Installing VOTCA on a cluster SGI

Tiago Espinosa

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Mar 9, 2016, 7:33:38 PM3/9/16

to votca

Dear votca users, I'm trying build votca on a SGI cluster:

build command: ./build.sh --prefix /home/u/espinosa/test/ --dev tools csg -DFFTW3_LIBRARY=/opt/local/intel/fftw-3.3.3/lib/libfftw3.so -DFFTW3_INCLUDE_DIR=/opt/local/intel/fftw-3.3.3/include/ -DWITH_SQLITE3=NO -DGROMACS_INCLUDE_DIR=/opt/local/gromacs-4.5.4/include/ -DGROMACS_LIBRARY=/opt/local/gromacs-4.5.4/lib/libgmx.so -DBoost_FILESYSTEM_LIBRARY=/usr/lib64/libboost_filesystem.so

ERROR:

-- 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 PkgConfig: /usr/bin/pkg-config (found version "0.23")

-- checking for module 'expat'

-- package 'expat' not found

-- Found EXPAT: /usr/lib64/libexpat.so

-- checking for module 'fftw3'

-- package 'fftw3' not found

-- Found FFTW3: /opt/local/intel/fftw-3.3.3/lib/libfftw3.so

-- Looking for fftw_plan_r2r_1d in /opt/local/intel/fftw-3.3.3/lib/libfftw3.so;m

-- Looking for fftw_plan_r2r_1d in /opt/local/intel/fftw-3.3.3/lib/libfftw3.so;m - found

-- checking for module 'gsl'

-- found gsl, version 1.11

-- Found GSL: /usr/lib64/libgsl.so

-- Looking for gsl_linalg_QR_decomp in /usr/lib64/libgsl.so;m

-- Looking for gsl_linalg_QR_decomp in /usr/lib64/libgsl.so;m - found

-- Intel(R) MKL was found:

MKL_INCLUDE_DIRS: /opt/intel/composerxe-2011.0.084/mkl/include

MKL_LIBRARY_DIRS: /opt/intel/composerxe-2011.0.084/mkl/lib/intel64;/opt/intel/composerxe-2011.0.084/compiler/lib/intel64

MKL_LIBRARIES: /opt/intel/composerxe-2011.0.084/mkl/lib/intel64/libmkl_rt.so;/opt/intel/composerxe-2011.0.084/compiler/lib/intel64/libiomp5.so;/opt/intel/composerxe-2011.0.084/compiler/lib/intel64/libimf.so

-- Performing Test HAVE_AIX

-- Performing Test HAVE_AIX - Failed

-- Found Doxygen: /usr/bin/doxygen (found version "1.5.6")

-- Configuring incomplete, errors occurred!

See also "/home/u/espinosa/test/src/tools/CMakeFiles/CMakeOutput.log".

See also "/home/u/espinosa/test/src/tools/CMakeFiles/CMakeError.log".

Regards

Tiago E. de Oliveira

CMakeError.log

CMakeOutput.log

Christoph Junghans

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Mar 9, 2016, 7:51:02 PM3/9/16

to vo...@googlegroups.com

2016-03-09 17:31 GMT-07:00 Tiago Espinosa <tespinos...@gmail.com>:
> Dear votca users, I'm trying build votca on a SGI cluster:
>
> build command: ./build.sh --prefix /home/u/espinosa/test/ --dev tools csg
> -DFFTW3_LIBRARY=/opt/local/intel/fftw-3.3.3/lib/libfftw3.so
> -DFFTW3_INCLUDE_DIR=/opt/local/intel/fftw-3.3.3/include/ -DWITH_SQLITE3=NO
> -DGROMACS_INCLUDE_DIR=/opt/local/gromacs-4.5.4/include/
> -DGROMACS_LIBRARY=/opt/local/gromacs-4.5.4/lib/libgmx.so
> -DBoost_FILESYSTEM_LIBRARY=/usr/lib64/libboost_filesystem.so
>
> ERROR:
>

There is no error below, can you post the complete output of build.sh.
If the output is too long, you could use the --log option of build.sh, e.g.
./build.sh --prefix /home/u/espinosa/test/ --log build.log --dev tools csg
and attach build.log

Christoph

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Christoph Junghans
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Tiago Espinosa

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Mar 9, 2016, 8:20:31 PM3/9/16

to votca

Log of './build.sh --prefix /home/u/espinosa/test/ --dev tools csg -DFFTW3_LIBRARY=/opt/local/intel/fftw-3.3.3/lib/libfftw3.so -DFFTW3_INCLUDE_DIR=/opt/local/intel/fftw-3.3.3/include/ -DWITH_SQLITE3=NO -DGROMACS_INCLUDE_DIR=/opt/local/gromacs-4.5.4/include/ -DGROMACS_LIBRARY=/opt/local/gromacs-4.5.4/lib/libgmx.so -DBoost_FILESYSTEM_LIBRARY=/usr/lib64/libboost_filesystem.so --log build.log'

^[[32;01mThis is VOTCA build.sh, version 1.9.7^[[0m

Install prefix is '/home/u/espinosa/test/'

^[[34;01mUsing 49 jobs for make^[[0m

^[[32;01mWorking on tools^[[0m

^[[34;01mSource dir (tools) is already there - skipping checkout^[[0m

^[[34;01mcmake -DCMAKE_INSTALL_PREFIX='/home/u/espinosa/test/' -DFFTW3_LIBRARY=/opt/local/intel/fftw-3.3.3/lib/libfftw3.so -DFFTW3_INCLUDE_DIR=/opt/local/intel/fftw-3.3.3/include/ -DWITH_SQLITE3=NO -DGROMACS_INCLUDE_DIR=/opt/local/gromacs-4.5.4/include/ -DGROMACS_LIBRARY=/opt/local/gromacs-4.5.4/lib/libgmx.so -DBoost_FILESYSTEM_LIBRARY=/usr/lib64/libboost_filesystem.so -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=ON .^[[0m

-- Found Git: /opt/local/bin/git (found version "1.8.4-rc0")

-- Looking for include file pthread.h

-- Looking for include file 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 - found

-- Found Threads: TRUE

-- 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

Christoph Junghans

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Mar 9, 2016, 8:56:51 PM3/9/16

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Something is strange right here.
At this point cmake is suppose to check for boost (program_options,
filesystem, system), which it didn't!
Can you drop the
-DBoost_FILESYSTEM_LIBRARY=/usr/lib64/libboost_filesystem.so option,
it is pointless as /usr/lib64 is part of the default search paths.

Which version of cmake are you using (see cmake --version)? You will
need at least 2.8.11 for votca-csg.

Christoph

Tiago Espinosa

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Mar 9, 2016, 8:59:24 PM3/9/16

to votca

cmake version 3.2.1

Christoph Junghans

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Mar 9, 2016, 10:12:51 PM3/9/16

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Is this a fresh checkout? If that doesn't help, could you try making a
CMakeLists.txt with following two lines:
cmake_minimum_required(VERSION 2.8.11)
find_package(Boost 1.39.0 REQUIRED COMPONENTS program_options
filesystem system )
and see if running cmake on it:
$ cmake .
and see if it finds boost.

Christoph

2016-03-09 18:59 GMT-07:00 Tiago Espinosa <tespinos...@gmail.com>:
> cmake version 3.2.1

Tiago Espinosa

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Mar 9, 2016, 11:02:20 PM3/9/16

to votca

OK, now I change CMakeList.txt:

cmake_minimum_required(VERSION 2.8.11)
find_package(Boost 1.36.0 REQUIRED COMPONENTS program_options

version on cluster is 1.36.0

and with these changes the process go a head a little bit more:

Log of './build.sh --prefix /home/u/espinosa/test/ --dev tools csg -DFFTW3_LIBRARY=/opt/local/intel/fftw-3.3.3/lib/libfftw3.so -DFFTW3_INCLUDE_DIR=/opt/local/intel/fftw-3.3.3/include/ -DWITH_SQLITE3=NO -DGROMACS_INCLUDE_DIR=/opt/local/gromacs-4.5.4/include/ -DGROMACS_LIBRARY=/opt/local/gromacs-4.5.4/lib/libgmx.so -DBoost_FILESYSTEM_LIBRARY=/usr/lib64/libboost_filesystem.so --log build.log -DVOTCA_TOOLS_LIBRARY=/home/u/espinosa/test/lib/libvotca_tools.so.4'

^[[32;01mThis is VOTCA build.sh, version 1.9.7^[[0m

Install prefix is '/home/u/espinosa/test/'

^[[34;01mUsing 49 jobs for make^[[0m

^[[34;01msourcing '/home/u/espinosa/test//bin/VOTCARC.bash'^[[0m

^[[32;01mWorking on tools^[[0m

^[[34;01mSource dir (tools) is already there - skipping checkout^[[0m

^[[34;01mcmake -DCMAKE_INSTALL_PREFIX='/home/u/espinosa/test/' -DFFTW3_LIBRARY=/opt/local/intel/fftw-3.3.3/lib/libfftw3.so -DFFTW3_INCLUDE_DIR=/opt/local/intel/fftw-3.3.3/include/ -DWITH_SQLITE3=NO -DGROMACS_INCLUDE_DIR=/opt/local/gromacs-4.5.4/include/ -DGROMACS_LIBRARY=/opt/local/gromacs-4.5.4/lib/libgmx.so -DBoost_FILESYSTEM_LIBRARY=/usr/lib64/libboost_filesystem.so -DVOTCA_TOOLS_LIBRARY=/home/u/espinosa/test/lib/libvotca_tools.so.4 -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=ON .^[[0m

-- Found Git: /opt/local/bin/git (found version "1.8.4-rc0")

-- Looking for include file pthread.h

-- Looking for include file 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 - found

-- Found Threads: TRUE

-- Boost version: 1.36.0

-- Found the following Boost libraries:

-- program_options

-- filesystem

-- system

-- Configuring done

-- Generating done

-- Build files have been written to: /home/u/espinosa/test/src/tools

^[[32;01mcleaning tools^[[0m

^[[32;01mbuidling tools^[[0m

[ 0%] Built target votca_tools_manpages

[ 0%] Built target gitversion

Scanning dependencies of target votca_tools

[ 15%] [ 15%] [ 18%] [ 21%] [ 24%] [ 27%] [ 27%] [ 33%] [ 33%] [ 36%] [ 36%] [ 36%] [ 39%] [ 42%] [ 48%] [ 48%] [ 51%] [ 54%] [ 57%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/akimaspline.cc.o

Building CXX object src/libtools/CMakeFiles/votca_tools.dir/crosscorrelate.cc.o

[ 60%] [ 63%] [ 69%] [ 69%] [ 72%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/version.cc.o

[ 75%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/table.cc.o

[ 78%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/datacollection.cc.o

Building CXX object src/libtools/CMakeFiles/votca_tools.dir/histogram.cc.o

Building CXX object src/libtools/CMakeFiles/votca_tools.dir/linspline.cc.o

Building CXX object src/libtools/CMakeFiles/votca_tools.dir/cubicspline.cc.o

[ 81%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/parsexml.cc.o

Building CXX object src/libtools/CMakeFiles/votca_tools.dir/mutex.cc.o

[ 84%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/colors.cc.o

Building CXX object src/libtools/CMakeFiles/votca_tools.dir/tokenizer.cc.o

Building CXX object src/libtools/CMakeFiles/votca_tools.dir/property.cc.o

Building CXX object src/libtools/CMakeFiles/votca_tools.dir/spline.cc.o

[ 87%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/application.cc.o

Building CXX object src/libtools/CMakeFiles/votca_tools.dir/matrix.cc.o

Building CXX object src/libtools/CMakeFiles/votca_tools.dir/linalg.cc.o

Building CXX object src/libtools/CMakeFiles/votca_tools.dir/parcer.cc.o

Building CXX object src/libtools/CMakeFiles/votca_tools.dir/linalg/gsl/invert.cc.o

Building CXX object src/libtools/CMakeFiles/votca_tools.dir/correlate.cc.o

Building CXX object src/libtools/CMakeFiles/votca_tools.dir/random.cc.o

Building CXX object src/libtools/CMakeFiles/votca_tools.dir/linalg/gsl/eigensystems.cc.o

Building CXX object src/libtools/CMakeFiles/votca_tools.dir/globals.cc.o

Building CXX object src/libtools/CMakeFiles/votca_tools.dir/random2.cc.o

Building CXX object src/libtools/CMakeFiles/votca_tools.dir/thread.cc.o

Building CXX object src/libtools/CMakeFiles/votca_tools.dir/linalg/gsl/svd.cc.o

Building CXX object src/libtools/CMakeFiles/votca_tools.dir/linalg/gsl/qrsolve.cc.o

Building CXX object src/libtools/CMakeFiles/votca_tools.dir/histogramnew.cc.o

[ 90%] [ 93%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/propertyiomanipulator.cc.o

Building CXX object src/libtools/CMakeFiles/votca_tools.dir/rangeparser.cc.o

Building CXX object src/libtools/CMakeFiles/votca_tools.dir/linalg/gsl/cholesky.cc.o

Linking CXX shared library libvotca_tools.so

[ 93%] Built target votca_tools

[ 96%] Building CXX object src/tools/CMakeFiles/votca_property.dir/votca_property.cc.o

Linking CXX executable votca_property

[ 96%] Built target votca_property

[100%] Building votca_property manpage

[100%] Built target votca_property_manpage

Scanning dependencies of target manpages

[100%] Built target manpages

^[[32;01minstalling tools^[[0m

[ 0%] Built target votca_tools_manpages

[ 0%] Built target gitversion

[ 93%] Built target votca_tools

[ 96%] Built target votca_property

[100%] Built target votca_property_manpage

[100%] Built target manpages

Linking CXX executable CMakeFiles/CMakeRelink.dir/votca_property

Linking CXX shared library CMakeFiles/CMakeRelink.dir/libvotca_tools.so

Install the project...

-- Install configuration: "Release"

-- Installing: /home/u/espinosa/test/lib/libvotca_tools.so.4

-- Up-to-date: /home/u/espinosa/test/lib/libvotca_tools.so

-- Up-to-date: /home/u/espinosa/test/lib/pkgconfig/libvotca_tools.pc

-- Installing: /home/u/espinosa/test/bin/votca_property

-- Installing: /home/u/espinosa/test/share/man/man1/votca_property.1

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/property.h

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/thread.h

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/histogramnew.h

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/random2.h

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/matrix.h

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/akimaspline.h

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/constants.h

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/parsexml.h

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/linalg.h

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/version.h

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/datacollection.h

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/objectfactory.h

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/mutex.h

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/colors.h

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/linspline.h

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/calculator.h

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/rangeparser.h

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/crosscorrelate.h

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/vec.h

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/tokenizer.h

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/application.h

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/cubicspline.h

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/table.h

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/getline.h

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/lexical_cast.h

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/globals.h

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/types.h

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/spline.h

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/average.h

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/histogram.h

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/random.h

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/propertyiomanipulator.h

-- Up-to-date: /home/u/espinosa/test/include/votca/tools/correlate.h

-- Up-to-date: /home/u/espinosa/test/bin/VOTCARC.csh

-- Up-to-date: /home/u/espinosa/test/bin/VOTCARC.bash

-- Up-to-date: /home/u/espinosa/test/share/man/man7/votca-tools.7

^[[32;01mdone with tools^[[0m

^[[34;01msourcing '/home/u/espinosa/test//bin/VOTCARC.bash'^[[0m

^[[32;01mWorking on csg^[[0m

^[[34;01mSource dir (csg) is already there - skipping checkout^[[0m

^[[34;01mcmake -DCMAKE_INSTALL_PREFIX='/home/u/espinosa/test/' -DFFTW3_LIBRARY=/opt/local/intel/fftw-3.3.3/lib/libfftw3.so -DFFTW3_INCLUDE_DIR=/opt/local/intel/fftw-3.3.3/include/ -DWITH_SQLITE3=NO -DGROMACS_INCLUDE_DIR=/opt/local/gromacs-4.5.4/include/ -DGROMACS_LIBRARY=/opt/local/gromacs-4.5.4/lib/libgmx.so -DBoost_FILESYSTEM_LIBRARY=/usr/lib64/libboost_filesystem.so -DVOTCA_TOOLS_LIBRARY=/home/u/espinosa/test/lib/libvotca_tools.so.4 -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=ON .^[[0m

-- Found Git: /opt/local/bin/git (found version "1.8.4-rc0")

-- Looking for include file pthread.h

-- Looking for include file 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 - found

-- Found Threads: TRUE

-- Found TXT2TAGS: /opt/local/bin/txt2tags

-- Found UnixCommands: /bin/bash

-- Found PkgConfig: /usr/bin/pkg-config (found version "0.23")

-- checking for module 'libvotca_tools'

-- package 'libvotca_tools' not found

-- Found VOTCA_TOOLS: /home/u/espinosa/test/lib/libvotca_tools.so.4

-- Looking for VotcaToolsFromC in /home/u/espinosa/test/lib/libvotca_tools.so.4

-- Looking for VotcaToolsFromC in /home/u/espinosa/test/lib/libvotca_tools.so.4 - not found

-- Configuring incomplete, errors occurred!

See also "/home/u/espinosa/test/src/csg/CMakeFiles/CMakeOutput.log".

See also "/home/u/espinosa/test/src/csg/CMakeFiles/CMakeError.log".

Christoph Junghans

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Mar 10, 2016, 9:46:55 AM3/10/16

to vo...@googlegroups.com

2016-03-09 21:02 GMT-07:00 Tiago Espinosa <tespinos...@gmail.com>:
> OK, now I change CMakeList.txt:
>
> cmake_minimum_required(VERSION 2.8.11)
> find_package(Boost 1.36.0 REQUIRED COMPONENTS program_options
>
> version on cluster is 1.36.0

Ok, I see, I guess that is why cmake fails.
However, Boost 1.36.0 is from 2008 and completely untested with VOTCA,
I am not sure that will work.
You might need to update your boost.

Can you send me that CMakeError.log!

Christoph

Tiago Espinosa

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Mar 10, 2016, 10:12:18 AM3/10/16

to vo...@googlegroups.com

Christoph, I did a new try, with a new boost:

I did:

export CC=gcc

export CXX=g++

export F77=gfortran

export LDFLAGS="-lpthread"

export INCLUDE=/opt/local/include:$INCLUDE

export LD_LIBRARY_PATH=/opt/local/lib:$LD_LIBRARY_PATH

export PREFIX=/home/u/espinosa/test/

./build.sh -DGMX_DOUBLE=OFF -DGMX_GPU=OFF -DBoost_LIBRARY_DIR=/opt/local/lib -DBOOST_INCLUDE_DIR=/opt/local/include/boost -Dboost_LIBRARY=/opt/local/lib/libboost_program_options.so -DGROMACS_INCLUDE_DIR=${PREFIX}/include/gromacs -DGROMACS_LIBRARY=${PREFIX}/lib64/libgromacs.so -DVOTCA_TOOLS_LIBRARY=${PREFIX}/lib/libvotca_tools.so -DFFTW3_LIBRARY='/opt/local/gnu/fftw/lib/libfftw3f.so;/opt/local/gnu/fftw/lib/libfftw3.so' -DFFTW3_INCLUDE_DIR=/opt/local/gnu/fftw/include -DGSL_LIBRARY='/opt/local/lib/libgsl.so;/opt/local/lib/libgslcblas.so' --dev tools csg --log build.log

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CMakeOutput.log

CMakeError.log

build.log

Christoph Junghans

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Mar 10, 2016, 11:42:01 AM3/10/16

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That looks better, boost got detected correctly!

Can you send the CMakeError.log from inside csg
(/home/u/espinosa/test/src/csg/CMakeFiles/CMakeError.log)?

Tiago Espinosa

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Mar 10, 2016, 11:56:23 AM3/10/16

to vo...@googlegroups.com

done!

CMakeError.log

Christoph Junghans

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Mar 10, 2016, 12:47:36 PM3/10/16

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At the end it says:
/home/u/espinosa/test/lib/libvotca_tools.so: undefined reference to
`boost::program_options::detail::cmdline::style(int)'

That means something went wrong when linking.
I guess this might be triggered by a typo in your command.
"-Dboost_LIBRARY=" needs to be "-DBoost_LIBRARY=" (chapitel B)
I thing the easiest way to specify a custom Boost location is
BOOST_ROOT, i.e. -DBOOST_ROOT=/opt/local/ in your case.

Cheers,

Christoph

Tiago Espinosa

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Mar 11, 2016, 12:48:09 PM3/11/16

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command:

./build.sh -DGMX_DOUBLE=OFF -DGMX_GPU=OFF -DBoost_LIBRARY_DIR=/opt/local/lib -DBOOST_INCLUDE_DIR=/opt/local/include/boost -DBoost_LIBRARY=/opt/local/lib/libboost_program_options.so -DGROMACS_INCLUDE_DIR=/home/u/espinosa/test/include/gromacs -DGROMACS_LIBRARY=/home/u/espinosa/test/lib64/libgromacs.so -DVOTCA_TOOLS_LIBRARY='/home/u/espinosa/test/lib/libvotca_tools.so;/home/u/espinosa/test/lib/libvotca_tools.so.3;/home/u/espinosa/test/lib/libvotca_tools.so.4;/home/u/espinosa/test/lib/libmd.so' -DFFTW3_LIBRARY='/opt/local/gnu/fftw/lib/libfftw3f.so;/opt/local/gnu/fftw/lib/libfftw3.so' -DFFTW3_INCLUDE_DIR=/opt/local/gnu/fftw/include -DGSL_LIBRARY='/opt/local/lib/libgsl.so;/opt/local/lib/libgslcblas.so' -DBOOST_ROOT=/opt/local/lib/ --dev tools csg --log build.log

Regards

Tiago

CMakeError.log

Christoph Junghans

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Mar 11, 2016, 12:58:14 PM3/11/16

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I saw the following line in the error log:
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld: warni
ng: libboost_program_options.so.1.54.0, needed by
/home/u/espinosa/test/lib/libvotca_tools.so, not found (try using
-rpath or -rpath-link)

My guess is that once you load libvotca_tools.so, cannot be found anymore.

Try two things:
1.) Post the output of
$ ldd /home/u/espinosa/test/lib/libvotca_tools.so
2.) Did you have
$ export LD_LIBRARY_PATH=/opt/local/lib
already?

Christoph

Tiago Espinosa

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Mar 11, 2016, 1:03:38 PM3/11/16

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1) output:

/home/u/espinosa/test/lib/libvotca_tools.so: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/u/espinosa/test/lib/libvotca_tools.so)

linux-vdso.so.1 => (0x00007fffa159c000)

libboost_program_options.so.1.54.0 => not found

libboost_filesystem.so.1.54.0 => not found

libboost_system.so.1.54.0 => not found

libgsl.so.0 => /opt/local/lib/libgsl.so.0 (0x00007fdbe15c9000)

libgslcblas.so.0 => /opt/local/lib/libgslcblas.so.0 (0x00007fdbe1388000)

libsqlite3.so.0 => /usr/lib64/libsqlite3.so.0 (0x00007fdbe10f6000)

libfftw3.so.3 => /opt/local/gnu/fftw/lib/libfftw3.so.3 (0x00007fdbe0d71000)

libexpat.so.1 => /lib64/libexpat.so.1 (0x00007fdbe0b47000)

libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fdbe092a000)

libstdc++.so.6 => /opt/local/gc/lib/gcc/x86_64-cesup-linux/4.8.1/libstdc++.so.6 (0x00007fdbe061b000)

libm.so.6 => /lib64/libm.so.6 (0x00007fdbe03c5000)

libgcc_s.so.1 => /opt/local/gc/lib/gcc/x86_64-cesup-linux/4.8.1/libgcc_s.so.1 (0x00007fdbe01af000)

libc.so.6 => /lib64/libc.so.6 (0x00007fdbdfe50000)

/lib64/ld-linux-x86-64.so.2 (0x00007fdbe1c87000)

2) yes

export LD_LIBRARY_PATH=/opt/local/lib:$LD_LIBRARY_PATH

Christoph Junghans

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Mar 11, 2016, 2:46:29 PM3/11/16

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2016-03-11 11:03 GMT-07:00 Tiago Espinosa <tespinos...@gmail.com>:
> 1) output:
>
> /home/u/espinosa/test/lib/libvotca_tools.so: /lib64/libc.so.6: version
> `GLIBC_2.14' not found (required by
> /home/u/espinosa/test/lib/libvotca_tools.so)
>
> linux-vdso.so.1 => (0x00007fffa159c000)
>
> libboost_program_options.so.1.54.0 => not found
>
> libboost_filesystem.so.1.54.0 => not found
>
> libboost_system.so.1.54.0 => not found

That is the problem! Even though you have specified LD_LIBRARY_PATH,
is seems it not getting picked up.
Is libboost_system.so.1.54.0 in /opt/local/lib? If it is in a
different directory, you need to add that to LD_LIBRARY_PATH, too!

Tiago Espinosa

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Mar 11, 2016, 4:47:23 PM3/11/16

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build.log

Christoph Junghans

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Mar 14, 2016, 1:11:38 AM3/14/16

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After some back and forth, we got it working with the following
command (one line):

CXX=/opt/local/gc/bin/g++ CC=/opt/local/gc/bin/gcc
PKG_CONFIG_PATH="/opt/local/gnu/fftw-3.3.3/lib/pkgconfig:/opt/local/gromacs-5.0.5/lib64/pkgconfig:/opt/local/lib/pkgconfig"
./build.sh --prefix /home/u/espinosa/votca3
-DBoost_INCLUDE_DIR=/opt/local/include
-DBoost_LIBRARY_DIR=/opt/local/lib
-DGSL_LIBRARY=/opt/local/lib/libgsl.so
-DGSLCBLAS_LIBRARY=/opt/local/lib/libgslcblas.so -DBUILD_MANPAGES=OFF
--dev -u tools csg

Explanation:
0.) in bash one can do
$ CXX=bla ./some_command
which is the same as:
$ export CXX=bla
$ ./some_command
Except it only export the variables for the one command.
This makes the line longer, but things much cleaner when experimenting.
1.) -DBoost_INCLUDE_DIR and -DBoost_LIBRARY_DIR specify the location
of boost (mind the capitalization!)
2.) The variable PKG_CONFIG_PATH tells cmake (which uses pkg-config)
where to find fftw, gromacs etc., e.g. test with
$ pkg-config --libs fftw
3.) -DGSL_LIBRARY and -DGSLCBLAS_LIBRARY tells cmake, which GSL library to use
4.) -DBUILD_MANPAGES=OFF disables the build of manpages
5.) Gromacs was build with a newer gcc from /opt/local/gc/bin/ and
hence VOTCA had to build with that same compiler to get the same C++
ABI, so CC and CXX needed to be set

Cheers,

Christoph

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