Hi Christoph,
Here is the tools build error message with boost-1.14.1 and gcc 4.9.2, I
also tried gcc 4.7.1 which results in the same error.
cd /home/mashaya1/Apps/votca/build/tools/src/libtools &&
/usr/local/software/GCC/4.9.2/bin/c++ -Dvotca_tools_EXPORTS -O3 -DNDEBUG
-fPIC -I/home/mashaya1/Apps/votca/src/tools/include
-I/home/mashaya1/Apps/votca/build/tools/include -I/usr/local/include
-I/home/mashaya1/Apps/votca/build/tools/src/libtools -o
CMakeFiles/votca_tools.dir/linalg.cc.o -c
/home/mashaya1/Apps/votca/src/tools/src/libtools/linalg.cc
/home/mashaya1/Apps/votca/src/tools/src/libtools/linalg.cc: In function
'double votca::tools::linalg_traceofProd(const
boost::numeric::ublas::matrix<double>&, const
boost::numeric::ublas::matrix<double>&)':
/home/mashaya1/Apps/votca/src/tools/src/libtools/linalg.cc:169:48: error:
invalid initialization of reference of type 'const
boost::numeric::ublas::vector<double>&' from expression of type 'const
array_type {aka const boost::numeric::ublas::unbounded_array<double,
std::allocator<double> >}'
const ub::vector<double>& Aarray=A.data();
^
/home/mashaya1/Apps/votca/src/tools/src/libtools/linalg.cc:170:48: error:
invalid initialization of reference of type 'const
boost::numeric::ublas::vector<double>&' from expression of type 'const
array_type {aka const boost::numeric::ublas::unbounded_array<double,
std::allocator<double> >}'
const ub::vector<double>& Barray=B.data();
On Wed, Feb 1, 2017 at 6:48 AM, Christoph Junghans <[email protected]>
wrote:
> 2017-01-31 17:25 GMT-05:00 Sikandar Mashayak <[email protected]>:
> > Hi,
> >
> > In the case of buildtb.log, the errors seem to be caused by Boost 1.41.0
> > library, however, if you build with later versions of Boost, e.g.,
> 1.58.0,
> > build is successful. @ Christoph, is this expected from Boost 1.41.0?
> boost-1.14.1 is very old (2009), but should be fine. However the gcc
> is 4.9.2 (rather new) and it might be the combination of both.
>
> Alireza,
>
> 1.) if you have multiple versions of gcc and boost on the cluster, try
> different combinations.
> 2.) Plus, I updated build.sh to log stderr as well, so could you
> download the latest version (build.sh v2.1.3) and reproduce the error
> in an empty directory and send us that log, too.
>
> Christoph
>
> >
> > Thanks,
> > Sikandar
> >
> > On Tue, Jan 31, 2017 at 3:48 PM, Alireza Moradzadeh <[email protected]>
> > wrote:
> >>
> >> I attached the files.
> >>
> >>
> >> Best Regards,
> >> Alireza Moradzadeh
> >>
> >>
> >> On Tue, Jan 31, 2017 at 3:23 PM, Christoph Junghans <[email protected]
> >
> >> wrote:
> >>>
> >>> 2017-01-31 15:55 GMT-05:00 Alireza Moradzadeh <[email protected]>:
> >>> > I am trying to install in a cluster, which I previously worked and on
> >>> > another Supercomputer. I attach both error file from CMakeFiles.
> >>> Unfortunately, the files in CMakeFiles have very little useful
> >>> information.
> >>> I need the full output of build.sh use:
> >>> $ ./build.sh --verbose --log build.log tools
> >>> and send the build.log.
> >>> Plus, the CMakeCache.txt from tools would be nice, too.
> >>>
> >>> Christoph
> >>> >
> >>> >
> >>> > Best Regards,
> >>> > Alireza Moradzadeh
> >>> >
> >>> >
> >>> > On Tue, Jan 31, 2017 at 1:04 PM, Christoph Junghans
> >>> > <[email protected]>
> >>> > wrote:
> >>> >>
> >>> >> 2017-01-31 13:49 GMT-05:00 Alireza Moradzadeh <[email protected]>:
> >>> >> > I am using boost/1.51.0. Basically, I exactly repeat instruction
> in
> >>> >> > the
> >>> >> > handout.
> >>> >> What version of VOTCA?
> >>> >> And is this a fresh checkout?
> >>> >> Can you attach the full output of build.sh?
> >>> >>
> >>> >> Christoph
> >>> >>
> >>> >> Christoph
> >>> >> > Thanks,
> >>> >> > Alireza
> >>> >> >
> >>> >> > On Tuesday, January 31, 2017 at 7:58:24 AM UTC-6, Christoph
> Junghans
> >>> >> > wrote:
> >>> >> >>
> >>> >> >> 2017-01-30 20:33 GMT-05:00 Alireza Moradzadeh <[email protected]
> >:
> >>> >> >> > Dear VOTCA Users,
> >>> >> >> >
> >>> >> >> > I get an error in installation of votca, any solution is highly
> >>> >> >> > appreicated.
> >>> >> >> Which version of boost are you using? Which version of VOTCA are
> >>> >> >> you
> >>> >> >> trying to build?
> >>> >> >> And did you build from scratch? (Otherwise try a fresh checkout
> or
> >>> >> >> the
> >>> >> >> build.sh options "--clean-out" or "--clean-ignored")
> >>> >> >>
> >>> >> >> Christoph
> >>> >> >> >
> >>> >> >> > Thanks,
> >>> >> >> > Alireza
> >>> >> >> >
> >>> >> >> > Scanning dependencies of target votca_property
> >>> >> >> > [ 97%] Building CXX object
> >>> >> >> > src/tools/CMakeFiles/votca_property.dir/votca_property.cc.o
> >>> >> >> > Linking CXX executable votca_property
> >>> >> >> > CMakeFiles/votca_property.dir/votca_property.cc.o: In function
> >>> >> >> >
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > `boost::program_options::validation_error::validation_
> error(boost::program_options::validation_error::kind_t,
> >>> >> >> > std::string const&, std::string const&, int)':
> >>> >> >> >
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > votca_property.cc:(.text._ZN5boost15program_
> options16validation_errorC2ENS1_6kind_tERKSsS4_i[_ZN5boost15program_
> options16validation_errorC5ENS1_6kind_tERKSsS4_i]+0x21):
> >>> >> >> > undefined reference to
> >>> >> >> >
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > `boost::program_options::validation_error::get_
> template(boost::program_options::validation_error::kind_t)'
> >>> >> >> >
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > votca_property.cc:(.text._ZN5boost15program_
> options16validation_errorC2ENS1_6kind_tERKSsS4_i[_ZN5boost15program_
> options16validation_errorC5ENS1_6kind_tERKSsS4_i]+0x39):
> >>> >> >> > undefined reference to
> >>> >> >> >
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > `boost::program_options::error_with_option_name::error_
> with_option_name(std::string
> >>> >> >> > const&, std::string const&, std::string const&, int)'
> >>> >> >> > CMakeFiles/votca_property.dir/votca_property.cc.o: In function
> >>> >> >> >
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > `boost::program_options::error_with_option_name::~
> error_with_option_name()':
> >>> >> >> >
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > votca_property.cc:(.text._ZN5boost15program_
> options22error_with_option_nameD2Ev[_ZN5boost15program_
> options22error_with_option_nameD5Ev]+0x12):
> >>> >> >> > undefined reference to `vtable for
> >>> >> >> > boost::program_options::error_with_option_name'
> >>> >> >> > CMakeFiles/votca_property.dir/votca_property.cc.o: In function
> >>> >> >> > `boost::program_options::validation_error::~validation_
> error()':
> >>> >> >> >
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > votca_property.cc:(.text._ZN5boost15program_
> options16validation_errorD2Ev[_ZN5boost15program_
> options16validation_errorD5Ev]+0x12):
> >>> >> >> > undefined reference to `vtable for
> >>> >> >> > boost::program_options::error_with_option_name'
> >>> >> >> > CMakeFiles/votca_property.dir/votca_property.cc.o: In function
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > `boost::program_options::invalid_option_value::~
> invalid_option_value()':
> >>> >> >> >
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > votca_property.cc:(.text._ZN5boost15program_
> options20invalid_option_valueD2Ev[_ZN5boost15program_
> options20invalid_option_valueD5Ev]+0x12):
> >>> >> >> > undefined reference to `vtable for
> >>> >> >> > boost::program_options::error_with_option_name'
> >>> >> >> > CMakeFiles/votca_property.dir/votca_property.cc.o: In function
> >>> >> >> >
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > `boost::program_options::error_with_option_name::~
> error_with_option_name()':
> >>> >> >> >
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > votca_property.cc:(.text._ZN5boost15program_
> options22error_with_option_nameD0Ev[_ZN5boost15program_
> options22error_with_option_nameD5Ev]+0x12):
> >>> >> >> > undefined reference to `vtable for
> >>> >> >> > boost::program_options::error_with_option_name'
> >>> >> >> > CMakeFiles/votca_property.dir/votca_property.cc.o: In function
> >>> >> >> > `boost::program_options::validation_error::~validation_
> error()':
> >>> >> >> >
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > votca_property.cc:(.text._ZN5boost15program_
> options16validation_errorD0Ev[_ZN5boost15program_
> options16validation_errorD5Ev]+0x12):
> >>> >> >> > undefined reference to `vtable for
> >>> >> >> > boost::program_options::error_with_option_name'
> >>> >> >> >
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > CMakeFiles/votca_property.dir/votca_property.cc.o:votca_
> property.cc:(.text._ZN5boost15program_options20invalid_option_
> valueD0Ev[_ZN5boost15program_options20invalid_option_valueD5Ev]+0x12):
> >>> >> >> > more undefined references to `vtable for
> >>> >> >> > boost::program_options::error_with_option_name' follow
> >>> >> >> >
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > CMakeFiles/votca_property.dir/votca_property.cc.o:(.rodata._
> ZTVN5boost16exception_detail19error_info_injectorINS_15program_
> options20invalid_option_valueEEE[_ZTVN5boost16exception_
> detail19error_info_injectorINS_15program_options20invalid_option_
> valueEEE]+0x20):
> >>> >> >> > undefined reference to
> >>> >> >> > `boost::program_options::error_with_option_name::what() const'
> >>> >> >> >
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > CMakeFiles/votca_property.dir/votca_property.cc.o:(.rodata._
> 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::string
> >>> >> >> > const&) const'
> >>> >> >> >
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > CMakeFiles/votca_property.dir/votca_property.cc.o:(.rodata._
> ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_
> 15program_options20invalid_option_valueEEEEE[_ZTVN5boost16exception_
> detail10clone_implINS0_19error_info_injectorINS_
> 15program_options20invalid_option_valueEEEEE]+0x28):
> >>> >> >> > undefined reference to
> >>> >> >> > `boost::program_options::error_with_option_name::what() const'
> >>> >> >> >
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > CMakeFiles/votca_property.dir/votca_property.cc.o:(.rodata._
> 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::string
> >>> >> >> > const&) const'
> >>> >> >> >
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > CMakeFiles/votca_property.dir/votca_property.cc.o:(.rodata._
> ZTVN5boost16exception_detail19error_info_injectorINS_15program_
> options16validation_errorEEE[_ZTVN5boost16exception_detail19error_info_
> injectorINS_15program_options16validation_errorEEE]+0x20):
> >>> >> >> > undefined reference to
> >>> >> >> > `boost::program_options::error_with_option_name::what() const'
> >>> >> >> >
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > CMakeFiles/votca_property.dir/votca_property.cc.o:(.rodata._
> 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::string
> >>> >> >> > const&) const'
> >>> >> >> >
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > CMakeFiles/votca_property.dir/votca_property.cc.o:(.rodata._
> ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_
> 15program_options16validation_errorEEEEE[_ZTVN5boost16exception_
> detail10clone_implINS0_19error_info_injectorINS_
> 15program_options16validation_errorEEEEE]+0x28):
> >>> >> >> > undefined reference to
> >>> >> >> > `boost::program_options::error_with_option_name::what() const'
> >>> >> >> >
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > CMakeFiles/votca_property.dir/votca_property.cc.o:(.rodata._
> 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::string
> >>> >> >> > const&) const'
> >>> >> >> >
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > CMakeFiles/votca_property.dir/votca_property.cc.o:(.rodata._
> ZTIN5boost15program_options16validation_errorE[_ZTIN5boost15program_
> options16validation_errorE]+0x10):
> >>> >> >> > undefined reference to `typeinfo for
> >>> >> >> > boost::program_options::error_with_option_name'
> >>> >> >> >
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > CMakeFiles/votca_property.dir/votca_property.cc.o:(.rodata._
> ZTVN5boost15program_options16validation_errorE[_ZTVN5boost15program_
> options16validation_errorE]+0x20):
> >>> >> >> > undefined reference to
> >>> >> >> > `boost::program_options::error_with_option_name::what() const'
> >>> >> >> >
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > CMakeFiles/votca_property.dir/votca_property.cc.o:(.rodata._
> ZTVN5boost15program_options16validation_errorE[_ZTVN5boost15program_
> options16validation_errorE]+0x30):
> >>> >> >> > undefined reference to
> >>> >> >> >
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > `boost::program_options::error_with_option_name::
> substitute_placeholders(std::string
> >>> >> >> > const&) const'
> >>> >> >> >
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > CMakeFiles/votca_property.dir/votca_property.cc.o:(.rodata._
> ZTVN5boost15program_options20invalid_option_valueE[_ZTVN5boost15program_
> options20invalid_option_valueE]+0x20):
> >>> >> >> > undefined reference to
> >>> >> >> > `boost::program_options::error_with_option_name::what() const'
> >>> >> >> >
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > CMakeFiles/votca_property.dir/votca_property.cc.o:(.rodata._
> ZTVN5boost15program_options20invalid_option_valueE[_ZTVN5boost15program_
> options20invalid_option_valueE]+0x30):
> >>> >> >> > undefined reference to
> >>> >> >> >
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > `boost::program_options::error_with_option_name::
> substitute_placeholders(std::string
> >>> >> >> > const&) const'
> >>> >> >> > ../libtools/libvotca_tools.so.5: undefined reference to
> >>> >> >> >
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > `boost::program_options::options_description::options_
> description(std::string
> >>> >> >> > const&, unsigned int, unsigned int)'
> >>> >> >> > ../libtools/libvotca_tools.so.5: undefined reference to
> >>> >> >> > `boost::system::system_category()'
> >>> >> >> > ../libtools/libvotca_tools.so.5: undefined reference to
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > `boost::program_options::detail::cmdline::get_
> canonical_option_prefix()'
> >>> >> >> > ../libtools/libvotca_tools.so.5: undefined reference to
> >>> >> >> > `boost::system::generic_category()'
> >>> >> >> > ../libtools/libvotca_tools.so.5: undefined reference to
> >>> >> >> > `boost::filesystem::path::operator/=(boost::filesystem::path
> >>> >> >> > const&)'
> >>> >> >> > ../libtools/libvotca_tools.so.5: undefined reference to
> >>> >> >> >
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > `boost::program_options::options_description::options_
> description(unsigned
> >>> >> >> > int, unsigned int)'
> >>> >> >> > collect2: error: ld returned 1 exit status
> >>> >> >> > make[2]: *** [src/tools/votca_property] Error 1
> >>> >> >> > make[1]: *** [src/tools/CMakeFiles/votca_property.dir/all]
> Error
> >>> >> >> > 2
> >>> >> >> >
> >>> >> >> > --
> >>> >> >> > You received this message because you are subscribed to the
> >>> >> >> > Google
> >>> >> >> > Groups
> >>> >> >> > "votca" group.
> >>> >> >> > To unsubscribe from this group and stop receiving emails from
> it,
> >>> >> >> > send
> >>> >> >> > an
> >>> >> >> > email to [email protected].
> >>> >> >> > To post to this group, send email to [email protected].
> >>> >> >> > Visit this group at https://groups.google.com/group/votca.
> >>> >> >> > For more options, visit https://groups.google.com/d/optout.
> >>> >> >>
> >>> >> >>
> >>> >> >>
> >>> >> >> --
> >>> >> >> Christoph Junghans
> >>> >> >> Web: http://www.compphys.de
> >>> >> >
> >>> >> > --
> >>> >> > You received this message because you are subscribed to the Google
> >>> >> > Groups
> >>> >> > "votca" group.
> >>> >> > To unsubscribe from this group and stop receiving emails from it,
> >>> >> > send
> >>> >> > an
> >>> >> > email to [email protected].
> >>> >> > To post to this group, send email to [email protected].
> >>> >> > Visit this group at https://groups.google.com/group/votca.
> >>> >> > For more options, visit https://groups.google.com/d/optout.
> >>> >>
> >>> >>
> >>> >>
> >>> >> --
> >>> >> Christoph Junghans
> >>> >> Web: http://www.compphys.de
> >>> >>
> >>> >> --
> >>> >> You received this message because you are subscribed to a topic in
> the
> >>> >> Google Groups "votca" group.
> >>> >> To unsubscribe from this topic, visit
> >>> >> https://groups.google.com/d/topic/votca/aLyUgGyNQxs/unsubscribe.
> >>> >> To unsubscribe from this group and all its topics, send an email to
> >>> >> [email protected].
> >>> >> To post to this group, send email to [email protected].
> >>> >> Visit this group at https://groups.google.com/group/votca.
> >>> >> For more options, visit https://groups.google.com/d/optout.
> >>> >
> >>> >
> >>> > --
> >>> > You received this message because you are subscribed to the Google
> >>> > Groups
> >>> > "votca" group.
> >>> > To unsubscribe from this group and stop receiving emails from it,
> send
> >>> > an
> >>> > email to [email protected].
> >>> > To post to this group, send email to [email protected].
> >>> > Visit this group at https://groups.google.com/group/votca.
> >>> > For more options, visit https://groups.google.com/d/optout.
> >>>
> >>>
> >>>
> >>> --
> >>> Christoph Junghans
> >>> Web: http://www.compphys.de
> >>>
> >>> --
> >>> You received this message because you are subscribed to a topic in the
> >>> Google Groups "votca" group.
> >>> To unsubscribe from this topic, visit
> >>> https://groups.google.com/d/topic/votca/aLyUgGyNQxs/unsubscribe.
> >>> To unsubscribe from this group and all its topics, send an email to
> >>> [email protected].
> >>> To post to this group, send email to [email protected].
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> >>> For more options, visit https://groups.google.com/d/optout.
> >>
> >>
> >> --
> >> You received this message because you are subscribed to the Google
> Groups
> >> "votca" group.
> >> To unsubscribe from this group and stop receiving emails from it, send
> an
> >> email to [email protected].
> >> To post to this group, send email to [email protected].
> >> Visit this group at https://groups.google.com/group/votca.
> >> For more options, visit https://groups.google.com/d/optout.
> >
> >
> > --
> > You received this message because you are subscribed to the Google Groups
> > "votca" group.
> > To unsubscribe from this group and stop receiving emails from it, send an
> > email to [email protected].
> > To post to this group, send email to [email protected].
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> > For more options, visit https://groups.google.com/d/optout.
>
>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
> --
> You received this message because you are subscribed to the Google Groups
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>
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