With intel 2015.1.133 and gcc 5.1.0 in the path, error on make check with cxx interface
Nick Papior Andersen
nickpapior at gmail.com
Mon Jun 1 17:00:07 CDT 2015
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
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