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[netCDF #IHQ-551892]: NetCDF build Test failures

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  • Subject: [netCDF #IHQ-551892]: NetCDF build Test failures
  • Date: Thu, 17 Apr 2014 10:32:02 -0600
Hi Phillip,

I am also on Mavericks, and am able to duplicate your issue, although I am 
using gfortran, not ifort.  I have taken a look at one of the failing problems 
in gdb, and it appears (in at least one case) that there is a bug related to 
overlapping strings when strcpy is invoked.  My conjecture is that the latest 
OSX dev tools catch this problem and force a crash, reporting the error.  Below 
is the call stack from my gdb session:

#0  0x00007fff8a07c866 in __pthread_kill ()
#1  0x00007fff8c08d35c in pthread_kill ()
#2  0x00007fff90334b1a in abort ()
#3  0x00007fff90334c91 in abort_report_np ()
#4  0x00007fff90358860 in __chk_fail ()
#5  0x00007fff90358870 in __chk_fail_overlap ()
#6  0x00007fff90358892 in __chk_overlap ()
#7  0x00007fff90358a6c in __strcpy_chk ()
#8  0x000000010000a6a0 in define_netcdf () at genlib.c:41
#9  0x0000000100001794 in main (argc=<value temporarily unavailable, due to 
optimizations>, argv=<value temporarily unavailable, due to optimizations>) at 
main.

My gdb session was invoked from the 'ncdump' directory as follows:

   $ gdb ../ncgen/ncgen 
   (gdb) run ./small.cdl

At this time all I can really suggest is to upgrade to the latest version of 
netcdf, version 4.3.1.1.  Note that there is a known test failure there, too, 
related to a change in our DAP servers; since you are not using DAP, you will 
likely not encounter it, and it is not a 'real' error in any case.

After installing netcdf-c libraries, you would need to install the 
netcdf-fortran libraries.  Since netcdf-4.2, the C, C++ and Fortran 
functionality has been split into separate libraries.

The different libraries may be downloaded from their respective projects on the 
Unidata github page:

http://github.com/Unidata

I hope this helps; if I can be any assistance installing the latest versions, 
please let me know.

-Ward

> Dear NETCDF Team,
> 
> As requested, I am attaching the failure for the tests for the file (MD5 
> netcdf-4.1.3.tar.gz ead16cb3b671f767396387dcb3c1a814).  My configure options 
> are
> 
> ./configure --prefix=/Users/pwolfram/ --disable-dap --disable-netcdf-4 
> --disable--cxx --disable--shared --enable-fortran
> 
> make all
> 
> make check &> checkresults
> 
> I am on Mavericks and made the change to ncgen3/genlib.h as suggested at 
> http://www.unidata.ucar.edu/software/netcdf/docs/known_problems.html#clang-ncgen3.
> 
> The fortran compiler is
> 
> ifort version 14.0.2
> 
> The C compiler is
> 
> Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr 
> --with-gxx-include-dir=/usr/include/c++/4.2.1
> Apple LLVM version 5.1 (clang-503.0.38) (based on LLVM 3.4svn)
> Target: x86_64-apple-darwin13.0.2
> Thread model: posix
> 
> Any ideas you have on this issue would be greatly appreciated!
> 
> Thanks,
> Phillip
> 
> 

Ticket Details
===================
Ticket ID: IHQ-551892
Department: Support netCDF
Priority: Normal
Status: Closed