With intel 2015.1.133 and gcc 5.1.0 in the path, error on make check with cxx interface

[Wei-keng Liao]

Hi, Nick

Your fix for the first bug makes all sense. I will add that to PnetCDF. Thanks.

As for the second error, can you use gdb to print the location of the segmentation fault?
Also, do both errors happen to Intel C compiler?

The two C compilers you used are the latest ones. I have not tried them.
Could you compile/run a simple C++ program to see if gcc works in your environment?
Or, if you installed gcc from source, have you tried run "make -k check"?
See https://gcc.gnu.org/install/test.html

If you do not need C++ component, you can build a PnetCDF without it, by adding option
"--disable-cxx" to the configure command.

By the way, I plan to release 1.6.1 today, but it will not fix the second error you are seeing.
I will try if I can find those new versions of C compiler and fix the problem.
The fix will have to wait for the next release, though.

Thanks again for reporting the problem.

Wei-keng

On Jun 1, 2015, at 1:00 AM, Nick Papior Andersen wrote:

> I am trying to compile and make check with these compilers:
> intel 2015.1.13
> and 
> gcc 5.1.0 in the path.
> 
> Compiling goes fine and everything seems to link correctly.
> However make check errors out in the CXX test.
> 
> First I get this error message:
> ./nctst        ./testfile.nc
> terminate called after throwing an instance of 'std::logic_error'
>   what():  basic_string::_M_construct null not valid
> [n-62-12-2:09803] *** Process received signal ***
> [n-62-12-2:09803] Signal: Aborted (6)
> [n-62-12-2:09803] Signal code:  (-6)
> [n-62-12-2:09803] [ 0] /lib64/libpthread.so.0(+0xf710)[0x2aae4ac54710]
> [n-62-12-2:09803] [ 1] /lib64/libc.so.6(gsignal+0x35)[0x2aae4ae94625]
> [n-62-12-2:09803] [ 2] /lib64/libc.so.6(abort+0x175)[0x2aae4ae95e05]
> [n-62-12-2:09803] [ 3] /zdata/groups/common/nicpa/2015-test/generic/gcc/5.1.0/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x15d)[0x2aae4a7428cd]
> [n-62-12-2:09803] [ 4] /zdata/groups/common/nicpa/2015-test/generic/gcc/5.1.0/lib64/libstdc++.so.6(+0x8c936)[0x2aae4a740936]
> [n-62-12-2:09803] [ 5] /zdata/groups/common/nicpa/2015-test/generic/gcc/5.1.0/lib64/libstdc++.so.6(+0x8c981)[0x2aae4a740981]
> [n-62-12-2:09803] [ 6] /zdata/groups/common/nicpa/2015-test/generic/gcc/5.1.0/lib64/libstdc++.so.6(+0x8cb98)[0x2aae4a740b98]
> [n-62-12-2:09803] [ 7] /zdata/groups/common/nicpa/2015-test/generic/gcc/5.1.0/lib64/libstdc++.so.6(_ZSt19__throw_logic_errorPKc+0x3f)[0x2aae4a767faf]
> [n-62-12-2:09803] [ 8] ./nctst[0x461b42]
> [n-62-12-2:09803] [ 9] ./nctst[0x4644b6]
> [n-62-12-2:09803] [10] ./nctst[0x40c313]
> [n-62-12-2:09803] [11] ./nctst[0x409f60]
> [n-62-12-2:09803] [12] /lib64/libc.so.6(__libc_start_main+0xfd)[0x2aae4ae80d5d]
> [n-62-12-2:09803] [13] ./nctst[0x409cb9]
> [n-62-12-2:09803] *** End of error message ***
> 
> 
> Secondly I change in file src/libcxx/ncmpiType.cpp:
> function inq_type has 'return NULL' which cannot be done using returns of string (unless it is a pointer, which it isn't)
> So I change it to an empty string:
> 'return ""'
> (I am not sure when this is reached, but the error message changes as can be seen below, hence my suspicion is at that code segment)
> 
> Now I recompile and get this alternate error message:
> ./nctst        ./testfile.nc
> [n-62-12-2:23419] *** Process received signal ***
> [n-62-12-2:23419] Signal: Segmentation fault (11)
> [n-62-12-2:23419] Signal code: Address not mapped (1)
> [n-62-12-2:23419] Failing at address: 0xffffffffffffffe8
> [n-62-12-2:23419] [ 0] /lib64/libpthread.so.0(+0xf710)[0x2ab6b02fa710]
> [n-62-12-2:23419] [ 1] /zdata/groups/common/nicpa/2015-test/generic/gcc/5.1.0/lib64/libstdc++.so.6(_ZNSo6sentryC2ERSo+0x19)[0x2ab6afe61e79]
> [n-62-12-2:23419] [ 2] /zdata/groups/common/nicpa/2015-test/generic/gcc/5.1.0/lib64/libstdc++.so.6(_ZSt16__ostream_insertIcSt11char_traitsIcEERSt13basic_ostreamIT_T0_ES6_PKS3_l+0x29)[0x2ab6afe62589]
> [n-62-12-2:23419] [ 3] /zdata/groups/common/nicpa/2015-test/generic/gcc/5.1.0/lib64/libstdc++.so.6(_ZStlsISt11char_traitsIcEERSt13basic_ostreamIcT_ES5_PKc+0x27)[0x2ab6afe629e7]
> [n-62-12-2:23419] [ 4] ./nctst[0x40d4a5]
> [n-62-12-2:23419] [ 5] ./nctst[0x409f60]
> [n-62-12-2:23419] [ 6] /lib64/libc.so.6(__libc_start_main+0xfd)[0x2ab6b0526d5d]
> [n-62-12-2:23419] [ 7] ./nctst[0x409cb9]
> [n-62-12-2:23419] *** End of error message ***
> make[2]: *** [testing] Segmentation fault
> 
> There seem to be something fishy with the cxx interface? 
> I am no expert in cxx... :( So had troubles debugging further...
> 
> -- 
> Kind regards Nick