Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Feature 2588 install rewrite #2791

Merged
merged 78 commits into from
Jan 22, 2024
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
78 commits
Select commit Hold shift + click to select a range
05c8b5d
updated first 3 sections
j-opatz Aug 21, 2023
fdc087b
updated spacing
j-opatz Aug 21, 2023
a59dffd
adding the Environment Variables to Run Script section
lisagoodrich Aug 21, 2023
a0c59c9
adding in the remainder of the google doc changes
lisagoodrich Aug 21, 2023
0f4f607
trying to fix duplicate explicit target name issue
lisagoodrich Aug 22, 2023
25d4e95
fixing required_external_libraries_to_build_met links
lisagoodrich Aug 22, 2023
257d15d
HDF4 testing double underscore
lisagoodrich Aug 23, 2023
ad36ae2
adding double underscores for HDF5 and HDF-EOS2 and changing library …
lisagoodrich Aug 23, 2023
abedb69
fixing HDF5 web link name
lisagoodrich Aug 23, 2023
77a2595
Added formatting, made minor edits, removed manual build instructions…
jprestop Aug 23, 2023
c3d5449
Removed reference to sample-test-case which no longer exists
jprestop Aug 23, 2023
3537332
Resolving errors
jprestop Aug 23, 2023
9be671a
Minor formatting change
jprestop Aug 23, 2023
cc3e403
Updated apptainer instructions, new version references
j-opatz Aug 24, 2023
52987fe
Formatting updates and removal of first person language
jprestop Aug 24, 2023
42e9ccb
fixed code blocks
j-opatz Aug 24, 2023
d268dbb
Formatting updates and removal of first person language
jprestop Aug 24, 2023
4c1f678
Merge branch 'feature_2586_install_rewrite' of github.com:dtcenter/ME…
jprestop Aug 24, 2023
62f4003
Resolving error
jprestop Aug 24, 2023
3f27898
Removed first person references
jprestop Aug 24, 2023
5c61e36
Removed reference to met_directory_structure
jprestop Aug 24, 2023
7459e74
updated bolding, removed end section
j-opatz Aug 24, 2023
c47f1e2
Changing X.Y.X references to X.Y.Z
jprestop Aug 25, 2023
f294ce3
updating thru Using the compile_MET_all.sh Script
lisagoodrich Dec 14, 2023
f134cf4
fixing spacing for ATLAS web address
lisagoodrich Dec 14, 2023
eb78af8
Pulled in changes from develop. This branch is old so there are a lo…
jprestop Dec 14, 2023
59c63d7
Fixed broken internal reference to installation due to typo
jprestop Dec 14, 2023
da9918f
adding version numbers
lisagoodrich Dec 14, 2023
a225cf4
fixing Recommended-Components MET
lisagoodrich Dec 14, 2023
9fca6f7
3.4.2 section updates
lisagoodrich Dec 14, 2023
1ed379a
fixing spacing
lisagoodrich Dec 14, 2023
d369959
adding a period and more dropdown menus
lisagoodrich Dec 15, 2023
9ecd151
fixing spacing
lisagoodrich Dec 15, 2023
2f4044f
loose ends
lisagoodrich Dec 15, 2023
6138072
removing space
lisagoodrich Dec 15, 2023
f20f620
removing bold
lisagoodrich Dec 15, 2023
245bd9b
External Library handling in compile_MET_all.sh section updates
lisagoodrich Dec 15, 2023
bcae26b
installation directory view
lisagoodrich Dec 15, 2023
0deeb00
installation directory after
lisagoodrich Dec 15, 2023
6a56b65
attempting to add figures via the web
lisagoodrich Dec 15, 2023
2913716
fixing bolds, italics etc.
lisagoodrich Dec 15, 2023
3e0ee52
Pulling in changes from develop and resolving conflicts
jprestop Dec 18, 2023
616df76
updating last half of doc
lisagoodrich Dec 18, 2023
9ececfd
loose ends
lisagoodrich Dec 18, 2023
fbc1478
loose ends
lisagoodrich Dec 18, 2023
082420f
adding more dropdown menus
lisagoodrich Dec 18, 2023
5a36c51
fixing dropdown menu and testing automatic version
lisagoodrich Dec 18, 2023
8ece662
testing automatic version
lisagoodrich Dec 18, 2023
a05af65
confirmed automatic version cannot be added to italics or code blocks
lisagoodrich Dec 18, 2023
0bc24de
another round of updates
lisagoodrich Dec 19, 2023
89bdf6b
fixing indents
lisagoodrich Dec 19, 2023
42f006d
creating a table
lisagoodrich Dec 19, 2023
c134d86
fixing table
lisagoodrich Dec 19, 2023
22d8747
fixing table 2
lisagoodrich Dec 19, 2023
e0badb5
more loose end changes
lisagoodrich Dec 19, 2023
c1d767e
more changes
lisagoodrich Dec 19, 2023
879fc97
hopefully final updates
lisagoodrich Dec 19, 2023
0421021
Merge branch 'develop' of github.com:dtcenter/MET into feature_2588_i…
jprestop Dec 20, 2023
15f3f98
trying a fancy new csv table
lisagoodrich Dec 20, 2023
42a280f
troubleshooting csv table
lisagoodrich Dec 20, 2023
f418062
correcting table name
lisagoodrich Dec 20, 2023
90df882
adding a grid table
lisagoodrich Dec 20, 2023
60fd351
fixing grid table
lisagoodrich Dec 20, 2023
93d7cdf
removing csv table
lisagoodrich Dec 20, 2023
142db33
Per #2588, update to the environment variables table.
JohnHalleyGotway Dec 20, 2023
b22eb80
Delete docs/Users_Guide/environment_variables_table.csv
lisagoodrich Dec 21, 2023
6f815c5
Per #2785, add new example installation files
jprestop Jan 11, 2024
8f2be51
Merge branch 'develop' of github.com:dtcenter/MET into feature_2588_i…
jprestop Jan 12, 2024
94f3d35
updating small changes in the first half of the documentation
lisagoodrich Jan 12, 2024
4907610
new dropdown menu and fixing some links
lisagoodrich Jan 16, 2024
b7c0ec5
trying to fix line spacing in dropdown
lisagoodrich Jan 16, 2024
2948310
take 2 fixing spacing
lisagoodrich Jan 16, 2024
18873cf
take 3 fix spacing
lisagoodrich Jan 16, 2024
df4fa36
env var order
lisagoodrich Jan 16, 2024
4c634ac
removing "s"
lisagoodrich Jan 16, 2024
fe877d9
small changes
lisagoodrich Jan 17, 2024
16301ba
un capitalizing S
lisagoodrich Jan 17, 2024
dfa1138
A few minor changes
jprestop Jan 17, 2024
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Binary file added docs/Users_Guide/figure/installation_dir.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
924 changes: 561 additions & 363 deletions docs/Users_Guide/installation.rst

Large diffs are not rendered by default.

2 changes: 1 addition & 1 deletion docs/Users_Guide/reformat_grid.rst
Original file line number Diff line number Diff line change
Expand Up @@ -215,7 +215,7 @@ Each NetCDF file generated by the Pcp-Combine tool contains the dimensions and v
Regrid-Data-Plane Tool
======================

This section contains a description of running the Regrid-Data-Plane tool. This tool may be run to read data from any gridded file MET supports, interpolate to a user-specified grid, and writes the field(s) out in NetCDF format. The user may specify the method of interpolation used for regridding as well as which fields to regrid. This tool is particularly useful when dealing with GRIB2 and NetCDF input files that need to be regridded. For GRIB1 files, it has also been tested for compatibility with the copygb regridding utility mentioned in :numref:`Installation-of-optional`.
This section contains a description of running the Regrid-Data-Plane tool. This tool may be run to read data from any gridded file MET supports, interpolate to a user-specified grid, and writes the field(s) out in NetCDF format. The user may specify the method of interpolation used for regridding as well as which fields to regrid. This tool is particularly useful when dealing with GRIB2 and NetCDF input files that need to be regridded. For GRIB1 files, it has also been tested for compatibility with the copygb regridding utility mentioned in :numref:`suggested_external_utiliites`.

regrid_data_plane Usage
-----------------------
Expand Down
2 changes: 1 addition & 1 deletion docs/Users_Guide/reformat_point.rst
Original file line number Diff line number Diff line change
Expand Up @@ -94,7 +94,7 @@ In this example, the PB2NC tool will process the input **sample_pb.blk** file ap
pb2nc Configuration File
------------------------

The default configuration file for the PB2NC tool named **PB2NCConfig_default** can be found in the installed *share/met/config* directory. The version used for the example run in :numref:`Sample test cases` is available in *scripts/config*. It is recommended that users make a copy of configuration files prior to modifying their contents.
The default configuration file for the PB2NC tool named **PB2NCConfig_default** can be found in the installed *share/met/config* directory. The version used for the installation test cases is available in *scripts/config*. It is recommended that users make a copy of configuration files prior to modifying their contents.

Note that environment variables may be used when editing configuration files, as described in the :numref:`config_env_vars`.

Expand Down
2 changes: 1 addition & 1 deletion docs/Users_Guide/tc-dland.rst
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ Input/Output Format

The input for the TC-dland tool is a file containing the longitude (degrees east) and latitude (degrees north) of all the coastlines and islands considered to be a significant landmass. The default input is to use all three land data files (**aland.dat, shland.dat, wland.dat**) found in the installed *share/met/tc_data/* directory. The use of all three files produces a global land data file. The **aland.dat** file contains the longitude and latitude distinctions used by NHC for the Atlantic and eastern North Pacific basins, the **shland.dat** contains longitude and latitude distinctions for the Southern Hemisphere (south Pacific and South Indian Ocean), and the **wland.dat** contains the remainder of the Northern Hemisphere (western North Pacific and North Indian Ocean). Users may supply their own input file in order to refine the definition of coastlines and a significant landmass.

The output file from TC-dland is a NetCDF format file containing a gridded field representing the distance to the nearest coastline or island, as specified in the input file. This file is used in the TC-Pairs tool to compute the distance from land for each track point in the adeck and bdeck. As noted in :numref:`met_directory_structure`, precomputed distance to land (NetCDF output from TC-dland) files are available in the release. In the installed *share/met/tc_data* directory:
The output file from TC-dland is a NetCDF format file containing a gridded field representing the distance to the nearest coastline or island, as specified in the input file. This file is used in the TC-Pairs tool to compute the distance from land for each track point in the adeck and bdeck. The precomputed distance to land (NetCDF output from TC-dland) files are available in the release. In the installed *share/met/tc_data* directory:

**dland_nw_hem_tenth_degree.nc:** TC-dland output from **aland.dat** using a 1/10th degree grid

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -47,6 +47,8 @@ export MAKE_ARGS="-j 5"
# need to update the paths to the appropriate location.
#export EXTERNAL_LIBS=${TEST_BASE}/external_libs
#export MET_PROJ=${EXTERNAL_LIBS}
#export TIFF_INCLUDE_DIR=${EXTERNAL_LIBS}/include
#export TIFF_LIB_DIR=${EXTERNAL_LIBS}/lib
#export SQLITE_INCLUDE_DIR=${EXTERNAL_LIBS}/include
#export SQLITE_LIB_DIR=${EXTERNAL_LIBS}/lib
#export MET_GSL=${EXTERNAL_LIBS}
Expand Down
Original file line number Diff line number Diff line change
@@ -0,0 +1,86 @@
# Find the directory this script is called from
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"

# Required
# Directory that is the root of the compile
export TEST_BASE=${DIR}

# Required
# Format is compiler_version (e.g. gnu_8.3.0)
# Compiler options = gnu, intel, ics, ips, PrgEnv-intel, or pgi
# Version is used for gnu in compilation of BUFRLIB and HDF5
export COMPILER=intel_2022.1.2

# Set the values for the compilers
export FC=ifort
export F77=ifort
export F90=ifort
export CC=icc
export CXX=icpc

# Required
# Root directory for creating/untaring met source code - usually same as TEST_BASE
export MET_SUBDIR=${TEST_BASE}

# Required
# The name of the met tarbal usually downloaded with version from dtcenter.org and includes a version
# example - v11.1.0.tar.gz
export MET_TARBALL=v12.0.0.tar.gz

# Required
# Specify if machine useds modules for loading software
export USE_MODULES=FALSE

# Root directory of your python install, containing the bin, include, lib, and share directories
export MET_PYTHON=`python3-config --prefix`

# Python ldflags created using python3-config
export MET_PYTHON_LD=`python3-config --ldflags --embed`

# Python cflags created using python3-config
export MET_PYTHON_CC=`python3-config --cflags`

# Use MAKE_ARGS to sped up the compilation of the external libaries and/or MET
# MAKE_ARGS can be set "-j #" where # is replaced with the number of
# cores to use (as an integer) or to simply "-j" to use all available cores.
# Recommend setting to "-j 5" as some users have experienced problems with
# higher values or no # specified.
export MAKE_ARGS="-j 5"

# If users have already installed these libraries and would like to make use of
# them, uncomment out the export statements. If those pre-existing libraries are
# in the external_libs directory, no further edits are needed; however, users
# that have the pre-existing libraries not in the external_libs directory will
# need to update the paths to the appropriate location.
#export EXTERNAL_LIBS=${TEST_BASE}/external_libs
#export MET_PROJ=${EXTERNAL_LIBS}
#export TIFF_INCLUDE_DIR=${EXTERNAL_LIBS}/include
#export TIFF_LIB_DIR=${EXTERNAL_LIBS}/lib
#export SQLITE_INCLUDE_DIR=${EXTERNAL_LIBS}/include
#export SQLITE_LIB_DIR=${EXTERNAL_LIBS}/lib
#export MET_GSL=${EXTERNAL_LIBS}
#export MET_BUFRLIB=${EXTERNAL_LIBS}/lib
#export BUFRLIB_NAME=-lbufr_4
#export LIB_JASPER=${EXTERNAL_LIBS}/lib
#export LIB_LIBPNG=${EXTERNAL_LIBS}/lib
#export LIB_Z=${EXTERNAL_LIBS}/lib
#export MET_GRIB2CLIB=${EXTERNAL_LIBS}/lib
#export MET_GRIB2CINC=${EXTERNAL_LIBS}/include
#export GRIB2CLIB_NAME=-lg2c
#export MET_HDF5=${EXTERNAL_LIBS}
#export MET_NETCDF=${EXTERNAL_LIBS}
#export MET_ECKIT==${EXTERNAL_LIBS}
#export MET_ATLAS==${EXTERNAL_LIBS}

# The optional libraries ecKit and atlas offer support for unstructured
# grids. The optional libraries HDF4, HDFEOS, FREETYPE, and CAIRO are
# used for the following, not widely used tools, MODIS-Regrid,
# lidar2nc, and MODE Graphics. To enable building of these libraries,
# set the compile flags for the library (e.g. COMPILE_ECKIT, COMPILE_ATLAS,
# COMPILE_HDF, COMPILE_HDFEOS) to any value in the environment config
# file. If these libraries have already been installed and don't need
# to be reinstalled, please supply values for the following environment
# variables in the input environment configuration file
# (install_met_env.<machine_name>): MET_ECKIT, MET_ATLAS, MET_HDF,
# MET_HDFEOS, MET_FREETYPEINC, MET_FREETYPELIB, MET_CAIROINC,
# MET_CAIROLIB.
Original file line number Diff line number Diff line change
@@ -0,0 +1,86 @@
# Find the directory this script is called from
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"

# Required
# Directory that is the root of the compile
export TEST_BASE=${DIR}

# Required
# Format is compiler_version (e.g. gnu_8.3.0)
# Compiler options = gnu, intel, ics, ips, PrgEnv-intel, or pgi
# Version is used for gnu in compilation of BUFRLIB and HDF5
export COMPILER=intel-oneapi_2023.0.0

# Set the values for the compilers
export FC=ifx
export F77=ifx
export F90=ifx
export CC=icx
export CXX=icpx

# Required
# Root directory for creating/untaring met source code - usually same as TEST_BASE
export MET_SUBDIR=${TEST_BASE}

# Required
# The name of the met tarbal usually downloaded with version from dtcenter.org and includes a version
# example - v12.0.0.tar.gz
export MET_TARBALL=v12.0.0.tar.gz

# Required
# Specify if machine useds modules for loading software
export USE_MODULES=FALSE

# Root directory of your python install, containing the bin, include, lib, and share directories
export MET_PYTHON=`python3-config --prefix`

# Python ldflags created using python3-config
export MET_PYTHON_LD=`python3-config --ldflags --embed`

# Python cflags created using python3-config
export MET_PYTHON_CC=`python3-config --cflags`

# Use MAKE_ARGS to sped up the compilation of the external libaries and/or MET
# MAKE_ARGS can be set "-j #" where # is replaced with the number of
# cores to use (as an integer) or to simply "-j" to use all available cores.
# Recommend setting to "-j 5" as some users have experienced problems with
# higher values or no # specified.
export MAKE_ARGS="-j 5"

# If users have already installed these libraries and would like to make use of
# them, uncomment out the export statements. If those pre-existing libraries are
# in the external_libs directory, no further edits are needed; however, users
# that have the pre-existing libraries not in the external_libs directory will
# need to update the paths to the appropriate location.
#export EXTERNAL_LIBS=${TEST_BASE}/external_libs
#export MET_PROJ=${EXTERNAL_LIBS}
#export TIFF_INCLUDE_DIR=${EXTERNAL_LIBS}/include
#export TIFF_LIB_DIR=${EXTERNAL_LIBS}/lib
#export SQLITE_INCLUDE_DIR=${EXTERNAL_LIBS}/include
#export SQLITE_LIB_DIR=${EXTERNAL_LIBS}/lib
#export MET_GSL=${EXTERNAL_LIBS}
#export MET_BUFRLIB=${EXTERNAL_LIBS}/lib
#export BUFRLIB_NAME=-lbufr_4
#export LIB_JASPER=${EXTERNAL_LIBS}/lib
#export LIB_LIBPNG=${EXTERNAL_LIBS}/lib
#export LIB_Z=${EXTERNAL_LIBS}/lib
#export MET_GRIB2CLIB=${EXTERNAL_LIBS}/lib
#export MET_GRIB2CINC=${EXTERNAL_LIBS}/include
#export GRIB2CLIB_NAME=-lg2c
#export MET_HDF5=${EXTERNAL_LIBS}
#export MET_NETCDF=${EXTERNAL_LIBS}
#export MET_ECKIT==${EXTERNAL_LIBS}
#export MET_ATLAS==${EXTERNAL_LIBS}

# The optional libraries ecKit and atlas offer support for unstructured
# grids. The optional libraries HDF4, HDFEOS, FREETYPE, and CAIRO are
# used for the following, not widely used tools, MODIS-Regrid,
# lidar2nc, and MODE Graphics. To enable building of these libraries,
# set the compile flags for the library (e.g. COMPILE_ECKIT, COMPILE_ATLAS,
# COMPILE_HDF, COMPILE_HDFEOS) to any value in the environment config
# file. If these libraries have already been installed and don't need
# to be reinstalled, please supply values for the following environment
# variables in the input environment configuration file
# (install_met_env.<machine_name>): MET_ECKIT, MET_ATLAS, MET_HDF,
# MET_HDFEOS, MET_FREETYPEINC, MET_FREETYPELIB, MET_CAIROINC,
# MET_CAIROLIB.