Votca 1.2 released

[Victor Ruehle]

Dear all,

finally, after a long day of coding, Votca 1.2 is released under the
name 'SuperDoris'.

A detailed list of changes can be found here:
http://www.votca.org/changelog

Expect for many minor enhancements and fixes, the most important
change is that we switched from autotools to cmake which should
improve the build process significantly. Further, it is now easier to
submit csg_inverse to a cluster in cases where one iteration takes
longer than the Wall time.

Due to a lack of developers we will NOT fix any bugs in votca 1.1.X
anymore, so we encourage everyone to update or at least to not bug us
with bugs in the old version anymore ;-)

Cheers,

The VOTCA team

[Nikos Bentenitis]

Hi Victor,

I have had trouble installing version 1.2 mainly because I am not
familiar with cmake.

I am trying to install Votca at $HOME/programs/votca-1.2 having
installed the prerequisite programs in the following directories:

GSL: $HOME/programs/gsl-1.0
FFTW3: $HOME/programs/fftw-3.2.1
Gromacs: $HOME/programs/gromacs-4.5.3
And I am using Votca's built-in Boost

How do I tell build.sh to look for libraries in the above locations?
(all libraries and include directories are in their standard location
for each program)

Thank you

Nikos

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[Christoph Junghans]

Hi Nikos,

there are basically two ways to set the paths to the libraries.
1.) add -DGSL_INCLUDE_DIR=$HOME/programs/gsl-1.0/include
-DGSL_LIBRARY=$HOME/programs/gsl-1.0/lib/libgsl.so to the command line
of build.sh
and the same for FFTW3_INCLUDE_DIR, FFTW3_LIBRARY and GMX_LIBRARY and
GMX_INCLUDE_DIR

or

2.) cmake comes with two nice gui's called cmake-gui and ccmake, which
can be used to set the paths.
$ cd path/to/votca/tools
$ cmake-gui . #mind the '.'
or
$ ccmake .
Don't forget to click generate!
$ make

Cheers,

Christoph

PS: I just added the '--cmake' option to build.sh to make use for the gui, e.g.
$build --cmake ccmake

2011/6/17 Nikos Bentenitis <bent...@southwestern.edu>:

--
Dr. Christoph Junghans
Votca Core Developer

Web: http://www.votca.org

[Nikos Bentenitis]

Hello Christoph,

I did not manage to use the cmake GUIs so I tried to enter the library
locations using the command line. Unfortunately, I am stuck with
sqlite3. If I use the sqlite3 libraries installed on my machine
build.sh quits with errors. After I install sqlite3 on my home
directory, build.sh quits with the same errors. I included the command
lines below as well as the common errors that I get.

Any suggestions?

Thanks!

Nikos

Here's the command I used without the sqlite3 in my home directory:

./build.sh --prefix $HOME/programs/votca-1.1.2
-DGSL_INCLUDE_DIR=$HOME/programs/gsl-1.0/include
-DGSL_LIBRARY=$HOME/programs/gsl-1.0/lib/libgsl.so
-DCBLAS_LIBRARY=$HOME/programs/gsl-1.0/lib/libgslcblas.so
-DFFTW3_INCLUDE_DIR=$HOME/programs/fftw-3.2.1d/include
-DFFTW3_LIBRARY=$HOME/programs/fftw-3.2.1d/lib
-DGMX_INCLUDE_DIR=$HOME/programs/gromacs-4.5.3/include
-DGMX_LIBRARY=$HOME/programs/gromacs-4.5.3/lib -DEXTERNAL_BOOST=OFF
tools

and here's the command I used with sqlite3 installed in my home directory:

./build.sh --prefix /home/bentenin/programs/votca-1.1.2
-DGSL_INCLUDE_DIR=$HOME/programs/gsl-1.0/include
-DGSL_LIBRARY=$HOME/programs/gsl-1.0/lib/libgsl.so
-DCBLAS_LIBRARY=$HOME/programs/gsl-1.0/lib/libgslcblas.so
-DFFTW3_INCLUDE_DIR=$HOME/programs/fftw-3.2.1d/include
-DFFTW3_LIBRARY=$HOME/programs/fftw-3.2.1d/lib
-DGMX_INCLUDE_DIR=$HOME/programs/gromacs-4.5.3/include
-DGMX_LIBRARY=$HOME/programs/gromacs-4.5.3/lib
-DSQLITE_INCLUDE_DIR=$HOME/programs/sqlite-3.7.6.3/include
-DSQLITE_LIBRARY=$HOME/programs/sqlite-3.7.6.3/lib
-DEXTERNAL_BOOST=OFF tools

And here's the last lines of the output that I got from build.sh

/home/bentenin/programs/src/tools/include/votca/tools/database.h:36:
error: 'SQLITE_OPEN_READWRITE' was not declared in this scope
/home/bentenin/programs/src/tools/include/votca/tools/database.h:36:
error: 'SQLITE_OPEN_CREATE' was not declared in this scope
/home/bentenin/programs/src/tools/src/libtools/database.cc: In member
function 'void votca::tools::Database::Open(std::string, int)':
/home/bentenin/programs/src/tools/src/libtools/database.cc:33: error:
'SQLITE_OPEN_READWRITE' was not declared in this scope
/home/bentenin/programs/src/tools/src/libtools/database.cc:33: error:
'SQLITE_OPEN_CREATE' was not declared in this scope
/home/bentenin/programs/src/tools/src/libtools/database.cc:33: error:
'sqlite3_open_v2' was not declared in this scope
/home/bentenin/programs/src/tools/src/libtools/random.cc: In static
member function 'static int
votca::tools::Random::rand_uniform_int(int)':
/home/bentenin/programs/src/tools/src/libtools/random.cc:153: warning:
converting to 'int' from 'double'
/home/bentenin/programs/src/tools/src/libtools/database.cc: In member
function 'votca::tools::Statement*
votca::tools::Database::Prepare(std::string)':
/home/bentenin/programs/src/tools/src/libtools/database.cc:56: error:
'sqlite3_prepare_v2' was not declared in this scope
make[2]: *** [src/libtools/CMakeFiles/votca_tools.dir/database.cc.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [src/libtools/CMakeFiles/votca_tools.dir/all] Error 2
make: *** [all] Error 2

[Nikos Bentenitis]

Hello again,

This is a followup to my last question: I found out that there is an
option to exclude sqlite3, and I used it as in the following command.
However, I now get a new problem with fftw. Could you please take a
look?

Thanks!

Nikos

Input:

./build.sh --prefix /home/bentenin/programs/votca-1.1.2
-DGSL_INCLUDE_DIR=$HOME/programs/gsl-1.0/include
-DGSL_LIBRARY=$HOME/programs/gsl-1.0/lib/libgsl.so
-DCBLAS_LIBRARY=$HOME/programs/gsl-1.0/lib/libgslcblas.so
-DFFTW3_INCLUDE_DIR=$HOME/programs/fftw-3.2.1d/include
-DFFTW3_LIBRARY=$HOME/programs/fftw-3.2.1d/lib
-DGMX_INCLUDE_DIR=$HOME/programs/gromacs-4.5.3/include
-DGMX_LIBRARY=$HOME/programs/gromacs-4.5.3/lib

-DSQLITE_INCLUDE_DIR=$HOME/programs/sqlite-3.7.6.4/include
-DSQLITE_LIBRARY=$HOME/programs/sqlite-3.7.6.4/lib
-DEXTERNAL_BOOST=OFF -DWITH_SQLITE3=OFF tools

Output:
libvotca_tools.so.2: undefined reference to `fftw_plan_dft_r2c_1d'
libvotca_tools.so.2: undefined reference to `fftw_plan_r2r_1d'
libvotca_tools.so.2: undefined reference to `fftw_plan_dft_c2r_1d'
libvotca_tools.so.2: undefined reference to `fftw_execute'
libvotca_tools.so.2: undefined reference to `fftw_destroy_plan'
libvotca_tools.so.2: undefined reference to `fftw_free'
libvotca_tools.so.2: undefined reference to `fftw_malloc'
collect2: ld returned 1 exit status
make[2]: *** [src/libtools/linktest] Error 1
make[1]: *** [src/libtools/CMakeFiles/linktest.dir/all] Error 2

make: *** [all] Error 2

[Christoph Junghans]

Hi Nikos,

The sqlite3 stuff is only needed for the charge transport modules. So
you can just disable the sqlite3 support by adding -DWITH_SQLITE3=OFF.

Cheers,

Christoph

2011/6/23 Nikos Bentenitis <bent...@southwestern.edu>: