anthill_sri005
Table of Contents
description
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software version
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sbatch example
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performance tests
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Anthill NAMD 212
preparation
Below information allow you to prepare NAMD software on Anthill computing cluster.
download NAMD source
Source tarball NAMD_2.12_Source.tar.gz can be downloaded from : http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD .
compile NAMD from source
By following bellow you will create NAMD in ~/anthill23_NAMD/source/NAMD_2.12_Source/Linux-x86_64-g++/ .
Login to anthill23.cent1.uw.edu.pl .
Create directory for NAMD :
[anteater@anthill23 ~]$ mkdir -p ~/anthill23_NAMD/source
Copy NAMD_2.12_Source.tar.gz to ~/anthill23_NAMD/source. ( Remember that pier23.cent1.uw.edu.pl and anthill23.cent1.uw.edu.pl share /home/users and /workspace ).
Start interactive session and go through compilation instructions :
[anteater@anthill23 ~]$ srun --pty -plong --ntasks=8 --mem=8G bash -l
anteater@ant007:~$
#untar source tarball
anteater@ant007:~$ cd ~/anthill23_NAMD/source
anteater@ant007:~/anthill23_NAMD/source$ tar xzf NAMD_2.12_Source.tar.gz
anteater@ant007:~/anthill23_NAMD/source$ cd NAMD_2.12_Source/
anteater@ant011:~/anthill23_NAMD/source/NAMD_2.12_Source$
#prepare charm ( this proces should end with [... charm++ built successfully. ] message.
anteater@ant011:~/anthill23_NAMD/source/NAMD_2.12_Source$ tar xf charm-6.7.1.tar
anteater@ant011:~/anthill23_NAMD/source/NAMD_2.12_Source$ cd charm-6.7.1/
anteater@ant011:~/anthill23_NAMD/source/NAMD_2.12_Source/charm-6.7.1$./build charm++ net-linux-x86_64 --no-build-shared --with-production
#test charm ( this proces should end with [... test 53: completed (0.13 sec), All tests completed, exiting ] message.
anteater@ant011:~/anthill23_NAMD/source/NAMD_2.12_Source/charm-6.7.1$ cd net-linux-x86_64/tests/charm++/megatest
anteater@ant011:~/anthill23_NAMD/source/NAMD_2.12_Source/charm-6.7.1/net-linux-x86_64/tests/charm++/megatest$ make pgm
anteater@ant011:~/anthill23_NAMD/source/NAMD_2.12_Source/charm-6.7.1/net-linux-x86_64/tests/charm++/megatest$ ./charmrun ++local +p4 ./pgm
#prepare fftw
anteater@ant007:~$ cd ~/anthill23_NAMD/source/NAMD_2.12_Source
anteater@ant007:~/anthill23_NAMD/source$ wget http://www.ks.uiuc.edu/Research/namd/libraries/fftw-linux-x86_64.tar.gz
anteater@ant007:~/anthill23_NAMD/source$ tar xzf fftw-linux-x86_64.tar.gz
anteater@ant007:~/anthill23_NAMD/source$ mv linux-x86_64 fftw
#prepare tcl
anteater@ant007:~$ cd ~/anthill23_NAMD/source/NAMD_2.12_Source
anteater@ant007:~/anthill23_NAMD/source$ wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64.tar.gz
anteater@ant007:~/anthill23_NAMD/source$ tar xzf tcl8.5.9-linux-x86_64.tar.gz
anteater@ant007:~/anthill23_NAMD/source$ mv tcl8.5.9-linux-x86_64 tcl
#compile NAMD
anteater@ant007:~$ cd ~/anthill23_NAMD/source/NAMD_2.12_Source
anteater@ant007:~/anthill23_NAMD/source$ ./config Linux-x86_64-g++ --charm-arch net-linux-x86_64
anteater@ant007:~/anthill23_NAMD/source$ cd Linux-x86_64-g++
anteater@ant007:~/anthill23_NAMD/source/Linux-x86_64-g++$ make
#test NAMD (src/alanin example is part of source tarball)
anteater@ant007:~$ cd ~/anthill23_NAMD/source/NAMD_2.12_Source/Linux-x86_64-g++
anteater@ant007:~/anthill23_NAMD/source/Linux-x86_64-g++$ ./charmrun ++local +p4 ./namd2 src/alanin
passwordless ssh login between nodes
charm used by namd requires passwordless login between allocated computing nodes durring NAMD calculations.
To enable passwordless login between nodes : logging (ssh) in to the Anthill cluster ssh your_login@anthill23.cent.uw.edu.pl and type the following commands ( ssh-keygen asks different questions, do not enter anything, just press ENTER ) :
ssh-keygen -t rsa
cat ~/.ssh/id_rsa.pub >> ~/.ssh/authorized_keys
chmod 600 ~/.ssh/authorized_keys
After performing the above commands one should check whether the desired effect has been achieved. Login to anthill cluster, and allocate two nodes in interactive session. Then login to the second allocated node. Login to second node should not require a password.
[anteater@anthill23 ~]$ srun -N2 --pty bash -l
[anteater@ant011 ~]$ echo $SLURM_NODELIST
ant[011-012] ## <--- !! your allocated node list probably will be different !!
[anteater@ant011 ~]$ ssh ant012
Welcome to Ubuntu 16.04.3 LTS (GNU/Linux 4.4.0-97-generic x86_64)
* Documentation: https://help.ubuntu.com
* Management: https://landscape.canonical.com
* Support: https://ubuntu.com/advantage
[anteater@ant012 ~]$ exit
logout
Connection to ant012 closed.
[anteater@ant011 ~]$ exit
logout
[anteater@anthill23 ~]$
using NAMD program
computation batch file
Below file anthill23_namd.batch uses 2 computing nodes (ant011, ant012) to run f1atpase/f1atpase.namd (ATPase benchmark).
#!/bin/bash -l
#SBATCH --partition=all
#SBATCH --nodes=2
#SBATCH --nodelist=ant011,ant012
#SBATCH --ntasks=8
#SBATCH --mem 8192M
BINPATH="/home/users/${USER}/anthill23_NAMD/source/NAMD_2.12_Source/Linux-x86_64-g++"
CHARMRUN_BIN="${BINPATH}/charmrun"
NAMD2_BIN="${BINPATH}/namd2"
WORKDIR="/home/users/${USER}/anthill23_NAMD/testjobs"
# start your computation:
echo "computation started : $(date +%Y%m%d%H%M%S)"
cd ${WORKDIR}
${CHARMRUN_BIN} ++verbose ++scalable-start ++mpiexec +p8 ${NAMD2_BIN} +setcpuaffinity +isomalloc_sync f1atpase/f1atpase.namd
echo "computation ended : $(date +%Y%m%d%H%M%S)"
NAMD performance on Anthill
example simulation files
Site http://www.ks.uiuc.edu/Research/namd/utilities/ in secition Example Simulations provides files for tests :
ApoA1 benchmark (92,224 atoms, periodic, PME)
ATPase benchmark (327,506 atoms, periodic, PME)
STMV (virus) benchmark (1,066,628 atoms, periodic, PME)
example simulation results
In this tests each node was occupied only by one job.
example simulation ApoA1 benchmark results
node name cores used average(s/step) result1 [s] result2 [s] result3 [s] average [s]
ant003 4 0.534 303.58 281.21 280.94 288.58
ant004 4 0.529 280.22 278.33 278.21 278.92
ant[003-004] 8 0.277 166.07 151.31 150.69 156.02
ant005 8 0.229 125.50 125.30 126.19 125.66
ant006 8 0.229 126.21 125.91 126.26 126.13
ant[005-006] 16 0.119 70.72 70.66 86.77 76.05
ant008 28 0.033 23.50 24.17 23.77 23.81
ant400 16 0.144 83.93 83.99 84.79 84.24
ant401 16 0.145 84.00 85.17 84.78 84.65
ant[400-401] 32 0.080 62.23 53.90 54.23 56.79
ant[400-402] 48 0.066 46.64 46.89 47.01 46.85
ant[400-403] 64 0.052 50.17 41.85 41.90 44.64
ant[400-404] 80 0.054 38.58 39.66 38.69 38.98
ant[400-405] 96 0.053 38.16 38.37 37.80 38.11
ant[400-406] 112 0.057 37.38 37.20 38.58 37.72
ant[400-407] 128 0.055 37.00 36.77 36.91 36.89
ant[400-408] 144 0.054 37.39 37.56 38.11 37.69
ant[400-409] 160 0.047 32.94 32.92 33.76 33.21
ant[400-410] 176 0.044 31.47 32.49 32.73 32.23
ant[400-411] 192 0.043 31.57 32.54 32.65 32.25
ant[300-311,400-411] 384 0.036 34.31 33.48 31.37 33.05
ant[110,200-211,300-311,400-411] 576 0.037 35.90 39.19 40.37 38.49
example simulation ATPase benchmark results
node name cores used average(s/step) result1 [s] result2 [s] result3 [s] average [s]
ant003 4 1.652 875.36 850.86 860.43 862.22
ant004 4 1.624 840.07 851.99 841.40 844.49
ant[003-004] 8 0.856 481.53 451.53 450.43 461.16
ant005 8 0.695 382.86 383.14 380.12 382.04
ant006 8 0.694 380.98 378.75 378.57 379.43
ant[005-006] 16 0.359 205.20 205.90 219.30 210.13
ant008 28 0.097 77.58 65.78 65.60 69.65
ant400 16 0.442 250.13 250.82 250.50 250.48
ant401 16 0.443 247.72 251.62 248.26 249.20
ant[400-401] 32 0.234 179.52 153.49 154.16 162.39
ant[400-402] 48 0.165 115.49 116.33 129.08 120.30
ant[400-403] 64 0.153 108.87 108.50 110.08 109.15
ant[400-404] 80 0.149 101.84 102.60 114.56 106.33
ant[400-405] 96 0.127 95.04 93.40 93.53 93.99
ant[400-406] 112 0.118 87.95 89.56 92.37 89.96
ant[400-407] 128 0.106 84.18 82.03 81.11 82.44
ant[400-408] 144 0.107 80.67 79.28 79.94 79.96
ant[400-409] 160 0.101 75.88 76.03 76.00 75.97
ant[400-410] 176 0.086 72.00 70.50 72.34 71.61
ant[400-411] 192 0.088 71.51 71.14 74.37 72.34
ant[300-311,400-411] 384 0.060 99.98 101.39 114.63 105.33
ant[110,200-211,300-311,400-411] 576 0.053 106.08 105.37 103.73 105.06
example simulation STMV (virus) benchmark results
node name cores used average(s/step) result1 [s] result2 [s] result3 [s] average [s]
ant003 4 5.206 2707.34 2677.83 2700.85 2695.34
ant004 4 5.165 2661.45 2662.53 2656.00 2659.99
ant[003-004] 8 2.681 1405.75 1406.41 1408.86 1407.01
ant005 8 2.296 1210.01 1211.15 1207.16 1209.44
ant006 8 2.292 1207.05 1207.00 1206.27 1206.77
ant[005-006] 16 1.179 647.70 651.09 648.72 649.17
ant007 28 - - - - -
ant008 28 0.319 179.59 180.58 179.67 179.95
ant00[7-8] 56 - - - - -
ant009 16 - - - - -
ant011 4 1.542 791.81 791.86 792.39 792.02
ant012 4 1.545 793.29 793.31 792.05 792.88
ant[011-012] 8 0.783 409.48 409.23 409.61 409.44
ant400 16 1.474 799.03 794.11 798.76 797.30
ant401 16 1.473 800.22 792.96 795.09 796.09
ant[400-401] 32 0.757 465.90 456.35 452.27 458.17
ant[400-402] 48 0.526 343.55 340.48 353.90 345.98
ant[400-403] 64 0.411 284.37 272.64 272.48 276.50
ant[400-404] 80 0.403 259.74 258.68 271.77 263.40
ant[400-405] 96 0.345 230.11 231.95 232.16 231.41
ant[400-406] 112 0.303 211.68 210.85 225.07 215.87
ant[400-407] 128 0.276 195.10 194.50 194.65 194.75
ant[400-408] 144 0.256 185.53 185.05 185.59 185.39
ant[400-409] 160 0.241 173.16 175.06 172.77 173.66
ant[400-410] 176 0.215 164.48 164.24 164.68 164.47
ant[400-411] 192 0.199 156.21 154.94 155.36 155.50
ant[300-311,400-411] 384 0.129 160.57 163.19 163.13 162.30
ant[200-211,300-311,400-411] 576 0.100 156.82 153.73 - 155.28
anthill_sri005.txt · Last modified: 2023/08/01 01:08 by 127.0.0.1
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