netcdf-fortran-4.5.3 fails to configure with netcdf-c-4.8.0: "configure: error: netcdf-c version 4.7.4 or greater is required"

[gus-correa]

netcdf-fortran-4.5.3, with netcdf-c-4.8.0 previously installed, on Linux CentOS 7.9, with gcc and gfortran 4.8.5.

$ export LD_LIBRARY_PATH=/opt/swinst/netCDF/C/gnu-4.8.5/lib [This is where the netcdf-c-4.8.0 libraries are installed.]

$ cd ../build_gnu-4.8.5/ [Trying to configure off the source tree (with VPATH), but got the same error if directly on the source tree.]

$ LD_LIBRARY_PATH=/opt/swinst/netCDF/C/gnu-4.8.5/lib ../netcdf-fortran-4.5.3/configure --prefix=/opt/swinst/netCDF/fortran/gnu-4.8.5 ... checking for library containing dlopen... -ldl checking netcdf.h usability... yes checking netcdf.h presence... yes checking for netcdf.h... yes checking for library containing nc_open... -lnetcdf checking for nc_def_opaque... yes checking for nccreate... yes checking for nc_set_log_level... no checking for oc_open... yes checking for nc_def_var_szip... no configure: error: netcdf-c version 4.7.4 or greater is required [<- ERROR MESSAGE]

However, nm shows that the nc_def_var_szip symbol is there, and so is nc_set_log_level

nm ../../C/gnu-4.8.5/lib/libnetcdf.a |grep nc_def_var_szip 0000000000000216 T nc_def_var_szip nm ../../C/gnu-4.8.5/lib/libnetcdf.a |grep nc_set_log_level 00000000000021cd T nc_set_log_level

Am I missing something? Do I have to downgrade to netcdf-c-4.7.4 or 4.7.X?

Thank you, Gus Correa

---

[WardF]

If you run 'which ncdump', is anything returned? The only thing that makes sense is if there is another libnetcdf installed elsewhere on the system in one of the default library locations, and that that library is the one that the linker is finding. Is nc-config available on your system?

Actually, what happens if you run the following?

$ CFLAGS="-I$(/opt/swinst/netCDF/C/gnu-4.8.5/bin/nc-config --includedir)" LDFLAGS="-L$(/opt/swinst/netCDF/C/gnu-4.8.5/bin/nc-config --libs)" ./configure --prefix=/opt/swinst/netCDF/fortran/gnu-4.8.5

If this fails, first check I didn't introduce a typo by copying by hand, and assuming there aren't any typos, what happens if you run the following?

$ /opt/swinst/netCDF/C/gnu-4.8.5/bin/nc-config --all

[gus-correa]

Thank you for your answer.

Sure there is another boilerplate netcdf library installed from Linux packages. which ncdump outputs the boilerplate: /bin/ncdump It is pretty common to have two, even many different versions of the same library in a system, to handle different compilers, programs that require different library versions, etc.

However, I tried to direct configure not to use the boilerplate but the 4.8.0 using the recipe in the netcdf C 4.8.0 web page: https://www.unidata.ucar.edu/software/netcdf/docs/building_netcdf_fortran.html and consists in setting the LD_LIBRARY_PATH to point to the alternative netcdf (4.8.0) library. That recipe clearly doesn't work.

Now, following your suggestion (with slightly different paths) here is what I nc-config from 4.8..0 outputs:

$/opt/swinst/netCDF/C/4.8.0/gnu-4.8.5/bin/nc-config --includedir /opt/swinst/netCDF/C/4.8.0/gnu-4.8.5/include $/opt/swinst/netCDF/C/4.8.0/gnu-4.8.5/bin/nc-config --libs -L/opt/swinst/netCDF/C/4.8.0/gnu-4.8.5/lib -lnetcdf

Trying to compile with explicit CFLAGS and LDFLAGS as suggested:

CFLAGS="-I$(/opt/swinst/netCDF/C/4.8.0/gnu-4.8.5/bin/nc-config --includedir)" LDFLAGS="-L$(/opt/swinst/netCDF/C/4.8.0/gnu-4.8.5/bin/nc-config --libs)" ./configure --prefix=/opt/swinst/netCDF/fortran/4.5.3/gnu-4.8.5 ... checking for nc_set_log_level... no checking for oc_open... yes checking for nc_def_var_szip... no configure: error: netcdf-c version 4.7.4 or greater is required [<- Same error again.]

Oh, I presume I should use --libdir instead of --libs, to get just the directory path: $/opt/swinst/netCDF/C/4.8.0/gnu-4.8.5/bin/nc-config --libdir /opt/swinst/netCDF/C/4.8.0/gnu-4.8.5/lib

So, trying again with --libdir: $CFLAGS="-I$(/opt/swinst/netCDF/C/4.8.0/gnu-4.8.5/bin/nc-config --includedir)" LDFLAGS="-L$(/opt/swinst/netCDF/C/4.8.0/gnu-4.8.5/bin/nc-config --libdir)" ./configure --prefix=/opt/swinst/netCDF/fortran/4.5.3/gnu-4.8.5 ... checking for nc_set_log_level... yes checking for oc_open... yes checking for nc_def_var_szip... yes [<- Passed the previous point of failure!] checking for nc_get_chunk_cache_ints... yes checking netCDF logging present... yes ... checking size of float... 0 checking size of double... 0 checking size of off_t... configure: error: in /opt/swinst/netCDF/fortran/4.5.3/netcdf-fortran-4.5.3': configure: error: cannot compute sizeof (off_t) * [<- Unfortunately it hit another error.]* See config.log' for more details

Is there a way to go across this other error?

Thank you, Gus Correa

On Thu, Jul 8, 2021 at 5:53 PM Ward Fisher @.***> wrote:

If you run 'which ncdump', is anything returned? The only thing that makes sense is if there is another libnetcdf installed elsewhere on the system in one of the default library locations, and that that library is the one that the linker is finding. Is nc-config available on your system?

Actually, what happens if you run the following?

$ CFLAGS="-I$(/opt/swinst/netCDF/C/gnu-4.8.5/bin/nc-config --includedir)" LDFLAGS="-L$(/opt/swinst/netCDF/C/gnu-4.8.5/bin/nc-config --libs)" ./configure --prefix=/opt/swinst/netCDF/fortran/gnu-4.8.5

If this fails, first check I didn't introduce a typo by copying by hand, and assuming there aren't any typos, what happens if you run the following?

$ /opt/swinst/netCDF/C/gnu-4.8.5/bin/nc-config --all

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Unidata/netcdf-fortran/issues/299#issuecomment-876770244, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHIZALXUZNE7QIQACCDQHB3TWYM5HANCNFSM5ABOPWOQ .

[WardF]

@gus-correa I believe I know what is going on here, can you attach the config.log file generated so that I can confirm? I believe the issue is an empty environmental variable, but once I can confirm that that is what's happening, I can provide the appropriate fix. Thanks!

[gus-correa]

Thank you for your answer. Please find attached the config.log file.

On Fri, Jul 9, 2021 at 1:05 PM Ward Fisher @.***> wrote:

@gus-correa https://github.com/gus-correa I believe I know what is going on here, can you attach the config.log file generated so that I can confirm? I believe the issue is an empty environmental variable, but once I can confirm that that is what's happening, I can provide the appropriate fix. Thanks!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Unidata/netcdf-fortran/issues/299#issuecomment-877329652, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHIZALUYMC5DPFKJYJDINLLTW4T7NANCNFSM5ABOPWOQ .

[WardF]

@gus-correa Hi Gus, I'm not seeing the file attached to the github issue comment thread, can you confirm it was uploaded?

[gus-correa]

I attached config.log to the email, but GitHub doesn't seem to like it this way. Anyway, I am trying to upload it directly here. config.log

[adamcpovey]

I encountered a similar error when attempting to build with gfortran 11 installed via a conda environment (such that libraries aren't necessarily in the default locations). A successful workaround was to add the directory where HDF is installed to LD_LIBRARY_PATH, which I think means that CMAKE_PREFIX_PATH isn't being linked against within CMakeLists.txt.

[simon-Leary42]

On my ubuntu machine I uninstalled all the netcdf packages from apt and I got a new error, which led me here: https://github.com/Unidata/netcdf-fortran/issues/73 Once I follow that workaround, this error doesn't come up whether or not other netcdf packages are installed with apt. I think that this configure process will check LD_LIBRARY_PATH first and standard locations second, which effectively hides the real problem. Maybe there should be some warning or output like, "hey, we didn't find anything in LD_LIBRARY_PATH, we'll look elsewhere"

[zexhan07]

@gus-correa did you find this error solution? i am trying to install WRF 4.3 but netcdf fortran is not installing, giving same error.

[adamcpovey]

@zexhan07 The following worked for me,

git clone [email protected]:Unidata/netcdf-fortran.git
cd netcdf-fortran
git checkout v4.5.3
mkdir build
cd build
cmake -DCMAKE_PREFIX_PATH="$LIB_DIR" \
      -DnetCDF_LIBRARIES="$LIB_DIR/lib/libnetcdf.so" \
      -DnetCDF_INCLUDE_DIR="$LIB_DIR/include" \
      -DCMAKE_BUILD_TYPE="Release" \
      -DBUILD_SHARED_LIBS=ON \
      -DNC_EXTRA_DEPS=jpeg \
      -DCMAKE_INSTALL_PREFIX="$LIB_DIR/netcdf-fortran" \
      -G "Unix Makefiles" -Wno-dev ..
make
make test
make install

I see the conda-forge feedstock defines a few paths in the compilation flags and had to use LD_LIBRARY_PATH before running their tests.

I still use configure when I build as a conda package and it works without these fiddles, but a conda-bld environment defines a lot of variables to stop my machine's native libraries leaking into the build.

[prehensilecode]

Same error with netcdf-c-4.8.1 and netcdf-fortran-4.5.4. I use ccmake 3.22.2:

 Found m4: /usr/bin/m4
 Found netCDF CMake package: netCDF::netcdf
 CMake Error at CMakeLists.txt:643 (message):
   netcdf-c version 4.7.4 or greater is required

 Configuring incomplete, errors occurred!
 See also "/ifs/opt/src/netcdf-fortran-4.5.4/BUILD/CMakeFiles/CMakeOutput.log".
 See also "/ifs/opt/src/netcdf-fortran-4.5.4/BUILD/CMakeFiles/CMakeError.log".

It found netCDF_DIR:

 BUILDNAME                        Linux-4.18.0-147.el8.x86_64-x86_64
 BUILDNAME_PREFIX
 BUILDNAME_SUFFIX
 BUILD_BENCHMARKS                 ON
 BUILD_SHARED_LIBS                ON
 BUILD_TESTING                    ON
 CMAKE_BUILD_TYPE                 DEBUG
 CMAKE_INSTALL_PREFIX             /ifs/opt/netcdf-fortran/intel/2020/4.5.4
 CTEST_MEMORYCHECK_COMMAND        valgrind
 ENABLE_LARGE_FILE_TESTS          ON
 ENABLE_PARALLEL_TESTS            OFF
 Fortran_INSTALL_MODDIR           include
 NC4F_M4                          /usr/bin/m4
 NC_DOT                           /usr/bin/dot
 NF_M4                            /usr/bin/m4
 PACKAGE                          netcdf-fortran
 TEST_WITH_VALGRIND               OFF
 TMP_BUILDNAME                    Linux-4.18.0-147.el8.x86_64-x86_64
 UNAME                            /usr/bin/uname
 netCDF_DIR                       /ifs/opt/netcdf/intel/2020/4.8.1/lib64/cmake/netCDF

nc-config --all reports:

This netCDF 4.8.1 has been built with the following features:

  --cc            -> /ifs/opt/intel/2020/compilers_and_libraries_2020.4.304/linux/bin/intel64/icc
  --cflags        -> -I/ifs/opt/netcdf/intel/2020/4.8.1/include
  --libs          -> -L/ifs/opt/netcdf/intel/2020/4.8.1/lib64 -lnetcdf
  --static        -> -lhdf5_hl-shared -lhdf5-shared -lm -lszip -lcurl

  --has-c++       -> no
  --cxx           ->

  --has-c++4      -> no
  --cxx4          ->

  --has-fortran   -> no
  --has-dap       -> yes
  --has-dap2      -> yes
  --has-dap4      -> yes
  --has-nc2       -> yes
  --has-nc4       -> yes
  --has-hdf5      -> yes
  --has-hdf4      -> no
  --has-logging   -> no
  --has-pnetcdf   -> no
  --has-szlib     -> yes
  --has-cdf5      -> yes
  --has-parallel4 -> no
  --has-parallel  -> no
  --has-nczarr    -> yes

  --prefix        -> /ifs/opt/netcdf/intel/2020/4.8.1
  --includedir    -> /ifs/opt/netcdf/intel/2020/4.8.1/include
  --libdir        -> /ifs/opt/netcdf/intel/2020/4.8.1/lib64
  --version       -> netCDF 4.8.1

The CMakeError.log file is attached. CMakeError.log

(Correction) Trying to set netCDF_LIBRARIES and netCDF_INCLUDE_DIR in the command line did not work.

[prehensilecode]

Setting CPPFLAGS and LDFLAGS appropriately for netcdf-c (using nc-config), and then using the old ./configure ... method works.

[jjpaulo2]

@prehensilecode which configuration or commands did you use? Would you share it here?

[encyclica]

As for me, this problem was solved simply by setting the NETCDF variable in the environment. Do not forget to do it after compiling netcdf-c!

[prehensilecode]

@prehensilecode which configuration or commands did you use? Would you share it here?

Sorry, it has been almost a year, so I don’t remember exactly.

I would look at the output of nc-config, which shows the values:

• --cflags -> -I/ifs/opt/netcdf/intel/2020/4.8.1/include
• --libs -> -L/ifs/opt/netcdf/intel/2020/4.8.1/lib64 -lnetcdf

So, set

• CPPFLAGS=-I/ifs/opt/netcdf/intel/2020/4.8.1/include
• LDFLAGS="-L/ifs/opt/netcdf/intel/2020/4.8.1/lib64 -Wl,-rpath,/ifs/opt/netcdf/intel/2020/4.8.1/lib64 -lnetcdf"

Of course, adjust the paths to the output of your own installation of nc-config.

[edwardhartnett]

OK, I cannot reproduce this error, except by deliberately linking to an older version of netcdf-c.

Are you sure you are setting LDFLAGS correctly to point to the lib directory of your netcdf-c install?

[tghi461]

Hi, I have been working to try to install NetCDF-Fortran for WRF modeling needs. I believe I successfully installed NetCDF-C (did make test and it reported success). I followed all in the above and any from the internet I can possibly understand and try to run configure. The nearest successful configure created was using the following command: CFLAGS="-I$(/home/tes/WRF_libs/netcdf2/bin/nc-config --includedir)" LDFLAGS="-L$(/home/tes/WRF_libs/netcdf2/bin/nc-config --libdir --libs)" ./configure --prefix=/home/tes/WRF_libs/netcdf2 --disable-dependency-tracking --disable-shared

Also attached are: Makefile created using the above configuration setup and it's config.log files. When I do "make check", returns an error as: Makefile:317: *** missing separator. Stop. So, I opened the 'Makefile' and added a forward-slash, as in " " for lines above 317 (i.e. at end of line 316), 332, & 334 in the attached "Makefile". But after another 'make check', it returns the details below and even if I try to add tabs or forward-slash as per my readings, I am completely stuck here.

Making check in libsrc make[1]: Entering directory /home/tes/WRF_libs/netcdf-fortran-4.6.0/libsrc' Makefile:200: *** missing separator. Stop. make[1]: Leaving directory /home/tes/WRF_libs/netcdf-fortran-4.6.0/libsrc' make: *** [check-recursive] Error 1

I use gcc/g++/gfortran v5.5.0 to compile my c/c++/gfortran programs in x86_64 GNU/Linux running on Scientific Linux 7.9 (Nitrogen) config.log Makefile.log

Thank you! Tes

[edwardhartnett]

OK, any time you are tempted to open up a Makefile and edit, just stop right there. That is never necessary.

So now you are getting through the configure for netcdf-fortran, but getting another problem? Please post here the entire output of the latest configure you have working.

[tghi461]

Thanks, here are a couple configure execution outputs (I hope these are what you are looking for): (1, when this command is used):
CFLAGS="-I$(/home/tes/WRF_libs/netcdf2/bin/nc-config --includedir)" LDFLAGS="-L$(/home/tes/WRF_libs/netcdf2/bin/nc-config --libdir --libs)" ./configure --prefix=/home/tes/WRF_libs/netcdf2 --disable-shared ===> configure: netCDF-Fortran 4.6.0 checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether to enable maintainer-specific portions of Makefiles... no configure: checking user options checking whether make supports the include directive... yes (GNU style) checking for gcc... /usr/bin/gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether /usr/bin/gcc accepts -g... yes checking for /usr/bin/gcc option to enable C11 features... none needed checking whether /usr/bin/gcc understands -c and -o together... yes checking dependency style of /usr/bin/gcc... gcc3 checking if netCDF was built with CDF5... yes checking if netCDF was built with Zstandard compression... no checking if netCDF was built with pnetcdf... no checking if netCDF was built with HDF5 parallel I/O features... no checking if netCDF was built with any parallel I/O features... no checking if netCDF-fortran should be built with HDF5 parallel I/O features... no checking if netCDF was built with support for szip writes... no checking if netCDF was built with support for quantize... yes checking for valgrind... no checking whether parallel IO tests should be run... no checking whether a user specified program to run mpi programs... mpiexec checking whether netCDF documentation should be generated... no checking for doxygen... doxygen checking for dot... no configure: WARNING: dot not found - will use simple charts in documentation configure: finding C compiler checking for gcc... (cached) /usr/bin/gcc checking whether the compiler supports GNU C... (cached) yes checking whether /usr/bin/gcc accepts -g... (cached) yes checking for /usr/bin/gcc option to enable C11 features... (cached) none needed checking whether /usr/bin/gcc understands -c and -o together... (cached) yes checking dependency style of /usr/bin/gcc... (cached) gcc3 checking for an ANSI C-conforming const... yes checking for a sed that does not truncate output... /usr/bin/sed configure: finding Fortran compiler checking whether the compiler supports GNU Fortran... yes checking whether /usr/bin/gfortran accepts -g... yes checking whether the compiler supports GNU Fortran 77... yes checking whether /usr/bin/gfortran accepts -g... yes checking whether Fortran compiler is checked for ISO_C_BINDING support... yes checking for Fortran flag to compile .f90 files... none checking fortran 90 modules inclusion flag... -I checking if Fortran compiler supports Fortran 2003 ISO_C_BINDING... yes checking if Fortran compiler supports Fortran 2008 ISO_FORTRAN_ENV additions... yes checking if Fortran compiler supports TS29113 standard extension... yes checking if Fortran compiler supports allow-mismatch flag... no checking if Fortran compiler supports mismatch_all flag... no checking whether fortran type sizes should be checked... yes checking whether large file (> 2GB) tests should be run... no checking whether benchmarks should be run... yes checking where to put large temp files if large file tests are run... . configure: setting up libtool checking how to print strings... printf checking for a sed that does not truncate output... (cached) /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by /usr/bin/gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from /usr/bin/gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... mt checking if mt is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/time.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if /usr/bin/gcc supports -fno-rtti -fno-exceptions... no checking for /usr/bin/gcc option to produce PIC... -fPIC -DPIC checking if /usr/bin/gcc PIC flag -fPIC -DPIC works... yes checking if /usr/bin/gcc static flag -static works... no checking if /usr/bin/gcc supports -c -o file.o... yes checking if /usr/bin/gcc supports -c -o file.o... (cached) yes checking whether the /usr/bin/gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking for /usr/bin/gfortran option to produce PIC... -fPIC checking if /usr/bin/gfortran PIC flag -fPIC works... yes checking if /usr/bin/gfortran static flag -static works... no checking if /usr/bin/gfortran supports -c -o file.o... yes checking if /usr/bin/gfortran supports -c -o file.o... (cached) yes checking whether the /usr/bin/gfortran linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking for /usr/bin/gfortran option to produce PIC... -fPIC checking if /usr/bin/gfortran PIC flag -fPIC works... yes checking if /usr/bin/gfortran static flag -static works... no checking if /usr/bin/gfortran supports -c -o file.o... yes checking if /usr/bin/gfortran supports -c -o file.o... (cached) yes checking whether the /usr/bin/gfortran linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate configure: finding other utilities configure: trying to set fortran flags for this platform checking what FC is set to... /usr/bin/gfortran checking for special C compiler options needed for large files... no checking for FILE_OFFSET_BITS value needed for large files... no checking for /usr/bin/nm... /usr/bin/nm -B checking nm flags... checking for C-equivalent to Fortran routine "SUB"... sub checking for Fortran "byte"... yes checking for Fortran "integer2"... yes checking for Fortran "integer8"... yes checking if Fortran "byte" is C "signed char"... yes checking if Fortran "byte" is C "short"... no checking if Fortran "byte" is C "int"... no checking if Fortran "byte" is C "long"... no checking if Fortran "integer2" is C "short"... yes checking if Fortran "integer2" is C "int"... no checking if Fortran "integer2" is C "long"... no checking if Fortran "integer8" is C "short"... no checking if Fortran "integer8" is C "int"... no checking if Fortran "integer8" is C "long long"... yes checking if Fortran "integer" is C "int"... yes checking if Fortran "real" is C "float"... yes checking if Fortran "doubleprecision" is C "double"... yes checking for Fortran-equivalent to netCDF "byte"... byte checking for Fortran-equivalent to netCDF "short"... integer*2 configure: checking types, headers, and functions checking for floor in -lm... yes checking for library containing dlopen... none required checking for netcdf.h... yes checking for library containing nc_open... -lnetcdf checking for nc_def_opaque... yes checking for nccreate... yes checking for nc_set_log_level... yes checking for oc_open... no checking for nc_def_var_szip... yes checking netCDF logging present... yes checking netCDF v2 API present... yes checking netCDF-4 present... no checking whether to test the filter API... no checking for stdlib.h... (cached) yes checking for sys/types.h... (cached) yes checking for sys/param.h... yes checking for locale.h... yes checking for stdio.h... (cached) yes checking for stdarg.h... yes checking for errno.h... yes checking for ctype.h... yes checking for fcntl.h... yes checking for malloc.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/stat.h... (cached) yes checking for getopt.h... yes checking for sys/time.h... (cached) yes checking for sys/resource.h... yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for egrep... (cached) /usr/bin/grep -E checking for sys/wait.h that is POSIX.1 compatible... yes checking for vprintf... yes checking for _Bool... yes checking for stdbool.h that conforms to C99... yes checking for size_t... yes checking for working alloca.h... yes checking for alloca... yes checking for size_t... (cached) yes checking for off_t... yes checking for ssize_t... yes checking for ptrdiff_t... yes checking for uchar... no checking for longlong... no checking whether char is unsigned... no checking size of short... 2 checking size of int... 4 checking size of long... 8 checking size of float... 4 checking size of double... 8 checking size of off_t... 8 checking size of size_t... 8 checking size of ptrdiff_t... 8 configure: generating header files and makefiles configure: WARNING: cache variable ac_cv_env_LDFLAGS_value contains a newline checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating nf-config config.status: creating netcdf-fortran.pc config.status: creating libnetcdff.settings config.status: creating docs/Makefile config.status: creating fortran/Makefile config.status: creating nf_test/Makefile config.status: creating nf_test4/Makefile config.status: creating nf03_test/Makefile config.status: creating nf03_test4/Makefile config.status: creating CMakeExtras/Makefile config.status: creating libsrc/Makefile config.status: creating examples/Makefile config.status: creating examples/F90/Makefile config.status: creating examples/F77/Makefile config.status: linking nf_test/ref_fills.nc to nf_test/fills.nc config.status: executing depfiles commands config.status: error: in /home/tes/WRF_libs/netcdf-fortran-4.6.0': config.status: error: Something went wrong bootstrapping makefile fragments for automatic dependency tracking. If GNU make was not used, consider re-running the configure script with MAKE="gmake" (or whatever is necessary). You can also try re-running configure with the '--disable-dependency-tracking' option to at least be able to build the package (albeit without support for automatic dependency tracking). See config.log' for more details configure: WARNING: cache variable ac_cv_env_LDFLAGS_value contains a newline ===<

(2, when '--disable-dependency-tracking is added from above last few lines):
CFLAGS="-I$(/home/tes/WRF_libs/netcdf2/bin/nc-config --includedir)" LDFLAGS="-L$(/home/tes/WRF_libs/netcdf2/bin/nc-config --libdir --libs)" ./configure --prefix=/home/tes/WRF_libs/netcdf2 --disable-dependency-tracking --disable-shared

===> Posted here starts from the 'error' down the final result, as the top above are all the same <=== config.status: executing depfiles commands config.status: executing libtool commands

NetCDF Fortran Configuration Summary

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

General

---

Library Version: 4.6.0 Configured On: Fri Apr 14 09:58:14 PDT 2023 Host System: x86_64-pc-linux-gnu Build Directory: /home/tes/WRF_libs/netcdf-fortran-4.6.0 Install Prefix: /home/tes/WRF_libs/netcdf2

Compiling Options

---

Fortran Compiler: /usr/bin/gfortran FFLAGS: -g -O2 LDFLAGS: -L/home/tes/WRF_libs/netcdf2/lib -L/home/tes/WRF_libs/netcdf2/lib -L/home/tes/WRF_libs/grib2/lib -lnetcdf -lm -ldl -lsz -lbz2 -lxml2 -lcurl -lnetcdf -lz C Compiler: /usr/bin/gcc CPPFLAGS: -I/home/tes/WRF_libs/netcdf2/include CFLAGS: -I/home/tes/WRF_libs/netcdf2/include -DLONGLONG_IS_LONG Shared Library: no Static Library: yes Extra libraries: -lnetcdf -lm

Features

---

F03: yes Dap Support: no Logging Support: yes NetCDF-2 API: yes NetCDF-4 API: no CDF5 Support: yes Parallel IO: no NetCDF4 Parallel IO: no PnetCDF Parallel IO: no SZIP Write Support: no Zstandard Support: no Quantize: yes configure: WARNING: cache variable ac_cv_env_LDFLAGS_value contains a newline ===< Thank you!

[edwardhartnett]

OK, now put up the full output of make check.

[edwardhartnett]

OK, now put up the full output of make check.

[tghi461]

It's just a one-line report: [t.ghidey@aeolus netcdf-fortran-4.6.0]$ make check Makefile:317: *** missing separator. Stop. [t.ghidey@aeolus netcdf-fortran-4.6.0]$

[edwardhartnett]

Start again with a new unpacking of netcdf-fortran.

[tghi461]

Thanks again! it is still the same. I have had this repeated zillion times, as in: [t.ghidey@aeolus WRF_libs]$ rm -r netcdf-fortran-4.6.0/ [t.ghidey@aeolus WRF_libs]$ ls netcdf-fortran-4.6.0 ls: cannot access netcdf-fortran-4.6.0: No such file or directory [t.ghidey@aeolus WRF_libs]$ tar xzf lib.gzfiles/netcdf-fortran-4.6.0.tar.gz [t.ghidey@aeolus WRF_libs]$ ls netcdf-fortran-4.6.0 acinclude.m4 configure fortran missing nf_test4 aclocal.m4 configure.ac install-sh netCDF-FortranConfig.cmake.in README.md CMakeExtras COPYRIGHT libnetcdff.settings.in netcdf-fortran.pc.in RELEASE_NOTES.md CMakeLists.txt CTestConfig.cmake.in libsrc nf03_test test-driver compile depcomp ltmain.sh nf03_test4 config.guess docs m4 nf-config.cmake.in config.h.cmake.in examples Makefile.am nf-config.in config.sub F03Interfaces_LICENSE Makefile.in nf_test [t.ghidey@aeolus WRF_libs]$ CFLAGS="-I$(/home/tes/WRF_libs/netcdf2/bin/nc-config --includedir)" LDFLAGS="-L$(/home/tes/WRF_libs/netcdf2/bin/nc-config --libdir --libs)" ./configure --prefix=/home/tes/WRF_libs/netcdf2 --disable-shared >& configure1.out

====> After reporting the bootstrapping issue, I added the Unidata recommended optimizer and results still the same as posted above earlier today <==== [t.ghidey@aeolus netcdf-fortran-4.6.0]$ vi configure1.out [t.ghidey@aeolus netcdf-fortran-4.6.0]$ CFLAGS="-I$(/home/tes/WRF_libs/netcdf2/bin/nc-config --includedir)" LDFLAGS="-L$(/home/tes/WRF_libs/netcdf2/bin/nc-config --libdir --libs)" ./configure --prefix=/home/tes/WRF_libs/netcdf2 --disable-dependency-tracking --disable-shared >& configure2.out [t.ghidey@aeolus netcdf-fortran-4.6.0]$ vi configure2.out [t.ghidey@aeolus netcdf-fortran-4.6.0]$ make check Makefile:317: *** missing separator. Stop. [t.ghidey@aeolus netcdf-fortran-4.6.0]$

[OMGTaylor0814]

Hi, I met another problem, when i compile netcdf-fortran-4.5.2 as wrf onLineTutorial suggested, Warning occurred: configure: WARNING: unrecognized options: --disable-dap, --disable-netcdf-4 that cause error when I try to compile WRF, I clean the environment, but I do have another version netcdf(4.1.3) in another file

Best Regards, config.log

[WardF]

--disable-dap and --disable-netcdf-4 are options for the netcdf-c library, not netcdf-fortran. configure for netcdf-fortran should detect whether the C library was built with DAP and NETCDF4 automatically.