Error in Installation

[Alireza Moradzadeh]

Dear VOTCA Users,

I get an error in installation of votca, any solution is highly appreicated.

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

[Christoph Junghans]

2017-01-30 20:33 GMT-05:00 Alireza Moradzadeh <a.m...@gmail.com>:
> 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

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[Alireza Moradzadeh]

I am using boost/1.51.0. Basically, I exactly repeat instruction in the handout.

Thanks,

Alireza

[Christoph Junghans]

2017-01-31 13:49 GMT-05:00 Alireza Moradzadeh <a.m...@gmail.com>:
> 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

[Alireza Moradzadeh]

I am trying to install in a cluster, which I previously worked and on another Supercomputer. I attach both error file from CMakeFiles.

Best Regards,
Alireza Moradzadeh

> email to votca+unsubscribe@googlegroups.com.

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[Christoph Junghans]

2017-01-31 15:55 GMT-05:00 Alireza Moradzadeh <a.m...@gmail.com>:
> 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

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[Alireza Moradzadeh]

I attached the files.

Best Regards,
Alireza Moradzadeh

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[Sikandar Mashayak]

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?

Thanks,

Sikandar

[Christoph Junghans]

2017-01-31 17:25 GMT-05:00 Sikandar Mashayak <symas...@gmail.com>:
> 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?

What error?
$ grep error build-bw.log buildtb.log
<nothing>

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[Christoph Junghans]

2017-01-31 17:25 GMT-05:00 Sikandar Mashayak <symas...@gmail.com>:

> 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

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[Sikandar Mashayak]

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();

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[Christoph Junghans]

2017-02-02 0:29 GMT-05:00 Sikandar Mashayak <symas...@gmail.com>:
> 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.

Wasn't Alireza's error ("undefined reference to
`boost::program_options....") a different issue?

>
> 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();

I guess boost-1.41.1 is too old then, which version worked for you? 1.58?
There is also the problem that not all gcc and boost combination work together.

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>> >>> >
>> >>> >
>> >>> > --
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>> >>> > send
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>> >>>
>> >>>
>> >>>
>> >>> --
>> >>> Christoph Junghans
>> >>> Web: http://www.compphys.de
>> >>>
>> >>> --

>> >>> You received this message because you are subscribed to a topic in the
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>> >>> To unsubscribe from this group and all its topics, send an email to

[Sikandar Mashayak]

Yes boost 1.58 worked for me.

>> >>> >> > email to votca+unsubscribe@googlegroups.com.

>> >>> >> > To post to this group, send email to vo...@googlegroups.com.
>> >>> >> > 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
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>> >>> >> votca+unsubscribe@googlegroups.com.

>> >>> >> To post to this group, send email to vo...@googlegroups.com.
>> >>> >> Visit this group at https://groups.google.com/group/votca.
>> >>> >> For more options, visit https://groups.google.com/d/optout.
>> >>> >
>> >>> >
>> >>> > --
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>> >>> > To post to this group, send email to vo...@googlegroups.com.
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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 a topic in the
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>> >>> votca+unsubscribe@googlegroups.com.

>> >>> To post to this group, send email to vo...@googlegroups.com.
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>> >>
>> >>
>> >> --
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>> >> To post to this group, send email to vo...@googlegroups.com.
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>> >
>> >
>> > --
>> > You received this message because you are subscribed to the Google
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>> > an

>> > email to votca+unsubscribe@googlegroups.com.

>> > To post to this group, send email to vo...@googlegroups.com.
>> > 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
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>> To unsubscribe from this group and stop receiving emails from it, send an

>> email to votca+unsubscribe@googlegroups.com.

>> To post to this group, send email to vo...@googlegroups.com.
>> 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 votca+unsubscribe@googlegroups.com.

> To post to this group, send email to vo...@googlegroups.com.
> 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

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