Linux vs MacOS for crystallographic software

From: Jacqueline Vitali
Date: 29 September 2011 01:26


Dear colleagues,

I need some advice for a new computer.

(1) I have the option of an HP Z210  8 GB with a low end Quadro Nvidia 400 512 MB.  

--How does Coot run with this card?

--I am happy with any Linux.  However, the system needs updates for security purposes (the University requires it).  Do I have to remake the NVidia driver every time there is a kernel update or is there a way around it for this NVidia card?  Do you suggest another NVidia card (inexpensive) that is good for coot and automatically updates when the kernel is updated?  

(2) Second option is an IMAC 4 GB 2.5 GHz with AMD Radeon HD 6750M 512 MB GDDRS.  

--How does Coot work with this graphics card?

--Should I get more memory for Lion?

--Is this platform advisable for crystallographic software for the next four years?   

Thank you in advance for any advice.

Jackie Vitali

Cleveland State University

----------
From: Nat Echols

I don't have exactly this, but something very similar (6770M), and it works very well for me so far, but I'm not a power user.  And I definitely don't use stereo, which I assume the iMac won't do.

Yes, absolutely - double it for sure.  (Don't upgrade when ordering from Apple unless you have money to burn - you can buy the memory elsewhere for a fraction of the price.)  Most of the time you will not need 8GB, but when you want to use all four processor cores at once for refinement etc., it is essential.

For a workstation (or laptop), yes (for clusters/servers I would still recommend Linux).  I don't know of any macromolecular crystallography programs that don't run on Mac - my only real complaint is that I really preferred running Coot on Linux (Apple's fault).  However, if you care about having hardware stereo, there may be other issues - I have no experience with this.

-Nat

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From: William G. Scott

OK
Try Ubuntu (or Kubuntu or Xubuntu, etc).  You can have Linux and proprietary drivers.
OK
Max it out.  Lion is a memory pig.
It is essentially BSD unix.  So it should be fine, unless they continue to lobotomize everything and make it into an iPod on a stick.

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From: Roger Rowlett

I use home built LINUX Intel boxes with 2Gb memory and low end Nvidia cards (GT 8000 series to GT 200 series) and they are fine with Coot, Pymol, CCP4i. I can even run CrysalisPro (Windows) in WINE. More memory is cheap to add. If you use a Ubuntu LTS release, you get 3 yr of updates. Proprietary Nvidia binaries can be downloaded from the Ubuntu repos, and they will reinstall every time you do a kernel update. Ubuntu has been pretty painless to maintain compared to Fedora, at least when I made the switch.

Roger Rowlett

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From: Francois Berenger


By the way, how about some Debian packages for CCP4?

That would make it installable painlessly on both Ubuntu and Debian systems for academic users, which would be quite cool.

Regards,
F.

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From: Sebastiano Pasqualato

Hey there,

does this mean that SHARP works on a Mac?

ciao,

s

-- 
Sebastiano Pasqualato, PhD
Crystallography Unit

IFOM-IEO Campus

Cogentech - Consortium for Genomic Technologies

via Adamello, 16
20139 - Milano
Italy

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From: Dirk Kostrewa

Yes, SHARP and BUSTER both work on a Mac.

Cheers,

Dirk.

Am 29.09.11 09:45, schrieb Sebastiano Pasqualato:

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From: Sebastiano Pasqualato

Thanks Dirk,

that's good news.

I'll take a look at it, then.

thanks,

ciao,

s

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From: Simon Kolstoe


I am routinely having the Mac vs Linux conversation with crystallographers and new students, especially given the price of Macs.

Generally I think that the extra money spent on a Mac pays for less time spent messing around installing software, sorting out dependencies, swearing at the less than effective office software etc. that plagues Linux which is more of a "computer experts" platform. I'd say if your interest is in solving structures with the least hassle get a Mac, but if you want to develop software get Linux. Meanwhile I think windows is slowly improving as a crystallography platform - and Microsoft is perhaps no longer hated in principle - however the one student in our lab who opted to go the windows route seems very limited in the software he can run.

Of course getting the highest spec machine one can afford at the time applies to all platforms. Mind you I've been using mid range MacBook Pro's for the last few years which work fine, with the added bonus that you can keep your coffee warm by placing it near the processor during MR!

Simon

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From: Clemens Vonrhein


Hi Sebastiano,
yes (since 2004), same for BUSTER (since 2009) and autoPROC.

Cheers

Clemens

--


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From: Johan Turkenburg

This discussion will rage forever, it seems, but that won't stop us
all chipping in. My experience is the opposite: all crystallographic
software I use is available as binaries for the major linux distros,
and installs without problems. Ubuntu is easy to maintain on desktops
(your mileage on laptops may vary). I constantly hear people complain
about Office being a pain when exchanging documents between PC and
Mac. So it is a personal preference, based on what you have experience
with etc., there is no a clear-cut answer.

And by the way, if it all works so well on Macs, why is the BB awash
with people asking about installation problems on Macs? If the answer
is that this is due to inexperience, then the same applies to problems
with Linux boxes ;-)

Dr. Johan P. Turkenburg                     X-ray facilities manager
York Structural Biology Laboratory
University of York                               

----------
From: Miguel Ortiz Lombardia

Le 29/09/2011 11:43, Johan Turkenburg a écrit :

I totally agree with Johan. I have experience now with both linux and
apple osx and I cannot say that things are easier in osx. It's rather
the opposite when it comes to the management of the OS in itself. Add to
this that when you have more or less learnt how to deal with a
particularity of the apple OS, they may change it in the next "upgrade".
Example: NFS. Non-unix idioms are becoming so frequent in osx that one
would say that it will soon depart completely from the BSD origins. But
this is a quite subjective view, of course.

However, if you compare the price/performance ratio, at least in Europe,
you will come easily with an answer.

--
Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France


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From: Lucas


2011/9/29 Simon Kolstoe <s.kolstoe@ucl.ac.uk>:
For some years I had dual-boot systems, but since the only thing in
Windows that I can't live without is their Office suite, what I've
been doing for a year or two is having an easy to maintain linux
distribution in my desktop (I use Kubuntu since Dapper Drake, and by
that time it seemed to be the only distro which was anything near
"easy to use", but there are probably other good options today) while
running Microsoft Office via Crossover Office, a very cheap little
program for running windows software on linux (they also have a
version for Mac). It works just perfectly, and it means I only need an
Office license (no need to install Windows, as some do in virtual
machines).

Also, back in 2003 setting up the video card was a nightmare even in
more user-friendly linux distributions. It seems not to be the case
nowadays, it's been a long time since I had that feeling for
destroying the computer with a sledgehammer after trying the nth
version of xorg.conf and still being unable to run coot.

Lucas

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From: Dima Klenchin

I have a feeling that the lack of Windows software continues to be mostly due to the irrational animosity toward it rather than the platform-specific issues. After all, there seemed to be many  developers who were happy to code for MacOS 7-9 but refused to release anything that runs in Windows. Meanwhile, that is the only platform we never hear about installation and dependencies issues. Given the large number of Windows versions of CCP4 downloaded, I assume this is not because nobody actually installs Windows software.

- Dima

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From: Bosch, Juergen

There's one piece of software that does not run on a Mac.

GRAPHent

I tried some years ago to port it to a Mac without success, that's the only reason I have a dead PC (*technically it has Windows on it but I call it dead as long as no linux is installed) in my office waiting to get some flavor of linux since about 1 year. As under linux I never had troubles compiling it.

Regarding $ US versus Europe

How frequently do you change your linux boxes ? 

I'm still running a Mac Laptop from 2004 which I bought for 2500$, only thing I had to do is replace the hard drive as the shipped 120 GB was way to small for my needs. It now sports a 500 GB drive and runs 10.6. So considering it's been running for 7.5 years now that brings the cost down to ~340$/year. I'm anticipating to use that Mac at least for another 3-4 years before I think it served my purposes well. Then in it's afterlife it will function as guest computer for people visiting us from Europe :-)

A Mac mini with Zalman serves as stereo workspace together $1000, has been running three years now and it will surely continue to run for a few more years. Sure I also have the MacPro's there the $-tag is much higher but you also get a few more cores for your money and not everybody needs one of those monsters.

Jürgen

......................

Jürgen Bosch

Johns Hopkins University

Bloomberg School of Public Health

Department of Biochemistry & Molecular Biology

Johns Hopkins Malaria Research Institute

615 North Wolfe Street, W8708

Baltimore, MD 21205

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From: George M. Sheldrick


I do all my program development on Linux and never liked Windows. However
I recently attended two small-molecule crystallographic workshops where
the large majority of the participants used exclusively Windows, and the
ones who didn't use Windows used mostly Macs. I think the decisive
advantage of Windows for them is the ease of downloading and installing
the software from the internet, especially on laptops. Indeed some small
molecule programs such as Olex2 (a widely used graphical GUI) perform
automatic web updates unless you go to some lengths to stop them (i.e.
just like Microsoft). The large majority of SHELX and shelXle (Christian
Huebschle's GUI for SHELXL refinement of small molecules) downloads are
for Windows, and Mac downloads clearly outnumber Linux. I suspect that a
silent majority of CCP4 users actually also run CCP4, and especially Coot,
under Windows!

George
> J rgen
> J rgen Bosch

--


----------
From: Thomas Cleveland


Hi,

I have been extremely happy with the latest Ubuntu release, on both a
Toshiba tablet (the touch screen worked right out of the box) and on a
desktop with the proprietary NVIDIA driver.  I haven't had to update,
so I don't know what happens with the NVIDIA driver in that case, but
I can tell you that it was no effort at all getting it to work on a
new install.  I literally just clicked a couple of buttons.

I have given up on Linux in the past because it was too much of a pain
to get everything working, but it seems that things have greatly
improved in recent years.

-Tom Cleveland

Johns Hopkins University School of Medicine

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From: Ethan Merritt <merritt@u.washington.edu>
Date: 29 September 2011 22:21
To: CCP4BB@jiscmail.ac.uk


Meaningless statistics:
       Of the requests made against my web server
       (Parvati, TLSMD, Anomalous Scattering, source tarballs),
       the requesting machines since Jan 2011 are running
               39% Windows
               32% Linux
               26% OSX
                3% other

Although I do have static content on the site also (e.g. class material),
I think it's fair to estimate that most of the access is from
crystallographers.   But who knows, really.  The fact that "other" includes
access from Sony playstations and SymbianOS phones does make me wonder.

FWIW, Firefox is the most common browser (55%), and since earlier in 2011
Chrome (15%) has taken over second place from IE (14%).  Safari is at 11%,
so I take it that more than half of the OSX users browse using something
else.
Yeah, but...
My current linux laptop was purchased new 2 years ago for $299.
It has roughly the same size and power as an 11" MacBook Air
(1.4GHz Core 2, 11" 1366x768 display, 6-8 hour battery life).
Yeah, I choose it for use while traveling rather than for heavy duty
computation, but hey, I could get a new one every year for the amortized
cost of your MacBook :-)

       cheers,

               Ethan

Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742

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From: Nicholas M Glykos


Hi William,
:-)) +1

Thankfully, it is possible to gcc-cross-compile for MacOSX (both i686 +
ppc) from a GNU/Linux machine (the procedure for getting it to work was so
convoluted that I keep three separate backups of all required directory
trees, knowing that I won't be able to repeat it ;-).

Having said that, the resulting executables work fine on a Snow Leopard
machine (even Ygl-based graphics !), but I bet my luck won't last long ...

All the best,
Nicholas


--


         Dr Nicholas M. Glykos, Department of Molecular Biology
    and Genetics, Democritus University of Thrace, University Campus,
 Dragana, 68100 Alexandroupolis, Greece,

----------
From: Adam Ralph


Dear All,

    There is a free alternative to MS Office, OpenOffice from Oracle. It 
can read and write MS Word files and save as PDF. There are some issues 
with names of spreadsheet functions when moving from OO to MS Office. 
If you use latex and beamer then there is no need to either ;-). I 
use both Ubuntu and Mac with OO.

Adam

----------
From: Tim Gruene <

The actual free alternative is called libreoffice, the successor of
openoffice after it was taken over by Oracle - a company, in my personal
opinion, is by orders of magnitudes less 'free' than microsoft.

- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen



----------
From: Johan Turkenburg


Rather than crossover office we now use VirutalBox and have a Windows
XP installation with Office for those of us who can't live without it.
You can backup the virtual machine (which is simply a big file) for
the virtual OS before you do an upgrade of your host OS (Ubuntu in my
case) and copy that back, so you do not need to do a full Windows XP
install every time you upgrade the host.

Your linux disks (including NFS mounts) can be seen from the virtual
windows machine, so you can have your files accessible in both
operating systems. Also, with two monitors you can have one with your
linux desktop and one with your virtual windows desktop, and you can
even cut and paste between the two. Very useful when writing papers
etc.

With NX you can then use that setup elsewhere (at home) as well,
without having to duplicate the whole lot. The virtual desktop works
ok via NX, things like coot are a bit more tricky.

Johan

----------
From: Kevin Cowtan

I can't speak for anyone else, but in my case this is not true. It's just down to convenience.

I develop on Linux because I install the OS and have a complete software development environment with everything I need pre-installed, or at most accessible after less than 5 minutes of playing with the unified software manager.

For OSX, we have machines about the lab I can ssh into where other people have set up the build environment so I can use it in almost exactly the same way. I don't know how much work that was for them.

For Windows, I have to arrange a license, install, deal with a much more painful registration and security update process, and then install a load more 3rd party tools before I can even start working. That or try and figure out the convoluted steps required to get cross compilation to work.

That's all there really is too it.
Kevin

----------
From: David Schuller


Yes, Open Office has forked, and LibreOffice is now the choice in Fedora Linux. I have used OpenOffice and LibreOffice, and they have some trouble with recent .docx files generated in MS Word, specifically with embedded image files. 

All Things Serve the Beam
=======================================================================
                              David J. Schuller
                              modern man in a post-modern world
                              MacCHESS, Cornell University
                               

----------
From: David Schuller

On 09/28/11 20:26, Jacqueline Vitali wrote:

...

For Fedora Linux, nVidia drivers are availabe through RPMfusion; and if you install with the akmod-nvidia package, the kernel module is automatically rebuilt for you when the kernel is updated.

----------
From: Ed Pozharski


...resisted the temptation to express redundant/easily
objectionable/useless opinion on the virtues of different OS
environments for two days... can't hold any longer... the power of one
ring is too strong... the only useful suggestion on automatic update of
proprietary nvidia drivers has already been made... to minimize damage,
must recycle the comment made on the same subject two years ago...


> On the emerged subject of which OS is best, I honestly think that modern
> computers have reached the point where $500 desktop satisfies all the
> needs of a protein crystallographer.  Since that is the case, any OS can
> be used, and the discussion has, imho, nothing to do with efficiency and
> everything to do with personal preferences.  As somebody who refuses to
> accept the marketing ploy of associating coolness with certain fruit
> logo, I have never used apple products (unless it's granny smith).
> Accordingly, I believe I have no right to comment on them.  I am old
> enough to remember the blue screen of death, so I can't be Windows
> supporter.  For an open source freedom fighter wannabee, Linux is a
> logical choice.
>
> In the end, our choice of OS today simply reflects who we are.

Cheers,

Ed.



--
"I'd jump in myself, if I weren't so good at whistling."
                              Julian, King of Lemurs

----------
From: William Scott

It might be of interest to look back on the original poster's question, because all she asked were a few questions about a specific computer (HP Z210  8 GB with a low end Quadro Nvidia 400 512 MB) running "any Linux", and a specific computer (IMAC 4 GB 2.5 GHz with AMD Radeon HD 6750M 512 MB) running OS X 10.7. Although she asked if the latter was "platform advisable for crystallographic software" for the coming years, there wasn't any question about the merits of various operating systems.

Presumably, she can determine that as well as anyone else, assuming accurate answers to her questions.

No one ever suggested operating system monogamy was a virtue.

Besides, both are simply unix variants, and are far more alike than evangelists for either Linux or OS X seem to want to admit.  If you like or dislike the iCandy apps, then there might be a compelling reason for/against OS X vs. Linux.  Likewise, if you refuse to use closed-source, proprietary operating systems and software on principle, as advocated by Richard Stallmann,  there is a compelling reason to use strict GNU/Linux (albeit without the NVidia proprietary driver). But then, you probably wouldn't be using much apart from COOT and other GPL software.

OS X users, in that respect, are kind of like vegetarians who eat fish.


--Bill


William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA
 
----------
From: Francis E Reyes


Bill

Thanks for focusing the thread....

to the original poster:

If you're going to go OSX I would wary away from the iMac. The all-in-one desktop solution in small form factor  has its downfalls, particularly when the mechanical disk (undoubtedly) fails.

I have an iMac from 2007 and the hard drive needs to be replaced.  The rest of the computer is fine and will probably work for the next 3-5 years for light desktop work (at least for the wife and kiddos). However, I expect the disassembly just to replace this component to be a nightmare.



F
---------------------------------------------
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

----------
From: Adrian Goldman

I would disagree about the disk issue. That's not the failure mode we have seen in the iMacs. Fwiw. Anyway, if it were to fail you could just attach an external disk and continue merrily along - macs will boot from external FireWire (and I assume thunderbolt?) disks.

We are putting money where my mouth is. Our last five purchases have been i7 iMacs. It seems like quite a nice amount of oomph for the money.

Adrian Goldman

Sent from my iPhone

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From: Francis E Reyes

Yes, but I treasure my desktop and USB/Firewire port space ;)

My point is that replacing anything (video card, logic board, display card, drive) within an iMac is difficult.  If the OP (like me) plans on keeping your computer for more than 5-7 years, then he/she might want to get something where replacing the hardware is easy.

I still have several fully functional dual processor PowerPC G5 from 2004 that work wonderfully for general desktop use. And it will still run most  (CCP4/Phenix/Coot) crystallographic software.
Core i7? Then your macs are still quite young (i7's were introduced in 2010).

I'm talking a core 2 duo mac from 2007 (the iSight G5). Time will tell if the drives in 2010 were any better than then drives from 2007. I doubt it though.