Graeme's suggestion of a standard benchmarking dataset is a good one,
but I'm not so sure a 24 GB download size is going to get a lot of hits.
In fact, in some countries you have to pay for internet by the GB, and
it costs as much as mobile phone data! The large size also makes it hard
to separ
Re: publishing benchmarks - great idea - expand on what James described earlier.
Most programs are GHz dependent (for most “sensible” definitions of GHz (not
the mega-hyper-pipeline stall prone P4 say) however I see your point that
“threaded” and “optimised for vector systems (e.g. AVX512)” woul
Hi Graeme,
I suspect that this conclusions depends very closely on (i) the shape of
> the problem and (ii) the extent to which the binary has been optimised for
> the given platform.
>
> I do hope some of these info are analyzed and either published or at least
put at ccp4 wiki.
I am pretty sure
HI James,
Re: dissenting opinion
I suspect that this conclusions depends very closely on (i) the shape of the
problem and (ii) the extent to which the binary has been optimised for the
given platform.
I am pretty sure that there are some applications (heavily threaded, making
extensive use o
I have a dissenting opinion about computers "moving on a bit". At least
when it comes to most crystallography software.
Back in the late 20th century I defined some benchmarks for common
crystallographic programs with the aim of deciding which hardware to
buy. By about 2003 the champion of m
Dear all,
Thanks for all the off/list replies.
> To be honest, how much are they paying you to take it? Can you sell it for
> scrap?
May be I will give it a pass.
> To compare, two dual CPU servers with Skylake Gold 6148 - that is 40 cores -
> will probably beat the whole lot even if you could ke
c.uk / rob...@well.ox.ac.uk / robert.esn...@bdi.ox.ac.uk
Tel: (+44)-1865-287783 (WHG); (+44)-1865-743689 (BDI)
-Original Message-
> From: "V F"
> To: CCP4BB@JISCMAIL.AC.UK
> Date: 23/11/18 13:11
> Subject: Re: [ccp4bb] buying a cluster
>
> Hello Peter
&g
Dear Veronica
The answer depends to a large extent on your own, or your group's, mode of
working. Specifically, are you interested in the fastest turn-around of
individual jobs, or are you interested the highest throughput of many jobs
running simultaneously, i.e. draining the batch queues as qui
Powell<193323b1e616-dmarc-requ...@jiscmail.ac.uk>
Sent: 23 November 2018 11:05:13
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] buying a cluster
Hi
For X-ray diffraction image processing, both XDS and DIALS can use multi cpus.
For cryo-EM, Relion can run on multi-cpus, but can also mak
Hello Peter
Thanks for quick replies.
> (1) a single large machine with 32 cpus, or:
No
>
> (2) a system with 32 separate computers linked together in a network?
>
Yes
Each node has HP ProLainat that contains 2x Intel Xeon Processor X5550
(quad-core, 2.66 GHz.
###
On Fri, Nov 23, 2018 at 11:30:01AM +0100, V F wrote:
> Which programs benefit from multi-cpu cluster?
in addition to what the others have mentioned, you can also configure ccp4i2
to run jobs remotely on the cluster. Currently it requires SGE, but
support for other job schedulers (such as Slurm) ca
Dear Veronica,
Is this:
(1) a single large machine with 32 cpus, or:
(2) a system with 32 separate computers linked together in a network?
If (1) others have already answered, although be aware that for many
applications the throughput doesn't scale linearly with the number of
cpus. This mea
Hi Veronica,
Fragment-based molecular replacement programs such as ARCIMBOLDO are
based on PHASER /SHELXE jobs parallelization over multiple CPUs in a
single machine or in a cluster.
All the best,
Nicolas
On 11/23/2018 11:30 AM, V F wrote:
Dear all,
Which programs benefit from multi-cpu c
CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] buying a cluster
Hi
For X-ray diffraction image processing, both XDS and DIALS can use multi cpus.
For cryo-EM, Relion can run on multi-cpus, but can also make good use of GPUs,
so don't forget this as an option if you're going over to the "dark sid
Hi
For X-ray diffraction image processing, both XDS and DIALS can use multi cpus.
For cryo-EM, Relion can run on multi-cpus, but can also make good use of GPUs,
so don't forget this as an option if you're going over to the "dark side"...
On 23 Nov 2018, at 10:30, V F wrote:
> Dear all,
> Whic
The first two programs that come to my mind (I know there are a lot more
programs) are xia2 and ccp4 cloud.
Sheers,
Luiso,
From: CCP4 bulletin board on behalf of V F
Sent: 23 November 2018 10:30:01
To: ccp4bb
Subject: [ccp4bb] buying a cluster
Dear all
Dear all,
Which programs benefit from multi-cpu cluster? Since the physics
department is getting rid of a old 32 compute node cluster, I was
hoping to find some benefit using for crystallographic work. Looking a
ccp4wiki or google-fu did not help
Many thanks
Veronica
##
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