Analyzing LHC experiment software in terms of obsolete memory - - PowerPoint PPT Presentation

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Analyzing LHC experiment software in terms of obsolete memory - - PowerPoint PPT Presentation

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Analyzing LHC experiment software in terms of obsolete memory utilization with a focus on ROOT objects Nathalie Rauschmayr, Sami Kama IT-SDC-OL, Southern Methodist University 18. September 2015 1/21 ROOT Workshop 2015 Nathalie Rauschmayr,

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SLIDE 1

Analyzing LHC experiment software in terms of

  • bsolete memory utilization with a focus on

ROOT objects

Nathalie Rauschmayr, Sami Kama

IT-SDC-OL, Southern Methodist University

  • 18. September 2015

1/21 ROOT Workshop 2015 Nathalie Rauschmayr, Sami Kama

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Introduction

  • Many LHC experiments are facing

serious memory footprint problems

2/21 ROOT Workshop 2015 Nathalie Rauschmayr, Sami Kama

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Introduction

NoLimit 3.5 3 2.5 2 1.5 50 100 150 200 250 Memory Limits Runtime in min

  • Many LHC experiments are facing

serious memory footprint problems

3/21 ROOT Workshop 2015 Nathalie Rauschmayr, Sami Kama

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SLIDE 4

Introduction

NoLimit 3.5 3 2.5 2 1.5 50 100 150 200 250 Memory Limits Runtime in min

  • Many LHC experiments are facing

serious memory footprint problems

  • Which objects are used and

which ones unused (=obsolete)?

3/21 ROOT Workshop 2015 Nathalie Rauschmayr, Sami Kama

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SLIDE 5

Introduction

NoLimit 3.5 3 2.5 2 1.5 50 100 150 200 250 Memory Limits Runtime in min

  • Many LHC experiments are facing

serious memory footprint problems

  • Which objects are used and

which ones unused (=obsolete)?

  • What is the contribution of

ROOT to this memory consumption?

  • Can ROOT help experiments to improve memory footprint/performance?

3/21 ROOT Workshop 2015 Nathalie Rauschmayr, Sami Kama

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SLIDE 6

Introduction

NoLimit 3.5 3 2.5 2 1.5 50 100 150 200 250 Memory Limits Runtime in min

  • Many LHC experiments are facing

serious memory footprint problems

  • Which objects are used and

which ones unused (=obsolete)?

  • What is the contribution of

ROOT to this memory consumption?

  • Can ROOT help experiments to improve memory footprint/performance?

New tool is necessary:

3/21 ROOT Workshop 2015 Nathalie Rauschmayr, Sami Kama

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SLIDE 7

Introduction

NoLimit 3.5 3 2.5 2 1.5 50 100 150 200 250 Memory Limits Runtime in min

  • Many LHC experiments are facing

serious memory footprint problems

  • Which objects are used and

which ones unused (=obsolete)?

  • What is the contribution of

ROOT to this memory consumption?

  • Can ROOT help experiments to improve memory footprint/performance?

New tool is necessary:

  • unused/obsolete memory != memory leak
  • Allocated objects can be unused and then freed by Python, ROOT etc.

3/21 ROOT Workshop 2015 Nathalie Rauschmayr, Sami Kama

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FOM Tools (Find Obsolete Memory)

LD PRELOAD=malloc-hook.so my process

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FOM Tools (Find Obsolete Memory)

LD PRELOAD=malloc-hook.so my process /cgroup/memory /cgroup/freezer

4/21 ROOT Workshop 2015 Nathalie Rauschmayr, Sami Kama

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FOM Tools (Find Obsolete Memory)

LD PRELOAD=malloc-hook.so my process /cgroup/memory /cgroup/freezer

Freeze Unfreeze Iterate over heap and read pagemap

4/21 ROOT Workshop 2015 Nathalie Rauschmayr, Sami Kama

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FOM Tools (Find Obsolete Memory)

LD PRELOAD=malloc-hook.so my process /cgroup/memory /cgroup/freezer

Freeze Unfreeze Iterate over heap and read pagemap

Bit 63: Page in RAM or not Bit 62: Page swapped or not 63 62 Never loaded Swapped 1 In RAM 1

4/21 ROOT Workshop 2015 Nathalie Rauschmayr, Sami Kama

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FOM Tools (Find Obsolete Memory)

LD PRELOAD=malloc-hook.so my process /cgroup/memory /cgroup/freezer

Freeze Unfreeze Iterate over heap and read pagemap

Bit 63: Page in RAM or not Bit 62: Page swapped or not 63 62 Never loaded Swapped 1 In RAM 1 Map objects to swapped pages Virtual adresses of objects plus backtraces

4/21 ROOT Workshop 2015 Nathalie Rauschmayr, Sami Kama

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FOM Tools (Find Obsolete Memory)

  • How many pages in RAM, Swap or never loaded
  • Memory utilization patterns
  • Memory hotspots
  • Allocation profiles
  • Which fraction of large datasets remain in RAM/Swap
  • etc....

https://twiki.cern.ch/twiki/bin/view/ITSDC/FomTool

5/21 ROOT Workshop 2015 Nathalie Rauschmayr, Sami Kama

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FOM Tools (Find Obsolete Memory)

  • How many pages in RAM, Swap or never loaded
  • Memory utilization patterns
  • Memory hotspots
  • Allocation profiles
  • Which fraction of large datasets remain in RAM/Swap
  • etc....

https://twiki.cern.ch/twiki/bin/view/ITSDC/FomTool

5/21 ROOT Workshop 2015 Nathalie Rauschmayr, Sami Kama

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Benchmark tests with a focus on ROOT objects

Sum of all ROOT objects Long lived objects Short lived objects How many in Swap/RAM Memory utilization patterns Allocation statistics

6/21 ROOT Workshop 2015 Nathalie Rauschmayr, Sami Kama

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Benchmark tests with a focus on ROOT objects

Time: 584984.636 Allocation Type: 1 PageBegin: 0x145b000 PageEnd: 0x145bfff Address: 0x145b020 Size: 385 : malloc+0x6d in /afs/cern.ch/sw/lcg/contrib/gcc/4.9.1/x86_64-slc6/include/c++/4.9.1/bits/atomic_base.h:308 18 _Znwm+0x1d in ../../../../gcc-4.8.4/libstdc++-v3/libsupc++/new_op.cc:52 425 _ZNSs4_Rep9_S_createEmmRKSaIcE+0x59 in ./libstdc++-v3/include/bits/basic_string.tcc:609 551 _ZNSs4_Rep8_M_cloneERKSaIcEm+0x1b in ./libstdc++-v3/include/bits/basic_string.tcc:630 552 _ZNSs7reserveEm+0x34 in ./libstdc++-v3/include/bits/basic_string.tcc:511 653 _ZNSs6appendEPKcm+0x4f in ./libstdc++-v3/include/bits/basic_string.tcc:308 654 _ZL11DynamicPathPKcb+0x3e5 in ./ROOT/6.02.12/core/unix/src/TUnixSystem.cxx:4520 634 _ZN11TUnixSystem14GetDynamicPathEv+0x1b in ./ROOT/6.02.12/core/unix/src/TUnixSystem.cxx:4560 635 _ZN11TUnixSystem18FindDynamicLibraryER7TStringb+0xb4 in ./ROOT/6.02.12/core/unix/src/TUnixSystem.cxx:4586 636 _ZN7TSystem15DynamicPathNameEPKcb+0x4a in ./ROOT/6.02.12/core/base/src/TSystem.cxx:1906 637 _ZN5TROOT15InitInterpreterEv+0xdf in, ./ROOT/6.02.12/core/base/src/TROOT.cxx:1683 638 _ZN4ROOT8GetROOT2Ev+0x2b in ./ROOT/6.02.12/core/base/src/TROOT.cxx:341 82 _ZN4ROOT7GetROOTEv+0xd in ./ROOT/6.02.12/core/base/src/TROOT.cxx:349 639 _ZN12TApplicationC1EPKcPiPPcPvi+0x2c3 in ./ROOT/6.02.12/core/base/src/TApplication.cxx:133 640 _ZN12TApplication17CreateApplicationEv+0x8b in ./ROOT/6.02.12/core/base/src/TApplication.cxx:1253 641 _ZN4xAOD4InitEPKcPiPPc+0xf5 in ??:0 642 _ZN4xAOD4InitEPKc+0xd in ??:0 643 main+0xd2 in ??:0 644 __libc_start_main+0xfd in ??:0 645 _start+0x29 in ??:0

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SLIDE 17

Benchmark tests with a focus on ROOT objects

Time: 584984.636 Allocation Type: 1 PageBegin: 0x145b000 PageEnd: 0x145bfff Address: 0x145b020 Size: 385 : malloc+0x6d in /afs/cern.ch/sw/lcg/contrib/gcc/4.9.1/x86_64-slc6/include/c++/4.9.1/bits/atomic_base.h:308 18 _Znwm+0x1d in ../../../../gcc-4.8.4/libstdc++-v3/libsupc++/new_op.cc:52 425 _ZNSs4_Rep9_S_createEmmRKSaIcE+0x59 in ./libstdc++-v3/include/bits/basic_string.tcc:609 551 _ZNSs4_Rep8_M_cloneERKSaIcEm+0x1b in ./libstdc++-v3/include/bits/basic_string.tcc:630 552 _ZNSs7reserveEm+0x34 in ./libstdc++-v3/include/bits/basic_string.tcc:511 653 _ZNSs6appendEPKcm+0x4f in ./libstdc++-v3/include/bits/basic_string.tcc:308 654 _ZL11DynamicPathPKcb+0x3e5 in ./ROOT/6.02.12/core/unix/src/TUnixSystem.cxx:4520 634 _ZN11TUnixSystem14GetDynamicPathEv+0x1b in ./ROOT/6.02.12/core/unix/src/TUnixSystem.cxx:4560 635 _ZN11TUnixSystem18FindDynamicLibraryER7TStringb+0xb4 in ./ROOT/6.02.12/core/unix/src/TUnixSystem.cxx:4586 636 _ZN7TSystem15DynamicPathNameEPKcb+0x4a in ./ROOT/6.02.12/core/base/src/TSystem.cxx:1906 637 _ZN5TROOT15InitInterpreterEv+0xdf in, ./ROOT/6.02.12/core/base/src/TROOT.cxx:1683 638 _ZN4ROOT8GetROOT2Ev+0x2b in ./ROOT/6.02.12/core/base/src/TROOT.cxx:341 82 _ZN4ROOT7GetROOTEv+0xd in ./ROOT/6.02.12/core/base/src/TROOT.cxx:349 639 _ZN12TApplicationC1EPKcPiPPcPvi+0x2c3 in ./ROOT/6.02.12/core/base/src/TApplication.cxx:133 640 _ZN12TApplication17CreateApplicationEv+0x8b in ./ROOT/6.02.12/core/base/src/TApplication.cxx:1253 641 _ZN4xAOD4InitEPKcPiPPc+0xf5 in ??:0 642 _ZN4xAOD4InitEPKc+0xd in ??:0 643 main+0xd2 in ??:0 644 __libc_start_main+0xfd in ??:0 645 _start+0x29 in ??:0

6/21 ROOT Workshop 2015 Nathalie Rauschmayr, Sami Kama

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SLIDE 18

Benchmark tests with a focus on ROOT objects

Time: 584984.636 Allocation Type: 1 PageBegin: 0x145b000 PageEnd: 0x145bfff Address: 0x145b020 Size: 385 : malloc+0x6d in /afs/cern.ch/sw/lcg/contrib/gcc/4.9.1/x86_64-slc6/include/c++/4.9.1/bits/atomic_base.h:308 18 _Znwm+0x1d in ../../../../gcc-4.8.4/libstdc++-v3/libsupc++/new_op.cc:52 425 _ZNSs4_Rep9_S_createEmmRKSaIcE+0x59 in ./libstdc++-v3/include/bits/basic_string.tcc:609 551 _ZNSs4_Rep8_M_cloneERKSaIcEm+0x1b in ./libstdc++-v3/include/bits/basic_string.tcc:630 552 _ZNSs7reserveEm+0x34 in ./libstdc++-v3/include/bits/basic_string.tcc:511 653 _ZNSs6appendEPKcm+0x4f in ./libstdc++-v3/include/bits/basic_string.tcc:308 654 _ZL11DynamicPathPKcb+0x3e5 in ./ROOT/6.02.12/core/unix/src/TUnixSystem.cxx:4520 634 _ZN11TUnixSystem14GetDynamicPathEv+0x1b in ./ROOT/6.02.12/core/unix/src/TUnixSystem.cxx:4560 635 _ZN11TUnixSystem18FindDynamicLibraryER7TStringb+0xb4 in ./ROOT/6.02.12/core/unix/src/TUnixSystem.cxx:4586 636 _ZN7TSystem15DynamicPathNameEPKcb+0x4a in ./ROOT/6.02.12/core/base/src/TSystem.cxx:1906 637 _ZN5TROOT15InitInterpreterEv+0xdf in, ./ROOT/6.02.12/core/base/src/TROOT.cxx:1683 638 _ZN4ROOT8GetROOT2Ev+0x2b in ./ROOT/6.02.12/core/base/src/TROOT.cxx:341 82 _ZN4ROOT7GetROOTEv+0xd in ./ROOT/6.02.12/core/base/src/TROOT.cxx:349 639 _ZN12TApplicationC1EPKcPiPPcPvi+0x2c3 in ./ROOT/6.02.12/core/base/src/TApplication.cxx:133 640 _ZN12TApplication17CreateApplicationEv+0x8b in ./ROOT/6.02.12/core/base/src/TApplication.cxx:1253 641 _ZN4xAOD4InitEPKcPiPPc+0xf5 in ??:0 642 _ZN4xAOD4InitEPKc+0xd in ??:0 643 main+0xd2 in ??:0 644 __libc_start_main+0xfd in ??:0 645 _start+0x29 in ??:0

Initiator Terminator

5/21 ROOT Workshop 2015 Nathalie Rauschmayr, Sami Kama

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Analysis Job

  • Vmem: 1 GB, Rss: 870 MB, Heap Vmem: 532 MB
  • Long lived ROOT objects:
  • ≈ 260 MB (≈ 48% of the heap)
  • Most of the time in Swap: ≈ 22k pages

(33% of long lived ROOT objects)

  • Always in Ram: ≈ 12k pages

(18% of long lived ROOT objects)

6/21 ROOT Workshop 2015 Nathalie Rauschmayr, Sami Kama

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Analysis Job

  • Vmem: 1 GB, Rss: 870 MB, Heap Vmem: 532 MB
  • Long lived ROOT objects:
  • ≈ 260 MB (≈ 48% of the heap)
  • Most of the time in Swap: ≈ 22k pages

(33% of long lived ROOT objects)

  • Always in Ram: ≈ 12k pages

(18% of long lived ROOT objects)

1 100 200 300 400 10 0 10 1 10 2 10 3

Number of continuous pages in Swap Number of Occurrences

7/21 ROOT Workshop 2015 Nathalie Rauschmayr, Sami Kama

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Analysis Job

Memory Utilization Patterns:

Red pixel: Page is in Swap and contains a ROOT object Green pixel: Page is in RAM and contains a ROOT object Gray pixel: Page was never loaded into RAM and contains a ROOT object

8/21 ROOT Workshop 2015 Nathalie Rauschmayr, Sami Kama

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Analysis Job

Memory Utilization Patterns:

One Allocation of 440 kB

7/21 ROOT Workshop 2015 Nathalie Rauschmayr, Sami Kama

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SLIDE 23

Analysis Job

Memory Utilization Patterns:

One Allocation of 440 kB

  • Read TTree from file (progressively)
  • ROOT creates TBuffer
  • In this case: size of allocations above MMAP THRESHOLD
  • malloc will use anonymous mapping (page is not in RAM until process tries

to access it for the first time)

  • Efficiency ratio <= 50% (What is allocated and actually needed for reading)

7/21 ROOT Workshop 2015 Nathalie Rauschmayr, Sami Kama

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Analysis Job

Figure: Percentage of allocations (size) involving ROOT libraries (excluding TObject Allocator)

8/21 ROOT Workshop 2015 Nathalie Rauschmayr, Sami Kama

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Analysis Job

Figure: Percentage of allocations (size) initiated by different function calls and terminating in libCling

3316: libCore.so _ZN6TClass8GetClassEPKcbb+0x6e3 in ./ROOT/6.02.12/core/meta/src/TClass.cxx:2881 4058: libRIO.so _ZN5TFile4OpenEPKcS1_S1_ii+0xcc0 in ./ROOT/6.02.12/io/io/src/TFile.cxx:3977 6358: libCore.so _ZN11TMethodCall17InitWithPrototypeEP6TClassPKcS3_bN4ROOT18EFunctionMatchModeE+0xbb in ./ROOT/6.02.12/core/meta/src/TMethodCall.cxx:344 1420: libCling.so _ZNK5clang15DeclarationName11getAsStringEv+0x69

9/21 ROOT Workshop 2015 Nathalie Rauschmayr, Sami Kama

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Analysis Job

Figure: Percentage of allocations (size) initiated by different function calls and terminating in libCore

8958: libTree.so _ZN14TBranchElement8GetEntryExi+0x222 in ./ROOT/6.02.12/tree/tree/src/TBranchElement.cxx:2310 8020: libRIO.so _ZN14TDirectoryFile3GetEPKc+0xf9 in ./ROOT/6.02.12/io/io/src/TDirectoryFile.cxx:866 7900: libHist.so _ZNK3TH15CloneEPKc+0x96 in ./ROOT/6.02.12/hist/hist/src/TH1.cxx:2568 3086: libCore.so R__unzip+0x2f5 in ./ROOT/6.02.12/core/zip/src/ZInflate.c:1198 2938: libCore.so _ZN6TExMapC2Ei+0xb3 in ./ROOT/6.02.12/core/cont/src/TExMap.cxx:46

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SLIDE 27

Analysis Job

Figure: Percentage of allocations (size) initiated by different function calls and terminating in libRIO

8953: libTree.so _ZN14TBranchElement12SetMakeClassEb+0xb3 in ./ROOT/6.02.12/tree/tree/src/TBranchElement.cxx:4987 8957: libTree.so _ZN14TBranchElement12SetMakeClassEb+0xbf in ./ROOT/6.02.12/tree/tree/src/TBranchElement.cxx:4989 3362: libRIO.so _ZN9__gnu_cxx13new_allocatorIN20TStreamerInfoActions17TConfiguredActionEE8allocateEmPKv+0x40 in ./gcc/4.8.4/x86_64-slc6/include/c++/4.8.4/ext/new_allocator.h:105

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SLIDE 28

ESD to AOD

  • Vmem: 8.2 GB, Rss: 5.4 GB, Heap Vmem: 6.35
  • Long lived ROOT objects (> 4kB):
  • ≈ 1.2 GB ≈ 19% of the heap
  • Most of the time in Swap: ≈ 93k pages

( 27% of long lived ROOT objects)

  • Always in Ram: ≈ 52k pages

( 15% of long lived ROOT objects)

12/21 ROOT Workshop 2015 Nathalie Rauschmayr, Sami Kama

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SLIDE 29

ESD to AOD

  • Vmem: 8.2 GB, Rss: 5.4 GB, Heap Vmem: 6.35
  • Long lived ROOT objects (> 4kB):
  • ≈ 1.2 GB ≈ 19% of the heap
  • Most of the time in Swap: ≈ 93k pages

( 27% of long lived ROOT objects)

  • Always in Ram: ≈ 52k pages

( 15% of long lived ROOT objects)

1 150 300 450 600 750 10 0 10 1 10 2 10 3 10 4

Number of continuous pages in Swap Number of Occurrences

12/21 ROOT Workshop 2015 Nathalie Rauschmayr, Sami Kama

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SLIDE 30

ESD to AOD

Memory Utilization Patterns:

Red pixel: Page is in Swap and contains a ROOT object Green pixel: Page is in RAM and contains a ROOT object Gray pixel: Page was never loaded into RAM and contains a ROOT object Black pixel: Page does not contain a ROOT object

13/21 ROOT Workshop 2015 Nathalie Rauschmayr, Sami Kama

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SLIDE 31

ESD to AOD

Memory Utilization Patterns:

  • Monitoring during event loop
  • It creates: histogram for data and a TTree for metadata (4 branches)
  • Only tiny amounts of the tree are filled
  • 35 KB allocated but only filled with few bytes

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ESD to AOD

Figure: Percentage of allocations (size) involving ROOT libraries (excluding TObject Allocator)

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ESD to AOD

(a) Size (b) Calls

Figure: Percentage of allocations (size/calls) initiated by different function calls and terminating in libCore

62488: libRIO.so _ZN5TFile5WriteEPKcii+0x1e7 in ./ROOT/6.02.08/io/io/src/TFile.cxx:2221 53729: libCore.so R__zipMultipleAlgorithm+0x3c2 in ./ROOT/6.02.08/core/zip/src/Bits.h:678 19255: libTree.so _ZN7TBranch8GetEntryExi+0x289 in ./ROOT/6.02.08/tree/tree/src/TBranch.cxx:1241 3469: libCore.so R__unzip+0x2f5 in ./ROOT/6.02.08/core/zip/src/ZInflate.c:1198

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SLIDE 34

ESD to AOD

(a) Size (b) Calls

Figure: Percentage of allocations (size/calls) initiated by different function calls and terminating in libCore

62488: libRIO.so _ZN5TFile5WriteEPKcii+0x1e7 in ./ROOT/6.02.08/io/io/src/TFile.cxx:2221 53729: libCore.so R__zipMultipleAlgorithm+0x3c2 in ./ROOT/6.02.08/core/zip/src/Bits.h:678 19255: libTree.so _ZN7TBranch8GetEntryExi+0x289 in ./ROOT/6.02.08/tree/tree/src/TBranch.cxx:1241 3469: libCore.so R__unzip+0x2f5 in ./ROOT/6.02.08/core/zip/src/ZInflate.c:1198 Buffers are allocated/freed for each request Size Occurrences Top 1 65 kB 105.000 Top 2 11 kB 74.000 Top 3 65 kB 72.000

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SLIDE 35

ESD to AOD

Figure: Percentage of allocations (size) initiated by different function calls and terminating in libCling

4302: libPyROOT.so _ZN6PyROOT12_GLOBAL__N_17mp_callEPNS_11MethodProxyEP7_objectS4_+0x138 in ./ROOT/6.02.08/bindings/pyroot/src/MethodProxy.cxx:464 4365: libCling.so _ZNK4TClingCallFunc4execEPvS0_+0x116c in ./ROOT/6.02.08/core/meta/src/TClingCallFunc.cxx:1882

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Summary

  • FOM Tools can analyze:
  • Obsolete allocations

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SLIDE 37

Summary

  • FOM Tools can analyze:
  • Obsolete allocations
  • Allocation profiles and correlations

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SLIDE 38

Summary

  • FOM Tools can analyze:
  • Obsolete allocations
  • Allocation profiles and correlations
  • Some unexpected code behaviors:

18/21 ROOT Workshop 2015 Nathalie Rauschmayr, Sami Kama

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SLIDE 39

Summary

  • FOM Tools can analyze:
  • Obsolete allocations
  • Allocation profiles and correlations
  • Some unexpected code behaviors:
  • Zip Buffers
  • Initial buffer sizes

18/21 ROOT Workshop 2015 Nathalie Rauschmayr, Sami Kama

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Backup Slides

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SLIDE 41

AliRoot PbPbBench Reconstruction Step

  • Vmem: 4 GB, Rss: 2.9 GB, Heap Vmem: 2.8 GB
  • Long lived ROOT objects (> 4kB):
  • 70k Objects
  • ≈ 2.1 GB (≈ 75% of the heap)
  • Most of the time in Swap: ≈ 101k pages

( 18% of long lived ROOT objects)

  • Always in Ram: ≈ 135k pages

( 24% of long lived ROOT objects)

20/21 ROOT Workshop 2015 Nathalie Rauschmayr, Sami Kama

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SLIDE 42

AliRoot PbPbBench Reconstruction Step

Long lived ROOT objects which move to Swap and remain there - an example:

  • Read bunch of classes with pointers to each other causing a lot TExMap

entries (3000 pages)

  • During reconstruction: large TMatrix allocations (5800 pages)
  • Many streamers buffers for reading (1000 pages)

21/21 ROOT Workshop 2015 Nathalie Rauschmayr, Sami Kama