????????? ??????????? ??????????? ????????????????

1
????????? ??????????? ???????????
???????????????? ???? ? ???????
???????????????? OpenTS

• ??????? ?. ?. ??????? ?????? ???????????, ???
  ???, 2006-04-20

2
??????? ???????? ? ??????? ??????????
????????????????
??? ?????? ? ??????

• ??????????? ??????????? ??? ????????????
  ???????????? ?????
• Nadmin ??????? ?????????????????
• Botik Tools ????? ???????? ??? ????????? (Botik
  Tester, Botik Key, Botik Look)
• Botik Mon ? Botik Map ?????????? ? ????. ???
• ?????????????? ? ?? ??????????
• ?????????????? ???????????????? ? ??????????
  ????? ????? (????????? ????????? ? ?? ?????????
  ??????????)
• ????????????? ?????? ???????????
• ????????? ??????????? ??????????? ???
  ???????????? ?????????? (??? ????????????????
  ????????? ????)
• ?-??????? ??????? ???????????????? ????????????
  ??????????
• OpenTS ?-??????? ? ???????? ????????????

3
????????????????? ????????? ???? ????????
???????????.????????? ??????????? ???????????
??? ???????????????? ????
4
????????????????? ?????? ???? ???????? ???????????

• 2000-2004
• 10 10 ????????????
• 10M (?? 5 ??? ?? 20 ???????????)
• ??? ??? ???????? ?? ??????
• ???? ??? ???????? ???????? ?? ??????????
• Hardware, Software, Applications, Aux.

5
?????? ???????? (16)
6
Linpack-?????????????????? ????????
2032
472
185 ???
57
26
11
7
??????? ???? ?-1000

• ??????? ?????????-????????? 2,5 Tflops
• Linpack-?????????-????????? 2,0 Tflops
• ???80.1

• ?????? 2004 ???????? ?????? ?????? ?? ??????????
  ???? (??????? ?????? ????? 2)
• ?????? 2004 ? 98 ? Top500

8
???????? ?? ??, ?????? ?1

• ???? ?? Linux-SKIF
• PVFS-SKIF ???????????? ???????? ???????
• OpenPBS-SKIF ??????? ????????
• FLAME-SKIF ??????? ??????????? ? ??????????
  (reset, power on/off) ??????????? ????????? ????

9
???????? ?? ??, ?????? ?1

• OpenTS ?-??????? ? ???????? ????????????
• ?????????? TG ??? ????? T
• ?????????? TF2TC(T-Fortran ? T)
• TDB ?????????????? ????????????? ????????
  MPI-????????, ? ?????????? ??????? ?-????????
  (?????? TotalView)

10
???????? ?? ??, ?????? ?1

• 6 ?????????? ??????????? ?????? ? ????? OpenTS
• 12 ?????????????? ????????? ???????, ????????? ?
  ??????????
• 14 ?????????? ??????????? ?????????? (?? ??? 3 ?
  ??????? ??)
• ????????????? ????????? ? ?????????????
  ??????????? ???????? (????? 6 ???????? ????????
  ??????????)

11
???????? ???? ?-??????? ? ????? ??????????? Open
TS
12
?-???????. ???????

• ???????? 80-?????????? ???? ?-???????
• 1990-???????? ?????????? ?-???????
• 2000-2002, ????????? ???? GRACE Graph
  Reduction Applied to Cluster Environment
• 2003-???????, ????????? ????Open TS Open
  T-system (???????? ???????????)

13
????????? ?-??????? ? MPI
Sequential
Parallel
14
Open TS ???????? ????????

• ?????????????? ???????????? ?????????????????
  ????????
• ????? ???????? ???? ??????????
• ?????? ??, multicore, SMP, ????????, GRID
• ????????? ???????? ?????????????? ? ????????????
  (???)
• ??????????????? ???????????????? ? ????
  ??????? C
• ????????? ?????? ????????? ? 90-??

15
? ????? ???????? ?????

• tfun ?-???????
• tval ?-?????????? (?-????????)
• tptr ?-?????????
• tout ???????? ???????? (?????? )
• tdrop ????????? ????? ?????????-
  ??????????? (??????? ???????)
• twait ?????? ????? ??????????
• tct ?-????????

16
?-??????

• ?????? ??????? (tfunc) ?? ?????? ????????
  ????????? ??????? ????????????
• ?-?????????
• ????????????? ?? ??????? ??????
• ??????????? ?? ?????? ?????? (C/C/ASM
  ???????????)
• C-??????????? ?????? ??????????
• ????????? ????????, ???????????? ????????????
• ??????? ?????????? ?????? C, Fortran, ?????

17
Open TS ??????????? ??????? ????????????????

• ???????? ??????????
• T ?????????? (??????? ?????? gcc)
• T ? C ?????????
• ??????????? ??? ?????? ??????
• ???????? ??????? ? ??????????? (TGDB, tracing)
• ????????? ?-??????? ? ?????????? ?????????
  ??????? ??????????

18
??????????????? ? ????????????

• ??????????? ?????? (lightweight threads)
  ????????????? ????????????
• ?????? ????????? 1 000 000 ??????? ?? ?????????
• ??????????? ??????????????
• ???? A ????????? ????????? ????????
• ?????????? ??????????? ?????? (Active messages
  Signals), ????? ????????????? ???????? ?????? ?
  ???? A
• ?????????? ????? ?? ???????????? (??? ?? ???? ?
  ????? ???????????) ? ??????? (context switch) ??
  ?????? ??????? ????
• ?????? ???????? ???????? (Latency Hiding) ?
  ?????????????

19
DMPI

• Dynamic MPI
• ?????????????? ?????? ?????????? MPI
• ???????????? ???????? ? ??????????(dynamic
  loading and linking)
• ???? ?????????? MPI ??????????
• LAM
• MPICH
• SCALI MPI
• MVAPICH
• IMPI
• MPICH-G2
• PACX-MPI
• ??? PVM ? TCP/IP ????? ???? ???????????? DMPI ?
  ???????? ?????????? ?????? MPI

??? ??????????????-?????????????? ?????????
(GRID)
20
2005 ?????????Open TS vs MPI
21
???????? Microsoft

• 2004 Microsoft ?????? ????????????? HPC
• 2005 ???????????? ????????? Microsoft ? ???????
  HPC
• ????? 2005 ????-?????? Microsoft MPI ? Microsoft
  Windows Computing Cluster Server
• ????? 2004 ?????????? Microsoft ? OpenTS
• 2005 ???????? ????????? Open TS ? MPI
• 2006 ???????? ??????? Open TS ?? Microsoft
  Windows Computing Cluster Server

22
??????????

• ?????????? ? ?????? ????????????
• ??????????? ???????????? MPI-????????-?? (???
  ?????? ? ?-????????)
• PovRay Persistence of Vision Ray-tracer,
  ?-????? C/MPI-patch
• ALCMD/MP_lite ???????????? ???????? (Ames
  Lab)???????-????????? MP_Lite/MPI

23
???????? ??????

• ????????? ?? ?-??????? ?????, ?????? ?????????
  ?????????? ????????
• ?????????? ?? ???? ?????????????
• ????????????? ?? ????? ??????????? ? ?????
  ?????????? ???? (less space for bugs)
• ? ??? ???? ?? ?? ?????? ????????
  ??????????????????? (?? 30 ?? MPI)?

24
T-PovRay vs MPI PovRay ????????? ????
????????? ????? ????????? ????
MPI ?????? ???PovRay 3.10g 1,500 ?????
MPI ???????? ??? PovRay 3.50c 3,000 ?????
T ?????? (??? ???? ?????? 3.10g ? 3.50c) 200 ?????
25
T-PovRay vs MPI PovRay ??????????????????
16 dual Athlon 1800, AMD Athlon MP 1800 RAM
1GB, FastEthernet, LAM 7.0.6
26
T-PovRay vs MPI PovRay ??????????????????
2CPUs AMD Opteron 248 2.2 GHz RAM 4GB, GigE, LAM
7.1.1
27
ALCMD/MPI vs ALCMD/OpenTS

• ?????????? MP_Lite (???????) ?????????? ?? T
• Fortran-??? ??????? ??????????

28
???????? ??????

• ????????? ?? ?-??????? ?????, ?????? ?????????
  ?????????? (???????? MP_Light) ??? ??????????
  ?????????? ?????????? ???????
• ?????????? ?? ???? ?????????????
• ????????????? ?? ????? ??????????? ? ?????
  ?????????? ???? (less space for bugs)
• ? ??? ???? ?? ?? ?????? ????????
  ??????????????????? (?? 30 ?? MPI)?

29
ALCMD/MPI vs ALCMD/OpenTS ????????? ????
????????? ????? ????????? ????
MP_Lite/MPI 3,500 ?????
MP_Lite/OpenTS 500 ?????
30
ALCMD/MPI vs ALCMD/OpenTS ??????????????????
2CPUs AMD Opteron 248 2.2 GHz RAM 4GB, GigE, LAM
7.1.1, Lennard-Jones MD, 512000 atoms
31
ALCMD/MPI vs ALCMD/OpenTS performance
2CPUs AMD Opteron 248 2.2 GHz RAM 4GB,
InfiniBand,MVAMPICH 0.9.4, Lennard-Jones
MD,512000 atoms
32
??????????, ?????????? ?? Open TS
33
?-??????????

• MultiGen ?????? ????????????? ??????????
  ???????
• ????????????? ???????????? ????? (???)
• ????????????? ??????
• ????????????? ??????
• ????????????
• Query engine for XML
• ??-?????????? (3 ?????)
• ? ??.

34
MultiGen??????????? ??????????????? ???????????
?0
Level 0
Level 1
?11
?12
Level 2
?22
?21
Multi-conformation model
35
MultiGen Speedup
National Cancer Institute USA Reg.No.
NCI-609067 (AIDS drug lead)
National Cancer Institute USA Reg.No.
NCI-641295 (AIDS drug lead)
TOSLAB company (Russia-Belgium) Reg.No. TOSLAB
A2-0261 (antiphlogistic drug lead)
Substance Atom number Rotations number Conformers Exectution time (min.?) Exectution time (min.?) Exectution time (min.?)
Substance Atom number Rotations number Conformers 1 node 4 nodes 16 nodes
NCI-609067 28 4 13 933 321 122
TOSLAB A2-0261 82 18 49 11527 3923 1609
NCI-641295 126 25 74 26619 9557 3448
36
??????????????? ???????? ??? ??. ?.?.??????????
37
??????????????? ???????? ??? ??. ?.?.??????????
38
?????????????? ??????????? ?? ?????? ???????? ???
(?????)
39
????????????? ????????????? ?????????????? ???
40
????????????? ??????????? (Landsat)

• ?????????????? Web-??????

41
?????????? ?????

• ????? ???????? ????????? ???????????? CPU
• (??????????????-) ?????????????? ???????
• ???????????
• ?????? ???????????????? ?????????? DMPI
• ?????????? ? Web-????????
• ????, ?????????? ? ??????? (fault-tolerance)
• ??????? ?? ?????? ??????????? (IBM Blue Gene),
  ??????????? ??? ????????? ??????????? CPU
• ??????? ??????????, ??????? ? ????????????
  ?????????? ???????? ??????
• sum fold
• minimum fold min
• prod fold

42
?? ??????? ???????

• ?????? ?-???????? T-Refal, T-Fortan
• ?????????? (?????????????) ???????
• ?????????????? ???????????? ????? call-?????? ?
  fork-?????? ??? ?????? ?-???????
• ??????????? ????? (Checkpointing)
• Heartbeat-????????
• ??????? (Flavours) tptr-?????????? normal,
  glue and magnetic ???????, ?????? ?
  ??????????? ???????? ??????

43
?????????????

• ????????????????? ????????? ???? ????????
  ???????????
• ????????? ???
• ????? ?????????????????????? ??????????????
  ??????? ? ?????? ?????????? ???????????
  ?????????????? ?????????
• ????????? ???????? ?????? ??? ?????????
  ?????????????? ??????? ?????????????-?????????????
  ? ???? ?? GRID ???????????
• ???? ????? 05-07-08005-???_?
• Microsoft ????????? Open TS vs MPI case study
  ? Porting Open TS _at_ Microsoft Windows Computing
  Cluster Server

44
??????? ?? ????????...

• ????? ???????? ?? ???????

45
?-??????? ??????????? ????
46
?-??????? ??????????? ????
47
?-??????? ??????????? ????
48
?-??????? ??????????? ????
49
?-??????? ??????????? ????
50
?-??????? ??????????? ????
51
?-??????? ??????????? ????
52
?-??????? ??????????? ????