[netCDF #TLH-274520]: Probable bug in netCDF compression

Hi Lynton,

> I have found a problem associated with compression of variables.
> The example I am attaching is apparent from running valgrind as
> it reports the condition:
> 
> "Conditional jump or move depends on uninitialised value(s)"
> in routine fill_window (deflate.c:1442)
> However, I suspect that the problem may be the cause of a segment core
> dump in my full programme when using compiler optimisatiion.
> 
> I attach a tar-zipped file of the test example.
> This includes the netCDF output file and the screen output
> from running valgrind
> valgrind ./test >valgrind.out
> 
> 
> I am using hdf5 version 1.8.10-patch1
> and  netCDF version 4.2.1.1 with the patch described by JIRA ticket NCF=217
> //  https://bugtracking.unidata.ucar.edu/browse/NCF-217 :
> //     for (dim = grp->dim; dim && dim->next; dim = dim->next)
> //         if (strcmp(dim->name, var->name) && !dim->dirty)
> for (dim = grp->dim; dim ; dim = dim->next)
> if (!strcmp(dim->name, var->name) && !dim->dirty)

Sorry, but I can't seem to duplicate the problem.  Using the same version of
HDF5 (1.8.10-patch1) and the same patch applied to netCDF-4.2.1.1 built using
that version of HDF5, the test works fine and valgrind shows no errors:

C_test2$ make test
gcc -g -I/machine/russ/installs/nc4211-patched/include 
-I/share/ed/local/spike/include  -c -o test.o test.c
gcc -g -I/machine/russ/installs/nc4211-patched/include 
-I/share/ed/local/spike/include  -c -o ncCheck.o ncCheck.c
gcc   test.o ncCheck.o  -L/machine/russ/installs/nc4211-patched/lib -lnetcdf 
-Wl,-rpath -Wl,/machine/russ/installs/nc4211-patched/lib -o test
C_test2$ ./test
C_test2$ valgrind ./test
==2964== Memcheck, a memory error detector
==2964== Copyright (C) 2002-2012, and GNU GPL'd, by Julian Seward et al.
==2964== Using Valgrind-3.8.1 and LibVEX; rerun with -h for copyright info
==2964== Command: ./test
==2964== 
==2964== 
==2964== HEAP SUMMARY:
==2964==     in use at exit: 541,960 bytes in 40 blocks
==2964==   total heap usage: 2,969 allocs, 2,929 frees, 2,012,562 bytes 
allocated
==2964== 
==2964== LEAK SUMMARY:
==2964==    definitely lost: 0 bytes in 0 blocks
==2964==    indirectly lost: 0 bytes in 0 blocks
==2964==      possibly lost: 0 bytes in 0 blocks
==2964==    still reachable: 541,960 bytes in 40 blocks
==2964==         suppressed: 0 bytes in 0 blocks
==2964== Rerun with --leak-check=full to see details of leaked memory
==2964== 
==2964== For counts of detected and suppressed errors, rerun with: -v
==2964== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 32149 from 5)

C_test2$ valgrind --version
valgrind-3.8.1
C_test2$ gcc --version
gcc (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4)

--Russ


Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: TLH-274520
Department: Support netCDF
Priority: Normal
Status: Closed