Hello Frank, Here at the CLS we have a 8-CPU AMD Quad-Core 2.9GHz machines (ie 32 cores per node). There are newer models capable of 48 cores. Each node has four Gb network ports bonded through Etherchannel. Our file server is a Sun 7310 storage server also with 4 bonded Gb network ports. We use NFSv4.
We also use XDS extensively and I have spent some time trying to optimize the system. In addition to the comments on the XDS wiki and in Kay's reply, I have made a few observations: - I determine the optimum number of CPUS and number of jobs to provide to XDS.INP using the following python snippet: min_cpus = int(round(DELPHI/delta)) stride = int(math.ceil(num_frames/float(total_cores))) jobs = (frames//min_cpus)//stride num_cpus = 1 + (num_frames//jobs)//stride For example if you have a cluster with 96 cores, and you want to process 360 frames with delta of 1 deg, this gives you maximum_number_of_cpus=6 maximum_number_of_jobs=18 So you get 18 jobs each with 4 batches, each batch will use 5 Cores each of which will be processing one frame from the frames in each batch, which maximises the CPU usage but does not over commit them. So each core will process 4 images before the integration job is complete. I find that adding many more cpus to the maximum_number_of_cpus above the number actually used in each batch is counterproductive. I simply add 1 because sometimes a few batches will get an extra frame if the number of jobs is not an integral multiple of the number of frames. I hope this helps. Michel Fodje, Canadian Macromolecular Crystallography Facility, Canadian Light Source -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank Murphy Sent: April-19-11 6:06 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Cluster Design Dear All, Here at NE-CAT, we make extensive use of XDS in a parallel environment. We are looking to purchase some new hardware, so I am soliciting your opinions. Our current cluster is made up of 16 nodes, each with 2 processors that have four cores, running at 2.2 GHz (I believe). We run with hyperthreading on, so 8 physical and 16 virtual cores per node. Our benchmarking with XDS (see https://rapd.nec.aps.anl.gov/wiki/RAPD_NecatStats for an example) shows a diminishing return on increasing the MAXIMUM_NUMBER_OF_PROCESSORS beyond the number of physical cores, and we are wondering if this is due to the test, the processor, the RAM, or XDS. In short, will going to 2 six core processors speed up processing using up to 12 for MAXIMUM_NUMBER_OF_PROCESSORS? Please do not feel the need to constrain the discussion to XDS, as we use our cluster for pretty much all the common crystallographic tasks. Thanks in advance, Frank Murphy Beamline Scientist, NE-CAT
