Hi All, There is really not much is done in parallel in Phenix. The major parallel thing is refinement with weights optimization. If you do this kind of refinement you may see benefit of several processors. Xiao: you may try both 8 and 4 processors and see what works for you best. Please note, that you will need sufficient amount of memory on your machine to run parallel refinements. Apart from that, Intel i7 with maximum frequency seems the best option for non-parallel refinements because of Intel TurboBoost technology which allows increase frequency of a single core of the processor if it executes only one (non-parallel) task. Oleg Sobolev. On Wed, Jun 24, 2015 at 10:21 AM, Xiao Lei wrote:

Hi Jim,

Thanks for the information! I just got a HP with core i7 4771 (4 cores 3.5GHz), now I know it will be a good speed boost for phenix. I used DEN refinement in phenix, which is very slow, I'm even thinking using university cluster to do it. There is an "DEN parameter optimization" choice in phenix, I do not know if this can be finished by parallel computing with multiple processors.

I have one question, in the phenix refinement, there is an input for the number of processor, is it the same number as cores CPU has? If a CPU is hyper-threaded like core i7 4771 (8 threads but 4 cores), should I put number of processors 8 or 4?

Xiao

On Wed, Jun 24, 2015 at 9:06 AM, Jim Fairman wrote:

...

A few years back one of the PHENIX devs referenced Amdahl's Law and how it affects the performance of PHENIX: https://en.wikipedia.org/wiki/Amdahl's_law

Even though some parts of the refinement are done in parallel on multiple processors, the really time-consuming calculations are done in serial, which ends up governing the overall speed of the process.

I have found that Intel Haswell-class processors like the Core i7 4770 perform refinements significantly speedier than our brand new 12-core Xeon server that is less than 6 months old. So it is my naive guess that getting the fastest "single processor performance" will get you maximal refinement speeds on PHENIX.

If you want to up the ante a bit more, you can always try overclocking with liquid nitrogen to hit 7.2 Ghz http://valid.canardpc.com/240rw0.

Cheers, Jim

On Wed, Jun 24, 2015 at 8:20 AM, Colin Levy wrote:

...

Apologies for the slightly off topic question.

I am configuring a Linux workstation and would like your thoughts on an optimal setup for running Phenix. A lot of my computing time is spent in refinement and I am keen to put something together that will see a considerable increase in speed from my creaking Mac Pro (2 2.4GHz Quad core Intel Xeon with 24Gb RAM).

Many thanks,

Colin

Manchester Protein Structure Facility

Dr. Colin W. Levy MIB G034 Tel. 0161 275 5090 Mob.07786 197 554 [email protected]

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Dear Jim, I would think that using the virtual cores from hyperthreading slows down the overall wall-clock time and would use the number of real cores, maybe +1 in case there are steps in the program that don't fully occupy the CPU. Otherwise I also have the impression that i7 CPUs are significantly faster than Xeon machines with comparable clock frequency. Regards, Tim On 06/24/2015 07:32 PM, Jim Fairman wrote:

Xiao,

I can't comment much on refinement with phenix.den as it is a feature I haven't used before.

There is indeed an input for number of processors. If you are running via command line, add --nproc=# to your command, where # is the number of processors. If you are using the GUI, there is a box in the bottom right-hand corner where you can select number of CPUs.

For hyper threaded CPUs you can pick double the actual physical cores. The 4770 chips have 4 hyper threaded physical cores, so you can run jobs with up to eight.

On Wed, Jun 24, 2015 at 10:21 AM, Xiao Lei wrote:

...

Hi Jim,

Thanks for the information! I just got a HP with core i7 4771 (4 cores 3.5GHz), now I know it will be a good speed boost for phenix. I used DEN refinement in phenix, which is very slow, I'm even thinking using university cluster to do it. There is an "DEN parameter optimization" choice in phenix, I do not know if this can be finished by parallel computing with multiple processors.

I have one question, in the phenix refinement, there is an input for the number of processor, is it the same number as cores CPU has? If a CPU is hyper-threaded like core i7 4771 (8 threads but 4 cores), should I put number of processors 8 or 4?

Xiao

On Wed, Jun 24, 2015 at 9:06 AM, Jim Fairman wrote:

...

A few years back one of the PHENIX devs referenced Amdahl's Law and how it affects the performance of PHENIX: https://en.wikipedia.org/wiki/Amdahl's_law

Even though some parts of the refinement are done in parallel on multiple processors, the really time-consuming calculations are done in serial, which ends up governing the overall speed of the process.

I have found that Intel Haswell-class processors like the Core i7 4770 perform refinements significantly speedier than our brand new 12-core Xeon server that is less than 6 months old. So it is my naive guess that getting the fastest "single processor performance" will get you maximal refinement speeds on PHENIX.

If you want to up the ante a bit more, you can always try overclocking with liquid nitrogen to hit 7.2 Ghz http://valid.canardpc.com/240rw0.

Cheers, Jim

On Wed, Jun 24, 2015 at 8:20 AM, Colin Levy wrote:

...

Apologies for the slightly off topic question.

I am configuring a Linux workstation and would like your thoughts on an optimal setup for running Phenix. A lot of my computing time is spent in refinement and I am keen to put something together that will see a considerable increase in speed from my creaking Mac Pro (2 2.4GHz Quad core Intel Xeon with 24Gb RAM).

Many thanks,

Colin

Manchester Protein Structure Facility

Dr. Colin W. Levy MIB G034 Tel. 0161 275 5090 Mob.07786 197 554 [email protected]

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

-- Jim Fairman, Ph D. Group Leader I - Crystallography Beryllium http://www.be4.com Tel: 206-780-8914 Cell: 240-479-6575 E-mail: [email protected] [email protected]

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-- -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A