HP XC System 3.x Software manuals

Hp XC System 3.x Software User Manual (131 pages)

Brand: Hp | Category: Software | Size: 1.35 MB |

English

Table of contents

HP Part Number: 5992-4009

1

Published: March 2008

1

Edition: 1

1

Table of Contents

3

4 Table of Contents

4

Table of Contents 5

5

6 Table of Contents

6

Table of Contents 7

7

8 Table of Contents

8

List of Figures

9

List of Tables

11

About This Document

13

Related Information

14

Publishing History

14

HP Encourages Your Comments

15

1 Introduction

17

18 Introduction

18

22 Introduction

22

2 Installing HPCPI and Xtools

25

Installing the Software

26

Installing the Software 27

27

Installing the Software 29

29

Verifying the Installation

30

Removing the Software

30

3 Getting Started with HPCPI

31

32 Getting Started with HPCPI

32

4 Using HPCPI

35

Starting the hpcpid Daemon

36

Selecting Events to Monitor

37

Commonly Used Event Sets

38

Event Duty Qualifier

39

Labeling Data

40

42 Using HPCPI

42

Default Input Data

43

Flushing Data: hpcpictl flush

43

HPCPI Header

44

HPCPI Procedure Header

46

48 Using HPCPI

48

50 Using HPCPI

50

HPCPI Utility Options

51

Specifying Events to Display

52

Selecting Data by Label

52

Displaying Raw Values

53

Limiting the hpcpiprof Output

54

Additional Options

54

Using Event Sets

55

Event Intervals

56

Multiple Duty Groups

56

Itanium Instruction Metrics

57

5 Using HPCPI Labels

59

Step 3: Flushing the Data

60

Label Selectors

62

-not Operator

63

-and Operator

63

-or Operator

63

-equiv Operator

63

Operator Syntax

63

Multiple Labels

64

Reusing Labels

64

Comparing Epochs and Labels

64

Label Examples

65

Kernel Idle Data: -pid 0

66

Creating Labels in Programs

67

Fortran Code Example

68

Overview

69

% setenv HPCPIDB ~/hpcpidb

70

% mkdir -p $HPCPIDB

70

% hpcpid -create-epoch

70

Submitting the Job

71

Collecting Data on One Node

73

7 Using Xtools

75

Xtools Overview

76

Using xclus and xcxclus

76

Using xclus and xcxclus 77

77

Starting xclus and xcxclus

78

Starting xclus and xcxclus 79

79

80 Using Xtools

80

82 Using Xtools

82

84 Using Xtools

84

86 Using Xtools

86

Recording Data

89

Replaying Data

89

Plotting Data

89

90 Using Xtools

90

Viewing Grouped Nodes

92

Using xperf and xcxperf

94

Starting xperf and xcxperf

94

Instructions

96

Sum I/O B/W

97

98 Using Xtools

98

HTn (HyperTransport Links)

100

102 Using Xtools

102

106 Using Xtools

106

108 Using Xtools

108

% xclus -generic

109

% xcxclus -enhanced -apmond

110

Xtools Daemons

111

A Product Specifications

113

114 Product Specifications

114

HPCPI Product Limitations

115

Calls to exec()

116

Unknown Locations

116

Mandated Duty Groups

116

Active Fraction Changes

116

B HPCPI Quick Reference

117

Viewing HPCPI Data

118

C Xtools Quick Reference

119

Starting xperf or xcxperf

121

Glossary

123

124 Glossary

124

126 Index

126

128 Index

128

130 Index

130

Hp XC System 3.x Software User Manual (118 pages)

Brand: Hp | Category: Software | Size: 1.39 MB |

English

Table of contents

HP XC System Software

1

User's Guide

1

Table of Contents

3

5 Submitting Jobs

4

6 Debugging Applications

5

7 Tuning Applications

5

8 Using SLURM

5

9 Using LSF

5

10 Advanced Topics

6

List of Figures

7

List of Tables

9

List of Examples

11

About This Document

13

HP XC Information

14

For More Information

15

Supplementary Information

15

Related Information

16

Related Linux Web Sites

17

Related MPI Web Sites

17

Related Compiler Web Sites

17

Additional Publications

17

Typographic Conventions

18

HP Encourages Your Comments

18

System Architecture

19

Node Specialization

20

Storage and I/O

20

File System

21

System Interconnect Network

22

User Environment

23

Run-Time Environment

24

Standard LSF

25

2 Using the System

27

Introduction

28

30 Using the System

30

Overview of Modules

31

Supplied Modulefiles

32

Viewing Available Modulefiles

33

Viewing Loaded Modulefiles

33

Loading a Modulefile

33

Unloading a Modulefile

34

Modulefile Conflicts

34

Creating a Modulefile

35

4 Developing Applications

37

Interrupting a Job

38

Setting Debugging Options

39

Modulefiles

40

Standard

41

42 Developing Applications

42

Developing Libraries

43

44 Developing Applications

44

46 Submitting Jobs

46

48 Submitting Jobs

48

Compiling applications

49

HP-MPI User's Guide

49

50 Submitting Jobs

50

Running Preexecution Programs

51

52 Submitting Jobs

52

SSH and TotalView

54

Setting Up TotalView

54

Using TotalView with SLURM

54

Using TotalView with LSF-HPC

55

Setting TotalView Preferences

55

Debugging an Application

55

TotalView process window

56

Exiting TotalView

57

60 Tuning Applications

60

The srun Roles and Modes

64

Job Accounting

65

Fault Tolerance

66

Security

66

Overview of LSF-HPC

68

Using LSF-HPC 69

69

Job Terminology

70

Using LSF-HPC 71

71

Notes on LSF-HPC

72

Using LSF-HPC 73

73

Job Startup and Job Control

74

Preemption

75

Getting Host Load Information

76

Submitting Jobs

77

LSF-SLURM External Scheduler

78

Using LSF-HPC 79

79

80 Using LSF

80

Examining the Status of a Job

81

82 Using LSF

82

Using LSF-HPC 83

83

84 Using LSF

84

Using LSF-HPC 85

85

86 Using LSF

86

Using LSF-HPC 87

87

88 Using LSF

88

Using LSF-HPC 89

89

92 Advanced Topics

92

94 Advanced Topics

94

Example Procedure 1

95

Example Procedure 2

95

Local Disks on Compute Nodes

96

Communication Between Nodes

97

Appendix A Examples

99

Submit the job:

100

View the job:

100

102 Examples

102

Show the environment:

103

Display the script:

103

Run the job:

103

Show the job allocation:

104

Show the SLURM job ID:

104

Exit the pseudo-terminal:

105

View the interactive jobs:

105

View the finished jobs:

105

View the node state:

105

View the running job:

106

View the finished job:

106

Glossary

109

110 Glossary

110

112 Glossary

112

116 Index

116

118 Index

118

Hp XC System 3.x Software User Manual (145 pages)

Brand: Hp | Category: Software | Size: 1.55 MB |

English

Table of contents

HP XC System Software

1

User's Guide

1

Table of Contents

3

4 Table of Contents

4

Table of Contents 5

5

6 Table of Contents

6

Table of Contents 7

7

List of Figures

9

List of Tables

11

List of Examples

13

About This Document

15

Related Information

17

Linux Web Sites

19

Manpages

20

HP Encourages Your Comments

21

1.1 System Architecture

23

1.1.4 Node Specialization

24

1.1.5 Storage and I/O

25

1.1.6 File System

25

File System Layout

26

1.3 User Environment

27

1.3.3 Commands

28

1.4.1 Parallel Applications

28

1.5 Run-Time Environment

29

1.5.3 Standard LSF

30

1.5.5 HP-MPI

30

2 Using the System

33

2.2.1 Introduction

34

2.2.5 Launching Jobs

35

2.2.8 Resuming Suspended Jobs

35

36 Using the System

36

3.1 Overview of Modules

37

3.2 Supplied Modulefiles

38

3.6 Loading a Modulefile

40

3.7 Unloading a Modulefile

41

3.9 Modulefile Conflicts

41

3.10 Creating a Modulefile

42

4 Developing Applications

43

4.2 Compilers

44

4.4 Interrupting a Job

45

4.5 Setting Debugging Options

45

46 Developing Applications

46

4.7.1.1 Modulefiles

47

4.7.1.2 HP-MPI

47

4.7.1.3 OpenMP

47

4.7.1.4 Pthreads

47

4.7.1.5 Quadrics SHMEM

47

48 Developing Applications

48

$ module load mpi

49

4.8 Developing Libraries

50

4.8 Developing Libraries 51

51

52 Developing Applications

52

5 Submitting Jobs

53

54 Submitting Jobs

54

5.3 Submitting a Parallel Job

55

56 Submitting Jobs

56

60 Submitting Jobs

60

62 Submitting Jobs

62

64 Submitting Jobs

64

-R "type=SLINUX64"

65

6 Debugging Applications

67

6.2.1.1 SSH and TotalView

68

6.2.1.2 Setting Up TotalView

68

70 Debugging Applications

70

6.2.1.8 Exiting TotalView

71

7 Monitoring Node Activity

73

74 Monitoring Node Activity

74

$ xcxperf -node n6

78

$ xcxperf -o test

78

$ xcxperf test

78

80 Monitoring Node Activity

80

82 Monitoring Node Activity

82

8 Tuning Applications

85

86 Tuning Applications

86

8.2.1 Installation Kit

87

Running a Program

88

9 Using SLURM

91

9.3.1.1 The srun Roles

92

9.3.1.2 The srun Modes

92

9.7 Job Accounting

94

9.8 Fault Tolerance

94

9.9 Security

94

10 Using LSF-HPC

95

96 Using LSF-HPC

96

10.4 Job Terminology

99

100 Using LSF-HPC

100

10.6 Submitting Jobs

101

DescriptionExit Code

102

Success0

102

102 Using LSF-HPC

102

SLURM_JOBID=53

103

SLURM_NPROCS=4

103

$ sinfo -p lsf -lNe

106

106 Using LSF-HPC

106

108 Using LSF-HPC

108

$ bjobs 24

109

112 Using LSF-HPC

112

11 Advanced Topics

117

118 Advanced Topics

118

120 Advanced Topics

120

11.3.1 Example Procedure 1

121

11.3.2 Example Procedure 2

121

11.3.3 Example Procedure 3

122

11.5.1 Shared File View

123

11.5.2 Private File View

123

% srun -A options

124

% ./wrapper

124

% bsub -I options... wrapper

124

A Examples

125

Submit the job:

126

View the job:

126

128 Examples

128

Exit from the shell:

129

Show the environment:

129

Display the script:

129

Run the job:

130

Show the job allocation:

130

Show the SLURM job ID:

131

Exit the pseudo-terminal:

131

View the interactive jobs:

131

View the finished jobs:

131

View the node state:

132

View the running job:

132

View the finished job:

133

Glossary

135

136 Glossary

136

138 Glossary

138

140 Glossary

140

142 Index

142

144 Index

144

Hp XC System 3.x Software User Manual (133 pages)

Brand: Hp | Category: Software | Size: 1.51 MB |

English

Table of contents

HP XC System Software

1

User's Guide

1

Table of Contents

3

4 Table of Contents

4

Table of Contents 5

5

6 Table of Contents

6

List of Figures

7

List of Examples

11

About This Document

13

14 About This Document

14

5 Related information

15

16 About This Document

16

Linux Web Sites 17

17

6 Manpages

18

7 HP Encourages Your Comments

18

1.1 System Architecture

19

1.1.4 Node Specialization

20

1.1.5 Storage and I/O

21

1.1.6 File System

21

1.3 User Environment

23

1.5 Run-Time Environment

24

1.5.3 Standard LSF

25

1.5.5 HP-MPI

26

2 Using the System

27

2.2.1 Introduction

28

30 Using the System

30

3.1 Overview of Modules

31

3.2 Supplied Modulefiles

32

3.6 Loading a Modulefile

34

3.7 Unloading a Modulefile

34

3.9 Modulefile Conflicts

35

3.10 Creating a Modulefile

35

4 Developing Applications

37

4.4 Interrupting a Job

38

4.5 Setting Debugging Options

39

4.7.1.1 Modulefiles

40

4.7.1.2 HP-MPI

40

4.7.1.3 OpenMP

40

4.7.1.4 Pthreads

40

42 Developing Applications

42

4.8 Developing Libraries

43

44 Developing Applications

44

4.8 Developing Libraries 45

45

5 Submitting Jobs

47

48 Submitting Jobs

48

5.3 Submitting a Parallel Job

49

50 Submitting Jobs

50

52 Submitting Jobs

52

54 Submitting Jobs

54

56 Submitting Jobs

56

6 Debugging Applications

57

6.2.1.1 SSH and TotalView

58

6.2.1.2 Setting Up TotalView

58

60 Debugging Applications

60

6.2.1.8 Exiting TotalView

61

7 Monitoring Node Activity

63

64 Monitoring Node Activity

64

66 Monitoring Node Activity

66

68 Monitoring Node Activity

68

70 Monitoring Node Activity

70

8 Tuning Applications

73

74 Tuning Applications

74

8.2.1 Installation Kit

75

Running a Program

76

9 Using SLURM

79

9.3.1.1 The srun Roles

80

9.3.1.2 The srun Modes

80

9.7 Job Accounting

81

9.8 Fault Tolerance

82

9.9 Security

82

10 Using LSF-HPC

83

84 Using LSF-HPC

84

10.4 Job Terminology

86

10.5.1 Useful Commands

87

10.5.3 Preemption

87

10.6 Submitting Jobs

88

SLURM_JOBID=53

89

SLURM_NPROCS=4

89

90 Using LSF-HPC

90

92 Using LSF-HPC

92

94 Using LSF-HPC

94

96 Using LSF-HPC

96

98 Using LSF-HPC

98

100 Using LSF-HPC

100

102 Using LSF-HPC

102

11 Advanced Topics

103

104 Advanced Topics

104

106 Advanced Topics

106

11.3.1 Example Procedure 1

107

11.3.2 Example Procedure 2

108

11.3.3 Example Procedure 3

108

11.5.1 Shared File View

109

11.5.2 Private File View

109

110 Advanced Topics

110

A Examples

113

Submit the job:

114

View the job:

115

116 Examples

116

Exit from the shell:

117

Show the environment:

117

Display the script:

118

Run the job:

118

Submit the job: 119

119

View the finished jobs:

120

View the node state:

120

View the running job:

121

View the finished job:

121

122 Examples

122

Glossary

123

124 Glossary

124

126 Glossary

126

130 Index

130

132 Index

132

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