VMD-L Mailing List

From: Dan Wright (dtwright_at_uiuc.edu)
Date: Wed Oct 03 2007 - 12:05:38 CDT

Hi Lorenzo,

Lorenzo Isella wrote:
> VMD Build Options
> -----------------
.....
> Once VMD is configured for compilation, do this:
> cd src; make veryclean; make
>
> iselllo_at_cappero:~/internet-download/vmd-1.8.6$ make platform
> make: *** No rule to make target `platform'. Stop.

Here is your main problem. You need to run "make <platform-name>", not
literally "make platform". So for you, this should probably be "make
linux.opengl". If you go back and do this, and then run "cd src; make
veryclean; make" you are much more likely to end up with a working build.

Dan

> iselllo_at_cappero:~/internet-download/vmd-1.8.6$ cd s
> scripts/ shaders/ src/
> iselllo_at_cappero:~/internet-download/vmd-1.8.6$ cd s
> scripts/ shaders/ src/
> iselllo_at_cappero:~/internet-download/vmd-1.8.6$ cd src/
> iselllo_at_cappero:~/internet-download/vmd-1.8.6/src$ make veryclean
> cd ../WIN32 ; \
> rm -f *.o *.warnings *.depend.old core
> rm -f vmd_python.C vmd.py
> cd ../WIN32 ; \
> rm -rf ; \
> rm -f vmd_WIN32
> cd ../src ; \
> rm -f *.o *.a *~ core; \
> rm -rf ; \
> rm -f vmd_WIN32
> cd ../doc ; \
> rm -f *~ core
> iselllo_at_cappero:~/internet-download/vmd-1.8.6/src$ sudo checkinstall
>
> checkinstall 1.6.1, Copyright 2002 Felipe Eduardo Sanchez Diaz Duran
> This software is released under the GNU GPL.
>
>
> The package documentation directory ./doc-pak does not exist.
> Should I create a default set of package docs? [y]:
>
> Preparing package documentation...OK
>
> *** No known documentation files were found. The new package
> *** won't include a documentation directory.
>
> Please write a description for the package.
> End your description with an empty line or EOF.
>>> new attempt to build vmd
>>>
>
> *****************************************
> **** Debian package creation selected ***
> *****************************************
>
> This package will be built according to these values:
>
> 0 - Maintainer: [ root_at_cappero.jrc.it ]
> 1 - Summary: [ new attempt to build vmd ]
> 2 - Name: [ src ]
> 3 - Version: [ 20071002 ]
> 4 - Release: [ 1 ]
> 5 - License: [ GPL ]
> 6 - Group: [ checkinstall ]
> 7 - Architecture: [ i386 ]
> 8 - Source location: [ src ]
> 9 - Alternate source location: [ ]
> 10 - Requires: [ ]
>
> Enter a number to change any of them or press ENTER to continue:
>
> Installing with make install...
>
> ========================= Installation results ===========================
> if [ ! -d "/usr/local/lib/vmd" ]; then \
> mkdir -p "/usr/local/lib/vmd" ; \
> fi ; \
> if [ ! -d "/usr/local/bin" ]; then \
> mkdir -p "/usr/local/bin" ; \
> fi ; \
> if [ ! -d "/usr/local/lib/vmd"/doc ]; then \
> mkdir -p "/usr/local/lib/vmd"/doc; \
> fi
> cp ../Announcement "/usr/local/lib/vmd"
> cp ../README "/usr/local/lib/vmd"
> cp ../LICENSE "/usr/local/lib/vmd"
> cp ../doc/ug.pdf "/usr/local/lib/vmd"/doc
> if [ -f /usr/local/lib/vmd/vmd_WIN32 ]; then \
> mv -f "/usr/local/lib/vmd/vmd_WIN32"
> "/usr/local/lib/vmd/OLD_vmd_WIN32" ; rm -f
> "/usr/local/lib/vmd/OLD_vmd_WIN32" ; fi
> cp ../WIN32/vmd_WIN32 "/usr/local/lib/vmd"
> cp: cannot stat `../WIN32/vmd_WIN32': No such file or directory
> make: [install] Error 1 (ignored)
> cp ../lib/stride/stride_WIN32 ../lib/surf/surf_WIN32
> ../lib/tachyon/tachyon_WIN32 "/usr/local/lib/vmd"
> cp: cannot stat `../lib/stride/stride_WIN32': No such file or directory
> cp: cannot stat `../lib/surf/surf_WIN32': No such file or directory
> cp: cannot stat `../lib/tachyon/tachyon_WIN32': No such file or directory
> make: [install] Error 1 (ignored)
> cd ..; tar -cf - scripts | \
> (cd "/usr/local/lib/vmd" ; tar -xf -)
> cd ../lib; tar -cf - scripts | \
> (cd "/usr/local/lib/vmd" ; tar -xf -)
> cd ..; tar -cf - python | \
> (cd "/usr/local/lib/vmd"/scripts ; tar -xf -)
> cd ..; tar -cf - plugins | \
> (cd "/usr/local/lib/vmd" ; tar -xf -)
> cd ..; tar -cf - shaders | \
> (cd "/usr/local/lib/vmd" ; tar -xf -)
> cp ../data/.vmdrc ../data/.vmdsensors "/usr/local/lib/vmd"
> cd ../bin ; \
> if [ -f run_vmd_tmp ]; then rm -f run_vmd_tmp; fi ; \
> echo '#!/bin/csh' >> run_vmd_tmp ; \
> echo 'set defaultvmddir="/usr/local/lib/vmd"' >> run_vmd_tmp ; \
> echo 'set vmdbasename=vmd' >> run_vmd_tmp ; \
> cat vmd >> run_vmd_tmp ; \
> chmod +x run_vmd_tmp ; \
> cp run_vmd_tmp "/usr/local/bin"/vmd ; \
> rm -f run_vmd_tmp
> echo Make sure "/usr/local/bin"/vmd is in your path.
> Make sure /usr/local/bin/vmd is in your path.
> echo "VMD installation complete. Enjoy!"
> VMD installation complete. Enjoy!
>
> ======================== Installation successful ==========================
> grep: /var/tmp/DgbJQLofilokkYaqGZZZP/newfile: No such file or directory
>
> Copying files to the temporary directory...OK
>
> Striping ELF binaries and libraries...OK
>
> Compressing man pages...OK
>
> Building file list...OK
>
> Building Debian package...OK
>
> Installing Debian package...OK
>
> Erasing temporary files...OK
>
> Writing backup package...OK
>
> Deleting temp dir...OK
>
>
> **********************************************************************
>
> Done. The new package has been installed and saved to
>
> /home/iselllo/internet-download/vmd-1.8.6/src/src_20071002-1_i386.deb
>
> You can remove it from your system anytime using:
>
> dpkg -r src
>
> **********************************************************************
>
>
> Again sorry for the long post. So, somehow, I got VMD installed successfully.
> Then I tried re-running the tutorial (a TCL script) this time using VMD for
> visualization.
> The part of the TCL script needing VMD is in the following:
>
>
> # 6 Visualization #
> # Now lets see what you have done so far. #
> # Set the variable vmd to "yes" for trying. #
> # TCL: #
> # Here you can already see how an 'if' condition works in #
> # tcl. #
> #############################################################
>
> set vmd "yes"
>
> if { $vmd == "yes" } {
> # This calls a small tcl script which starts the program #
> # VMD and opens a socket connection between ESPResSo and #
> # VMD. #
> prepare_vmd_connection tutorial 3000
>
> # Just wait a moment until VMD has started. #
> # The 'exec' command is quite useful since with that you can#
> # call any other program from within your simulation script.#
> exec sleep 4
>
> # The additional command imd steers the socket connection #
> # to VMD, e.g. sending the actual coordinates #
> imd positions
> }
>
>
> , but here is what happened when I ran the script; an xterm terminal opened with
> the message:
>
> xterm: Can't execvp /usr/local/lib/vmd/vmd_LINUX: No such file or directory
>
> In fact this is the content of the folder which is giving me some headache:
>
> ls /usr/local/lib/vmd/
> Announcement doc LICENSE plugins README scripts shaders
>
> Can anyone help me out? I am sure there must be other Debian/Ubuntu
> users or simply people building from source who went through
> this...and I am also sure that if has to be rather trivial to sort
> this out, for someone knowledgeable.
> Many thanks