Hi,
With "HAS_BOOST=" in the config.h , the compilation works just fine ...
Does this mean no boost is used at all or is the OS boost instead of the
Amber boost used ?
Best,
Vlad
On 2020-10-22 01:04, Scott Brozell wrote:
> Hi,
>
> While it is possible that there is some issue with your version of
> intel and Amber's boost, a number of other possibilities exist.
> It would be useful to verify that Amber's boost is being used.
> Unfortunately, there is no way to get that info without re-configuring
> and specifying -verbose. If you are going to do that then you
> might as well redo the installation via:
> make veryclean
> This removes all stuff except the executables from the previous
> build. Leftover libraries from other compilers can also cause
> problems.
>
> As far as workarounds, the simplest would be to have make ignore errors:
> make -i
>
> Another easy one is to edit config.h and change
> HAS_BOOST=yes
> to
> HAS_BOOST=
>
> scott
>
> On Wed, Oct 21, 2020 at 01:31:27PM +0200, Vlad Cojocaru wrote:
>> 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.
>>
>> On 2020-10-20 23:37, Scott Brozell wrote:
>>> 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).
>>>>
>>>> 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
>>>>
>>>> On 2020-10-20 04:10, Scott Brozell wrote:
>>>>> 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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--
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 Fri Oct 23 2020 - 01:30:03 PDT
