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tcr_sri003 [2020/12/17 09:43] – tmatejuktcr_sri003 [2023/08/01 01:08] (current) – external edit 127.0.0.1
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 variable y index 1 variable y index 1
 variable z index 1 variable z index 1
-variable t index 20000+variable t index 200000
  
 variable xx equal 20*$x variable xx equal 20*$x
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 fix      1 all nve fix      1 all nve
-thermo   1000+thermo   100
 run      $t run      $t
 </code> </code>
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 Use LAMMPS 29Oct20. This description assumes that path to binaries is ''/home/users/${USER}/soft/lammps_29Oct20/bin'' and example file ''in.lj'' is under ''/home/users/${USER}/lammps_29Oct20_example''. Use bellow ''lammps_29Oct20-test.sbatch'' file to run computation. Use LAMMPS 29Oct20. This description assumes that path to binaries is ''/home/users/${USER}/soft/lammps_29Oct20/bin'' and example file ''in.lj'' is under ''/home/users/${USER}/lammps_29Oct20_example''. Use bellow ''lammps_29Oct20-test.sbatch'' file to run computation.
   #!/bin/bash -l   #!/bin/bash -l
-  #SBATCH --job-name="lammps example N2_n32"+  #SBATCH --job-name="lammps-example-N2_n32"
   #SBATCH --nodes=2                   # number of computing_nodes   #SBATCH --nodes=2                   # number of computing_nodes
   #SBATCH --ntasks=32                 # number of CPU's ( 16*computing_nodes )   #SBATCH --ntasks=32                 # number of CPU's ( 16*computing_nodes )
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   T2=`date +%s`   T2=`date +%s`
   echo -e "stop ${T2}\t start ${T1}\t ${SLURM_NNODES}"   echo -e "stop ${T2}\t start ${T1}\t ${SLURM_NNODES}"
- 
- 
-FIXME 
- 
-FIXME 
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-FIXME 
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-FIXME 
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-FIXME 
  
 ==== performance tests ==== ==== performance tests ====
-Bellow results show time of computation in function of used resources (computation scalability) for a specific computational task done with ''pw.x'' program.+Bellow results show time of computation in function of used resources (computation scalability) for a specific computational task ''lammps_29Oct20-test.sbatch''.
  
 Assigning a larger amount of computing nodes does not always lead to a (efficient) reduction in computing time (wall-time of the job). To find the most appropriate number of nodes for a specific type of job, it is essential to run one's own benchmarks. In general, parallel <color #22b14c>jobs should scale to at least 70% efficiency for the sake of other TCR users</color>. One user using twice the resources to squeeze out 10% more performance may be keeping other users from working at all. Assigning a larger amount of computing nodes does not always lead to a (efficient) reduction in computing time (wall-time of the job). To find the most appropriate number of nodes for a specific type of job, it is essential to run one's own benchmarks. In general, parallel <color #22b14c>jobs should scale to at least 70% efficiency for the sake of other TCR users</color>. One user using twice the resources to squeeze out 10% more performance may be keeping other users from working at all.
  
-Bellow results should be consider as results of this specific computational task on this specific hardware (TCR cluster) and not overall benchmark for Quantum Espresso software suite.+Bellow results should be consider as results of this specific computational task on this specific hardware (TCR cluster) and not overall benchmark for LAMMPS software.
  
-{{ tcr:qe65_tcr_result_001.png?nolink|}} 
 ^nodes ^min [s] ^avg [s] ^median [s] ^max [s] ^efficiency [%] ^ ^nodes ^min [s] ^avg [s] ^median [s] ^max [s] ^efficiency [%] ^
-|1 |1862 |2065.75 |2126 |2149 |<color #22b14c>100.00%</color>| +|1 |349 |351.67 |349 |357 |<color #22b14c>100.00%</color>| 
-|2 |1105 |1192.75 |1157.5 |1351 |<color #22b14c>84.25%</color>| +|2 |206 |209.33 |207 |215 |<color #22b14c>84.71%</color>| 
-|3 |763 |770 |768.5 |780 |<color #22b14c>81.35%</color>| +|3 |156 |156.33 |156 |157 |<color #22b14c>74.57%</color>| 
-|4 |798 |1026.25 |868.5 |1570 |58.33%| +|4 |128 |128.67 |129 |129 |68.16%| 
-|5 |571 |589.75 |574 |640 |65.22%| +|5 |121 |121.33 |121 |122 |57.69%| 
-|6 |488 |536 |525.5 |605 |63.59%| +|6 |111 |111 |111 |111 |52.40%| 
-|7 |372 |502.25 |414.5 |808 |<color #22b14c>71.51%</color>| +|7 |92 |93 |93 |94 |54.19%| 
-|8 |375 |489.75 |408.5 |767 |62.07%| +|8 |88 |88.67 |89 |89 |49.57%| 
-|9 |324 |403.75 |346.5 |598 |63.85%| +|9 |83 |84 |84 |85 |46.72%|
-|10 |327 |456.25 |465.5 |567 |56.94%| +
-|12 |285 |429.4 |375 |609 |54.44%| +
-|16 |228 |274.25 |281.5 |306 |51.04%| +
- +
- +
  
 *) values (min, avg, median, max, efficiency) do not include failed runs \\ *) values (min, avg, median, max, efficiency) do not include failed runs \\
 +*) results are from 3 runs \\
 *) efficiency as ''t1 / ( nodes * tn )'' ( where t1 is min computation time at one node, tn is min computation time on N nodes ) \\ *) efficiency as ''t1 / ( nodes * tn )'' ( where t1 is min computation time at one node, tn is min computation time on N nodes ) \\
  
-example source) https://arc.vt.edu/userguide/lammps/+==== other ==== 
 +above desciption uses default settings and do not include any extra LAMMPS packages that you may require. More about LAMMPS' package at  [[https://lammps.sandia.gov/doc/Build_package.html]] . 
 + 
 +*) [[https://arc.vt.edu/userguide/lammps/]]

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