RE: [PyMOL] Quadro-based 3D Mac Feedback

[Warren D. <wa...@de...>]

HI Tim!

Thank you for making the pro-Linux case.

> I thought the mailing list was for discussions regarding the=20
> usage of a program, not a forum for polemicism.

Indeed it is, and thank you also for that reminder -- let's all try to
stick to the real-world practical issues surrounding use of PyMOL on
each platform, and set aside the polemicism.

> Try telling your average OS X user to install coot (and don't=20

PyMOL on Mac OS X is simply drag & drop or download & double-click.  I
don't think it is fair to criticize Coot on the pymol list, so please
email Paul directly with concerns regarding his installation process.

> And for the record, setting up the nvidia drivers in linux=20
> (fedora, in my case) is three lines:
>=20
> rpm -ivh http://rpm.livna.org/livna-release4.rpm
> rpm --import http://rpm.livna.org/RPM-LIVNA-GPG-KEY
> yum install kernel-module-nvidia-$(uname -r)
>=20
> Then just restart X.

Even if it were just this simple on every common Linux variant, and even
if this worked for every common graphics card and CPU archicture -- and
it doesn't -- it still seems unreasonable to me to expect PyMOL Users to
have to muck about with "root" commands like the above just to able to
do OpenGL visualization. =20

> Aren't you just saying Apple's binary only drivers are better=20
> than NVidia's linux-based binary only driver? =20

Yes, with respect to PyMOL, the nVidia and ATI drivers in Mac OS X are
better in terms of performance and stability, and there is no end-user
driver installation requirement.

> If thats the logic, can't I=20
> say "since the NVidia drivers for windows are more stable=20
> than the NVidia drivers for linux (SLI support, HDTV=20
> decompression, etc), everyone should go out and buy windows=20
> since its gets more support from vendors."?

You can certainly make that argument up through Windows XP -- it has
been a strong reason for PyMOL Users to use Windows, and many have
(including myself, when on the road).  However, with Vista, Microsoft is
discouraging use of OpenGL by barely allowing it to run within their new
interface, so Apple now ends up being the vendor providing the best
OpenGL support.

> Its that linux users don't want to
> ***depend*** on anyone.  Not Apple, Microsoft or NVidia - I=20
> want, as they would say on the twilight zone, control over=20
> the horizontal as well as the vertical (I own the computer,=20
> after all).  From what I understand, its the whole reason=20
> linux was written in the first place.

To be consistent, PyMOL users who insist upon avoiding software
dependence most limit themselves to using open-source PyMOL with
open-source OpenGL renderers.  If one is willing to compromise one's
principles by using proprietary software drivers in the interests of
practicality, then why not simply run our precompiled PyMOL on a
proprietary Unix with well-supported OpenGL drivers? =20

> How is that not saying "Go Mac!"?

Yes, "Go Mac!" but with eyes open and with reasonable reservations.  New
releases from any vendor (or open-source project) always have some
issues, so do your research.  Try before you buy, and listen closely to
the experiences of your peers before making a heavy commitment.  Note
that while DeLano Scientific strongly favors Mac OS X as a visualization
platform, our views are currently in the minority. =20

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: Tim Fenn [mailto:fe...@st...]=20
> Sent: Thursday, January 19, 2006 5:06 AM
> To: Warren DeLano
> Cc: pym...@li...
> Subject: Re: [PyMOL] Quadro-based 3D Mac Feedback
>=20
> On Mon, Jan 16, 2006 at 04:34:44PM -0800, Warren DeLano wrote:
> >=20
> > Through extensive travel, contacts, and personal=20
> experiences over past=20
> > few years, I have come to understand just how poorly Linux=20
> is doing at=20
> > meeting the needs of the scientific visualization=20
> community.  Despite=20
> > my unabashed pro-open-source stance, it would be unethical=20
> for me to=20
> > continue advocating the adoption of Linux as the general=20
> solution for=20
> > UNIX OpenGL visualization when in practice it is only effective for=20
> > those having strong system administration skills.
> >=20
>=20
> Eh?  OS X is that much better in regards to system administration?
> Try telling your average OS X user to install coot (and don't=20
> tell him what subversion of OS X he's using), and feel free=20
> to post back how simple it was for him/her.
>=20
> And for the record, setting up the nvidia drivers in linux=20
> (fedora, in my case) is three lines:
>=20
> rpm -ivh http://rpm.livna.org/livna-release4.rpm
> rpm --import http://rpm.livna.org/RPM-LIVNA-GPG-KEY
> yum install kernel-module-nvidia-$(uname -r)
>=20
> Then just restart X.
>=20
> Or you could read any of the 800,000 pages that come up when=20
> googling "linux nvidia howto."
>=20
> > This is primarily due to incessant complications with proprietary=20
> > OpenGL drivers.  In my considered opinion, resolution of=20
> these issues=20
> > is beyond the reach of the open-source community, as no=20
> Linux vendor=20
> > has sufficient clout or motivation to effect the necessary and=20
> > permanent changes (i.e. shipping validated *proprietary* graphics=20
> > drivers with all common distributions of Linux).  In this case, the=20
> > open-source community is (correctly?) putting free software=20
> ideology=20
> > (free-software/open-source drivers!) ahead of users' needs=20
> to simply=20
> > get work done now.
>=20
> Its not a motivation issue.  Its that linux users don't want to
> ***depend*** on anyone.  Not Apple, Microsoft or NVidia - I=20
> want, as they would say on the twilight zone, control over=20
> the horizontal as well as the vertical (I own the computer,=20
> after all).  From what I understand, its the whole reason=20
> linux was written in the first place.
>=20
> > In time, this approach may yield the desired end-result, but=20
> > scientists, doctors, and engineers need a working solution today.
> >=20
> > Caught in the middle of all this, our obligation as a vendor is to=20
> > identify, advance, and promote solution which actually do=20
> work for our=20
> > customers today or very soon and not at some unspecified=20
> point in the=20
> > future.  We need an alternative answer to OpenGL under=20
> Linux, and we=20
> > obviously believe that answer lies with Mac OS X.
> >
> <snip>
> >
> > Apple, in contrast, is fully committed to OpenGL -- an open=20
> standard=20
> > that runs on any platform.  Furthermore, by switching to Intel=20
> > processors, Apple customers will now have even greater=20
> choice to run=20
> > one, two, or even three major operating systems on Apple hardware.
> > Simply put, Apple "gets it" when it comes to consumer=20
> choice, and over=20
> > the past several years they have made it a practice of synergizing=20
> > with Free Software and Open Source efforts (GCC, Darwin,=20
> KHTML, PyMOL,=20
> > etc).
>=20
> If the mailing list is meant as an infomercial, I'll start=20
> sending it to my spam folder.
>=20
> > Steve Jobs understands that open-source is transforming the=20
> software=20
> > industry, but he also apparently grasps the new role that=20
> proprietary=20
> > solution vendors must adopt in delivering extra value on=20
> top of what=20
> > is already both ubiquitous and free.  That, in a nutshell, is the=20
> > future of the software industry.  Proprietary and open-source=20
> > solutions will co-exist and complement one another to the=20
> benefit of=20
> > consumers and developers alike.
> >=20
>=20
> Aren't you just saying Apple's binary only drivers are better=20
> than NVidia's linux-based binary only driver?  The argument=20
> presented above is simply hyperbole based on nvidia chipset=20
> support from different vendors.  If thats the logic, can't I=20
> say "since the NVidia drivers for windows are more stable=20
> than the NVidia drivers for linux (SLI support, HDTV=20
> decompression, etc), everyone should go out and buy windows=20
> since its gets more support from vendors."?
>=20
> > > this blatant
> > > shilling contrasts jarringly with the open source context=20
> in which=20
> > > PyMOL is developed, distributed, and supported: PyMOL is=20
> attractive=20
> > > in part because it promises long-term, flexible access to=20
> the tools=20
> > > to do our work, without users falling into a vassal role with=20
> > > respect to one industry-dominant company.
> >
> > I apologize for excess enthusiasm -- it is perhaps an=20
> overreaction to=20
> > biased and premature dismissal of Mac OS X as a credible=20
> solution by=20
> > some members of the pharma/biotech IT & Informatics communities.
>=20
> I thought the mailing list was for discussions regarding the=20
> usage of a program, not a forum for polemicism.
>=20
> >=20
> > > Launching such a hyperbolic cheerleading campaign may belie the=20
> > > stability of the support one might expect from Apple for this=20
> > > technology, if one feels such campaigns are necessary to=20
> keep that=20
> > > support alive.
> >=20
> > But that is exactly my point:  If potential customers such=20
> as yourself=20
> > do not show strong interest in these systems through purchases or=20
> > communicate to Apple (directly or through us) why they may=20
> have missed=20
> > the mark, then Apple would be correct and justified in=20
> concluding that=20
> > we are uninterested in Mac OS X-based solutions for scientific=20
> > visualization.
> >=20
>=20
> or I could find a development community that *IS* its user=20
> base, and therefore doesn't require my input/money/praises in=20
> order to understand why its necessary to support poor little=20
> ol' me.  Which is linux/BSD!
>=20
> > So let me make clear:  We are not saying, "Go Mac!" blindly and=20
> > without reservations.
>=20
> But you said:
>=20
> On Thu, Dec 08, 2005 at 11:58:40PM -0800, Warren DeLano wrote:
> >
> > To avoid Linux headaches -- my brutually honest advice is=20
> to buy Macs=20
> > instead.  It's just that simple.
> >
>=20
> How is that not saying "Go Mac!"?
>=20
> Regards,
> Tim
>=20
> --
> ---------------------------------------------------------
>=20
>         Tim Fenn
>         fe...@st...
>         Stanford University, School of Medicine
>         James H. Clark Center
>         318 Campus Drive, Room E300
>         Stanford, CA  94305-5432
>         Phone:  (650) 736-1714
>         FAX:  (650) 736-1961
>=20
> ---------------------------------------------------------
>=20
>=20
> --
> ---------------------------------------------------------
>=20
>         Tim Fenn
>         fe...@st...
>         Stanford University, School of Medicine
>         James H. Clark Center
>         318 Campus Drive, Room E300
>         Stanford, CA  94305-5432
>         Phone:  (650) 736-1714
>         FAX:  (650) 736-1961
>=20
> ---------------------------------------------------------
>=20
>=20
>=20
>=20
>=20