Re: [ccp4bb] buying a cluster

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

Re: [ccp4bb] buying a cluster

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

[ccp4bb] Polder or FEM

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

[ccp4bb] Structural Biology Post-doctoral Fellow Position at Uppsala University

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

Re: [ccp4bb] buying a cluster

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.

Re: [ccp4bb] buying a cluster

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)

Re: [ccp4bb] buying a cluster

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

Re: [ccp4bb] buying a cluster

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

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 side"... On 23 Nov 2018, at 10:30, V F wrote: > Dear all, >

Re: [ccp4bb] buying a cluster

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,

[ccp4bb] buying a cluster

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

[ccp4bb] FW: Registration still open for CCP4 Study Weekend 2019

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)