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

Mon Jun 1 17:16:31 CDT 2015

That message "ncmpi_inq_typeids not implemented" should not appear.
It is fishy.

I forgot to ask the PnetCDF version you are using.
Please let me know. Also, please send me the file config.log. Thanks.

Wei-keng

On Jun 1, 2015, at 5:02 PM, Nick Papior Andersen wrote:

> Oh, and I do not have these problems using pure gcc 5.1.0 on my local machine.
> 
> 2015-06-02 0:00 GMT+02:00 Nick Papior Andersen <nickpapior at gmail.com>:
> Dear Wei-keng and Rob,
> 
> My default options did not include -g flag, so the coredump was quite un-useful ;(
> 
> I did the catchsegv thing... Here is the output:
> 
> $> catchsegv ./nctst ./testfile.nc
> ncmpi_inq_typeids not implemented
> *** Segmentation fault
> Register dump:
> 
>  RAX: 00002b61bec50000   RBX: 00002b61bec50000   RCX: 000000000000000c
>  RDX: 0000000000000000   RSI: 00002b61bec50000   RDI: 00007fff5e677fa0
>  RBP: 00007fff5e677fa0   R8 : 0000000000e79b60   R9 : 00000000000000f0
>  R10: 00007fff5e677d70   R11: 00002b61be9e1560   R12: 00007fff5e6780e0
>  R13: 00007fff5e678920   R14: 000000000000004c   R15: 00007fff5e677fa0
>  RSP: 00007fff5e677f60
> 
>  RIP: 00002b61be9e0e79   EFLAGS: 00010206
> 
>  CS: 0033   FS: 0000   GS: 0000
> 
>  Trap: 0000000e   Error: 00000005   OldMask: 00000000   CR2: ffffffe8
> 
>  FPUCW: 0000037f   FPUSW: 00000000   TAG: 00002b61
>  RIP: bf8f7fff   RDP: 5e677ff0
> 
>  ST(0) 0000 0000000000000033   ST(1) 0000 000000000000000d
>  ST(2) 0000 0000000000c80000   ST(3) 0000 0000000000000640
>  ST(4) 0000 0000000000000000   ST(5) 0000 0000000000000000
>  ST(6) 0000 0000000000000000   ST(7) 8000 8000000000000000
>  mxcsr: 9fe0
>  XMM0:  00000000000000000000000000000000 XMM1:  00000000000000000000000000000000
>  XMM2:  00000000000000000000000000000000 XMM3:  00000000000000000000000000000000
>  XMM4:  00000000000000000000000000000000 XMM5:  00000000000000000000000000000000
>  XMM6:  00000000000000000000000000000000 XMM7:  00000000000000000000000000000000
>  XMM8:  00000000000000000000000000000000 XMM9:  00000000000000000000000000000000
>  XMM10: 00000000000000000000000000000000 XMM11: 00000000000000000000000000000000
>  XMM12: 00000000000000000000000000000000 XMM13: 00000000000000000000000000000000
>  XMM14: 00000000000000000000000000000000 XMM15: 00000000000000000000000000000000
> 
> Backtrace:
> /zdata/groups/common/nicpa/2015-test/generic/gcc/5.1.0/lib64/libstdc++.so.6(_ZNSo6sentryC2ERSo+0x19)[0x2b61be9e0e79]
> /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)[0x2b61be9e1589]
> /zdata/groups/common/nicpa/2015-test/generic/gcc/5.1.0/lib64/libstdc++.so.6(_ZStlsISt11char_traitsIcEERSt13basic_ostreamIcT_ES5_PKc+0x27)[0x2b61be9e19e7]
> ??:0(_Z3genRKP19ompi_communicator_tPKcN7PnetCDF9NcmpiFile10FileFormatE)[0x40d4a5]
> ??:0(main)[0x409f60]
> /lib64/libc.so.6(__libc_start_main+0xfd)[0x2b61bf0a5d5d]
> ??:0(_start)[0x409cb9]
> 
> 
> Where I think the top line is pretty self-explanatory ;)
> And looking at the code, it makes sense, whether it should be called at all is another matter... 
> 
> 2015-06-01 18:25 GMT+02:00 Wei-keng Liao <wkliao at eecs.northwestern.edu>:
> 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
> 
> 
> 
> 
> -- 
> Kind regards Nick
> 
> 
> 
> -- 
> Kind regards Nick