VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Mon Jan 25 2016 - 12:57:00 CST

Hi Kris,

What are the permissions that got set for /usr/local/bin/vmd? At a base
level, it needs to be set as executable, and I'm not sure why it didn't.
For instance, this is what I get when I go hunting for my permissions:

josh_at_jaguar:~$ ls -l /usr/local/bin/vmd
-rwxr-xr-x 1 root root 13034 Jun 21 2013 /usr/local/bin/vmd

Note that it is executable for everyone (the third x), which is why I
can start it from that location if I choose to do so. Normally though,
since I have a newer version of VMD elsewhere in my path (/usr/bin/vmd),
I can just type vmd on the terminal to load up this newer version. Is
/usr/local/bin in your path? (Check with echo $PATH)

-Josh Vermaas

On 01/25/2016 11:41 AM, Kris Feher wrote:
> Dear Sir/Madam,
>
> I tried to install vmd on an Ubuntu 14.04 Linux from the tar files
> VMD 1.9.2 for Linux (64-bit x86_64) using OpenGL, CUDA
> or
> VMD 1.9.2 for Linux (64-bit x86_64) using TextMode
> using the description on
> http://www.ks.uiuc.edu/Research/vmd/current/ig.pdf
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ks.uiuc.edu_Research_vmd_current_ig.pdf&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=lquh4XhM2ouDQ2vK-TxLrVCzpTSaqllGH41EtM8QViw&s=8SrL-SFAlRUHQ_jhD-LZ9YLhAc31RpKyxe-4XSJ7B2I&e=>,
> but I could not start vmd. I did the following steps:
> - I extracted the tar file into my home directory, I did not modify
> the .configure file (thus installation into /usr/local/bin), I
> executed the configure script as follows:
> ./configure LINUXAMD64 MESA FLTK PYTHON
> - I changed to the source directory and executed 'make install', the
> output please see below. The script ran through.
> - I tried to execute command 'vmd', but vmd does not start (also see
> below). I also do not find any executable or startup script at the
> specified (/usr/local/bin/vmd) location.
>
> I have searched the vmd mailing list already, but did see any solution
> to this problem. I would very much appreciate any help.
>
> Thank you in advance,
> Best regards,
> Kris
>
>
>
>
>
>
> sirius2:~/bin/vmd-1.9.2/src> ls
> config.h Makedata.depend Makefile
> sirius2:~/bin/vmd-1.9.2/src> make install
> 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
> mkdir: cannot create directory ‘/usr/local/lib/vmd’: Permission denied
> mkdir: cannot create directory ‘/usr/local/lib/vmd’: Permission denied
> make: *** [install] Error 1
> sirius2:~/bin/vmd-1.9.2/src> lsERROR) Error reading Tcl input: I/O error
> make install
> sirius2:~/bin/vmd-1.9.2/src>
> sirius2:~/bin/vmd-1.9.2/src>
> sirius2:~/bin/vmd-1.9.2/src> sudo make install
> [sudo] password for kriszti:
> 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_LINUXAMD64 ]; then \
> mv -f "/usr/local/lib/vmd/vmd_LINUXAMD64"
> "/usr/local/lib/vmd/OLD_vmd_LINUXAMD64" ; rm -f
> "/usr/local/lib/vmd/OLD_vmd_LINUXAMD64" ; fi
> cp ../LINUXAMD64/vmd_LINUXAMD64 "/usr/local/lib/vmd"
> if [ -d "../lib/redistrib/lib_LINUXAMD64" ]; then \
> cd ../lib/redistrib/lib_LINUXAMD64; tar -cf - ./* | \
> (cd "/usr/local/lib/vmd" ; tar -xf -) \
> fi ;
> cp ../lib/stride/stride_LINUXAMD64 ../lib/surf/surf_LINUXAMD64
> ../lib/tachyon/tachyon_LINUXAMD64 "/usr/local/lib/vmd"
> 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 -)
> if [ -f ../LINUXAMD64/OptiXShaders.ptx ]; then \
> cp ../LINUXAMD64/OptiXShaders.ptx "/usr/local/lib/vmd/shaders"; \
> fi;
> cp ../data/.vmdrc ../data/.vmdsensors ../data/vmd_completion.dat
> "/usr/local/lib/vmd"
> cd ../bin ; \
> if [ -f run_vmd_tmp ]; then rm -f run_vmd_tmp; fi ; \
> if [ ! -x "/bin/csh" ]; then \
> echo "Info: /bin/csh shell not found, installing Bourne shell
> startup script instead" ; \
> echo '#!/bin/sh' >> run_vmd_tmp ; \
> echo 'defaultvmddir="/usr/local/lib/vmd"' >> run_vmd_tmp ; \
> echo 'vmdbasename=vmd' >> run_vmd_tmp ; \
> cat vmd.sh >> run_vmd_tmp ; \
> else \
> 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.csh >> run_vmd_tmp ; \
> fi ; \
> 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!
> sirius2:~/bin/vmd-1.9.2/src> vmd
> vmd: Command not found.
> sirius2:~/bin/vmd-1.9.2/src> /usr/local/bin/vmd
> /usr/local/bin/vmd: Permission denied.