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CCP4BB  November 2008

CCP4BB November 2008

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Subject:

Re: Crystallographic computing platform recommendations?

From:

Kevin Cowtan <[log in to unmask]>

Reply-To:

Kevin Cowtan <[log in to unmask]>

Date:

Tue, 18 Nov 2008 18:04:11 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (110 lines)

 From a system management point of view there is one very significant 
benefit to Ubuntu: The LTS releases come out every 2 years and are 
supported for 3 years. Compare this with Fedora: releases are only 
supported for 18 months.

Once you take into account testing and transition times, that means in 
practice with Fedora you are on a 1-year upgrade cycle, versus 2 years 
with Ubuntu.

(I used Fedora for years on my desktop machines and more recently Ubuntu 
on my laptops. It did take a couple of days getting used to the 
differences, but I find now that I prefer the setup of the Ubuntu system).

Andreas Förster wrote:
> Re:  Switching from Fedora to Ubuntu.
> 
> Don't.  Stick with Fedora if it works for you.  If you're tempted by 
> Ubuntu because of the coolness, the bling, the color, the limited 
> customizability or the lack of root, a Mac will get you all of this much 
> more abundantly.
> 
> If you're used to Redhat/Fedora, stick with it.  Everything 
> crystallography related works on it.  I tried to set an ancient Vaio up 
> with xUbuntu and went back to Redhat 9 after too much frustration. 
> Things are not where they're supposed to be and don't work as they 
> should.  This is from a Redhat perspective, obviously, which I've been 
> using since 5.2.
> 
> 
> Andreas
> 
> 
> 
> Edward Snell wrote:
>> That would have saved me a lot of time and frustration!  Now if only I 
>> can remember this for the next time J  
>>  
>>
>> I have a 64bit Fedora 9 system running on an Lenovo Thinkstation D10 – 
>> you can buy this without the operating system.  I used the 64bit 
>> option as I’m processing very high resolution X-ray data and needed to 
>> use more memory.  I was able to get a 16 GB system for a reasonable cost.
>>
>>  
>>
>> If you are a tinkerer and want a few days of ‘fun’ this is a way to 
>> go.  If not, commercially available Linux systems are available but I 
>> found few with a large memory capacity.
>>  
>>
>> Coot and CCP4 were a pain to compile in 64 bit mode (not the 
>> developers problem, just mine for trying to get them to work in 64 
>> bit).  I had to play with some header definitions, lop h’s off etc, 
>> add using namespace std and, install a lot of libraries but they now 
>> work well.  Coot reads all the svg files and displays all the pretty 
>> icons.  I like the PC Linux route mainly because the hardware is less 
>> expensive and easier to swap out components.  I am used to Fedora and 
>> manage my own system so for the moment I plan to stick with that but 
>> it sounds like Ubuntu looks like an interesting way to go. Has anyone 
>> had any experiences in transitioning from Fedora to Ubuntu?  Is it 
>> something to think about, a Thanksgiving project mainly?
>>
>>  
>>
>> Cheers,
>>
>>  
>>
>> Eddie
>>
>> Edward Snell Ph.D.
>> Assistant Prof. Department of Structural Biology, SUNY Buffalo,
>> Hauptman-Woodward Medical Research Institute
>> 700 Ellicott Street, Buffalo, NY 14203-1102
>> Phone:     (716) 898 8631         Fax: (716) 898 8660
>> Email: [log in to unmask]  Telepathy: 42.2 GHz
>>
>> Heisenberg was probably here!
>>
>> ------------------------------------------------------------------------
>>
>> *From:* CCP4 bulletin board [mailto:[log in to unmask]] *On Behalf 
>> Of *Michel Fodje
>> *Sent:* Tuesday, November 18, 2008 10:28 AM
>> *To:* [log in to unmask]
>> *Subject:* Re: [ccp4bb] Crystallographic computing platform 
>> recommendations?
>>
>>  
>>
>> On Tue, 2008-11-18 at 09:40 -0500, James M. Vergis wrote:
>>
>>  
>>
>> 2) Graphics Cards:
>>
>> I like the Nvidia cards since they provide linux drivers.  ATI also does
>>
>> now.  I would say the only thing I don't like about them is when you do a
>>
>> kernel update you have to remake the driver.
>>
>> I would just add that for those using Fedora, you can avoid having to 
>> remake the driver by using the RPMFusion repositories to install the 
>> Nvidia drivers. This way updating the kernel automatically installs 
>> the corresponding Nvidia kernel module.  The same applies to AMD/ATI 
>> drivers.
>>
> 

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