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

Mon Jun 1 19:35:00 CDT 2015

You are right. None of the locations that call ncmpi_inq_typeids() are supposed to reach at all,
because that function is for compound data types (not supported by PnetCDF.)
I added a printf statement to all places this function is called, but none shows.

What you suggested may be a right solution, could you please give it a try?
i.e. change line 112 of file ncmpi_notyet.cpp from

ncmpi_inq_typeids(int ncid, int *ntypes, int *typeids){printf("%s not implemented\n",__func__); return NC_EINVAL;}
to
ncmpi_inq_typeids(int ncid, int *ntypes, int *typeids){*ntypes = 0; printf("%s not implemented\n",__func__); return NC_EINVAL;}

Once you made the changes, you can run "make" command in directory src/libcxx
and then go to test/CXX, run "make check".

Wei-keng

On Jun 1, 2015, at 7:14 PM, Nick Papior Andersen wrote:

> 
> 
> 2015-06-02 1:48 GMT+02:00 Nick Papior Andersen <nickpapior at gmail.com>:
> I did this (adding traceback to the debugging compilation)
> 
> ../configure CXXFLAGS='-g -O0 -traceback' CFLAGS='-g -O0 -traceback' CC=mpicc CXX=mpicxx F77=mpif77 F90=mpif90 FC=mpif90 --prefix=/zdata/groups/common/nicpa/2015-test/XeonX5550/pnetcdf/1.6.0/intel-15.0.1 --with-mpi=/zdata/groups/common/nicpa/2015-test/XeonX5550/openmpi/1.8.5/intel-15.0.1 --enable-debug --disable-fortran
> make
> cd test/CXX
> make check
> 
> And got (well the same thing :( ):
> ./nctst        ./testfile.nc
> ncmpi_inq_typeids not implemented
> [n-62-12-2:31968] *** Process received signal ***
> [n-62-12-2:31968] Signal: Segmentation fault (11)
> [n-62-12-2:31968] Signal code: Address not mapped (1)
> [n-62-12-2:31968] Failing at address: 0xffffffffffffffe8
> [n-62-12-2:31968] [ 0] /lib64/libpthread.so.0(+0xf710)[0x2b13425f0710]
> [n-62-12-2:31968] [ 1] /zdata/groups/common/nicpa/2015-test/generic/gcc/5.1.0/lib64/libstdc++.so.6(_ZNSo6sentryC2ERSo+0x19)[0x2b1342157e79]
> [n-62-12-2:31968] [ 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)[0x2b1342158589]
> [n-62-12-2:31968] [ 3] /zdata/groups/common/nicpa/2015-test/generic/gcc/5.1.0/lib64/libstdc++.so.6(_ZStlsISt11char_traitsIcEERSt13basic_ostreamIcT_ES5_PKc+0x27)[0x2b13421589e7]
> [n-62-12-2:31968] [ 4] ./nctst[0x40ad62]
> [n-62-12-2:31968] [ 5] ./nctst[0x40b93c]
> [n-62-12-2:31968] [ 6] /lib64/libc.so.6(__libc_start_main+0xfd)[0x2b1342a21d5d]
> [n-62-12-2:31968] [ 7] ./nctst[0x405899]
> [n-62-12-2:31968] *** End of error message ***
> make: *** [check] Segmentation fault
> 
> 
> Note that I have "corrected" the return to an empty string and the above compilation.
> However, it is clear from the code that the values that are to be updated (number of types) isn't set. Hence the error is in the logic behind calling the inq_typ, not the preceding code, which should function once the number of types code has been implemented, correctly setting the number of types.
> I think I was a bit unclear here.
> The integer size for the number of types hasn't been set properly, hence the segmentation fault (I think).
> The error is before this call, it shouldn't be made at all as you state. Hence any debugging will probably not show anything useful as it is a path that shouldn't be taken.
> So the problem is why inq_typ is called. (I think we agree on this no?) 
> 
> (code snippet:
> int ntypesp;
>     ncmpiCheck(ncmpi_inq_typeids(getId(), &ntypesp,typeidsp),__FILE__,__LINE__);
> )
> with no initialization.
> Maybe the "not implemented" routine should set the ntypesp to 0?
> 
> 
> Note, that this may also be a compiler bug. :(
> 
> 2015-06-02 1:24 GMT+02:00 Wei-keng Liao <wkliao at eecs.northwestern.edu>:
> Hi, Nick
> 
> I tried to see if any place that can indirectly invoke that message, but could not find one.
> 
> I wonder if you can kindly help me find more information about this error, by rebuilding your PnetCDF with the following configure command (with debug option enabled):
> 
> ./configure --enable-debug --disable-fortran --with-mpi=/zdata/groups/common/nicpa/2015-test/XeonX5550/openmpi/1.8.5/intel-15.0.1
> 
> Disabling Fortran gives you a shorter build time.
> 
> Once you build it, please cd directly to test/CXX and run "make check" there.
> This can skip all other tests.
> 
> thanks
> 
> Wei-keng
> 
> On Jun 1, 2015, at 5:21 PM, Nick Papior Andersen wrote:
> 
> > Oh, yeah sorry. it is the latest 1.6.0 version.
> > Here is a tar with the config.log and the tmp.test (it was 1 mb, so sorry for taring).
> >
> >
> >
> > 2015-06-02 0:16 GMT+02:00 Wei-keng Liao <wkliao at eecs.northwestern.edu>:
> > 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
> >
> >
> >
> >
> > --
> > Kind regards Nick
> > <log-test.tar.gz>
> 
> 
> 
> 
> -- 
> Kind regards Nick
> 
> 
> 
> -- 
> Kind regards Nick