From: Cosseddu, Salvatore (S.M.Cosseddu_at_warwick.ac.uk)
Date: Fri May 13 2011 - 06:41:40 CDT

Thank you so much! Now it works perfectly. I'd like invite you a beer.

You are very kind.

Just the last thing, a suggestion from a user.

quote: http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/compiling.html

> If you wish to build the plugins for AMBER 9, and MMTK NetCDF trajectories,
> then the NETCDFLIB and NETCDFINC environment variables must be set.

could be a bit ambiguous. Someone could understand that, if unset, netcdf support will not be installed.
It could be useful to add just a line about setting the variable as empty or removing them from Make-arch

Many thanks again

Salvatore Cosseddu
Centre for Scientific Computing and
School of Engineering
University of Warwick
Coventry CV4 7AL
United Kingdom

email: S.M.Cosseddu_at_warwick.ac.uk

-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu on behalf of Axel Kohlmeyer
Sent: Fri 13/05/2011 01:40
To: Cosseddu, Salvatore
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: Compiling plugins without netcdf support returns an error.
 
On Thu, May 12, 2011 at 7:48 PM, Cosseddu, Salvatore
<S.M.Cosseddu_at_warwick.ac.uk> wrote:
> Many thanks both of you for the kindness and the prompt reply.
>
> First of all many thanks for all those tools you provide.
> I manage to compile the plugins.
> What I would like to use is the fortran interface to molfile.
> I manage to compile it, but, once I try to run the tester it returns
>
> #$ ./tester
> ./tester: error while loading shared libraries: libtcl8.5.so: cannot open
> shared object file: No such file or directory

> But I'm sure I compiled linking the tcl library from the right path. Any
> idea?

this is not a linktime but a runtime error. you have compiled
tcl as a shared library but it is not in any of the directory that
the shared linker is searching. you have set set the LD_LIBRARY_PATH
environment variable accordingly or recompile tcl to generate a
static library and link with that.

axel.

>
>
> Salvatore Cosseddu
> Centre for Scientific Computing
> School of Engineering
> University of Warwick
> Coventry CV4 7AL
> United Kingdom
>
> email: S.M.Cosseddu_at_warwick.ac.uk
>
>
>
>
> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu on behalf of Axel Kohlmeyer
> Sent: Thu 12/05/2011 21:56
> To: Cosseddu, Salvatore
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: Compiling plugins without netcdf support returns an
> error.
>
> On Thu, May 12, 2011 at 4:12 PM, Cosseddu, Salvatore
> <S.M.Cosseddu_at_warwick.ac.uk> wrote:
>> Sorry, is it possible that there's a small bug in some vmd 1.9 plugin
>> Makefiles?
>>
>> According to
>> http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/compiling.html and to
>> the general Makefile, if NETCDFLIB and NETCDFINC are not declared, vmd
>> could
>> be compiled without netcdf. But catdcd requires the library to be linked
>> to
>> compile as you can see from this error. The compilation aborts.
>
> not declaring is not sufficient to disable it.
> you have to define those variables to be empty.
>
>>
>> #$ make LINUXAMD64 TCLINC=$TCLINC TCLLIB=$TCLLIB
>
> try: make LINUXAMD64 TCLINC=$TCLINC TCLLIB=$TCLLIB NETCDFLDFLAGS=""
>
>>> src/sgsmooth.C: In function 'float_vect lsqr_fprime(const float_vect&,
>>> int)':
>>> src/sgsmooth.C:545: warning: comparison between signed and unsigned
>>> integer expressions
>>> src/sgsmooth.C: In function 'float_vect sg_derivative(const float_vect&,
>>> int, int, double)':
>>> src/sgsmooth.C:567: warning: comparison between signed and unsigned
>>> integer expressions
>>> src/sgsmooth.C:600: warning: comparison between signed and unsigned
>>> integer expressions
>>> /usr/bin/ld: cannot find -lnetcdf
>>> collect2: ld returned 1 exit status
>>> make[2]: *** [../compile/lib_LINUXAMD64/bin/catdcd4.0/catdcd] Errore 1
>>> make[1]: *** [bins] Errore 1
>>> make: *** [LINUXAMD64] Errore 2
>>
>> Best regards
>> Salvatore Cosseddu
>>
>> Salvatore Cosseddu
>> Centre for Scientific Computing and
>> School of Engineering
>> University of Warwick
>> Coventry CV4 7AL
>> United Kingdom
>>
>> email: S.M.Cosseddu_at_warwick.ac.uk
>>
>> Ps. I'm sorry if it is a repost but I received a failure notice.
>
> you'll always receive failure notices due to some people
> not unsubscribing from mailing lists when they move on.
> you have to check carefully where the failure notice is coming from.
>
>
> axel.
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com  http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>
>
>

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.