Thanks to Scott's answer I solved the previous issue that indeed was
related to linking the intel compiler against an old gcc version.
However, after passing this, I am receiving lots of undefined reference
errors from the metatwist source code.
The compilation is after successful ./configure -noX11 intel (intel
19.1.1) (no complains from configure at all, all tests for requirements
passed including for bzip2 and zlib).
Does anyone have any clue about solving these issue ?
Best wishes
Vlad
ld:
metatwist.o:(.data.rel.ro._ZTVN5boost15program_options11typed_valueISt6vectorIdSaIdEEcEE[_ZTVN5boost15program_options11typed_valueISt6vectorIdSaIdEEcEE]+0x38):
undefined reference to
`boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&,
std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
ld:
metatwist.o:(.data.rel.ro._ZTVN5boost15program_options11typed_valueImcEE[_ZTVN5boost15program_options11typed_valueImcEE]+0x38):
undefined reference to
`boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&,
std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
ld:
metatwist.o:(.data.rel.ro._ZTVN5boost15program_options20invalid_option_valueE[_ZTVN5boost15program_options20invalid_option_valueE]+0x30):
undefined reference to
`boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&) const'
ld:
metatwist.o:(.data.rel.ro._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE]+0x30):
undefined reference to
`boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&) const'
ld:
metatwist.o:(.data.rel.ro._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE]+0x38):
undefined reference to
`boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&) const'
ld:
metatwist.o:(.data.rel.ro._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE]+0x30):
undefined reference to
`boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&) const'
ld:
metatwist.o:(.data.rel.ro._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE]+0x38):
undefined reference to
`boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&) const'
Makefile:30: recipe for target
'/u/vcojocar/apps/amber/20_tools-20_pnetcdf-1.12.1_impi-2019.7_intel-2019.1.1/bin/metatwist'
failed
make[2]: ***
[/u/vcojocar/apps/amber/20_tools-20_pnetcdf-1.12.1_impi-2019.7_intel-2019.1.1/bin/metatwist]
Error 1
make[2]: Leaving directory
'/cobra/u/vcojocar/apps/amber/20_tools-20_pnetcdf-1.12.1_impi-2019.7_intel-2019.1.1/AmberTools/src/moft'
Makefile:36: recipe for target 'serial' failed
make[1]: *** [serial] Error 2
make[1]: Leaving directory
'/cobra/u/vcojocar/apps/amber/20_tools-20_pnetcdf-1.12.1_impi-2019.7_intel-2019.1.1/AmberTools/src'
Makefile:7: recipe for target 'install' failed
make: *** [install] Error 2
On 2020-10-20 04:10, Scott Brozell wrote:
> Hi again,
>
> That bit about "on a supercomputer" didn't penetrate my noggin
> initially. Go ahead call me Fickian (the 'F' can be pronounced
> with a 'Th' sound as well :).
>
> Anyway, this now seems like a not-so-super-computer issue. Ie,
> support there should verify their Intel and GNU compatibility.
> Here's some context:
>
> Intel compilers use the GNU tools on the cluster: header files, libraries, and
> linker. The details of Intel and GNU compatibility and interoperability can be
> controlled in several ways. On Foo clusters the default mechanism of control is
> based on modules. An alternative way to control compatibility and
> interoperability is with Intel compiler options; see the 'GNU gcc
> Interoperability' section of the Intel compiler man pages for details.
>
> To view the GNU compatibility, use the '-v' intel compiler option.
>
> scott
>
> On Mon, Oct 19, 2020 at 09:44:09PM -0400, Scott Brozell wrote:
>> On Mon, Oct 19, 2020 at 07:47:43PM +0200, Vlad Cojocaru wrote:
>>> I am trying to install Amber 20 on a supercomputer with the intel 19.1.1
>>> compiler but the serial compilation fails at cpptraj with the error below.
>>> Has anyone seen this before and has an idea how to fix it ?
>>>
>>> In file included from Traj_GmxXtc.cpp(1):
>>> Traj_GmxXtc.h(40): error: identifier "off_t" is undefined
>>> ?????????? std::vector<off_t> frameOffsets_; ///< Frame offsets for reading
>>> ?????????????????????????????????? ^
>>>
>>> compilation aborted for Traj_GmxXtc.cpp (code 2)
>>> ../config.h:45: recipe for target 'Traj_GmxXtc.o' failed
>>> make[4]: *** [Traj_GmxXtc.o] Error 2
>> I routinely build with intel; last was 19.0.5 on oct 15 on
>> Red Hat Enterprise Linux Server release 7.7 (Maipo)
>>
>> I don't have 19.1.1 but i suspect your problem is GNU/OS related.
>> off_t comes from sys/types.h via bits/types.h
>> My system has several versions of these but they haven't changed significantly:
>> 8 -rw-r--r-- 1 root root 6771 Apr 30 2019 /usr/include/sys/types.h
>> 8 -rw-r--r-- 1 root root 6838 Jan 24 2014 /usr/lib/x86_64-redhat-linux6E/include/sys/types.h
>> 8 -rw-r--r-- 1 root root 7729 Apr 30 2019 /usr/include/bits/types.h
>> 8 -rw-r--r-- 1 root root 7601 Jan 24 2014 /usr/lib/x86_64-redhat-linux6E/include/bits/types.h
>>
>> My first guess is that you have intel compilers layered on top of
>> really old gnu compilers.
>> So check into updating your gnu with your OS's package management tool.
>> If you send verbose and verbatim details then someone can probably quote
>> exactly what to execute. Those details should include
>> cat /etc/*release
>> gcc -v
>> icc -v
>>
>> For the compilers, eg, ...
>> gcc version 8.4.0 (GCC)
>> icc version 19.0.5.281 (gcc version 8.4.0 compatibility)
>>
>> scott
>>
>>
>> _______________________________________________
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> _______________________________________________
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--
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
-----------------------------------------------
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru
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Received on Tue Oct 20 2020 - 08:00:02 PDT
