nc_var_info.cc:15:10: fatal error: 'netcdf' file not found

[wxbinge]

I have compiled installed NetCDF-C and NetCDF-CXX to compile several packages. However, when I try to compile MET, the package cannot find NetCDF, and I am trying to figure out what I need to do differently. I am using a bash environment. Here are my setup and procedures:

MET Version: 11.1.1

Compilers: Intel OneAPI (icx and icpx)

Issue: Unable to find NetCDF

NetCDF directory: I've read that NetCDF-C and NetCDF-CXX must be in the same directory.

In the .bashrc: export MET_NETCDF=/home/wxbinge/work/built_with_intel_2024_old_libs_version_2.1/netcdf

I've attached my config.log, config.status, and make log files.
config.log
config.status.txt
make.log

Additional Notes: I've also tried including the MET_NETCDFINC and MET_NETCDFLIB paths in the bashrc file, but I am still getting the same error. I've tried to use the CPPFLAGS when setting up the configuration.

Any assistance would be greatly appreciated.

[wxbinge]

It seems the netCDF libraries I am using are too old to compile with MET v11.1.1.

I used some newer netCDF builds on my system and got past the error. However, I am now faced with this error:

/usr/bin/ld: /home/wxbinge/work/built_with_intel_2024_old_libs_version_2.1/netcdf/lib/libnetcdf_c++4.so: undefined reference to nc_inq_var_filter' /usr/bin/ld: /home/wxbinge/work/built_with_intel_2024_old_libs_version_2.1/netcdf/lib/libnetcdf_c++4.so: undefined reference to nc_def_var_filter'
icpx: error: linker command failed with exit code 1 (use -v to see invocation)

Has MET been tested with Intel OneAPI compilers (icx and icpx)?

[JohnHalleyGotway]

@wxbinge I see you're having difficulty installing MET version 11.1.1, specifically related to the external NetCDF library.

You created a GitHub issue in the MET repository. However, I've moved this over to the METplus repository... and converted it to a GitHub discussion instead.

MET is the statistical engine of the METplus system, but we provide support for all METplus components (including MET) via the METplus Discussions forum.

I'm going to ping @jprestop on this discussion and ask her to respond. She handles the majority of the installations of METplus on a variety of platform and is best suited to answer questions about compiler and dependent library versions.

[wxbinge]

Thank you for moving the thread to the correct location.

[jprestop]

Hi @wxbinge.

Thank you for all of the information and the files you included here. Official support in MET for the Intel oneAPI compilers was NOT included in our latest official release, MET-11.1.1, but will be included in our upcoming MET-12.0.0 official release scheduled for December this year. We found that many of the libraries we distributed with our tar file package needed to be updated in order to compile with the oneAPI compilers, so we'll be offering a new set of tar file of dependencies with our upcoming release.

Do you have access to the older Intel compilers or the GNU compilers for compiling MET-11.1.1? Are you familiar with our compilation script and tar files that we provide? If not, please take a look at our documentation under "Sample Script for Compiling External Libraries and MET" on our MET Download page if you're interested in using it. Please note, however, that this documentation will be moved to our User's Guide for the MET-12.0.0 release.

Regarding your attempted compilation, in your config.log file, I see that LDFLAGS contains the following:

• -L/home/wxbinge/work/built_with_intel_2024_old_libs_version_2.1/netcdf_c/v4.3.3.1/lib
• -L/home/wxbinge/work/built_with_intel_2024_old_libs_version_2.1/netcdf_cxx/v4.2/lib

but it does not contain:

• -L/home/wxbinge/work/built_with_intel_2024_old_libs_version_2.1/netcdf/lib

where it appears the files are now located.

Please let us know if you have any further questions.

[wxbinge]

Hey @jprestop,

Thank you for getting back to me. After building with all the latest dependencies, I successfully compiled MET v11.1.1 with the last Intel OneAPI compilers (2024.1). I am putting my steps in a separate post.

[jprestop]

Hi @wxbinge. Thank you for letting us know that after building with more recent versions of the dependencies you were able to successful compile METv11.1.1 with the Intel OneAPI compilers (2024.1). We appreciate your detailed follow up post. I'll go ahead and select an answer and mark this conversation as locked to prevent future posts here. Please feel free to start a new discussion with any new questions.

[wxbinge]

Compiling MET v11.1.1 with Intel OneAPI (2024.1)

Compilers: ICX and ICPX

==================================================================

USE THESE SETTING WHEN INSTALLING MET v11.1.1 or newer with Intel OneAPI compilers

==================================================================

-----------------

>>>> MODULES <<<<

-----------------

ZLIB

export vZLIB="v1.3.1"
export ZLIB=${UTIL}/zlib/$vZLIB

LIBPNG

export vLIBPNG="v1.6.43"
export LIBPNG=${UTIL}/libpng/$vLIBPNG

JPEG

export vJPEG="v9f"
export JPEG=${UTIL}/jpeg/$vJPEG

JASPER

export vJASPER="v4.2.4"
export JASPER=${UTIL}/jasper/$vJASPER

SZIP

export vSZIP="v2.1.1"
export SZIP=${UTIL}/szip/$vSZIP

ZSTD

export vZSTD="v1.5.6"
export ZSTD=${UTIL}/zstd/$vZSTD

GSLIB

export vGSL="v2.8"
export GSL_PATH=${UTIL}/gslib/$vGSL

***************** START NCEPLIBS *****************

NCEP BUFRLIB

export vBUFRLIB="v12.0.1"
export BUFRLIB=${UTIL}/nceplibs/bufrlib/$vBUFRLIB

NCEP BACIO

export vBACIO="v2.6.0"
export BACIO=${UTIL}/nceplibs/bacio/$vBACIO

NCEP W3EMC

export vW3EMC="v2.12.0"
export W3EMC=${UTIL}/nceplibs/w3emc/$vW3EMC

NCEP G2

export vG2="v3.5.1"
export G2_PATH=${UTIL}/nceplibs/g2/$vG2

NCEP G2C

export vG2C="v1.9.0"
export G2C_PATH=${UTIL}/nceplibs/g2c/$vG2C

NCEP IP

export vIP="v5.1.0"
export IP_PATH=${UTIL}/nceplibs/ip/$vIP

NCEP SP

export vSP="v2.5.0"
export SP_PATH=${UTIL}/nceplibs/sp/$vSP

NCEP GRIB2 LIB

export vGRIB2LIB="v1.5.0"
export GRIB2LIB=${UTIL}/nceplibs/grib2lib/$vGRIB2LIB

***************** END NCEPLIBS *****************

CURL

export vCURL="v8.8.0"
export CURL=${UTIL}/curl/$vCURL

HDF4

export vHDF4="v4.3.0"
export HDF4=${UTIL}/hdf4/$vHDF4

HDF5

export vHDF5="v1.14.4"
export iHDF5=${UTIL}/hdf5/$vHDF5

LIBXMl2

export vXML2="v2.9.12"
export XML2=${UTIL}/libxml2/$vXML2

NETCDF-C

export vNETCDF_C="v4.9.2"
export NETCDF_C=${UTIL}/netcdf_c/$vNETCDF_C

NETCDF-CXX

export vNETCDF_CXX="v4.3.1"
export NETCDF_CXX=${UTIL}/netcdf_cxx/$vNETCDF_CXX

MET

export vMET="v11.1.1"
export MET_PATH=${UTIL}/met/$vMET
export MET_NETCDF=$UTIL/netcdf

---------------------------------------------

Dynamic Library Paths and Include directories

---------------------------------------------

export LD_LIBRARY_PATH=$INTELHPC/2024.1:$ZLIB/lib:$LIBPNG/lib:$JPEG/lib:$JASPER/lib:$SZIP/lib:$ZSTD/lib:$CURL/lib:$GSL_PATH/lib:$XML2/lib:$HDF4/lib:$iHDF5/lib:$UTIL/netcdf/lib:$BUFRLIB/lib:$LD_LIBRARY_PATH
export PATH=$PATH:$INTELHPC/2024.1/bin:$XML2/bin
export LDFLAGS="-L$ZLIB/lib -L$LIBPNG/lib -L$JASPER/lib -L$JPEG/lib -L$SZIP/lib -L$ZSTD/lib -L$CURL/lib -L$XMl2/lib -L$HDF4/lib -L$iHDF5/lib -L$UTIL/netcdf/lib -L$GSL_PATH/lib -L$BUFRLIB/lib"
export CPPFLAGS="-I$ZLIB/include -I$LIB/include -I$JASPER/include -I$JPEG/include -I$SZIP/include -I$ZSTD/include -I$CURL/include -I$XMl2/include -I$HDF4/include -I$iHDF5/include -I$UTIL/netcdf/include -I$GSL_PATH/include"

======================================================

CONFIGURING LIBRARIES AND DEPENDENCIES

======================================================

##############

ZLIB

##############
./configure --prefix=$ZLIB

##############

LIBPNG

##############
./configure --prefix=$LIBPNG

##############

SZIP

##############
./configure --prefix=$SZIP

##############

JPEG

##############
./configure --prefix=$JPEG

##############

JASPER

##############
cmake -H$UTIL/SOURCE/MET/jasper-version-4.2.4 -B$UTIL/SOURCE/MET/build -DCMAKE_INSTALL_PREFIX=$JASPER

cmake --build $UTIL/SOURCE/MET/build

cd $UTIL/SOURCE/MET/build

ctest --output-on-failure

cmake --build $UTIL/SOURCE/MET/build --target install

##############

CURL

##############
./configure --prefix=$CURL --without-ssl --with-zstd=$ZSTD

##############

XML2

##############
./configure --prefix=$XMl2

##############

GSL

##############
./configure --prefix=$GSL_PATH

##############

NCEP BUFRLIB

##############
cmake -DCMAKE_INSTALL_PREFIX=$BUFRLIB ..

##############

NCEP BACIO

##############
cmake -DCMAKE_INSTALL_PREFIX=$BACIO ..

##############

NCEP IP

##############
cmake -DCMAKE_INSTALL_PREFIX=$IP_PATH ..

##############

NCEP SP

##############
cmake -DCMAKE_INSTALL_PREFIX=$SP_PATH ..

##############

NCEP W3EMC

##############
cmake .. -DCMAKE_INSTALL_PREFIX=$W3WMC -DCMAKE_PREFIX_PATH="${BACIO}"

##############

NCEPLIB G2

##############

Dependencies: LIBPNG, JASPER, JPEG, NCEP-BACIO, NCEP-W3EMC

cmake .. -DCMAKE_INSTALL_PREFIX=$G2_PATH -DCMAKE_PREFIX_PATH="${JPEG_LIBRARY};${JPEG_INCLUDE_DIR};${JASPERLIB};${JASPERINC};${BACIO};${W3EMC}"

##############

NCEPLIB G2C

##############

Dependencies: JASPER, JPEG

cmake .. -DCMAKE_INSTALL_PREFIX=$G2C_PATH -DCMAKE_PREFIX_PATH="${JPEG_LIBRARY};${JPEG_INCLUDE_DIR};${JASPERLIB};${JASPERINC}"

###############################

NCEP GRIB2LIB AND UTILITIES

###############################

Dependencies: LIBPNG, JASPER, JPEG, NCEP-BACIO, NCEP-IP, NCEP-SP, NCEP-W3EMC

cmake .. -DCMAKE_INSTALL_PREFIX=$GRIB2LIB -DCMAKE_PREFIX_PATH="${JPEG_LIBRARY};${JPEG_INCLUDE_DIR};${JASPERLIB};${JASPERINC};${BACIO};${IP_PATH};${SP_PATH};${W3EMC};${G2_PATH}"

##############

HDF4

##############
./configure --prefix=$HDF4 --with-zlib=$ZLIB --with-szlib=$SZIP --with-jpeg=$JPEG --enable-shared --disable-netcdf --disable-fortran

##############

HDF5

##############
./configure --prefix=$iHDF5 --enable-shared --enable-fortran

##############

NETCDF-C

##############
./configure --prefix=$NETCDF_C --disable-dap --enable-shared --enable-hdf4 --enable-netcdf4

##############

NETCDF-CXX

##############
./configure --prefix=$NETCDF_CXX

##############

MET v11.1.1

##############
./configure --prefix=$MET_PATH CFLAGS="-qopenmp" CPPFLAGS="-I$GSL_PATH/include" LDFLAGS="-L$GSL_PATH/lib -L$BUFRLIB/lib" BUFRLIB_NAME=-lbufr_4