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IB0054606-02 A 2-1
2 Step-by-Step Cluster Setup
and MPI Usage Checklists
This section describes how to set up your cluster to run high-performance
Message Passing Interface (MPI) jobs.
Cluster Setup
Perform the following tasks when setting up the cluster. These include BIOS,
adapter, and system settings.
1. Make sure that hardware installation has been completed according to the
instructions in the QLogic InfiniBand
®
Adapter Hardware Installation Guide
and software installation and driver configuration has been completed
according to the instructions in the QLogic InfiniBand
®
Fabric Software
Installation Guide. To minimize management problems, the compute nodes
of the cluster must have very similar hardware configurations and identical
software installations. See “Homogeneous Nodes” on page 3-37 for more
information.
2. Check that the BIOS is set properly according to the instructions in the
QLogic InfiniBand
®
Adapter Hardware Installation Guide.
3. Set up the Distributed
Subnet Administration (SA) to correctly synchronize
your virtual fabrics. See “QLogic Distributed Subnet Administration” on
page 3-12
4. Adjust settings, including setting the appropriate MTU size. See “Adapter
and Other Settings” on page 3-38.
5. Remove unneeded services. See “Remove Unneeded Services” on
page 3-39.
6. Disable powersaving features. See “Host Environment Setup for MPI” on
page 3-40.
7. Check other performance tuning settings. See “Performance Settings and
Management Tips” on page 3-24.
- OFED+ Host Software 1
- Release 1.5.4 1
- Document Revision History 2
- Table of Contents 3
- IB0054606-02 A v 5
- 5 Using Other MPIs 6
- E ULP Troubleshooting 10
- F Write Combining 10
- G Commands and Files 10
- H Recommended Reading 11
- List of Figures 12
- List of Tables 13
- User Guide 14
- Intended Audience 15
- Related Materials 15
- Documentation Conventions 15
- License Agreements 16
- Technical Support 17
- Knowledge Database 18
- 1 Introduction 19
- Overview 20
- Interoperability 21
- 1–Introduction 22
- 1-4 IB0054606-02 A 22
- 2 Step-by-Step Cluster Setup 23
- Using MPI 24
- 3 InfiniBand 25
- Installed Layout 26
- IPoIB Administration 29
- IB Bonding 30
- Red Hat EL5 and EL6 31
- Subnet Manager Configuration 34
- 3–InfiniBand 36
- 3-12 IB0054606-02 A 36
- Default Configuration 37
- 3-14 IB0054606-02 A 38
- DQG[ 39
- [I 39
- [ 40
- IB0054606-02 A 3-17 41
- ScanFrequency 42
- Other Settings 43
- Changing the MTU Size 44
- Managing the ib_qib Driver 45
- Performance Tuning 49
- Default Parameter Settings 50
- AMD CPU Systems 52
- AMD Interlagos CPU Systems 52
- Intel CPU Systems 52
- IB0054606-02 A 3-31 55
- Compute Nodes 59
- Node Type Selection 60
- Test Execution 60
- Homogeneous Nodes 61
- Adapter and Other Settings 62
- Remove Unneeded Services 63
- Configuring for ssh 64
- Process Limitation with ssh 68
- 3-48 IB0054606-02 A 72
- 4 Running MPI on QLogic 73
- Create the mpihosts File 75
- Running Open MPI Applications 75
- To Use Another Compiler 77
- Table 4-3. Intel 78
- Process Allocation 79
- Open MPI 81
- IB0054606-02 A 4-9 81
- 4-10 IB0054606-02 A 82
- PSM_SHAREDCONTEXTS=0 82
- PSM_SHAREDCONTEXTS=NO 82
- Running in Shared Memory Mode 83
- Using Open MPI’s mpirun 85
- Environment for Node Programs 87
- Setting MCA Parameters 89
- Name Description 91
- IB0054606-02 A 4-21 93
- compile line 93
- is used by other 93
- Debugging MPI Programs 94
- The TotalView 95
- 4-24 IB0054606-02 A 96
- MVAPICH2 100
- Running MVAPICH2 Applications 101
- Platform MPI 8 102
- Intel MPI 103
- Installation 104
- 5–Using Other MPIs 108
- 5-12 IB0054606-02 A 108
- 6 SHMEM Description and 109
- SHMEM Programs 111
- Compiling SHMEM Programs 112
- Running SHMEM Programs 113
- Slurm Integration 116
- Sizing Global Shared Memory 117
- 6-10 IB0054606-02 A 118
- Progress Model 119
- Active Progress 120
- Passive Progress 120
- Environment Variables 121
- Implementation Behavior 123
- 6-16 IB0054606-02 A 124
- IB0054606-02 A 6-17 125
- Operation Calls 126
- SHMEM Benchmark Programs 135
- QLogic SHMEM reduce benchmark 138
- Option Description 139
- 6-32 IB0054606-02 A 140
- 7 Virtual Fabric support in 141
- Virtual Fabric Support 142
- Using SL and PKeys 142
- Using Service ID 143
- Adapters 144
- 8 Dispersive Routing 145
- 8–Dispersive Routing 146
- 8-2 IB0054606-02 A 146
- IB0054606-02 A 8-3 147
- 8-4 IB0054606-02 A 148
- IB0054606-02 A 9-1 149
- Required Steps 150
- Installing DHCP 151
- Configuring DHCP 152
- Netbooting Over IB 153
- HTTP Boot Setup 162
- IB0054606-02 A 9-15 163
- /etc/init.d/httpd start 163
- 9-16 IB0054606-02 A 164
- A Benchmark Programs 165
- Between Two Nodes 168
- (osu_mbw_mr) 170
- A–Benchmark Programs 172
- A-8 IB0054606-02 A 172
- IB0054606-02 A A-11 175
- A-12 IB0054606-02 A 176
- B SRP Configuration 177
- QLogic SRP Configuration 178
- Specifying a Session 179
- B–SRP Configuration 180
- B-4 IB0054606-02 A 180
- script as follows: 182
- Port Indexes 184
- Specifying a SRP Target Port 185
- Specifying an Adapter 186
- Restarting the SRP Module 187
- SRP Initiator port to another 190
- FVIC in Chassis 194
- 1. Review ib_qlgc_srp_query 197
- Native IB Storage SRP Driver” 198
- Native IB Storage SRP Driver 198
- OFED SRP Configuration 200
- B-26 IB0054606-02 A 202
- C Integration with a Batch 203
- C-4 IB0054606-02 A 206
- D Troubleshooting 207
- BIOS Settings 208
- InfiniPath 212
- SDP Module Not Loading 213
- Performance Issues 215
- Erratic Performance 216
- Open MPI Troubleshooting 218
- E–ULP Troubleshooting 225
- IB0054606-02 A E-7 225
- Troubleshooting SRP Issues 227
- Following is an example: 230
- E-14 IB0054606-02 A 232
- IB0054606-02 A E-15 233
- E-16 IB0054606-02 A 234
- IB0054606-02 A E-17 235
- Solution: 237
- E-20 IB0054606-02 A 238
- F–Write Combining 240
- F-2 IB0054606-02 A 240
- # ipath_mtrr 240
- F-4 IB0054606-02 A 242
- Restarting InfiniPath 244
- Program Name Function 245
- G–Commands and Files 247
- IB0054606-02 A G-5 247
- Sample output: 248
- G-20 IB0054606-02 A 262
- OS_version/updates 267
- G-30 IB0054606-02 A 272
- # modprobe -v ib_qib 272
- Common Tasks and Commands 274
- Function Command 275
- Table G-4. Useful Files 276
- G-38 IB0054606-02 A 280
- OpenFabrics 282
- Clusters 282
- Networking 282
- Other Software Packages 282
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