Re: [ESPResSo] Installation Question

[Tristan Bereau]

Hello,

 

ESPResSo tries to access the visualization software VMD to output the simulation while running.

You can find VMD on this website:

http://www.ks.uiuc.edu/Research/vmd/

 

If you're not really interested in visualizing your simulations, you can still disable the vmd option.

To do that, as stated in the log:

"if { $vmd == "yes" } {

# This calls a small tcl script which starts the program    #
# VMD and opens a socket connection between ESPResSo and    #
# V..."

    (file "samples/tutorial.tcl" line 203)

-> Go to samples/tutorial.tcl whithin your espresso directory, and change line 203 of the code, setting $vmd to "offline":

if { $vmd == "offline" } {

Setting $vmd to "offline" actually means that vmd files will be written, so that you can visualize your simulation anytime later. There's a third option to completely disable vmd, but I don't remember it from the top of my head (it should be in the user's guide).

Best,

Tristan

On 9/30/07, Lorenzo Isella <address@hidden> wrote:

Dear All,
I have downloaded the espresso tar.gz file and installed Espresso, but I
am having some problems to run the tutorial.
I am running Debian testing on my box.
I unzipped the Espresso source, and from the newly created folder I
entered the command:
./configure CPPFLAGS=-I/usr/include/tcl8.4 --without-mpi
which produced a lot of output; here I report only the configuration
summary:

*                   Configuration summary                      *
****************************************************************
platform detected       = Pentium_M-pc-linux

Compiler settings:
------------------
MPI                     = fake
compiler                = gcc
linker                  = gcc
c compiler flags        = -finline-limit=1000000 -fomit-frame-pointer
-funroll-loops -floop-optimize -ffast-math -Wall -Wno-unused-function
-O3 -malign-double -msse2 -mfpmath=sse -march=pentium-m -m32
c preprocessor flags    = -I/usr/include/tcl8.4
linker flags            =
libraries               = -lfftw -ltcl8.4  -lrfftw -lfftw
using debug flags       = no
using profiling flags   = no
inline                  =

Libraries:
----------
Tcl version             = tcl8.4
Tk version              = none
FFTW version            = 2
efence                  = no

Other settings:
---------------
using Espresso chooser  = yes
local config header     = myconfig.h
pdflatex                = /usr/bin/pdflatex
doxygen                 = no

Then I ran the make command, which did not return any error message.
Finally, instead of make install, I used checkinstall (Debian tool to
create a Debian package which integrates better into the system), which
returned:
**********************************************************************

Done. The new package has been installed and saved to

/home/iselllo/internet-download/Espresso/espresso_2.3-1_i386.deb

You can remove it from your system anytime using:

      dpkg -r espresso

************************************************************ **********

So everything should be fine. In fact, I tried launching espresso from
the directory where I built everything:
$ ./Espresso
0: Script directory:
/home/iselllo/internet-download/Espresso/obj-Pentium_M-pc -linux/../scripts

*******************************************************
*                                                     *
*                    - Espresso -                     *
*                    ============                     *
*      A MPI Parallel Molecular Dynamics Program      *
*                                                     *
*                                                     *
* (c) 2002-2006                                       *
* Max-Planck-Institute for Polymer Research           *
* Mainz, Germany                                      *
*                                                     *
*******************************************************

%

However, when I tried running the tutorial, this is what I got:

./Espresso samples/tutorial.tcl
0: Script directory:
/home/iselllo/internet-download/Espresso/obj-Pentium_M-pc-linux/../scripts

*******************************************************
*                                                     *
*                    - Espresso -                     *
*                    ============                     *
*      A MPI Parallel Molecular Dynamics Program      *
*                                                     *
*                                                     *
* (c) 2002-2006                                       *
* Max-Planck-Institute for Polymer Research           *
* Mainz, Germany                                      *
*                                                     *
*******************************************************


=======================================================
=               ESPResSo Tutorial                     =
=          Learning ESPResSo in 10 steps              =
=======================================================

ESPResSo: 2.0.2l, Last Change: April 17th, 2007
{ Compilation status { MPI fake } { FFTW2 } { ELECTROSTATICS } {
LENNARD_JONES } }
{ Debug status { MPI_CORE FORCE_CORE } }
Simulate PE Solution N=40 at density 0.001
Simulation box: 43.0886938006
43.0886938006 43.0886938006 43.0886938006
0.01
0.4
{ set nvt }
{ langevin 1.0 1.0 }
10 pos 38.4413797919 38.0387042236 18.3332119557 type 0 q 1.0 v 0.0 0.0
0.0 f 0.0 0.0 0.0 bond { {0 9} }
50 pos 32.9191376228 26.1971311794 5.78403040845 type 1 q -1.0 v 0.0 0.0
0.0 f 0.0 0.0 0.0
couldn't execute "vmd": no such file or directory
    while executing
"exec vmd -e vmd_start.script &"
    (procedure "prepare_vmd_connection" line 25)
    invoked from within
"prepare_vmd_connection tutorial 3000"
    invoked from within
"if { $vmd == "yes" } {
# This calls a small tcl script which starts the program    #
# VMD and opens a socket connection between ESPResSo and    #
# V..."
    (file "samples/tutorial.tcl" line 203)

Should I change the value of that variable? Or did I do anything wrong
with my installation?
Actually, after the installation I see a newly created folder containing
the espresso binary, but nothing changes when I use that to call the
tutorial. Sorry for my newbie's question, but I am new to espresso and
molecular dynamics in general (actually I was suggested espresso after
posting on the gromacs list).
Many thanks

Lorenzo



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