On Wed, May 2, 2012 at 5:44 PM, Peter C. Lai <[email protected]> wrote: > When considering compute hardware today, you're gonna have to shop like a > gamer. A rig that can get high Battlefield 3 or Arma 2/3 framerates should > also be able to get you some nice ns/day. >
(To a great extent) wong! While many if not most games are GPU-bound and not well multi-threaded, GROMACS uses highly efficient CPU code and can make use of virtually any amount of CPU juice (i.e. extra cores and frequency). > I think most people consider Bulldozer mostly a flop. AMD masks lower > cycle speeds with more cores per chip, but that just shifts the burden onto > interprocessor communication, to which MPI is the most sensitive. > Partly true, but GROMACS has no issues whatsoever with scaling pretty much linearly to any number of cores currently available per node (with at least 500 atoms/core). > You can wait for ivy bridge, then stick some Kepler GPUs (nvidia gtx 680) > in it. That should max the performance. asm is pretty much stagnant for > general purpose procs since core2 came out. > AFAIK IB doesn't improve much on flop/s performance over SB, but it's a power efficiency king. However, it's not at all sure that when it comes to performance/$ AMD doesn't win. Also, Kepler might not be the best choice, we'll see what can we get out with some more tuning. What do you mean by asm? > Keep an eye on the I7-3770K. It has the most cache and fastest core speed > of the intel ones. The K chips are preferred for adventurous overclocking. > Although hyperthreading and onboard intel gpu is useless for hpc. The > I5-3570K is slower and has 2M less cache - it's basically an ivy bridge > drop in replacement for the I5-2500K (just pci-e 3.0 upgrade) > Ehmm, HT *is* useful, it will boost GROMACS performance by up to 10-15% or so. > gmx 4.6 is supposed come with native gpu support; you should look at some > list archives to see what is planned to be supported. Waiting for 4.6 to > come out is going to extend your wait on hardware considerations, but it > also means prices should drop. > > for nics find the best/most compatible tcp offloading engine, also while > using jumbo frames. Personally I've always found Intel better than > Broadcom. Stay away from anything Realtek. If you can, try to begin to look > at going to fiber earlier (with an eye on splitting out storage from > compute). > -- > Sent from my Android phone with K-9 Mail. Please excuse my brevity. > > > melichercik <[email protected]> wrote: >> >> Hi people, >> we plan to buy some computer mostly for gromacs, so I want to ask you >> for some hints. I'd tried to do some research, but no success. :( >> >> Have someone ever compared AMD Bulldozer and Sandy/Ivy Bridge >> architectures? Are there planed any optimizations in gmx core in asm >> parts? (if there are need). >> Most interesting for me whould be to compare FX-8150 and i5-2550, >> I7-2600, i7-3570K or i7-3770 processors. >> >> GPGPU - are there some real plans for supporting Radeon GPUs? Because >> OpenMP 3.x supports them - but I don't have any idea how complicate is >> to use newer OpenMP in GMX (and another work about it). >> >> And are there bigger differences (if someone knows) in use 1 Gbps >> onboard NIC vs. "better"? add-on NIC cards e.g. Intel Pro/1000 CT or >> similar? In MPI calculations with use 4 to 8 cores per computing node. >> >> >> Thanks a lot. >> >> Milan Melichercik >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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