Thanks,
No errors, no warnings for the boost configure, all seemed to have
worked perfectly ...
I kept with the legacy build because it worked most of the time for me,
and I did not want to change something that works and also did not
works... But sure, I can try to build with cmake and/or also disable
metatwist as Dave suggested.
Cheers
Vlad
On 2020-10-20 23:37, Scott Brozell wrote:
> Hi,
>
> The legacy build made metatwist for me (on the git master):
> ./configure --miniconda -verbose intel
> ...
> [MoFT] CXX metatwist.cpp
> ...
> icpc -std=c++0x -o /tmp/amber/bin/metatwist metatwist.o -L/tmp/amber/lib -lboost_program_options -lboost_iostreams -lboost_regex -lboost_system -lboost_timer -lboost_chrono -lboost_filesystem -lboost_graph -mkl=sequential -lz -lbz2
>
> 2972 -rwxr-xr-x 1 scott 3041344 Oct 19 22:02 ./bin/metatwist
>
>
> The errors below are all boost related.
> What happened during this stage of configure ?
> Configuring boost (may be time-consuming)...
>
> You can look in file AmberTools/src/boost_config.log
>
> scott
>
> On Tue, Oct 20, 2020 at 01:50:49PM -0400, David A Case wrote:
>> On Tue, Oct 20, 2020, Vlad Cojocaru wrote:
>>> 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).
>> Something is broken with the legacy build and metatwist. Simple option
>> is just to comment out that part of the build (in
>> $AMBERHOME/src/Makefile).
> On Tue, Oct 20, 2020 at 04:46:37PM +0200, Vlad Cojocaru wrote:
>> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Oct 21 2020 - 05:00:02 PDT
