MPAS | MPAS-JEDI | obs2ioda

• NWP | BUFR data | GFS - Binary Universal Form for the Representation of meteorological data
• MPAS | MPAS-JEDI
• MPAS | MPAS-JEDI V3.0.2
• MPAS | MPAS-JEDI | spack-stack 1.9.3
• MPAS | Joint MPAS/WRF Users Workshop 2025 | MPASv8.3.0
• Spack-Stack: building JEDIbundles on your own machine | 202506NCAS

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obs2ioda

• To convert NCEP PREPBUFR/BUFR files and Himawari Standard Data FLDK files to ioda-v1 or ioda-v2 format.
• To convert GOES-ABI netCDF to ioda-v1 format.
• File types that obs2ioda can handle:
  • prepbufr.gdas.YYYYMMDD.tHHz.nr
  • gdas.satwnd.tHHz.YYYYMMDD.bufr
  • gdas.gpsro.tHHz.YYYYMMDD.bufr
  • gdas.1bamua.tHHz.YYYYMMDD.bufr
  • gdas.1bmhs.tHHz.YYYYMMDD.bufr
  • gdas.airsev.tHHz.YYYYMMDD.bufr
  • gdas.cris.tHHz.YYYYMMDD.bufr
  • gdas.crisf4.tHHz.YYYYMMDD.bufr
  • gdas.mtiasi.tHHz.YYYYMMDD.bufr
  • HS_H08_YYYYMMDD_HH00_BNN_FLDK_R20_S0210.DAT
  • OR_ABI-L1b-Rad nc files

Observation data sources

Observation data sources:

• https://nomads.ncep.noaa.gov/pub/data/nccf/com/gfs/prod/
• https://gdex.ucar.edu/datasets/d337000/
• https://gdex.ucar.edu/datasets/d735000/
• https://registry.opendata.aws/noaa-goes/
• https://registry.opendata.aws/noaa-himawari/

github

• https://github.com/jamiebresch/obs2ioda
• https://github.com/jamiebresch/obs2ioda/blob/main/obs2ioda-v2/README.md
  • Compile: cd obs2ioda-v2/src; make
  • NCEP BUFR library (https://github.com/NOAA-EMC/NCEPLIBS-bufr) is required to compile obs2ioda-v2.x.
    • cmake 3.15
    • bufr_v11.5.0
  • Edit obs2ioda-v2/src/Makefile to set proper BUFR_LIB before make.

For bufr_v11.5.0

bufr.tar is not available

[ 97%] (curl) downloading https://ftp.emc.ncep.noaa.gov/static_files/public/bufr.tar curl: (22) The requested URL returned error: 404 make[2]: *** [test/CMakeFiles/get_bufr_test_data.dir/build.make:73: test/bufr.tar] Error 22 make[1]: *** [CMakeFiles/Makefile2:934: test/CMakeFiles/get_bufr_test_data.dir/all] Error 2 make: *** [Makefile:146: all] Error 2

• Download
  • https://ftp.emc.ncep.noaa.gov/static_files/public/
  • move to NCEPLIBS-bufr/build/test

conda env

• may apply channel - conda-forge only.

▶

conda env: obs2ioda.yml

name: obs2ioda
channels:
- anaconda
- conda-forge
dependencies:
- _libgcc_mutex=0.1=main
- _openmp_mutex=5.1=1_gnu
- attr=2.5.2=h47b2149_0
- binutils_impl_linux-64=2.44=h4b9a079_2
- blas=1.0=openblas
- blosc=1.21.6=hef167b5_0
- bzip2=1.0.8=h5eee18b_6
- c-ares=1.34.6=hd44998d_0
- ca-certificates=2025.12.2=h06a4308_0
- certifi=2026.01.04=py314h06a4308_0
- cftime=1.6.5=py314h6a40391_0
- gcc=10.4.0=hb92f740_13
- gcc_impl_linux-64=10.4.0=h5231bdf_19
- gfortran=10.4.0=h0c96582_13
- gfortran_impl_linux-64=10.4.0=h7d168d2_19
- hdf4=4.2.15=h2a13503_7
- hdf5=1.14.6=nompi_h19486de_106
- icu=78.2=h33c6efd_0
- kernel-headers_linux-64=4.18.0=h3108a97_1
- keyutils=1.6.3=hb9d3cd8_0
- krb5=1.22.2=ha1258a1_0
- ld_impl_linux-64=2.44=h153f514_2
- libaec=1.1.5=h088129d_0
- libcurl=8.18.0=hcf29cc6_1
- libedit=3.1.20250104=pl5321h7949ede_0
- libev=4.33=h7f8727e_1
- libexpat=2.7.4=h7354ed3_0
- libffi=3.5.2=h3435931_0
- libgcc=15.2.0=h69a1729_7
- libgcc-devel_linux-64=10.4.0=hd38fd1e_19
- libgcc-ng=15.2.0=h166f726_7
- libgfortran=15.2.0=h166f726_7
- libgfortran5=15.2.0=hc633d37_7
- libgomp=15.2.0=h4751f2c_7
- libiconv=1.18=h3b78370_2
- libjpeg-turbo=3.1.3=h47b2149_0
- liblzma=5.8.2=hb03c661_0
- liblzma-devel=5.8.2=hb03c661_0
- libmpdec=4.0.0=h5eee18b_0
- libnetcdf=4.9.3=nompi_hbf2fc22_104
- libnghttp2=1.67.0=had1ee68_0
- libopenblas=0.3.31=hf7dbefb_0
- libsanitizer=10.4.0=h5246dfb_19
- libsqlite=3.51.2=hf4e2dac_0
- libssh2=1.11.1=hcf80075_0
- libstdcxx=15.2.0=h39759b7_7
- libstdcxx-ng=15.2.0=hc03a8fd_7
- libuuid=2.41.3=h5347b49_0
- libxml2=2.15.1=he237659_1
- libxml2-16=2.15.1=hca6bf5a_1
- libzip=1.11.2=h6991a6a_0
- libzlib=1.3.1=hb25bd0a_0
- lz4-c=1.9.4=h6a678d5_1
- ncurses=6.5=h7934f7d_0
- netcdf-fortran=4.6.2=nompi_h90de81b_102
- netcdf4=1.7.2=py314ha2d4c0d_2
- numpy=2.4.2=py314hda7dee8_0
- numpy-base=2.4.2=py314h5cadfd5_0
- openssl=3.6.1=h35e630c_1
- packaging=25.0=py314h06a4308_1
- pip=26.0.1=pyhc872135_0
- python=3.14.3=h32b2ec7_101_cp314
- python_abi=3.14=2_cp314
- readline=8.3=hc2a1206_0
- setuptools=80.10.2=py314h06a4308_0
- snappy=1.2.2=h4bcf44c_1
- sysroot_linux-64=2.28=h3108a97_1
- tk=8.6.13=noxft_h366c992_103
- tzdata=2025c=he532380_0
- wheel=0.46.3=py314h06a4308_0
- xz=5.8.2=ha02ee65_0
- xz-gpl-tools=5.8.2=ha02ee65_0
- xz-tools=5.8.2=hb03c661_0
- zstd=1.5.7=h11fc155_0

▶

install_obs2ioda-v2.sh

#!/bin/bash

#------------------------------------------------#
#Author:         wpsze
#Email：         waipangsze@gmail.com
#date:           
#Version:        0.0 
#Description:    Install libraries that MPAS needs 
#Copyright (C)： 2022 All rights reserved
#------------------------------------------------#

############################## Directory Listing ############################
source /home/wpsze/micromamba/bin/activate obs2ioda
export SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"

export HOME=`pwd`

### NCEP BUFR library environment
export NCEP_BUFR_library_dir="/home/wpsze/cpas/CPAS-DA/cpas-da/NCEPLIBS-bufr/NCEPLIBS-bufr/selflibbufr/"
export PATH=$NCEP_BUFR_library_dir/bin:$PATH
export LD_LIBRARY_PATH=$NCEP_BUFR_library_dir/lib64:$LD_LIBRARY_PATH
export LIBRARY_PATH=$NCEP_BUFR_library_dir/lib64:$LIBRARY_PATH

export NETCDF="/home/wpsze/micromamba/envs/obs2ioda"

echo "====== gfortran version ====="
#
# gfortran: error: unrecognized command line option ‘-fallow-argument-mismatch’; did you mean ‘-Wno-argument-mismatch’?
# gfortran: error: unrecognized command line option ‘-fallow-invalid-boz’; did you mean ‘-Wno-invalid-pch’?
# 1. The most recommended approach is to update your compiler to GFortran version 10 or newer, which officially supports the flag
# 2. Replace -fallow-argument-mismatch with -Wno-argument-mismatch in your build configuration or command line.  

#ldd /home/wpsze/DA-obs2ioda/obs2ioda-H9/obs2ioda-v2/src/obs2ioda-v2.x 
gfortran --version

echo "====== netcdf.mod ======="
# 
# Fatal Error: Cannot open module file 'netcdf.mod' for reading at (1): No such file or directory
#
nf-config --fflags
nf-config --flibs

#cd ./obs2ioda-H9/obs2ioda-v2/src/
#cd ./obs2ioda-v2/src/
cd ./obs2ioda-v2-jamiebresch/src/

# ld is the command for the GNU linker (link editor)
ld -lbufr #--verbose
ld -lbufr_4 #--verbose
ld -lbufr_d_DA #--verbose

echo "==== LD_LIBRARY_PATH ==="
echo $LD_LIBRARY_PATH
echo "==== LIBRARY_PATH    ==="
echo $LIBRARY_PATH
echo "========================"

rm log.log

make clean

## you can add sometings like -g -traceback in the FFLAGS for full debug msg,

make 2>&1 |tee log.log