Dear Christoph
I put folders of "tools" and "csg" in a directory with build.sh and tried
to compile them with the --selfdownload option.
However, an error occurred in compiling the linalg.cc file.
The error is the following:
/home/ohkuma/cc/tools/votca/tools/src/libtools/linalg.cc(193): error: no
suitable user-defined conversion from "const
boost::numeric::ublas::unbounded_array<double, std::allocator<double>>" to
"const boost::numeric::ublas::vector<double,
boost::numeric::ublas::unbounded_array<double, std::allocator<double>>>"
exists
const ub::vector<double>& Aarray=A.data();
^
/home/ohkuma/cc/tools/votca/tools/src/libtools/linalg.cc(194): error: no
suitable user-defined conversion from "const
boost::numeric::ublas::unbounded_array<double, std::allocator<double>>" to
"const boost::numeric::ublas::vector<double,
boost::numeric::ublas::unbounded_array<double, std::allocator<double>>>"
exists
const ub::vector<double>& Barray=B.data();
Intel compiler was used. But, I confirmed errors in the same lines of
linalg.cc in case of gcc compiler.
The log file is attached.
Thank you for your considerations.
Takahiro
2017年10月11日水曜日 0時24分16秒 UTC+9 Christoph Junghans:
> 2017-10-10 8:54 GMT-06:00 Takahiro Ohkuma <[email protected]
> <javascript:>>:
> > I need to install VOTCA on a computer (RedHat) which is not connecting
> to
> > the internet. Could anyone tell me a way to manually install the
> packages?
> > Thank you very much for your advice in advance.
> build.sh has the "--selfdownload" option, just put all the tarball,
> e.g. votca-tools-1.4.1.tar.gz, votca-csg-1.4.1.tar.gz, in same
> directory and run build.sh.
>
> Otherwise here are some hints on manual install:
> <https://github.com/votca/csg/wiki/Installing#manual-install>
>
> Christoph
> >
> > Takahiro
> >
> > --
> > 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] <javascript:>.
> > To post to this group, send email to [email protected]
> <javascript:>.
> > 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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Log of '/home/ohkuma/cc/tools/votca/./build.sh --selfdownload
--prefix=/home/ohkuma/cc/tools/votca -DWITH_SQLITE3=off tools csg --log log'
[31;01mget_webversion: Could not fetch new version number[0m
[31;01mget_webversion: Could not fetch new version number[0m
[32;01mThis is VOTCA build.sh, version 2.1.6[0m
Install prefix is '/home/ohkuma/cc/tools/votca'
[34;01mUsing 17 jobs for make/ninja[0m
[32;01mWorking on tools[0m
[34;01mSource dir (tools) is already there - skipping checkout[0m
[34;01mcmake -DCMAKE_INSTALL_PREFIX='/home/ohkuma/cc/tools/votca'
-DWITH_SQLITE3=off -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=ON
/home/ohkuma/cc/tools/votca/tools[0m
-- The C compiler identification is Intel 14.0.0.20130728
-- The CXX compiler identification is Intel 14.0.0.20130728
-- Check for working C compiler:
/app/intel/icsxe_2013-R1/composer_xe_2013_sp1.0.080/bin/intel64/icc
-- Check for working C compiler:
/app/intel/icsxe_2013-R1/composer_xe_2013_sp1.0.080/bin/intel64/icc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler:
/app/intel/icsxe_2013-R1/composer_xe_2013_sp1.0.080/bin/intel64/icpc
-- Check for working CXX compiler:
/app/intel/icsxe_2013-R1/composer_xe_2013_sp1.0.080/bin/intel64/icpc -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Boost version: 1.41.0
-- Found the following Boost libraries:
-- program_options
-- filesystem
-- system
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.23")
-- Could NOT find GSL (missing: GSL_INCLUDE_DIR GSL_LIBRARY GSL_CBLAS_LIBRARY)
-- Intel(R) MKL was found:
MKL_INCLUDE_DIRS:
/app/intel/icsxe_2013-R1/composer_xe_2013_sp1.0.080/mkl/include
MKL_LIBRARY_DIRS:
/app/intel/icsxe_2013-R1/composer_xe_2013_sp1.0.080/mkl/lib/intel64;/app/intel/icsxe_2013-R1/composer_xe_2013_sp1.0.080/compiler/lib/intel64
MKL_LIBRARIES:
/app/intel/icsxe_2013-R1/composer_xe_2013_sp1.0.080/mkl/lib/intel64/libmkl_rt.so;/app/intel/icsxe_2013-R1/composer_xe_2013_sp1.0.080/compiler/lib/intel64/libiomp5.so;/app/intel/icsxe_2013-R1/composer_xe_2013_sp1.0.080/compiler/lib/intel64/libimf.so
-- MKL found, overloading uBLAS prod()
-- Checking for module 'fftw3'
-- No package 'fftw3' found
-- Found FFTW3: /usr/lib64/libfftw3.so
-- Looking for fftw_plan_r2r_1d in /usr/lib64/libfftw3.so;
-- Looking for fftw_plan_r2r_1d in /usr/lib64/libfftw3.so; - found
-- Looking for assert.h
-- Looking for assert.h - found
-- Looking for math.h
-- Looking for math.h - found
-- Looking for stdio.h
-- Looking for stdio.h - found
-- Looking for stdlib.h
-- Looking for stdlib.h - found
-- Looking for string.h
-- Looking for string.h - found
-- Looking for C++ include cmath
-- Looking for C++ include cmath - found
-- Looking for C++ include fstream
-- Looking for C++ include fstream - found
-- Looking for C++ include functional
-- Looking for C++ include functional - found
-- Looking for C++ include iostream
-- Looking for C++ include iostream - found
-- Looking for C++ include limits
-- Looking for C++ include limits - found
-- Looking for C++ include list
-- Looking for C++ include list - found
-- Looking for C++ include map
-- Looking for C++ include map - found
-- Looking for C++ include ostream
-- Looking for C++ include ostream - found
-- Looking for C++ include sstream
-- Looking for C++ include sstream - found
-- Looking for C++ include stack
-- Looking for C++ include stack - found
-- Looking for C++ include stdexcept
-- Looking for C++ include stdexcept - found
-- Looking for C++ include string
-- Looking for C++ include string - found
-- Looking for C++ include vector
-- Looking for C++ include vector - found
-- Looking for sqrt in m
-- Looking for sqrt in m - found
-- Found EXPAT: /usr/lib64/libexpat.so (found version "2.0.1")
-- Performing Test HAVE_AIX
-- Performing Test HAVE_AIX - Failed
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
-- Configuring done
-- Generating done
-- Build files have been written to: /home/ohkuma/cc/tools/votca/tools/build
[32;01mcleaning tools[0m
[32;01mbuidling tools[0m
Scanning dependencies of target intel
[ 2%] Creating directories for 'intel'
[ 2%] Built target votca_tools_manpages
[ 2%] Built target gitversion
[ 4%] Performing download step (download, verify and extract) for 'intel'
-- verifying file...
file='/home/ohkuma/cc/tools/votca/tools/build/intel/src/intel-mkl-and-boost-example.zip'
-- File already exists and hash match (skip download):
file='/home/ohkuma/cc/tools/votca/tools/build/intel/src/intel-mkl-and-boost-example.zip'
MD5='b957ee63a2167ad21b650b47726cd55c'
-- extracting...
src='/home/ohkuma/cc/tools/votca/tools/build/intel/src/intel-mkl-and-boost-example.zip'
dst='/home/ohkuma/cc/tools/votca/tools/build/intel/src/intel'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
[ 6%] No patch step for 'intel'
[ 9%] No update step for 'intel'
[ 11%] No configure step for 'intel'
[ 13%] No build step for 'intel'
[ 16%] No install step for 'intel'
[ 18%] Completed 'intel'
[ 18%] Built target intel
Scanning dependencies of target votca_tools
[ 20%] Building CXX object
src/libtools/CMakeFiles/votca_tools.dir/akimaspline.cc.o
[ 23%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/colors.cc.o
[ 25%] Building CXX object
src/libtools/CMakeFiles/votca_tools.dir/crosscorrelate.cc.o
[ 27%] Building CXX object
src/libtools/CMakeFiles/votca_tools.dir/application.cc.o
[ 30%] Building CXX object
src/libtools/CMakeFiles/votca_tools.dir/correlate.cc.o
[ 34%] Building CXX object
src/libtools/CMakeFiles/votca_tools.dir/cubicspline.cc.o
[ 34%] Building CXX object
src/libtools/CMakeFiles/votca_tools.dir/datacollection.cc.o
[ 37%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/globals.cc.o
[ 41%] Building CXX object
src/libtools/CMakeFiles/votca_tools.dir/histogram.cc.o
[ 41%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/matrix.cc.o
[ 44%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/parcer.cc.o
[ 46%] Building CXX object
src/libtools/CMakeFiles/votca_tools.dir/histogramnew.cc.o
[ 48%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/parsexml.cc.o
[ 51%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/mutex.cc.o
[ 53%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/property.cc.o
[ 55%] Building CXX object
src/libtools/CMakeFiles/votca_tools.dir/linspline.cc.o
[ 58%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/linalg.cc.o
[ 60%] Building CXX object
src/libtools/CMakeFiles/votca_tools.dir/propertyiomanipulator.cc.o
[ 62%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/random.cc.o
[ 65%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/random2.cc.o
[ 67%] Building CXX object
src/libtools/CMakeFiles/votca_tools.dir/rangeparser.cc.o
[ 69%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/spline.cc.o
[ 72%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/table.cc.o
[ 74%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/thread.cc.o
[ 76%] Building CXX object
src/libtools/CMakeFiles/votca_tools.dir/tokenizer.cc.o
[ 79%] Building CXX object
src/libtools/CMakeFiles/votca_tools.dir/linalg/mkl/cholesky.cc.o
[ 81%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/version.cc.o
[ 83%] Building CXX object
src/libtools/CMakeFiles/votca_tools.dir/linalg/mkl/eigensystems.cc.o
[ 86%] Building CXX object
src/libtools/CMakeFiles/votca_tools.dir/linalg/mkl/invert.cc.o
/home/ohkuma/cc/tools/votca/tools/src/libtools/linalg.cc(193): error: no
suitable user-defined conversion from "const
boost::numeric::ublas::unbounded_array<double, std::allocator<double>>" to
"const boost::numeric::ublas::vector<double,
boost::numeric::ublas::unbounded_array<double, std::allocator<double>>>" exists
const ub::vector<double>& Aarray=A.data();
^
/home/ohkuma/cc/tools/votca/tools/src/libtools/linalg.cc(194): error: no
suitable user-defined conversion from "const
boost::numeric::ublas::unbounded_array<double, std::allocator<double>>" to
"const boost::numeric::ublas::vector<double,
boost::numeric::ublas::unbounded_array<double, std::allocator<double>>>" exists
const ub::vector<double>& Barray=B.data();
^
[ 88%] Building CXX object
src/libtools/CMakeFiles/votca_tools.dir/linalg/mkl/qrsolve.cc.o
[ 90%] Building CXX object
src/libtools/CMakeFiles/votca_tools.dir/linalg/mkl/svd.cc.o
compilation aborted for
/home/ohkuma/cc/tools/votca/tools/src/libtools/linalg.cc (code 2)
make[2]: *** [src/libtools/CMakeFiles/votca_tools.dir/linalg.cc.o] エラー 2
make[2]: *** 未完了のジョブを待っています....
make[1]: *** [src/libtools/CMakeFiles/votca_tools.dir/all] エラー 2
make: *** [all] エラー 2
