Cannot disable netcdf API in [email protected] ?

[climbfuji]

Steps to reproduce

I install [email protected] with the ~netcdf variant. The verbose spack install says:

==> hdf: Executing phase: 'autoreconf'
==> hdf: Executing phase: 'configure'
==> [2022-06-29-16:46:46.730940] '/Users/heinzell/prod/spack-stack-v1/cache/build_stage/spack-stage-hdf-4.2.15-lrqus5d362tixy4tu7m3zojzjsddixoh/spack-src/configure' '--prefix=/Users/heinzell/prod/spack-stack-v1/envs/skylab-1.0.0/install/apple-clang/13.1.6/hdf-4.2.15-lrqus5d' '--enable-production' '--enable-static' '--with-zlib=/Users/heinzell/prod/spack-stack-v1/envs/skylab-1.0.0/install/apple-clang/13.1.6/zlib-1.2.12-fb5aox3' '--with-jpeg=/Users/heinzell/prod/spack-stack-v1/envs/skylab-1.0.0/install/apple-clang/13.1.6/libjpeg-turbo-2.1.0-l2jhx75' '--disable-shared' '--disable-netcdf' '--disable-fortran' '--disable-java' '--without-szlib' '--enable-hdf4-xdr'

with the configuration summary looking good:

	    SUMMARY OF THE HDF4 CONFIGURATION
	    =================================

General Information:
-------------------
		   HDF4 Version: 4.2.15
		  Configured on: Wed Jun 29 16:47:15 MDT 2022
		  Configured by: heinzell@JCSDA-L-18146
		 Configure mode: production
		    Host system: i386-apple-darwin21.2.0
              Uname information: Darwin JCSDA-L-18146 21.2.0 Darwin Kernel Version 21.2.0: Sun Nov 28 20:28:41 PST 2021; root:xnu-8019.61.5~1/RELEASE_ARM64_T6000 x86_64
		      Libraries: 
	     Installation point: /Users/heinzell/prod/spack-stack-v1/envs/skylab-1.0.0/install/apple-clang/13.1.6/hdf-4.2.15-lrqus5d

Compiling Options:
------------------
               Compilation Mode: production
                     C compiler: /Users/heinzell/prod/spack-stack-v1/spack/lib/spack/env/clang/clang
                         CFLAGS:  -O2
                       CPPFLAGS:  -I/Users/heinzell/prod/spack-stack-v1/envs/skylab-1.0.0/install/apple-clang/13.1.6/zlib-1.2.12-fb5aox3/include -I/Users/heinzell/prod/spack-stack-v1/envs/skylab-1.0.0/install/apple-clang/13.1.6/libjpeg-turbo-2.1.0-l2jhx75/include 
               Shared Libraries: no
               Static Libraries: yes
  Statically Linked Executables: no
                        LDFLAGS:  -L/Users/heinzell/prod/spack-stack-v1/envs/skylab-1.0.0/install/apple-clang/13.1.6/zlib-1.2.12-fb5aox3/lib -L/Users/heinzell/prod/spack-stack-v1/envs/skylab-1.0.0/install/apple-clang/13.1.6/libjpeg-turbo-2.1.0-l2jhx75/lib
 	 	Extra libraries: -ljpeg -lz 
 		       Archiver: ar
 		 	 Ranlib: ranlib

Languages:
----------
                        Fortran: no

                           Java: no

Features:
---------
               SZIP compression: disabled
   Support for netCDF API 2.3.2: no

But then:

...
Making all in ncdump
/Users/heinzell/prod/spack-stack-v1/spack/lib/spack/env/clang/clang -DHAVE_CONFIG_H -I. -I../../hdf/src  -I../../hdf/src -I../../mfhdf/libsrc -I../../mfhdf/libsrc -I/Users/heinzell/prod/spack-stack-v1/cache/build_stage/spack-stage-hdf-4.2.15-lrqus5d362tixy4tu7m3zojzjsddixoh/spack-src/mfhdf/xdr -DNDEBUG -DHDF -I/Users/heinzell/prod/spack-stack-v1/envs/skylab-1.0.0/install/apple-clang/13.1.6/zlib-1.2.12-fb5aox3/include -I/Users/heinzell/prod/spack-stack-v1/envs/skylab-1.0.0/install/apple-clang/13.1.6/libjpeg-turbo-2.1.0-l2jhx75/include   -O2 -MT dumplib.o -MD -MP -MF .deps/dumplib.Tpo -c -o dumplib.o dumplib.c
...
Making install in ncdump
 /usr/local/bin/gmkdir -p '/Users/heinzell/prod/spack-stack-v1/envs/skylab-1.0.0/install/apple-clang/13.1.6/hdf-4.2.15-lrqus5d/bin'
 /usr/local/bin/gmkdir -p '/Users/heinzell/prod/spack-stack-v1/envs/skylab-1.0.0/install/apple-clang/13.1.6/hdf-4.2.15-lrqus5d/share/man/man1'
  /bin/sh ../../libtool   --mode=install /usr/local/bin/ginstall -c ncdump '/Users/heinzell/prod/spack-stack-v1/envs/skylab-1.0.0/install/apple-clang/13.1.6/hdf-4.2.15-lrqus5d/bin'
 /usr/local/bin/ginstall -c -m 644 ncdump.1 '/Users/heinzell/prod/spack-stack-v1/envs/skylab-1.0.0/install/apple-clang/13.1.6/hdf-4.2.15-lrqus5d/share/man/man1'
libtool: install: /usr/local/bin/ginstall -c ncdump /Users/heinzell/prod/spack-stack-v1/envs/skylab-1.0.0/install/apple-clang/13.1.6/hdf-4.2.15-lrqus5d/bin/ncdump

Error message

With the hdf/4.2.15 module being loaded (in addition to the netcdf modules):

> module li
Currently Loaded Modules:
...
netcdf-c/4.8.1
...
hdf/4.2.15

I get

> which ncdump
/gpfsm/dswdev/jcsda/spack-stack/spack-stack-v1/envs/skylab-1.0.0-intel-2022.0.1/install/intel/2022.0.1/hdf-4.2.15-nn6m4qw/bin/ncdump

Anyone seeing what is going wrong?

Information on your system

Same on all systems: Discover, Orion, macOS, Red Hat 8, with spack-stack-1.0.0 tags of spack-stack and spack.

Example output from spack debug report

* **Spack:** 0.18.0 (779c953a82cb1b0924f38abdd6048fd1b43ea89d)
* **Python:** 3.9.7
* **Platform:** linux-sles12-haswell
* **Concretizer:** clingo

General information

• I have run spack debug report and reported the version of Spack/Python/Platform
• I have searched the issues of this repo and believe this is not a duplicate
• I have run the failing commands in debug mode and reported the output

[climbfuji]

@kgerheiser @edwardhartnett FYI - maybe you can see what I am doing wrong?

[kgerheiser]

It looks configured correctly, could it be a bug in the build?

[edwardhartnett]

I looks correct. But I just built it on my machine with the same result - it says that it's not going to build netcdf, but then it does!

I'm trying the previous release...

[edwardhartnett]

OK, all the way back to 4.2.8 this still happens. Did it --disable-netcdf ever work?

[kgerheiser]

We can either patch configure (or wherever the problem lies), or modify the install with an @run_after(install)

[climbfuji]

We can either patch configure (or wherever the problem lies), or modify the install with an @run_after(install)

... and report the error back ...

My manual override will be to delete ncdump and ncgen in the installations (HPC, AMIs, ...) and add a note to the documentation.

[edwardhartnett]

I have asked the HDF support people and copied you guys in the email, so you can see what they say...

[edwardhartnett]

Just to record their answer: using --disable-netcdf turns off the netCDF functions in HDF4, but the utilities still get built. We need to delete the HDF4 versions of the ncdump/ncgen utilities.

[edwardhartnett]

Just to record their answer: using --disable-netcdf turns off the netCDF functions in HDF4, but the utilities still get built. We need to delete the HDF4 versions of the ncdump/ncgen utilities.