Issues after installation

[Justin Lemkul]

Hi,

First off, thanks very much for providing MDAnalysis to the simulation
community. It looks like it has several very useful features that I
hope to make use of. I would like to report a few problems I have had
and solicit some advice on how to proceed.

My computer is running Mac OSX 10.5.8 with gcc-4.0.1. As a note,
attempting to install MDAnalysis with gcc-4.4 results in a failure
that the "-arch" option is not supported. I do not know whether this
is something intrinsic in the compiler or set within the MDAnalysis
source (I couldn't find it), but I thought I should at least report
that this happened. I installed the gcc-4.4 package from Fink and it
is my normal compiler that I use for everything.

The second problem I am having is that, although the installation went
seamlessly, any attempt to use MDAnalysis results in the following:

$ python
Enthought Python Distribution -- http://www.enthought.com
Version: 6.2-2 (32-bit)

Python 2.6.5 |EPD 6.2-2 (32-bit)| (r265:79063, May 28 2010, 15:13:03)
[GCC 4.0.1 (Apple Inc. build 5488)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from MDAnalysis import *
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "MDAnalysis/__init__.py", line 183, in <module>
from coordinates.core import writer as Writer
File "MDAnalysis/coordinates/__init__.py", line 473, in <module>
import PDB, PQR, DCD, CRD, XTC, TRR, GRO, XYZ, TRJ #, NETCDF
File "MDAnalysis/coordinates/DCD.py", line 329, in <module>
import _dcdmodule
ImportError: No module named _dcdmodule


Any ideas what might be going on? I am fairly inexperienced with
Python, so please excuse me if I'm missing something obvious. I can
provide any details from the build/install process if necessary. All
my Python components come from EPD, if that makes a difference, but I
believe I have satisfied all prerequisites.

Thanks for your time!

-Justin

[Justin Lemkul]

Hi again,

The error can be disregarded. I got enthusiastic and ran the demo
commands from the source directory, which causes all sorts of
problems. That seems all too obvious to me now :)

The issue with gcc is still probably worth noting, though.

Thanks!

-Justin

On Apr 19, 6:29 pm, Justin Lemkul <justin.lem...@gmail.com> wrote:
> Hi,
>
> First off, thanks very much for providing MDAnalysis to the simulation
> community.  It looks like it has several very useful features that I
> hope to make use of.  I would like to report a few problems I have had
> and solicit some advice on how to proceed.
>
> My computer is running Mac OSX 10.5.8 with gcc-4.0.1.  As a note,
> attempting to install MDAnalysis with gcc-4.4 results in a failure
> that the "-arch" option is not supported.  I do not know whether this
> is something intrinsic in the compiler or set within the MDAnalysis
> source (I couldn't find it), but I thought I should at least report
> that this happened.  I installed the gcc-4.4 package from Fink and it
> is my normal compiler that I use for everything.
>
> The second problem I am having is that, although the installation went
> seamlessly, any attempt to use MDAnalysis results in the following:
>
> $ python

> Enthought Python Distribution --http://www.enthought.com

[Oliver Beckstein]

Hi Justin,

On 19 Apr, 2011, at 23:56, Justin Lemkul wrote:

> The error can be disregarded. I got enthusiastic and ran the demo
> commands from the source directory, which causes all sorts of
> problems. That seems all too obvious to me now :)

It took me *much* longer to realize what the problem was when I did it the first time – and of course forgot about it until you mentioned it.

Furthermore, running from within actually works if one has done a 'developer' installation

python setup.py develop

because that installs libraries inside the package. (Incidentally, I use develop a lot during, well, development because it allows me to change python code and immediately see changes without re-installing the package) – http://code.google.com/p/mdanalysis/wiki/DevelopmentWorkflow#Code_development_and_debugging

> The issue with gcc is still probably worth noting, though.

Thanks, I'll add a note to INSTALL. I am using 10.5.8 + fink, too, but always use /usr/bin/gcc for python installations and hence never ran into this problem.

Just ask if other problems/questions arise.

Cheers,
Oliver

--
Oliver Beckstein * orbe...@gmx.net
skype: orbeckst * orbe...@gmail.com