[phenixbb] off topic - linux flavors for crystallography

Fulvio Saccoccia fulvio.saccoccia at uniroma1.it
Thu Dec 12 14:53:51 PST 2013


I have been used both Phenix and CCP4 suite on a variaty of Linux
distribution, both Debian- and RedHat-based (Ubuntu, Debian, Fedora,
CentOS, openSuse, Scientific Linux) on the basis of different architecture
and hardware specification (graphic card, processor, etc.). In my personal
opinion, Ubuntu is the "safest" way because of the huge hardware support,
so that the great majority of updated hardware available today is
recognized out-of-the-box. A great support comes also from the community.
However, some libraries lacked in the past for specific purposes (e.g. I
think there is an issue for mapslicer in ccp4 or a fortran interpreter so
that COMO does not run). I have been using openSuse since the version 12.3
and I found that all work correctly and without user efforts. Also the open
source graphic driver for ATI cards now work great (this has been a
puzzling trouble for a log time since my laptop has a radeon HD5145 which
worked only with Ubuntu and proprietary drivers). PyMol and Coot run very
well with open source drivers. I have no experience with RHEL but I highly
recommend openSuse for a crystallography workstation.

Best wishes

Fulvio Saccoccia


2013/12/12 Engin Özkan <eozkan at stanford.edu>

>  Let me clear this: the perfect storm of hacks *and* lost/stolen devices
> with private patient information appears to have led to changes at our
> institution. I guess these got our IT and lawyers to get religion on data
> security. Obviously, encryption won't protect against hacking.
>
> That out of the way, nobody has encrypted linux machines?
>
> Engin
>
>
> On 12/12/13, 10:00 AM, Engin Özkan wrote:
>
> At the risk of hijacking the thread, is the other type of "safety"
> considered? Our university is cutting net access to unencrypted computers,
> after now-publicized hacks originating from a foreign country. They do not
> seem to understand or know solutions for encrypting linux machines (they
> are also banishing XP; all FPLCs may have to come offline!).
>
> So, to cut to the chase, does anyone run RHEL/CentOS/Scientific Linux on
> encrypted disks? I am assuming dm-crypt with LUKS would be the way to go,
> and I would appreciate to hear about how easy it is to set it up and
> maintain. Can this be done without wiping clean the system? We are not
> system admins, and don't want to be. Otherwise, we may be forced to switch
> entirely to Macs (a Mac OS X Server as our SBGrid server?).
>
> Thanks,
> Engin
>
> On 12/12/13, 8:32 AM, David Waterman wrote:
>
> CCP4 builds and tests on a handful of Linux distributions, but the
> distributed binaries are, I think, built on CentOS 5.9. I agree that RHEL
> derivatives are "safest" for a crystallography platform.
>
> -- David
>
>
> On 11 December 2013 23:15, Nathaniel Echols <nechols at lbl.gov> wrote:
>
>>  On Wed, Dec 11, 2013 at 2:24 PM, Andreas Förster <docandreas at gmail.com>wrote:
>>
>>> Everyone has a favorite distro, and they all work
>>
>>
>>  I'm not sure about this - we have definitely found some distributions
>> to be easier to support than others, even just compiling Phenix from
>> source.  My advice would be to stick to distributions derived from RedHat
>> (i.e. Fedora, RHEL, CentOS, Scientific Linux) or Ubuntu, simply because we
>> will go out of our way to ensure that the binary Phenix installers work on
>> these.  (They also have Coot binaries.)  That doesn't mean other
>> distributions are necessarily unsuitable, but the software support may be
>> patchier.
>>
>>  I can't remember what CCP4 builds on, but I would be surprised if it
>> doesn't support at least the same OSes.
>>
>>  -Nat
>>
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-- 
Fulvio Saccoccia, PhD
Dept. of Biochemical Sciences
Sapienza University of Rome
00185, Rome (Italy)
Phone: +39 06 4991 0556
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