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NCEPLIBS

Introduction

This is a collection of libraries commonly known as NCEPLIBS that are required for several NCEP applications, e.g., UFS, GSI, UPP, etc. For general information about NCEPLIBS, the user is referred to the Wiki.

For full documentation of each package see https://noaa-emc.github.io/NCEPLIBS/.

For installing NCEPLIBS on NOAA HPC systems, see the documentation for the spack-stack project. The documentation provides instructions for using spack-stack to build software stacks from scratch, as well as to build stacks that are chained to existing environments in order to re-use dependencies already provided by official spack-stack deployments. Note that users are recommended to use existing spack-stack installations as much as possible when using NOAA R&D systems, and to use spack-stack as much as possible when developing for applications that spack-stack is intended to support, namely, UFS applications, Global Workflow, and JEDI applications (i.e., users developing the UFS Weather Model on a personal machine are recommended to use their own installation of spack-stack). Outside of these platforms and applications, users are recommended to install NCEPLIBS either through CMake or through regular Spack (not spack-stack); see instructions below.

NCEPLIBS is comprised of the following libraries:

NCEP library Spack package name Description
NCEPLIBS-bacio bacio Binary I/O for the NCEP models
NCEPLIBS-bufr bufr Working with the BUFR format
NCEPLIBS-g2 g2 Coding/decoding GRIB2 messages
NCEPLIBS-g2c g2c C decoder/encoder routines for GRIB edition 2
NCEPLIBS-g2tmpl g2tmpl Utilities for GRIB2 templates
NCEPLIBS-gfsio gfsio Convert GFS Gaussian output into grib output
NCEPLIBS-ip ip General interpolation library
NCEPLIBS-landsfcutil landsfcutil Initializing land-surface states
NCEPLIBS-ncio ncio Read the GFS forecast files
NCEPLIBS-nemsio nemsio I/O for the NCEP models using NEMS
NCEPLIBS-nemsiogfs nemsiogfs I/O for the NEMS-GFS model
NCEPLIBS-sfcio sfcio Surface files I/O
NCEPLIBS-sigio sigio I/O on the sigma restart file of the global spectral model
NCEPLIBS-w3emc w3emc Decoder/encoder routines for GRIB edition 1
NCEPLIBS-wrf_io wrf-io Lightweight WRF-IO API library for Unified Post Processor (UPP)

The NCEPLIBS-w3nco, NCEPLIBS-ip2, and NCEPLIBS-sp libraries ('w3nco', 'ip2', and 'sp' in Spack, respectively) are deprecated. NCEPLIBS-w3emc replaces NCEPLIBS-w3nco, and NCEPLIBS-ip replaces NCEPLIBS-ip2 and NCEPLIBS-sp.

The following projects are also related to the NCEPLIBS project:

Required Software

  • A supported C/C++ and Fortran compiler (see table below). Other versions may work, in particular if close to the versions listed below.
Compiler vendor Supported (tested) versions
Intel 18.0.3.222, 18.0.5.274, 19.0.2.187, 19.0.5.281, 19.1.0.166
GNU 8.3.0, 9.X.0
  • A supported MPI library (see table below). Other versions may work, in particular if close to the versions listed below.
MPI library Supported (tested) versions
MPICH 3.3.1, 3.3.2
MVAPICH2 2.3.3
Open MPI 3.1.5, 4.0.2
Intel MPI 2018.0.4, 2019.6.154, 2020.0.166
SGI MPT 2.19
  • A software stack consisting of the following third-party libraries, compiled with the same compiler and MPI library (where applicable). Other versions may work, in particular if close to the versions listed below. To install the third-party libraries needed by NCEPLIBS, see NCEPLIBS-external.
Library Supported (tested) versions
CMake cmake-3.16.3
zlib zlib-1.2.11
libpng libpng-1.6.35
libjpeg jpeg-9.1
Jasper jasper-2.0.16
HDF5 hdf5-1.10.4
NetCDF netcdf-c-4.7.3, netcdf-fortran-4.5.2

The NCEPLIBS-external project provides an convenient way to install the required third-party libraries on supported platforms such as generic Linux/macOS systems.

Obtaining, Building, and Using NCEPLIBS

With Spack

All of the NCEPLIBS can be installed through the Spack package manager. One significant benefit of using Spack is that it will automatically install any dependencies needed, including CMake, or even compilers. See the Spack documentation for details of configuring and executing Spack installations. Spack also has extensive capabilities including source and build caching, parallel installation, dynamically generating Tcl and Lmod environment modules, and creating Docker and Singularity container images.

In the simplest case, with the spack command loaded into the current environment, run, for example, spack install ip to install the latest release of the NCEPLIBS-ip library along with any needed dependencies. See the above table for each package's name in Spack. The develop branch for each library can be installed by specifying the 'develop' version, i.e., spack install w3emc@develop.

Here is a typical set of steps for installing and using NCEPLIBS using Spack, assuming that Spack's prerequisites are already installed:

git clone https://github.com/spack/spack
. spack/share/spack/setup-env.sh # assuming bash, zsh, or dash shell
spack external find cmake gmake # find external packages to save time
spack install ip@develop precision=4 ^[email protected] precision=4
spack load ip

The spack load command configures the $CMAKE_PREFIX_PATH variable, in this example making the ip library available to downstream CMake builds.

For any bugs or other issues with Spack-based installations, such as incorrect dependencies in a package's recipe, please file an issue under the appropriate NCEPLIBS repository.

With CMake

External dependencies

See NCEPLIBS-external for building external dependencies.

Obtaining the code

Clone the repository:

git clone https://github.com/NOAA-EMC/NCEPLIBS

Building the libraries

CMake employs an out-of-source build. Create a directory for configuring the build and cd into it:

mkdir -p build && cd build

Set the compilers, if needed, to match those being used for compiling the third-party libraries listed above: FC, CC, and CXX environment variables can be used to point to the desired Fortran, C, and C++ compilers.

Execute cmake from inside your build directory.

cmake -DCMAKE_INSTALL_PREFIX=<nceplibs-prefix> ../NCEPLIBS

If the third-party libraries are not located in a path recognized by cmake e.g. /usr/local, it may be necessary to provide the appropriate environment variables e.g. <package_ROOT> or CMAKE_PREFIX_PATH so that cmake is able to locate these dependencies.

The installation prefix for NCEPLIBS is provided by the cmake command-line argument -DCMAKE_INSTALL_PREFIX=<nceplibs-prefix>

To build and install:

make -j<x>

This will build and install all the NCEPLIBS and place them into the installation prefix <nceplibs-prefix>.

Additional cmake command-line options while configuring NCEPLIBS:

-DFLAT=ON|OFF - determines the installation tree heirarchy

-DDEPLOY=ON|OFF - prepares and deploys Lua modulefiles for each of the NCEPLIBS libraries. To deploy modulefiles:

make deploy

LMod Environment module system is required to load/unload these modules.

Some HPC systems use Tcl based Environment modules. NCEPLIBS provides a means to deploy Tcl module files and can be exercised as follows:

-DTCLMOD=ON - enables option to change Lua modulefiles to Tcl modulefiles for each of the NCEPLIBS libraries. To make the change:

make tcl

On machines that do not provide access to Github, a DOWNLOAD_ONLY and USE_LOCAL option is provided. To download the NCEPLIBS without building them use the cmake command line option -DDOWNLOAD_ONLY=ON. This will download all the NCEPLIBS in a local download folder. make tarball will tar and zip this folder into nceplibs.tgz which can then be transferred to the machine without GitHub access. Untar the tarball, and use the cmake command line option USE_LOCAL as -DUSE_LOCAL=ON. This will use the source code from the download directory.

Usage

NCEPLIBS can be used in any application that uses cmake to configure and build by adding -DCMAKE_PREFIX_PATH=<nceplibs-prefix> to the cmake command line during configuration. Note that if NCEPLIBS are installed through Spack, loading the packages, either through Spack-built environment modules or using the spack load command, will populate the $CMAKE_PREFIX_PATH environment variable with the appropriate paths.

Disclaimer

The United States Department of Commerce (DOC) GitHub project code is provided on an "as is" basis and the user assumes responsibility for its use. DOC has relinquished control of the information and no longer has responsibility to protect the integrity, confidentiality, or availability of the information. Any claims against the Department of Commerce stemming from the use of its GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.

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