Re: [netcdfgroup] netcdf.h declares non-existing functions

  • To: Heiko Klein <Heiko.Klein@xxxxxx>
  • Subject: Re: [netcdfgroup] netcdf.h declares non-existing functions
  • From: Doug Hunt <dhunt@xxxxxxxx>
  • Date: Wed, 2 May 2012 10:11:00 -0600 (MDT)
Hi Heiko: I'm fine with your proposal. This will make the netcdf interface more useful (ability to check HDF presence at compile- and run-times) at the cost of a little bit of extra complexity in PDL-NetCDF.

Could you add the extra logic to check for netcdf versions between 4.1.2 and 4.2 to the (not released to CPAN) PDL-NetCDF-4.16 that I sent you and test it with HDF?

Once you've got that working, send it back and I'll test it in my environment and then release it to CPAN.

How does that sound?

--Doug

dhunt@xxxxxxxx
Software Engineer
UCAR - COSMIC, Tel. (303) 497-2611

On Wed, 2 May 2012, Heiko Klein wrote:

Hi Dennis, Doug,

I really like Dennis proposal. It will give both a compile and a run-time ability to check for netcdf4 support.


Concernings Dougs comment: Yes, we need a test for the broken versions 4.1.2 to 4.2. Since NC_NETCDF4 is correct before 4.1.2 and will be correct after 4.2, a way to go would be to just add
#undef NC_NETCDF4
right after #include "netcdf.h", depending of the result of a test_nc_netcdf4_wrongly_declared.

The pre-build test code (e.g. autotools/configure) for that function is then something like:

#include "netcdf.h"
int main () {
#ifdef NC_NETCDF4
   nc_inq_var_deflate(0, 0, NULL, NULL, NULL);
# else
   this_fails();
# endif
}

Doug, I can put that into PDL::NetCDF during that week, if you like. I see you have already a framework for pre-build tests in the current PDL::NetCDF 4.16

Heiko

On 2012-05-01 17:49, Doug Hunt wrote:
Hi Dennis: After sleeping on this, I find I may have spoken too soon.

It may be best (at least from my perspective as maintainer of PDL::NetCDF)
to leave things as they are.

As logical as your change is, it would still introduce a 3rd behavior
regarding netcdf-4 detection. PDL::NetCDF will have to support all 3
behaviors:

1) (version 4.0.1) NC_NETCDF4 defined means netcdf-4 is supported. If
'nc_inq_var_deflate' is present at run-time then netcdf-4 is supported.
2) (version 4.2) NC_NETCDF4 always defined. If 'nc_inq_var_deflate' is
present at run-time then netcdf-4 is supported.
3) (your proposed) NC_NETCDF4 defined means netcdf-4 is supported.
'nc_inq_var_deflate' is always defined, but returns NC_ENOTNC4 if
netcdf-4 is not supported.

Dealing with three of these behaviors will complicate the logic used to
detect netcdf-4 support.

The new version of PDL::NetCDF that I'm working on right now (version
4.16) will do the run-time check and so catch cases 1) and 2), but would
have to be modified to catch case 3).

So, since netcdf version 4.2 is already out there and needs to be
supported, I would think just leaving things the way they are might be
wisest.

Heiko--What do you think?

Regards,

Doug

dhunt@xxxxxxxx
Software Engineer
UCAR - COSMIC, Tel. (303) 497-2611

On Mon, 30 Apr 2012, Doug Hunt wrote:

Hi Dennis: This sounds good to me!

Regards,

Doug Hunt

dhunt@xxxxxxxx
Software Engineer
UCAR - COSMIC, Tel. (303) 497-2611

On Mon, 30 Apr 2012, Dennis Heimbigner wrote:

Unidata proposes to change this as follows.

1. All the netcdf-4 functions will exist in the netcdf-3
only library, but will return the error NC_ENOTNC4
if invoked. This allows runtime testing for netcdf-4 support.
2. The NC_NETCDF4 flag in netcdf.h will only be defined
it the corresponding library has netcdf-4 support enabled.
This is so compile-time testing for netcdf-4 can occur.

Comments?

=Dennis Heimbigner
Unidata


Doug Hunt wrote:
Hi Heiko: I made a fix to the logic PDL-NetCDF uses to detect if
netcdf-4 support is available. In the previous version, a simple
check for the pre-processor symbol NC_NETCDF4 being defined is
made--if it is, then netcdf-4 support is found.

Recent netcdf releases, however, have been defining NC_NETCDF4
whether or not netcdf-4 support is actually present (meaning netcdf
is compiled with HDF5).

The change I made includes a test compile and link of
nc_inq_var_deflate to determine if netcdf-4 support is available.
The logic is in Makefile.PL, not netcdf.pd. I've used this procedure
before in my PDL-Graphics-PLplot interface and it works well.

I'm sending this to you instead of just putting it on CPAN because
(1) I can't get netcdf-4 support compiled in on my machine, so I
can't test it properly and (2) you added the netcdf-4 support so I'd
like you to look it over.

Could you take a look and see if this makes sense to you? If you've
got a netcdf-4 enabled netcdf on one of your systems, it would be
great if you could test it out.

Thanks much,

Doug

dhunt@xxxxxxxx
Software Engineer
UCAR - COSMIC, Tel. (303) 497-2611

On Fri, 27 Apr 2012, Heiko Klein wrote:

Russ,

I'll try to give a better example:

I don't have hdf-libraries installed (at least not in default
pathes). First, from a pure ABI point of view:
---------------------------------------------------------------
With netcdf-4.1.2:
./configure --prefix=/disk1/netcdf-4.1.2_install
make
make install

In /disk1/netcdf-4.1.2_install/include:
$ grep nc_def_var_deflate netcdf.h
* function nc_def_var_deflate. These defines are used there. */
nc_def_var_deflate(int ncid, int varid, int shuffle, int deflate,

In /disk1/netcdf-4.1.2_install/lib:
$ nm libnetcdf.so | grep nc_def_var_deflate

Nothing found, symbol not defined.

--------------------------------------------------------------
New try, all directories removed and new untar:

./configure --prefix=/disk1/netcdf-4.1.2_install --disable-netcdf4
make
make install

In /disk1/netcdf-4.1.2_install/lib:
$ nm libnetcdf.so | grep nc_def_var_deflate

Nothing found, symbol not defined. Still the same.
---------------------------------------------------------------
New try, now 4.2:
$ ./configure --prefix=/disk1/netcdf-4.2_install --disable-netcdf-4
make
make install

In /disk1/netcdf-4.2_install/lib
$ nm libnetcdf.so | grep nc_def_var_deflate

Nothing found, symbol not defined.
---------------------------------------------------------------
A previous build, with hdf5 enabled:
$ nm /disk1/heiko/local/netcdf4.2-rc1/lib/libnetcdf.so | grep
nc_def_var_deflate
000299b0 T nc_def_var_deflate
----------------------------------------------------------------




Now, from a API point of view:

a slightly modified simple_xy_wr.c (from
http://www.unidata.ucar.edu/software/netcdf/examples/programs/),
just enabling compression if netcdf4 is supported by the library:
#ifdef NC_NETCDF4
/* compress all variables in netcdf4 */
if ((retval = nc_def_var_deflate(ncid, varid, 0, 1, 3)))
ERR(retval);
#endif

The program works nicely with netcdf-4.1.1, independently of
netcdf4 is enabled or disabled.
$ gcc -c -I/opt/netcdf4.1.1/include/ simple_xy_wr.c
$ gcc -o simple_xy_wr simple_xy_wr.o -L/opt/netcdf4.1.1/lib/ -lnetcdf
No problems


With above 4.2:
$ gcc -c -I/disk1/netcdf-4.2_install/include/ simple_xy_wr.c
No problems.
$ gcc -o simple_xy_wr simple_xy_wr.o
-L/disk1/netcdf-4.2_install/lib -lnetcdf
simple_xy_wr.o: In function `main':
simple_xy_wr.c:(.text+0x27d): undefined reference to
`nc_def_var_deflate'
collect2: ld returned 1 exit status


With 4.2, but with enabled hdf/netcdf4 support (ok, that's 4.2rc1,
but that not the point here):
$ gcc -c -I/disk1/heiko/local/netcdf4.2-rc1/include simple_xy_wr.c
No problems
$ gcc -o simple_xy_wr simple_xy_wr.o
-L/disk1/heiko/local/netcdf4.2-rc1/lib -lnetcdf
No problems, generating netcdf4 files.


I see the code of nc_def_var_deflate defined in libdispatch/dvar.c,
but it doesn't seem to make it to the library.


Best regards,

Heiko





On 2012-04-26 18:51, Russ Rew wrote:
Heiko,

since netcdf-4.1.2, the netcdf.h file declares all netcdf4
functions,
like nc_def_var_deflate and NC_NETCDF4, even if the library was
compiled
without hdf5 support, and does not have these functions.

I have code like

#ifdef NC_NETCDF4
nc_def_var_deflate(...)
#endif

which worked perfectly with netcdf3 and netcdf4 until 4.1.1. Since
netcdf 4.1.2, this code compiles still, but when the
netcdf-library was
not compiled with hdf5 support, the code won't link with the
library.
This means, that netcdf since 4.1.2 has a single API, but has
different
ABIs depending on netcdf-configure flags. I would suggest adding the
'Extra netcdf4 stuff.' function calls to the netcdf3 code, even
if they
are empty, e.g.

int
nc_def_var_deflate(int ncid, int varid, int shuffle, int deflate,
int deflate_level)
{
return NC_NOERR;
}

This means, that netcdf since 4.1.2 has a single API, but has
different
ABIs depending on netcdf-configure flags. I would suggest adding the
'Extra netcdf4 stuff.' function calls to the netcdf3 code, even
if they
are empty, e.g.

int
nc_def_var_deflate(int ncid, int varid, int shuffle, int deflate,
int deflate_level)
{
return NC_NOERR;
}

Sorry, but I can't duplicate the problem. This is supposed to be
handled by the "dispatch layer" in netCDF-4.x. For example, when you
run "make check" on a netCDF-4.2 distribution that has been
configured
with "--disable-netcdf-4", it will link and run netCDF-3 tests
against
the library, so this would indicate all the public functions
declared in
netcdf.h must be implemented.

The following function appears in libdispatch/dvar.c, even when
configured with "--disable-netcdf-4":

int
nc_def_var_deflate(int ncid, int varid, int shuffle, int deflate,
int deflate_level)
{
NC* ncp;
int stat = NC_check_id(ncid,&ncp);
if(stat != NC_NOERR) return stat;
return
ncp->dispatch->def_var_deflate(ncid,varid,shuffle,deflate,deflate_level);
}

I've also just tried building the 4.2 library with --disable-netcdf-4
and --disable-shared, and verified that a netCDF-3 program
compiles and
links with the resulting static library. However, I had to remove
previously built shared libraries from the directory in which I
installed the static library, because the dynamic linker/loader
will use
an older installed shared library in preference to a new static
library.

I also built a new shared library with --disable-netcdf-4 but without
--disable-shared and verified that a netCDF-3 program could be
successfully linked and run against the resulting shared library. For
this, I set LD_LIBRARY_PATH to run the resulting program, but other
alternatives would also work, assuming the library is installed in
LIBDIR:

- add LIBDIR to the `LD_RUN_PATH' environment variable
during linking
- use the `-Wl,-rpath -Wl,LIBDIR' linker flag
- have system administrator add LIBDIR to `/etc/ld.so.conf'

This was all on a Linux system, but our cross-platform tests should
catch such problems on some other systems, such as Solaris, MacOS,
and
AIX.

It's possible I've misunderstood the problem. If so, I'll need more
information to reproduce it. For now, I think the dispatch layer
implementation already provides the stub functions for 'extra
netCDF-4
stuff' that you're requesting ...

--Russ

Note: as Dennis Heimbigner pointed out last week on this list, for
now
it's necessary to build netCDF-4.2 with
"--disable-dap-remote-tests", at
least until we resolve a problem with the test server, which was
moved
from port 8080 to 8081.

--
Dr. Heiko Klein Tel. + 47 22 96 32 58
Development Section / IT Department Fax. + 47 22 69 63 55
Norwegian Meteorological Institute http://www.met.no
P.O. Box 43 Blindern 0313 Oslo NORWAY


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--
Dr. Heiko Klein                              Tel. + 47 22 96 32 58
Development Section / IT Department          Fax. + 47 22 69 63 55
Norwegian Meteorological Institute           http://www.met.no
P.O. Box 43 Blindern  0313 Oslo NORWAY




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