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

Tue Jun 2 10:54:53 CDT 2015

2015-06-02 17:51 GMT+02:00 Rob Latham <robl at mcs.anl.gov>:

>
>
> 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! :>

Yes, I was linking through shared libraries all the way, and actually I
have never had problems.
I guess better safe than sorry...

And yes, I wanted to reduce the footprint of the installation as it already
was at 9gb for installations using as many shared libraries as I could. :(

>
>
> ==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
>

-- 
Kind regards Nick
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