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cluster:175 [2018/09/26 16:01]
hmeij07 [Gromacs]
cluster:175 [2018/11/29 13:00] (current)
hmeij07
Line 2: Line 2:
 \\ \\
 **[[cluster:0|Back]]** **[[cluster:0|Back]]**
 +
 +As of 
 + --- //[[hmeij@wesleyan.edu|Henk]] 2018/10/08 08:56// \\
 +The P100 with 12 GB is end of life, replaced by the P100 16 GB or V100 and \\
 +The GTX 1080Ti will be replaced by the GTX 2080 (no specs yet and not certified for Amber18, yet)\\
 +As of
 + --- //[[hmeij@wesleyan.edu|Henk]] 2018/11/29 12:55//\\
 +New GROMACS performance benchmarks featuring 2x and 4x NVIDIA RTX 2080 GPUs are now available (GTX too). The RTX 2080 graphics card utilizes the new NVIDIA Turing GPU architecture and provides up to 6x the performance of the previous generation. (Exxact newsletter)
 +
  
 ==== P100 vs GTX & K20 ==== ==== P100 vs GTX & K20 ====
Line 120: Line 129:
  
 ==== Gromacs 2018.3 ==== ==== Gromacs 2018.3 ====
 +
 +The multidir not running in Gromacs 2018 is a bug in the code clashing with the call MPI_Barrier (communication timing error).  It is fixed in Gromacs 2018.3 so we have some multidir results although gpu utilization has room for improvements (about 25% used, same as on GTX).
  
 <code> <code>
-multidir -gpu_id 0123+ 
 +multidir -gpu_id 0123 with four simultaneous gromacs processes 
 -np  8 -ntomp  4 -npme 1 -maxh 0.1 -pin on -nb gpu -np  8 -ntomp  4 -npme 1 -maxh 0.1 -pin on -nb gpu
 01/md.log:Performance:       36.692        0.654 01/md.log:Performance:       36.692        0.654
 02/md.log:Performance:       36.650        0.655 02/md.log:Performance:       36.650        0.655
 03/md.log:Performance:       36.623        0.655 03/md.log:Performance:       36.623        0.655
-04/md.log:Performance:       36.663        0.655+04/md.log:Performance:       36.663        0.655 or about 146 ns/day/node (quad) 
 -np 16 -ntomp  8 -npme 1 -maxh 0.1 -pin on -nb gpu -np 16 -ntomp  8 -npme 1 -maxh 0.1 -pin on -nb gpu
 01/md.log:Performance:       25.151        0.954 01/md.log:Performance:       25.151        0.954
 02/md.log:Performance:       25.257        0.950 02/md.log:Performance:       25.257        0.950
 03/md.log:Performance:       25.247        0.951 03/md.log:Performance:       25.247        0.951
-04/md.log:Performance:       25.345        0.947+04/md.log:Performance:       25.345        0.947 or about 100 ns/day/node (quad) 
 + 
 +multidir -gpu_id 00112233 with eight simultaneous gromacs processes 
 +sharing the gpus, 2 processes per gpu
  
-multidir -gpu_id 00112233 
 -np  8 -ntomp  4 -npme 1 -maxh 0.1 -pin on -nb gpu -np  8 -ntomp  4 -npme 1 -maxh 0.1 -pin on -nb gpu
 Error in user input: Error in user input:
 The string of available GPU device IDs '00112233' may not contain duplicate The string of available GPU device IDs '00112233' may not contain duplicate
 device IDs device IDs
 +
 </code> </code>
 +
 +That last error when loading multiple processes per gpu is *not* according to their documentation. So the multidir performance is similar to previous single dir performance but still lags GTX performance by quite a bit. Albeit, there is room in utilization rate of the gpus.
 +
  
 ==== What to Buy ==== ==== What to Buy ====
  
   * Amber folks: does not matter   * Amber folks: does not matter
-  * Lammps folks: P100 nodes please+  * Lammps folks: P100 nodes please, although in hybrid runs does not matter
   * Gromacs folks: GTX nodes please   * Gromacs folks: GTX nodes please
  
cluster/175.1537992086.txt.gz · Last modified: 2018/09/26 16:01 by hmeij07