and run NEMO on a single processor. However most realistic configurations 20 will require the parallel capabilities of NEMO and these use the Message Passing 21 Interface (MPI) library. NEMO v4.0, by default, uses some MPI features introduced 22 into the MPI-3 standard. On older systems, that do not support these features, 23 the key_mpi2 preprocessor key should be used at compile time. This will limit MPI 24 features to those defined within the MPI-2 standard (but will lose some performance 25 benefits). 26 | 27 The following prerequisites may already be installed or be available from the 28 official repositories of your Linux distribution. However access to all the 29 options available with the XIOS IO-server will require the parallel form of the 30 netcdf4 library and its underlying HDF5 library. It is also necessary to compile 31 these libraries with the same version of the MPI library that both NEMO and XIOS 32 (see below) are compiled and linked with. To satisfy these requirements, it is common 33 to have to compile the following from source. 34 35 - `HDF5`_ (C library) (use: --enable-fortran --enable-parallel with configure) 36 - `NetCDF4`_ (C and Fortran libraries) 37 38 Note that particular versions of these libraries may have their own 39 restrictions. For example, the latest versions of the netCDF libraries: 40 netcdf-c-4.6.2 and netcdf-fortran-4.4.4, state the following requirements for netCDF-4 support: 41 42 * HDF5 1.8.9 or later. 43 * HDF5 1.10.1 or later. 44 * zlib 1.2.5 or later (for netCDF-4 compression) 45 * curl 7.18.0 or later (for DAP remote access client support) 46 47 | 48 `Important Note: When building netCDF-C library versions older than 4.4.1, 49 use only HDF5 1.8.x versions. Combining older netCDF-C versions with newer 50 HDF5 1.10 versions will create superblock 3 files that are not readable by 51 lots of older software.` 52 53 Extract and install XIOS 54 ======================== 55 56 With the sole exception of running NEMO in mono-processor mode (in which case 57 output options are limited to those supported by the IOIPSL library), diagnostic 58 outputs from NEMO are handled by the third party XIOS library. This can be used 59 in two different modes: 60 61 * attached - Every NEMO process also acts as a XIOS server 62 * dettached - Every NEMO process runs as a XIOS client. Output is collected and collated by external, 63 stand-alone XIOS server processors. 64 65 In either case, it is important to note that XIOS needs to be compiled before 66 NEMO, since the libraries are needed to successfully create the NEMO executable. 67 68 Instructions on how to obtain and install the software can be found on the `XIOS Wiki`_ . 69 70 It is recommended to use XIOS version 2.5 with NEMOv4.0. This version should be more stable (in terms of 71 future code changes) than the XIOS trunk. It is also the version used by the NEMO system team when 72 testing all developments and new releases. This particular version has its own branch and can be 73 checked out and downloaded with: 74 75 .. code:: console 76 77 $ svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5 78 79 Download the NEMO source code 80 ============================= 26 81 27 82 .. code:: console … … 52 107 | | - ``NST``: AGRIF for embedded zooms | 53 108 | | - ``OCE``: |OPA| for ocean dynamics | 54 | | - `` MBG``: |TOP| for tracers |109 | | - ``TOP``: |TOP| for tracers | 55 110 +-----------+------------------------------------------------------------+ 56 111 | ``tests`` | :doc:`Test cases <test_cases>` (unsupported) | … … 58 113 | ``tools`` | :doc:`Utilities <tools>` to [pre|post]process data | 59 114 +-----------+------------------------------------------------------------+ 60 61 Extract and install XIOS62 ========================63 64 Diagnostic outputs from NEMO are handled by the third party XIOS library.65 66 Important notice: XIOS needs to be compiled before NEMO, since the libraries are needed to successfully create NEMO executable.67 Instructions on how to obtain and install the software, see Users/Model Interfacing/Inputs Outputs.68 69 When you compile NEMO you will need to specify the following CPP keys:70 71 key_iomput72 key_mpp_mpi (if you want to run with multiple processes and/or use "detached mode" for the IOs system XIOS)73 for nemo_v3_6_STABLE only: you can add key_xios2 if you wish to use the most recent XIOS2 release of XIOS. Doing so, you will have to change the xml files used as input for XIOS : in this release, the xml files are only XIOS1 compatible. If you add key_xios2 you can use xml files located in GYRE_XIOS/EXP00 as first templates. In future releases of NEMO XIOS2 will be the default XIOS release in use.74 115 75 116 Setup your architecture configuration file 76 117 ========================================== 77 118 78 All compiler options in NEMO are controlled using files in NEMOGCM/ARCH/arch-'my_arch'.fcm where 'my_arch' is the name of the computing architecture. 79 It is recommended to copy and rename an configuration file from an architecture similar to your owns. You will need to set appropriate values for all of the variables in the file. In particular the FCM variables %NCDF_HOME, %HDF5_HOME and %XIOS_HOME should be set to the installation directories used for XIOS installation. 80 81 %NCDF_HOME /opt/local 82 %HDF5_HOME /opt/local 83 %XIOS_HOME /Users/$( whoami )/xios-1.0 84 %OASIS_HOME /not/defined 119 All compiler options in NEMO are controlled using files in 120 NEMOGCM/ARCH/arch-'my_arch'.fcm where 'my_arch' is the name of the computing 121 architecture. It is recommended to copy and rename an configuration file from 122 an architecture similar to your owns. You will need to set appropriate values 123 for all of the variables in the file. In particular the FCM variables: 124 ``%NCDF_HOME``; ``%HDF5_HOME`` and ``%XIOS_HOME`` should be set to the 125 installation directories used for XIOS installation. 126 127 .. code-block:: sh 128 129 %NCDF_HOME /opt/local 130 %HDF5_HOME /opt/local 131 %XIOS_HOME /Users/$( whoami )/xios-2.5 132 %OASIS_HOME /not/defined 85 133 86 134 Compile and create NEMO executable … … 115 163 Folder intended to contain your customised routines (modified from initial ones or new entire routines) 116 164 165 When you compile NEMO you will need to specify the following CPP keys: 166 167 * key_iomput 168 * key_mpp_mpi 169 117 170 After successful execution of makenemo command, the executable called opa is created in the EXP00 directory (in the example above, the executable is created in CONFIG/MY_GYRE/EXP00). 118 171 More options … … 179 232 180 233 .. _HDF5: http://www.hdfgroup.org/downloads/hdf5 181 .. _NetCDF: http://www.unidata.ucar.edu/downloads/netcdf 234 .. _NetCDF4: http://www.unidata.ucar.edu/downloads/netcdf 235 .. _XIOS Wiki: http://forge.ipsl.jussieu.fr/ioserver/wiki/documentation 236 .. _XIOSSRC: http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5 -
NEMO/trunk/doc/rst/source/global.rst
r10279 r10557 18 18 .. _CMCC: http://www.cmcc.it 19 19 .. _CNRS: http://www.cnrs.fr 20 .. _Mercator Oc éan: http://www.mercator-ocean.fr20 .. _Mercator Ocean: http://www.mercator-ocean.fr 21 21 .. _Met Office: http://www.metoffice.gov.uk 22 22 .. _MOI: http://www.mercator-ocean.fr
Note: See TracChangeset
for help on using the changeset viewer.