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

[Rob Latham]

On 06/02/2015 10:18 AM, Wei-keng Liao wrote:
> Hi, Nick
>
> I found a Xeon machine that has icc and built 1.6.0 without errors.
> icc version 15.0.2 (gcc version 4.4.7 compatibility)
>
> I also notice from your config.log that CFLAGS was set even you did not set it at configure command line. If you search keyword for "ac_cv_env_CFLAGS_value", you can see it contains compile options
> "-m64 -fPIC -O2 -xHost -prec-div ... " See lines 72 and 3419.  In my case, that variable is empty.
> Something strange in configure triggers the setting of use these explicit compile options.
> Maybe you should regenerate file configure by running command "autoreconf".
>
> The option -fPIC is for building share libraries, which I suspect is the cause of error you are seeing. I built my OpenMPI 1.8.5 with configure option "--enable-static --disable-shared".
> I was seeing problems when I used an OpenMPI with shared library option enabled to build netCDF or HDF5, so I disable it. (I remember shared option is discouraged by parallel HDF5.)
> Do you know how your OpenMPI was built?

The shared option was indeed discouraged by HDF5, but linkers have 
gotten better and systems are no longer (typically) a hodge-podge of 
random workstations.

-fPIC is needed if you want to link with Unidata NetCDF, right?  Or one 
can explicitly select and build that whole stack entirely with static 
libraries.  Must make for some large executable files! :>

==rob

>
>
> Wei-keng
>
> On Jun 2, 2015, at 9:29 AM, Nick Papior Andersen wrote:
>
>>
>>
>> 2015-06-02 16:25 GMT+02:00 Rob Latham <robl at mcs.anl.gov>:
>>
>>
>> On 06/02/2015 02:58 AM, Nick Papior Andersen wrote:
>> ./nctst        ./testfile.nc <http://testfile.nc>
>> ncmpi_inq_typeids not implemented
>> [n-62-12-2:21767] *** Process received signal ***
>> [n-62-12-2:21767] Signal: Segmentation fault (11)
>> [n-62-12-2:21767] Signal code: Address not mapped (1)
>> [n-62-12-2:21767] Failing at address: 0xffffffffffffffe8
>> [n-62-12-2:21767] [ 0] /lib64/libpthread.so.0(+0xf710)[0x2b3e93945710]
>> [n-62-12-2:21767] [ 1]
>> /zdata/groups/common/nicpa/2015-test/generic/gcc/5.1.0/lib64/libstdc++.so.6(_ZNSo6sentryC2ERSo+0x19)[0x2b3e934ace79]
>> [n-62-12-2:21767] [ 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)[0x2b3e934ad589]
>> [n-62-12-2:21767] [ 3]
>> /zdata/groups/common/nicpa/2015-test/generic/gcc/5.1.0/lib64/libstdc++.so.6(_ZStlsISt11char_traitsIcEERSt13basic_ostreamIcT_ES5_PKc+0x27)[0x2b3e934ad9e7]
>> [n-62-12-2:21767] [ 4] ./nctst[0x40ad62]
>> [n-62-12-2:21767] [ 5] ./nctst[0x40b93c]
>> [n-62-12-2:21767] [ 6]
>> /lib64/libc.so.6(__libc_start_main+0xfd)[0x2b3e93d76d5d]
>> [n-62-12-2:21767] [ 7] ./nctst[0x405899]
>> [n-62-12-2:21767] *** End of error message ***
>>
>> I understand the oddity here is that inq_typids is getting called somehow, and so the backtrace is in some ways irrelevant.  I ran it through c++filt anyway:
>> I agree completely.
>>
>>
>> ./nctst        ./testfile.nc
>> ncmpi_inq_typeids not implemented
>> [n-62-12-2:21767] *** Process received signal ***
>> [n-62-12-2:21767] Signal: Segmentation fault (11)
>> [n-62-12-2:21767] Signal code: Address not mapped (1)
>> [n-62-12-2:21767] Failing at address: 0xffffffffffffffe8
>> [n-62-12-2:21767] [ 0] /lib64/libpthread.so.0(+0xf710)[0x2b3e93945710]
>> [n-62-12-2:21767] [ 1] /zdata/groups/common/nicpa/2015-test/generic/gcc/5.1.0/lib64/libstdc++.so.6(std::basic_ostream<char, std::char_traits<char> >::sentry::sentry(std::basic_ostream<char, std::char_traits<char> >&)+0x19)[0x2b3e934ace79]
>> [n-62-12-2:21767] [ 2] /zdata/groups/common/nicpa/2015-test/generic/gcc/5.1.0/lib64/libstdc++.so.6(std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*, long)+0x29)[0x2b3e934ad589]
>> [n-62-12-2:21767] [ 3] /zdata/groups/common/nicpa/2015-test/generic/gcc/5.1.0/lib64/libstdc++.so.6(std::basic_ostream<char, std::char_traits<char> >& std::operator<< <std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*)+0x27)[0x2b3e934ad9e7]
>> [n-62-12-2:21767] [ 4] ./nctst[0x40ad62]
>> [n-62-12-2:21767] [ 5] ./nctst[0x40b93c]
>> [n-62-12-2:21767] [ 6] /lib64/libc.so.6(__libc_start_main+0xfd)[0x2b3e93d76d5d]
>> [n-62-12-2:21767] [ 7] ./nctst[0x405899]
>> [n-62-12-2:21767] *** End of error message ***
>>
>> --
>> Rob Latham
>> Mathematics and Computer Science Division
>> Argonne National Lab, IL USA
>>
>>
>>
>> --
>> Kind regards Nick
>

-- 
Rob Latham
Mathematics and Computer Science Division
Argonne National Lab, IL USA