From: Geordano Palacios (biodano.geo_at_gmail.com)
Date: Tue Dec 17 2019 - 11:59:56 CST
Hi as can install cuda GTX 210 on Ubuntu 18 please help me tutorial of
Google are bad.
El lun., 16 de diciembre de 2019 15:38, David Hardy <dhardy_at_ks.uiuc.edu>
> Hi Gerald,
> I think your slow down might be due to accidentally using both GPUs for
> each process.
> By default, NAMD will use all devices that it finds. You should add to
> the first invocation of NAMD "+devices 0" to restrict to using only GPU 0
> and to the second "+devices 1" to restrict to using only GPU 1.
> NAMD is already CPU-intensive enough on each thread that it generally does
> not benefit from hyperthreading.
> Best regards,
> David J. Hardy, Ph.D.
> Beckman Institute
> University of Illinois at Urbana-Champaign
> 405 N. Mathews Ave., Urbana, IL 61801
> dhardy_at_ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/
> On Dec 14, 2019, at 9:51 AM, Gerald Keller <gerald.keller_at_uni-wuerzburg.de>
> Thank you all for your suggestions!
> I tried out to set cpu affinity but the simulation speed still slows down
> when starting the second replica.
> On a node with Intel(R) Core(TM) i9-7940X CPU @ 3.10GHz (1 socket, 14
> cores, 28 with hyperthreading) i tried,
> For the first replica on GPU 0 I used: namd2 +setcpuaffinity +pemap 0-11
> +p 12 +idlepoll
> The second on GPU 1: namd2 +setcpuaffinity +pemap 11-23 +p 12 +idlepoll
> also tried:
> 1st repilca: namd2 +setcpuaffinity +pemap 0-11:2 +p 6 +idlepoll
> 2nd repilca: namd2 +setpcuaffinity +pemap 11-23:2 +p 6 + idlepoll
> Giacomo mentioned that hyperthreading has to be disabled. I thaught namd
> would support hyperthreading?
> Best regards
> >>> Giacomo Fiorin <giacomo.fiorin_at_gmail.com> 12.12.19 20.27 Uhr >>>
> Hello Gerald, I would go with Victor's and Julio's suggestion, but also
> try making sure that HyperThreading is disabled i.e. there are 40 CPU
> physical cores and not 20. In /proc/cpuinfo look for the keyword "ht"
> among the CPU features.
> It is likewise good to keep in mind that unless a program runs entirely on
> the GPU, transferring data between the GPU and the CPU goes via circuitry
> that is most of the time shared among the devices on one motherboard.
> On Thu, Dec 12, 2019 at 2:14 PM Julio Maia <jmaia_at_ks.uiuc.edu> wrote:
>> If you’re not setting the correct affinities, PEs from different replicas
>> might compete for the same cores in your machine.
>> Please try to set CPU affinities for PEs for each replica and try again.
>> You can check how it’s done here:
>> On Dec 12, 2019, at 2:09 AM, Gerald Keller <
>> gerald.keller_at_uni-wuerzburg.de> wrote:
>> Hi everyone,
>> in our working group we compute on our own GPU nodes, with no queue
>> system and do not compute on multiple nodes.
>> When we calculate two replicas of plain MD runs on 1 node with in total 2
>> GPUs and 40 CPUs we recognized that the simulation speed slows down when
>> starting the second replica.
>> 1x NAMD on 1 node using 1 GPU and 18 CPUs:
>> Info: Benchmark time: 18 CPUs 0.00742875 s/step
>> Info: Benchmark time: 18 CPUs 0.0073947 s/step
>> Info: Benchmark time: 18 CPUs 0.00747593 s/step
>> Info: Benchmark time: 18 CPUs 0.00752931 s/step
>> Info: Benchmark time: 18 CPUs 0.00744549 s/step
>> Info: Benchmark time: 18 CPUs 0.00746218 s/step
>> TIMING: 500 CPU: 3.86542, 0.0073741/step Wall: 3.90971, 0.0074047/step
>> TIMING: 980 CPU: 7.43293, 0.00730715/step Wall: 7.49914, 0.00738945/step
>> TIMING: 1000 CPU: 7.58503, 0.007605/step Wall: 7.65193, 0.0076393/step
>> TIMING: 1500 CPU: 11.2973, 0.0073617/step Wall: 11.3969, 0.00763561/step
>> TIMING: 2000 CPU: 15.0195, 0.00745355/step Wall: 15.1411, 0.0075375/step
>> 2x NAMD on 1 node 1 GPU and 18 CPUs for each replica:
>> Info: Benchmark time: 18 CPUs 0.0115988 s/step
>> Info: Benchmark time: 18 CPUs 0.0116316 s/step
>> Info: Benchmark time: 18 CPUs 0.0118586 s/step
>> Info: Benchmark time: 18 CPUs 0.0115375 s/step
>> Info: Benchmark time: 18 CPUs 0.0114114 s/step
>> Info: Benchmark time: 18 CPUs 0.0117798 s/step
>> TIMING: 500 CPU: 6.0915, 0.0113823/step Wall: 6.18421, 0.0114815/step
>> TIMING: 1000 CPU: 11.8594, 0.0126053/step Wall: 12.0109, 0.0127244/step
>> TIMING: 1500 CPU: 17.564, 0.0114935/step Wall: 17.7579, 0.0116048/step
>> TIMING: 2000 CPU: 23.3157, 0.0119276/step Wall: 23.5628, 0.0119936/step
>> If we run 1x NAMD on 1 node using 1 GPU and 18 CPUs and start another
>> simulation with amber on the other GPU, there is no influence on the namd
>> simulation speed.
>> Does anyone have an idea why this is happening and how to solve that
>> problem? Because of limited resources, somtimes we have to run only one
>> simulation per GPU.
>> Thank you in advance for your suggestions!
>> Best regards
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Research collaborator, National Institutes of Health, Bethesda, MD
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