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
To put the record straight, despite our efforts SHELXE is not currently
multiply threaded, but ARCIMBOLDO is able to run several copies of
SHELXE simultaneusly (which can be more effective). On the other hand
SHELXL, SHELXD and SHELXT (widely used to solve small molecule
structures) are themsel
Dear Pavel,
By coincidence today I was looking at a soak-dataset and got totally
confused with FEM (map) and Polder now.
I am working on a dataset that processed it at 2.7A (in summer with
XDS) and there was weak density for (OCA-Octanoic acid) when looked
with FEM. This week, I retried it with D
We are seeking a postdoctoral fellow to join the Structural Biochemistry lab at
the Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden:
Postdoctoral research fellow in Structural Biochemistry
Duties
Structural and functional characterization of enzymes involved in uracil and
thym
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
PHASER and SHELXE can take advantage of multiple CPUs, as can most of the
Molecular Replacement pipelines such as AMPLE and ARCIMBOLDO.
It does depend on whether all the CPUs have access to shared memory, though. If
the program is parallellised with threads (such as SHELXE for example),
exploit
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,
W
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
##
We still have quite a number of places available for the annual CCP4 Study
Weekend in January 2019.
Registration closes on 10th December 2018.
Regards
Karen McIntyre
Science & Technology Facilties Council
Scientific Computing Department - CCP4
RCaH 1.22
Tel +44 (0) 1235 44 5790
Fax +44 (0) 1235
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