input format not supported: topol.tpr

[Christoph Junghans]

Hi Valentina,

it seems like you have compiled VOTCA without gromacs support.
Please check that again. tpr and xtc files need gromacs support.

Cheers,

Christoph

2011/8/4 Valentina Erastova <valentina...@durham.ac.uk>:
> Dear VOTCA Developers,
> I am trying to use VOTCA for GC my system and I have a problem with
> running csg_boltzmann.  As described in the manual I am providing gromacs
> topology, but it seems to to be a supported topology.
> Here is an example, when I try running the tutorial:
> My existing files in the directory (created by running run.sh)
> -rw-r--r-- 1 d47fvj users   3713 2011-05-02 15:35 topol.top
> -rw-r--r-- 1 d47fvj users    739 2011-05-02 15:35 settings.xml
> -rwxr-xr-x 1 d47fvj users     69 2011-05-02 15:35 run.sh
> -rwxr-xr-x 1 d47fvj users    318 2011-05-02 15:35 run_fmatch.sh
> -rwxr-xr-x 1 d47fvj users    219 2011-05-02 15:35 run_boltzmann.sh
> -rw-r--r-- 1 d47fvj users   1171 2011-05-02 15:35 propane.xml
> -rw-r--r-- 1 d47fvj users    575 2011-05-02 15:35 conf.gro
> -rw-r--r-- 1 d47fvj users    157 2011-05-02 15:35 boltzmann_cmds
> -rw-r--r-- 1 d47fvj users  10310 2011-08-04 13:04 mdout.mdp
> -rw-r--r-- 1 d47fvj users  18836 2011-08-04 13:04 topol.tpr
> -rw-r--r-- 1 d47fvj users 192384 2011-08-04 13:05 traj.trr
> -rw-r--r-- 1 d47fvj users   4348 2011-08-04 13:05 state.cpt
> -rw-r--r-- 1 d47fvj users  12897 2011-08-04 13:05 md.log
> -rw-r--r-- 1 d47fvj users   1308 2011-08-04 13:05 ener.edr
> -rw-r--r-- 1 d47fvj users    804 2011-08-04 13:05 confout.gro
> -rw-r--r-- 1 d47fvj users   9864 2011-08-04 13:06 grompp.mdp
> Followed by  ./run_boltzmann.sh
> an error occurred:
> input format not supported: topol.tpr
> I also have tried with topol.top but same error.
> Could you advise me how can I solve this problem?
> Many thanks,
>
> __________________________
> Valentina Erastova
> PhD Research Postgraduate
> Computational Chemistry Group
> Department of Chemistry
> Durham University
> Sciences Editor,
> Kaleidoscope
> STEM Ambassador
> Associate Member of RSC
> +44 786 131 6686
> +7 926 587 6662
>
>
>

--
Dr. Christoph Junghans
Votca Core Developer

Web: http://www.votca.org

[Valentina Erastova]

Hello,

I am trying to compile with gromacs, but not being successful, getting
this error:
-- Could NOT find GMX (missing: GMX_LIBRARY GMX_INCLUDE_DIR)
CMake Error at src/libcsg/CMakeLists.txt:44 (message):
gromacs-4.5 (single or double) not found, make sure you have also
installed
the gromacs-5.0 and it's dev package or disable it with -
DWITH_GMX=OFF. If
you have gromacs-5.0 installed enable to build against it with
-DWITH_GMX_DEVEL=ON

I have gromacs 4.5.3 installed on my computer,

my library path seems to be ok:
echo $LD_LIBRARY_PATH
/usr/local/votca/lib:/usr/local/gromacs/lib:/usr/lib

I can locate gmx libraries there
locate libgmx_d
/usr/lib/libgmx_d.so.4
/usr/lib/libgmx_d.so.4.0.0
/usr/local/gromacs/lib/libgmx_d.a
/usr/local/gromacs/lib/libgmx_d.la
/usr/local/gromacs/lib/pkgconfig/libgmx_d.pc

also in build.sh if I echo the LD_LIBRARY_PATH it is correct.

Does anyone have a solution?

Many thanks,
V

On Aug 4, 3:03 pm, Christoph Junghans <jungh...@votca.org> wrote:
> Hi Valentina,
>
> it seems like you have compiled VOTCA without gromacs support.
> Please check that again. tpr and xtc files need gromacs support.
>
> Cheers,
>
> Christoph
>

> 2011/8/4 Valentina Erastova <valentina.erast...@durham.ac.uk>:

[Valentina]

Hi there,

I have reinstalled gromacs 4.5.4 with shared libraries, single
precision. I have now the following libraries.

ls /usr/gromacs/lib
/usr/local/gromacs/lib/libgmx.a
/usr/local/gromacs/lib/libgmx.la
/usr/local/gromacs/lib/libgmx.so
/usr/local/gromacs/lib/libgmx.so.6
/usr/local/gromacs/lib/libgmx.so.6.0.0
/usr/local/gromacs/lib/libgmx_d.a
/usr/local/gromacs/lib/libgmx_d.la
/usr/local/gromacs/lib/libgmxana.a
/usr/local/gromacs/lib/libgmxana.la
/usr/local/gromacs/lib/libgmxana.so
/usr/local/gromacs/lib/libgmxana.so.6
/usr/local/gromacs/lib/libgmxana.so.6.0.0
/usr/local/gromacs/lib/libgmxana_d.a
/usr/local/gromacs/lib/libgmxana_d.la
/usr/local/gromacs/lib/libgmxpreprocess.a
/usr/local/gromacs/lib/libgmxpreprocess.la
/usr/local/gromacs/lib/libgmxpreprocess.so
/usr/local/gromacs/lib/libgmxpreprocess.so.6
/usr/local/gromacs/lib/libgmxpreprocess.so.6.0.0
/usr/local/gromacs/lib/libgmxpreprocess_d.a
/usr/local/gromacs/lib/libgmxpreprocess_d.la


LD_LIBRARY_PATH includes the correct path:

echo $LD_LIBRARY_PATH
/usr/local/votca/lib:/usr/local/gromacs/lib

Unfortunately, upon compiling votca, I still get the same error:

-- checking for module 'libgmx'
-- package 'libgmx' not found

-- Could NOT find GMX (missing: GMX_LIBRARY GMX_INCLUDE_DIR)
CMake Error at src/libcsg/CMakeLists.txt:44 (message):
gromacs-4.5 (single or double) not found, make sure you have also
installed

the gromacs-4.5 and it's dev package or disable it with -

DWITH_GMX=OFF. If
you have gromacs-5.0 installed enable to build against it with
-DWITH_GMX_DEVEL=ON

-- Configuring incomplete, errors occurred!


Could you advise me how I can solve this?

Many thanks,
V


On Aug 4, 6:12 pm, Valentina Erastova <valentina_erast...@yahoo.co.uk>
wrote:

[Christoph Junghans]

Hi Valentina,

You can have a look at CMakeFiles/CMakeError.log.

I have some ideas what could be the problem:
1.) Do you have pkg-config installed?
2.) On some distributions /usr/local/gromacs/lib/pkgconfig is not
included in the search path of pkg-config, you can add it by
export PKG_CONFIG_PATH=/usr/local/gromacs/lib/pkgconfig
3.) Specify GMX_LIBRARY and GMX_INCLUDE_DIR by hand by adding
-DGMX_LIBRARY=/usr/local/gromacs/lib/libgmx.so
-DGMX_INCLUDE_DIR=/usr/local/include
to the build.sh commandline.

Cheers,

Christoph

2011/8/5 Valentina <valentina...@yahoo.co.uk>:

> --
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> To post to this group, send email to vo...@googlegroups.com.
> To unsubscribe from this group, send email to votca+un...@googlegroups.com.
> For more options, visit this group at http://groups.google.com/group/votca?hl=en.

[Valentina]

Awesome! Thank you very much, editing PKG_CONFIG_PATH did the trick!
V

On Aug 5, 7:20 pm, Christoph Junghans <jungh...@votca.org> wrote:
> Hi Valentina,
>

> You can have a look at CMakeFiles/CMakeError.log.
>
> I have some ideas what could be the problem:
> 1.) Do you have pkg-config installed?
> 2.) On some distributions /usr/local/gromacs/lib/pkgconfig is not
> included in the search path of pkg-config, you can add it by
> export PKG_CONFIG_PATH=/usr/local/gromacs/lib/pkgconfig
> 3.) Specify GMX_LIBRARY and GMX_INCLUDE_DIR by hand by adding
> -DGMX_LIBRARY=/usr/local/gromacs/lib/libgmx.so
> -DGMX_INCLUDE_DIR=/usr/local/include
> to the build.sh commandline.
>
> Cheers,
>
> Christoph
>

> 2011/8/5 Valentina <valentina_erast...@yahoo.co.uk>:

> > For more options, visit this group athttp://groups.google.com/group/votca?hl=en.

[Valentina]

Hello again.

I am trying to install Votca on other 2 machines (i am now the
installer of the lab) and have a similar problem as above. I do have
pkg-config, I have added pkg-config path, I have the right version
(4.5.4) of gromacs installed, I have tried specifying the path to the
gmx include and library by hand, as advised above, but nothing seem to
work, I get an error of similar type as above (but different):


Working on csg
Source dir (csg) is already there - skipping checkout
cmake -DCMAKE_INSTALL_PREFIX=/usr/local/votca -DWITH_SQLITE3=NO -
DCMAKE_INSTALL_RPATH_USE_LINK_PATH=ON .

-- checking for module 'libgmx'
-- package 'libgmx' not found

-- Could NOT find GROMACS (missing: GROMACS_LIBRARY
GROMACS_INCLUDE_DIR)
CMake Error at src/libcsg/CMakeLists.txt:25 (message):
gromacs not found, make sure you have installed at least the
gromacs-4.0.7
and it's dev package. If the gromacs module was not found above,
make sure
you have sourced GMXRC or set PKG_CONFIG_PATH yourself. If you have
a
double precision version of gromacs enable to build against it with
-DGMX_DOUBLE=ON. If you have gromacs-5.0 installed enable to build
against
it with -DWITH_GMX_DEVEL=ON. Gromacs support can be disable it with
-DWITH_GMX=OFF.


There must be a wise trick, that I don't know.
Thank you for help,
Valentina

[Christoph Junghans]

Hi Valentina,

after we had recently so much problem with detecting gromacs I cleaned
up cmake's gromacs detection code.
I also added the support for gromacs 4.0.X back.

You can specify the gromacs include dir and library in GROMACS_LIBRARY
and GROMACS_INCLUDE_DIR independently of their version.

But

>-- checking for module 'libgmx'
> -- package 'libgmx' not found

shows me that there is something wrong with your pkg-config path.
You can test if it works beforehand by running:
$pkg-config --cflags --libs libgmx
The output should look like this:
-pthread -DGMX_SOFTWARE_INVSQRT -DGMX_THREADS -pthread -lgmx -lm

Is pkg-config installed?

And actually GMXRC should set the PKG_CONFIG_PATH for you.

Cheers,

Christoph

2011/9/6 Valentina <valentina...@yahoo.co.uk>:

> For more options, visit this group at http://groups.google.com/group/votca?hl=en.

[Valentina]

Great! Thank you very much.
I managed to install it on the cluster, there was smth funny with pkg-
config indeed. (One more machine to go, but I think I know where the
problem lays now)

Valentina

On Sep 6, 3:25 pm, Christoph Junghans <jungh...@votca.org> wrote:
> Hi Valentina,
>

> after we had recently so much problem with detecting gromacs I cleaned
> up cmake's gromacs detection code.
> I also added the support for gromacs 4.0.X back.
>
> You can specify the gromacs include dir and library in GROMACS_LIBRARY
> and GROMACS_INCLUDE_DIR independently of their version.
>
> But>-- checking for module 'libgmx'
> > --   package 'libgmx' not found
>
> shows me that there is something wrong with your pkg-config path.
> You can test if it works beforehand by running:
> $pkg-config --cflags --libs libgmx
> The output should look like this:
> -pthread -DGMX_SOFTWARE_INVSQRT -DGMX_THREADS -pthread -lgmx -lm
>
> Is pkg-config installed?
>
> And actually GMXRC should set the PKG_CONFIG_PATH for you.
>
> Cheers,
>
> Christoph
>

> 2011/9/6 Valentina <valentina_erast...@yahoo.co.uk>: