VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Nov 30 2004 - 16:34:41 CST

Luis,
  If MSMS crashes when used with the socketPort option, that
completely explains the reason VMD fails to talk to it. There are
two ways around this:
  1) use one of the the latest test versions of VMD 1.8.3, which has
     a new environment variable called "VMDMSMSUSEFILE". If this variable
     is set, then VMD will talk to MSMS through files instead of via
     sockets. (this allows VMD to use MSMS on Windows, where MSMS had
     never previously implemented the socketport feature...)

  2) Run MSMS manually in a debugger and report the crash to the
     MSMS authors so they can fix it. Like this:
         gdb msms.whatever.you.named.it
         run -socketPort 1357
    ...then, when it crashes:
         where
    Then email the 'where' output to the MSMS team along with
    the output of 'ldd msms.whatever.you.named.it' so they can
    see what dynamic link libraries your MSMS is linking against.
    They'll probably need to know which Linux distro you're running too.

  John Stone
  vmd_at_ks.uiuc.edu
 

On Mon, Nov 29, 2004 at 06:38:55PM -0600, Luis Rosales wrote:
> Hi all,
>
> I just checked msms with the exact options used by vmd, and from wahat I
> could see, msms is having touble with the -socketPort option. I am able to
> run msms with just the -no_area option (it just complains about the lack of
> a input file), however, when I use the socketport option (alone or with the
> -no_area), it crashes and generates a core dump file.
>
> I tried the following (using the same options that vmd uses):
>
> turning off the firewall,
> enabling the port 1357,
> Using a different port,
>
> With no difference on the outcome...
>
> Thanks,
>
> Luis
>
> > -----Mensaje original-----
> > De: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu]
> > En nombre de John Stone
> > Enviado el: Lunes, 29 de Noviembre de 2004 00:08
> > Para: Luis Rosales
> > CC: vmd-l_at_ks.uiuc.edu; 'Brian Bennion'
> > Asunto: Re: vmd-l: MSMS variable
> >
> >
> > Luis, Brian,
> > Sorry for the delayed reply, I've been mostly offline for
> > the last 4 days...
> >
> > MSMS is not listening to the socket when you give it that additional
> > -if option... In order to test it properly, you need to run it with
> > the exact options VMD uses. Once you run it that way (giving the port
> > flag etc) you should be able to telnet to the MSMS port and connect
> > to it. If you can't connect to it, then that's the source of
> > the problem
> > that VMD is encountering. Try just using the exact flags
> > that VMD uses,
> > and telnet to MSMS. Let me know what happens.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Wed, Nov 24, 2004 at 04:13:44PM -0600, Luis Rosales wrote:
> > >
> > > Hi all!
> > >
> > > Dear John and Brian:
> > >
> > > Thanks for your time,
> > > Yes, I checked the directory permissions as well as the
> > binary permissions,
> > > and they are set right for everybody to read/execute (drwxr-xr-x).
> > > And I have defined localhost on my hosts file... (127.0.0.1
> > > localhost.localdomain localhost)
> > >
> > > So far I had run msms with:
> > >
> > > msms -if file.xyzr
> > > msms -no_area -if 1crn.xyzr
> > > msms -no_area -socketPort 1357 -if 1crn.xyzr
> > >
> > > And every time if indicates a normal termination (this is
> > the output of the
> > > -no_area -sockerPort 1357 -if):
> > >
> > > Arioco_at_ruiz2 15% msms -no_area -socketPort 1357 -if 1crn.xyzr
> > > MSMS 2.5.5 started on ruiz2.biomedicas.unam.mx
> > > Copyright M.F. Sanner (1994)
> > > Compilation flags -O3 -mips3 -xansi -DVERBOSE -DTIMING
> > -DFUNCPROTO -fullwarn
> > > INPUT 1crn.xyzr 327 spheres 0 collision only, radii 1.400
> > to 2.000
> > > PARAM Probe_radius 1.500 density 1.000
> > > REDUCED SURFACE ...
> > > RS component 0 identified 211 208 210
> > > 0 free edge(s) found in component 0
> > > RS component #faces #edges #free_edges #vertices genus
> > > 0 430 645 0 210 3.5
> > > Time Reduced Surface real: 0.04 user: 0.04 sys: 0.00
> > > ANALYTICAL SOLVENT EXCLUDED SURFACE...
> > > Component 0
> > > Time Surface real: 0.01 user: 0.01 sys: 0.00
> > > Time Singularities real: 0.00 user: 0.00 sys: 0.00
> > > SES comp. #fac. #edg. #s_edg. #vert. #s_vert. R_h C_h genus
> > > 0 1304 2616 12 1314 24 0 0 0
> > > TRIANGULATION...
> > > Component 0
> > > component#, vertices, edges, faces, genus, density
> > > 0 2465 7389 4926 0 0.000
> > > Time Triangulation real: 0.04 user: 0.04 sys: 0.00
> > > MSMS terminated normally
> > > Total Time real: 0.10 user: 0.09 sys: 0.00
> > >
> > > -------------------------------------------
> > >
> > > So,it appears that the socketport and the no_area options
> > run fine in a
> > > manual run....
> > > How can I know if the port is open, so that the
> > communication between vmd
> > > and msms is happening??
> > >
> > > Thanks
> > >
> > >
> > >
> >
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> >
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> >
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078