Re: [netcdfgroup] Difficulty configuring NETCDF on Linux QEMU

• To: Alvaro Fernandez <afernandez@xxxxxxxxxxxxxxx>
• Subject: Re: [netcdfgroup] Difficulty configuring NETCDF on Linux QEMU
• From: Dave Allured - NOAA Affiliate <dave.allured@xxxxxxxx>
• Date: Tue, 27 May 2025 14:40:45 -0600

Config.log shows unexpected errors that are confusing several config
tests.  The actual error happens not on compile, but on execute:

> checking size of short
> gcc -o conftest  -fno-strict-aliasing -I/home/root/WRF/include
-L/home/root/WRF/lib conftest.c -lsz
> ./conftest
> error while loading shared libraries: libsz.so.2: cannot open shared
object file: No such file or directory

This is a dynamic linking problem.  It might be caused by libsz.so.2
installed in a nonstandard location.  This has come up several times on the
Unidata support list.  Look for titles with "sizeof":

     https://support.unidata.ucar.edu/archives/netcdf/maillist.html

Unidata's suggestion is to append a path to LD_LIBRARY_PATH.  However, a
web search also suggests "sudo ldconfig" as a preferred solution on Linux.


On Mon, May 26, 2025 at 7:09 PM Alvaro Fernandez <afernandez@xxxxxxxxxxxxxxx>
wrote:

> Dave,
>
> Thanks for offering to take a look at the logfile.
>
> I'm attaching it, along with the config.cache I used.
>
> The command used was:
>
> ./configure --disable-dap --disable-libxml2
> CPPFLAGS="-I/home/root/WRF/include" LDFLAGS="-L/home/root/WRF/lib"
> --host=riscv64-linux-gnu --build=riscv64-linux-gnu
>  --cache-file=config.cache  2>&1  | tee configure-net.out
>
> Alvaro
>
>
> *From:* Dave Allured - NOAA Affiliate <dave.allured@xxxxxxxx>
> *Sent:* Monday, May 26, 2025 2:03 PM
>
> > configure: error: cannot compute sizeof (size_t)
>
> There is a known generic problem in configure scripts.  Internally they
> use a small C program for type checking.  Sometimes that test program fails
> for some other reason, something like library not found; and the error
> message does not report the real problem.  That is probably what is
> happening here.  A careful examination of config.log may reveal the real
> problem.  Feel free to post config.log as link or attachment, and I will
> take a look.
>
> Alternatively, try building netCDF with Cmake rather than configure.  It
> uses completely different code for testing system features.
>
>
> On Mon, May 26, 2025 at 11:24 AM Alvaro Fernandez <
> afernandez@xxxxxxxxxxxxxxx> wrote:
>
> Hi,
>
> I'm trying to build NETCDF on (a QEMU emulation of) a RISC-V platform
> we're developing.
>
> I've successfully built other libraries (like HDF5, zlib, etc.) on this
> QEMU with gcc 14.2.0.
>
> However, I am having difficulty completing the configuration phase of the
> NETCDF build process.
>
> This machine will not be accessing the web or pulling down anything, so I
> disabled DAP and XML, and am not giving it curl.
>
> I started with this configure command:
>
> ./configure --disable-dap --disable-libxml2
> CPPFLAGS="-I/home/root/WRF/include" LDFLAGS="-L/home/root/WRF/lib" 2>&1  |
> tee configure-net.out
>
> But I get errors like:
>
> checking size of size_t... configure: error: in
> '/home/root/repos/netcdf-c-4.9.3':
> configure: error: cannot compute sizeof (size_t)
> See 'config.log' for more details
>
> I reasoned that the configure script  might be confused about the host or
> built targets, so I decided to be explicit.
>
> Below is the latest attempt. I added the cache file:
>
> root@qemuriscv64:~/repos/netcdf-c-4.9.3# cat config.cache
> ac_cv_sizeof_off_t=8
>
> And then I ran:
>
> ./configure --disable-dap --disable-libxml2
> CPPFLAGS="-I/home/root/WRF/include" LDFLAGS="-L/home/root/WRF/lib"
> --host=riscv64-linux-gnu --build=riscv64-linux-gnu
> --cache-file=config.cache  2>&1  | tee configure-net.out
>
> It fails with the same error.
>
> This error is detected in line 26715 of the configure script.
>
> I see from the comments that this test serves to guard against an error in
> the HP compiler. Is this still a useful test?
>
> I would suspect our toolchain usually, but it's built hdf5 and multiple
> other applications.
>
> Thanks in advance,
>
> Alvaro Fernandez, PhD
> Inspire Semi
>
>

• Follow-Ups:
  • Re: [netcdfgroup] Difficulty configuring NETCDF on Linux QEMU
    • From: Alvaro Fernandez

• References:
  • [netcdfgroup] Difficulty configuring NETCDF on Linux QEMU
    • From: Alvaro Fernandez
  • Re: [netcdfgroup] Difficulty configuring NETCDF on Linux QEMU
    • From: Dave Allured - NOAA Affiliate
  • Re: [netcdfgroup] Difficulty configuring NETCDF on Linux QEMU
    • From: Alvaro Fernandez