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,

To print the trace of a segmentation fault is easy. You can run command
"gdb corefile" and when at the gdb prompt, type command "where".
If you can send me the printout, it will be helpful.

Just to clarify, if gcc 5.1.0 is used, are you saying there is no problem of building PnetCDF?
Can you tell me the configure command line you used?

Wei-keng

On Jun 1, 2015, at 11:11 AM, Nick Papior Andersen wrote:

> 
> 
> 2015-06-01 17:09 GMT+02:00 Wei-keng Liao <wkliao at eecs.northwestern.edu>:
> 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?
> I haven't done that. I would rather not go that path? I ain't an avid user of gdb (yet). 
> Also, do both errors happen to Intel C compiler?
> It is only the intel cxx compiler. I only show the gcc version as intel uses that for compatibility issues. (see -gcc-name)
> I thought that this could be problem... Maybe it isn't.
> 
> 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
> 
> Gcc/g++ runs fine. I can compile 20 other different libraries with full support. If anything, it is related to the intel compiler. :(
> If you do not need C++ component, you can build a PnetCDF without it, by adding option
> "--disable-cxx" to the configure command.
> This is already my diverting methodology :) Thanks. 
> 
> 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.
> Ok. :) 
> 
> Thanks again for reporting the problem.
> You are welcome. 
> Thanks for the software.
> 
> 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
> 
> 
> 
> 
> -- 
> Kind regards Nick