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tcr_sri003 [2020/12/16 16:10] – tmatejuktcr_sri003 [2023/08/01 01:08] (current) – external edit 127.0.0.1
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-====== LAMMPS version (29 Oct 2020) ======+====== LAMMPS version 29 Oct 20 ======
 ==== description ==== ==== description ====
 LAMMPS is a classical molecular dynamics code with a focus on materials modeling. It's an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. ( https://lammps.sandia.gov/index.html ) . LAMMPS is a classical molecular dynamics code with a focus on materials modeling. It's an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. ( https://lammps.sandia.gov/index.html ) .
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   srun -n16 -N1 --pty bash -l   srun -n16 -N1 --pty bash -l
  
- +When interactive session is started go through LAMMPS installation process described with bellow commands. It will take about 14 minutes.
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-use : https://lammps.sandia.gov/doc/Install_tarball.html  +
- +
-use : https://github.com/lammps/lammps/archive/stable_29Oct2020.tar.gz +
- +
-<hr /> +
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-When interactive session is started go through Quantum Espresso installation process described with bellow commands. It will take about 12 minutes.+
   #folder for source files   #folder for source files
-  mkdir -p ~/downloads/quantum_espresso_6.5+  mkdir -p ~/downloads/lammps_29Oct20
   #folder for compiled binares   #folder for compiled binares
-  mkdir -p ~/soft/qe-6.5+  mkdir -p ~/soft/lammps_29Oct20
      
-  cd ~/downloads/quantum_espresso_6.5 +  cd ~/downloads/lammps_29Oct20 
-  wget https://github.com/QEF/q-e/releases/download/qe-6.5/qe-6.5-ReleasePack.tgz +  wget https://github.com/lammps/lammps/archive/stable_29Oct2020.tar.gz 
-  tar xvzf qe-6.5-ReleasePack.tgz +  tar xvzf stable_29Oct2020.tar.gz 
-  cd qe-6.5 +  cd lammps-stable_29Oct2020
-  module load mpi/openmpi-x86_64+
      
-  ./configure --prefix="/home/users/${USER}/soft/qe-6.5"+  module load mpi/openmpi-x86_64 
 +  module load compilers/gcc-9.3.0
      
-  time make -j${SLURM_NTASKS} all +  mkdir build 
 +  cd build 
 +  cmake3 -D CMAKE_INSTALL_PREFIX=~/soft/lammps_29Oct20 -D LAMMPS_MACHINE=mpi ../cmake 
 +  make -j${SLURM_NTASKS}
   make install   make install
  
 remember to end interactive session with ''exit'' command. remember to end interactive session with ''exit'' command.
  
-If no errors occurred, compiled Quantum Espresso binaries are available in ''/home/users/${USER}/soft/qe-6.5/bin'' .+If no errors occurred, compiled LAMMP binary is available in ''/home/users/${USER}/soft/lammps_29Oct20/bin'' . 
 + 
 +==== example file ==== 
 +Create new folder for example file : 
 +   mkdir ~/lammps_29Oct20_example 
 + 
 +It is recommended that you test this script before you try to run your own LAMMPS problems. 
 + 
 +The example is a Lennard-Jones melt in a 3D box. The Lennard-Jones force has a cutoff at r = 2.5 sigma, where sigma is the distance at which the interparticle potential is zero. The system includes 32,000 atoms, and is to be modeled for 1000 time steps. 
 + 
 +Store below in the filename ''in.lj'', under ''~/lammps_29Oct20_example/'': 
 +<code> 
 +# 3d Lennard-Jones melt 
 +variable x index 1 
 +variable y index 1 
 +variable z index 1 
 +variable t index 200000 
 + 
 +variable xx equal 20*$x 
 +variable yy equal 20*$y 
 +variable zz equal 20*$z 
 + 
 +units         lj 
 +atom_style    atomic 
 + 
 +lattice       fcc 0.8442 
 +region        box block 0 ${xx} 0 ${yy} 0 ${zz} 
 +create_box    1 box 
 +create_atoms  1 box 
 +mass     1 1.0 
 + 
 +velocity all create 1.44 87287 loop geom 
 + 
 +pair_style    lj/cut 2.5 
 +pair_coeff    1 1 1.0 1.0 2.5 
 + 
 +neighbor 0.3 bin 
 +neigh_modify  delay 0 every 20 check no 
 + 
 +fix      1 all nve 
 +thermo   100 
 +run      $t 
 +</code>
  
 ==== sbatch example ==== ==== sbatch example ====
-Use Quantum Espresso 6.5. This description assumes that path to binaries is ''/home/users/${USER}/soft/qe-6.5/bin'' . Use bellow ''qe-test.sbatch'' file to run computation.+Use LAMMPS 29Oct20. This description assumes that path to binaries is ''/home/users/${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="qe-test_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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   #SBATCH --time=2:00:00   #SBATCH --time=2:00:00
      
-  WORKDIR="/home/users/${USER}/soft_tests/qe_run_`date +%s`_${RANDOM}/" +  WORKDIR="/home/users/${USER}/lammps_29Oct20_example"
-  mkdir -p ${WORKDIR}+
   cd ${WORKDIR}   cd ${WORKDIR}
      
-  export BIN_DIR="/home/users/${USER}/soft/qe-6.5/bin"+  export BIN_DIR="/home/users/${USER}/soft/lammps_29Oct20/bin"
   export PATH=${BIN_DIR}:$PATH   export PATH=${BIN_DIR}:$PATH
-  export PSEUDO_DIR=${WORKDIR} 
   export TMP_DIR="/tmp"   export TMP_DIR="/tmp"
            
-  #copy input files and pseudo files to ${WORKDIR}  
-  cp /home/users/${USER}/downloads/quantum_espresso_input_files/* ${WORKDIR} 
-     
   module load mpi/openmpi-x86_64   module load mpi/openmpi-x86_64
 +  module load compilers/gcc-9.3.0
      
   T1=`date +%s`   T1=`date +%s`
          
-  mpirun -np ${SLURM_NTASKS} pw.x -npool ${SLURM_NNODES} -inp Ti2N.in > Ti2N.out+  mpirun -np ${SLURM_NTASKS} lmp_mpi -in in.lj
          
   T2=`date +%s`   T2=`date +%s`
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 ==== 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 ) \\
  
 +==== 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/]]
tcr_sri003.1608131447.txt.gz · Last modified: 2023/08/01 06:38 (external edit)

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