Hi,
It means that the boost dependent software is not made.
Those are moft and packmol_memgen with memembed.
scott
On Fri, Oct 23, 2020 at 10:28:11AM +0200, Vlad Cojocaru wrote:
> 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)
> >>>>>>
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Received on Fri Oct 30 2020 - 14:00:02 PDT
