Thanks, Heiko--this looks good to me. If no one objects, I'll put it out on CPAN soon. Regards, Doug dhunt@xxxxxxxx Software Engineer UCAR - COSMIC, Tel. (303) 497-2611 On Fri, 11 May 2012, Heiko Klein wrote:
Hi Doug,please find attached a modified version of PDL-NetCDF-4.16. Changes I made are:* adding '#undef NC_NETCDF4' if your nc_def_var_deflate test fails. * fixing header and libs for the nc_def_var_deflate test * using again NC_NETCDF4 in the xs code* adding support for new NETCDF4 datatypes (please have a look at the mapping in the cases where PDL does not have the required datatypes, e.g. unsigned int and unsigned long long (I use int and long long instead. And I added not tests for those yet).* fixing a compiler warning concerning 'croak(errmsg)'I tested it successfully against netcdf-4.1.1 (with netcdf4), netcdf-4.2 (with netcdf4) and netcdf-4.2 (without netcdf4)In case Dennis and Russ decide on keeping NC_NETCDF4 with nc_def_var_deflate enabled (the FEATURE solution), we might get runtime problems: hasNetcdf4 will return true, even if it does not exist (It will nicely croak and move the problem to the user). But that problem can't be fixed before we have a decision.Best wishes, Heiko On 2012-05-02 18:11, Doug Hunt wrote: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------------------------------------------------------------------------ _______________________________________________ netcdfgroup mailing list netcdfgroup@xxxxxxxxxxxxxxxx For list information or to unsubscribe, visit: http://www.unidata.ucar.edu/mailing_lists/_______________________________________________ netcdfgroup mailing list netcdfgroup@xxxxxxxxxxxxxxxx For list information or to unsubscribe, visit: http://www.unidata.ucar.edu/mailing_lists/-- 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-- 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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