From: Josh Vermaas (
Date: Fri Aug 15 2014 - 16:28:42 CDT

There isn't a definitive list that I'm aware of. I do know that I've
compiled it with 5.5 on at least one machine (CentOS), so that on its
own is probably not the reason. In my experience, the problem tends to
be that in the configure file, no effort is made to detect what is
actually available on your system, and instead it defaults to what is
available in the build environment that makes the binaries for public
consumption. For CUDA, it defaults to 4.0, and assumes its in a place
that would not be standard on a debian-based OS. I'm working off memory
here, as I don't have it in front of me, but I had issues with my cuda
builds until I changed the $cuda_library variable to point to where dpkg
put the cudart library (-L/usr/local/cuda/lib?) and make sure that
$arch_nvcc points to where you want it. The trick here is that those
variables are defined multiple times, so you need to find the definition
that you are actually using (probably the LINUXAMD64 one?). Of course,
it could be something completely different. What are the compiler errors
exactly saying?

On 8/15/14, 5:05 PM, Chris Knorowski wrote:
> Thanks Josh,
> Do you know if there is a list of the highest version of the
> dependencies that vmd has been compiled with. I'm getting come
> compilation errors when CUDA is enabled and I'm wondering if its
> related to the version of CUDA(5.5) that I'm using.
> Chris
> On Thu, Aug 14, 2014 at 8:48 PM, Josh Vermaas <
> <>> wrote:
> Hi Chris,
> I have not, as for me it picks up 2.7 without issue. What does a
> normal vmd python start look like for you? (The text from "vmd
> -dispdev text -python") It clearly isn't picking up the system
> libraries, as I think those are 2.7 at minimum, so somewhere,
> somehow, you missed something in the config file.
> This is what I have, based on my build for 12.04:
> $python_defines = "-DVMDPYTHON";
> $python_include = "-I/usr/include/python2.7/";
> $python_library = "-L/usr/lib/python2.7/config-x86_64-linux-gnu/";
> $python_libs = "-lpython2.7 -lpthread";
> The config file also has stuff involving stock_python nonsense,
> which I tend to comment out since its horrifically out of date and
> not useful to me since I define my libraries explicitly.
> Although... Now that I'm looking more closely at the Ubuntu
> directory structure, your problem may be that there isn't actually
> a shared library under /usr/lib/python2.7 (which is why my
> $python_library goes one level deeper).
> Good luck! Compiling VMD for python is hard, but totally worth it
> in the end.
> -Josh Vermaas
> On 08/14/2014 04:52 PM, Chris Knorowski wrote:
>> Hi All,
>> I am trying to compile vmd against python 2.7. I have changed the
>> configure file from python2.5 to python2.7. I have exported
>> export PYTHON_LIBRARY_DIR=/usr/lib/python2.7
>> and export PYTHON_INCLUDE_DIR=/usr/include/python2.7 then
>> run./configure and compiled the src. Still when I run vmd, and
>> use gopython the python version is 2.5? I am running on ubuntu
>> with version LINUXAMD64. Has anyone else had this issue?
>> Thanks,
>> Chris
>> --
>> Christopher Knorowski
>> Iowa State Physics Department
> --
> Christopher Knorowski
> Iowa State Physics Department