OACIS_Tutorial_Session1_20170614

Transcript

1. RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE Computer simulations create the

   future  H[T `W `]M 5U O] _ 6a _ CUY` M_U[ B M]OT D MY B: 6 2:4C 24:C 9M P [ U[ (" 
      
   
   

2. RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE 2S PM  •

   U[ ( , YU " – N]U R [a ]aU b [ 24:C – TM P [ ( • 9[b _[ `NYU_ V[N ` U S 24:C • U[ ) YU " – TM P [ ) • 9[b _[ _ ` d[`] CUY` M_[] • 9[b _[ _ ` 9[ _ • U[ YU " – TM P [ • 24:C 2A: _[ M`_[YM_ M]MY _ ] M]OT

3. RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE 9M P [ (0

   9[b _[ `NYU_ V[N 

4. RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE FU]_`M MOTU ` P

   U _TU _`_[]UM • 2 FU]_`M MOTU [ 5[OW ] – 5[OW ] U M [R_bM] _[ YM MS aU]_`M YMOTU – G PU _]UN`_ M UYMS [ bTUOT 24:C U ] U _M P https://www.docker.com/ https://hub.docker.com/r/oacis/oacis_jupyter/

5. RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE =M` OTU S 24:C

   • =M` OT 24:C • 2OO 24:C b N U _ ]RMO – T__ 0 [OM T[ _0 – T__ 0 (/) (-. // ( 0 5[OW ] _[[ N[c" OACIS web Interface docker run --name my_oacis -p 127.0.0.1:3000:3000 -p 127.0.0.1:8888:8888 -dt oacis/oacis_jupyter (for Docker toolbox users) docker run --name my_oacis -p 3000:3000 -p 8888:8888 -dt oacis/oacis_jupyter docker logs -f my_oacis # wait until boot is ready. It may take 20-30 secs.

6. RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE • H[`e M Y

   _d U _ [R UY` M_[] • D[ O[ P`O_ UY` M_U[ # b P _[ ] SU _ ] M UY` M_[] [ 24:C – B` _T R[ [bU S O[YYM P _[ ] SU _ ] M MY UY` M_[] ` P U _TU _`_[]UM – G bU M] T[b _[ ] SU _ ] [`] UY` M_[] U _T c_ U[ docker exec -it -u oacis my_oacis bash -l ( in the container) git clone https://github.com/yohm/sim_ns_model.git sim_ns_model/install_on_oacis.sh

7. RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE . 9 0 9

   9 9 89 • . 9 0 9 9 9 E 9 89 : :: 9E E98 E • /9:9 21 98 3 E,%%9 98 % %. 9 -( )0 9 9 9 89 Key Description l Road length v Maximum velocity rho Car density p deceleration probability t_init thermalization steps t_measure measurement steps http://www.civil.iitb.ac.in/tvm/1111_nptel/544_TrCA/plain/ plain.html

8. RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE • :_ ] ][P`O

   _T TM _]M U_U[ N _b _T R] R [b TM M P _T O[ S _U[ TM • C[`]O O[P [R _TU UY` M_[] – T__ 0 SU_T`N O[Y d[TY U YK KY[P – `_ `_ RU [R _TU UY` M_[] • M C RU O[ _MU U S Ma ]MS a [OU_d M P R [b • M M T[_ A 8 RU position time

9. RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE C O_U S M

   CUY` M_[]  • C O_ M CUY` M_[] • 4T OW CUY` M_[] __U S Click Click Definition of input parameters & configurations of the simulator are registered.

10. RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE 4] M_U S M

    AC M P B`  • C O_ M CUY` M_[] • =U _ [R AM]MY _ ]C _ M] T[b • 4 UOW f b AM]MY _ ]C _g N`__[ _[ O] M_ M b AC Click Click

11. RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE  • 4] M_U

    S M AM]MY _ ]C _ M P B` – U U _T aM ` [R M]MY _ ] • a 1 , • ]T[ 1 ) – C _ fDM]S _ [R B` g_[ L(L – 4 UOW f4] M_ g N`__[  Select “1”  Click
    Set the values

12. RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE  The page for

    the created ParameterSet. Values of the parameters are displayed. List of Runs under this ParameterSet. Click • 2 b AM]MY _ ]C _ M P M B` M] O] M_ P – DT _M_` [R _T B` bU OTM S U M R b O[ P

13. RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE OT OWU S _T

    ] ` _  The page of Run Contents of “_output.json” file is saved in OACIS DB. List of output files. Click it to access. Figures (bmp,jpg,png…) are displayed inline. A button to download the archive of these results.

14. RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE  Path in the

    file system. Each result has its own URL. Ex. URL for this figure file: http://192.168.99.100:3000/Result_development/56 1cdf093135350450000000/561dfaad356339008d260 000/561dfaad356339008d530000/traffic.png It is useful to summarize the results in your notebook by keeping this URL.

15. RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE  • : _T

    R[]Y _[ O] M_ AM]MY _ ]C _ – RU U _T aM ` [R M]MY _ ] M O[YYM M]M_ P aM ` • a 1 f(#)# # #,g • ]T[ 1 f ,# (# (,# )# ),# # ,# # ,# ,g – C _ fDM]S _ [R B` g _[ L(L – 4 UOW 4] M_  Select ”1”  Click
    fill in values in a CSV form MWU S Y` _U V[N

16. RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE MWU S Y` _U

    V[N  45 ParameterSets are created in total. List of ParameterSets Values of parameters Progress bars for job executions.

17. RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE MWU S Y` _U

    V[N  Progress Greenfinished Orangerunning Bluesubmitted Redfailed

18. RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE 4T OWU S _T

    ] ` _  Click ID may be different on your environment

19. RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE  At the page

    of ParameterSet Click “Plot”

20. RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE  Select “line plot”

    X-Axis: “rho” Y-Axis: “flow” Click Data saved in DB are plotted.

21. RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE 4T OWU S _T

    ] ` _  Select “scatter plot” X-Axis: “rho” Y-Axis: “v” Result: “.flow” Click Data points are plotted.

22. RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE  You can download

    SVG file. Each plot has its own URL. When you double click each data point, you’ll go to a page for the ParameterSet.

23. RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE  Select “figure viewer”

    X-Axis: “rho” Y-Axis: “v” Result: “.traffic.png” Click A magnified image is displayed by mouse-over. Double-click leads you to the ParameterSet page.

24. RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE 4[YYM P =U :

    _ ]RMO  • O] M_U S M [_ [R AM]MY _ ]C _ – G UYU_ _T YMcUY`Y `YN ] [R O] M_ P AC _[ ( [ _T b N U _ ]RMO 4=: P[ [_ TMa `OT O[ _]MU _ • = _ ` O] M_ (, B` – a 1 I(#)# # #,J – ]T[ 1 I ,# (# (,# )# ),# # ,# # ,# ,J – 1 I (# )# J

25. RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE  You’ll find a

    CLI command to make PS in bulk. Copy and Paste to the terminal to run the command. docker exec -it -u oacis oacis_tutorial bash -l cd oacis [Paste the command shown in the web interface]

26. RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE :R d[` TMa _UY

    h  • P[O`Y _M_U[ MS – DT ] U M U W [ _T ` ] ]UST_ O[] ] • B` UY` M_U[ bU_T ]T[1 – DT UY` M_[] bU RMU • D]d [_T ] MY UY` M_[]

27. RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE  • T__ 0

    SU_T`N O[Y d[TY UYK [b ]KY M K MY U S – D[][W#H `]M #9 9 [ _ M # GTM_ 3US 5M_M _ 0 CMY U S _T [OUM _b[]W Nd O[YY` UOM_U[ OTM g# ATd B a 6 ) (-" docker exec -it -u oacis my_oacis bash -l (in the container) git clone https://github.com/yohm/sim_power_mean_sampling.git sim_power_mean_sampling/install.sh Create ParameterSets with various alpha and beta for "NetworkSamplingTunedF0" simulator, and see how the assortativity of the sampled network depends on these parameters. alpha = [0.6, 0.8, 1.0], beta = [-2.0, -1.0, 0.0, 1.0, 2.0] I[ _U[ M J 2 [_T ] MY

28. RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE  • T__ 0

    SU_T`N O[Y d[TY UYK [ KY[P – D CTUYMPM 2 ` Ua ] M _]M U_U[ U _T ][N` _ [R a[ aU S [ d _ Y COU B 0 .) ) ( " docker exec -it -u oacis my_oacis bash -l (in the container) git clone https://github.com/yohm/sim_eos_model.git sim_eos_model/install.sh I[ _U[ M J MY ) Run "EOS_model" simulator for m=[3,5,7,9,11,13,15,17,19,21,23], and see that "Divergence Speed" is positive only for 5<= m <= 17. courtesy of T. Shimada To see a clear transition, set "t" to a much bigger value than the default value.

29. RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE  • T__ 0

    SU_T`N O[Y d[TY Pd MYUOM KS]M TKY[P – H `]M _ M # 2 UY Y[P R[] W b P OU UR _UY PU _]UN`_U[ # b ATd ) ( " docker exec -it -u oacis my_oacis bash -l (in the container) git clone https://github.com/yohm/dynamical_graph_model.git dynamical_graph_model/install.sh I[ _U[ M J MY Run "DynamicalGraphModel" simulator with the default parameters, and see how the lifetime distribution looks like.

30. RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE C_[ U S 24:C

     • ][Y _T _ ]YU M – _[ U S 24:C 1111111111111111111111111111111111111111111111111 – ] _M]_U S 24:C – [SSU S U _[ _T O[ _MU ] – ] Y[aU S _T O[ _MU ] # user docker exec -it -u oacis my_oacis bash -l docker stop my_oacis; docker rm -v my_oacis docker start my_oacis docker stop -t 60 my_oacis

31. RIKEN ADVANCED INSTITUTE FOR COMPUTATIONAL SCIENCE 4[ O ` U[

     • : _M M_U[ [R 5[OW ] M P 24:C • TM P [ [R UY` M_U[ c O`_U[ Nd 24:C – O_U S _T CUY` M_[] – O] M_U S AM]MY _ ]C _ M P B` – MOO U S _T ] ` _ • [`_ `_ RU • [_ i : _T c_ TM P [ b bU U _]`O_ T[b _[ UY Y _ H EB UY` M_[]