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1.4 Run-Time E nvironment
In the HP XC environment, LSF-HPC, SLURM, and HP-MPI work together to provide a
powerful, flexible, extensive run-time environment. This section describes LSF-HPC, SLURM ,
and HP-MPI, and h o w these components work together to provid e the HP XC run-time
environment.
1.4.1 SLURM
SLURM (Simple Linux Utility for Resource Management) is a resource management system
that is integrated into the HP XC system. SLURM is suitable for use on large and s m a ll
Linux clusters. It was developed by Lawrence Livermore National Lab and Linux Networks.
As a resource manager, S LURM allocates exclusive or non-exclusive access to resources
(application/compute nodes) for users to perform work, and provides a framework to start,
execute and monitor work (normally a parallel job) on the set of allocated nodes. A SLURM
system consists of two daemo ns, one configuration file, and a set of commands and APIs. The
central controller daemon, slurmctld, maintains the global s tate and directs operations. A
slurmd daemon is deployed to each computing node and responds to job-related requests,
such as launching jobs, sig nalling , and terminating jobs. E nd users and system software (such
as LSF-HPC) communicate withSLURMbymeansofcommandsorAPIs—forexample,
allocating resources, launching parallel jobs on allocated resources, an d killing running jobs.
SLURM groups compute nodes (the nodes where jobs are run) togeth er into partitions.The
HP XC system can have one or several partitions. When HP XC is installed, a single par tit ion
of com pute nodes is created by default for LSF batch jobs. The system administrator has the
option of cr eating addition a l partitions. For example, another partition could be created for
interactive jobs.
1.4.2 Load Sharing Facility (LSF-HPC)
The Load Sharing Facility for High Performance Computing (LSF-HPC) from Platform
Computing Corporation is a batch system resource manager that has been integrated with
SLURM for use on the HP XC system. LSF-HPC for SLURM is included with the HP XC
System Softw are, and is an integral part of theHP XC environment. LSF-HPC interacts with
SLURM to obtain and allocate available resources, and to launch and control all the jobs
submitted to LSF-HPC. LSF-HPC accepts, q ueues, schedules, dispatches, and controls all the
batch j obs that users submit, according to policies and configurations established by the HP
XC site administrator. On an HP XC system, LSF-HPC for SLU RM is installed and runs on
one HP XC node, known as the LSF-HPC execution host.
A complete description of LSF-HPC is provided in Chapter 7. In addition , for your convenience,
the HP XC documentation CD contains LSF Version 6.0 manuals from Platform Computing.
1.4.3 How LSF-HPC and SLURM Interact
In the HP XC environment, LSF-HPC cooperates with SLURM to combine LSF-HPC’s
powerful scheduling functionali ty with SLURM’s scalable parallel job launching capabilities.
LSF-HPC acts primarily as a w orkload scheduler on top of the SLURM system, providing
policy and topology-based scheduling for end users. SLURM provides an execution and
monitori ng layer for LSF-HPC. LSF-HPC uses SLURM to detect system topology information,
make scheduling decisions, and launch j obs on allocated resources.
When a job is submitted to LSF-HPC, LSF-HPC schedules the job based on job resource
requirements and communicates with SLURM to allocate the required HP XC com pu te nodes
for the job from the SLURM lsf partition. LSF-HPC provides node-level scheduling for
parallel jobs, and CPU-level scheduling for serial jobs. Because of node-level scheduling, a
parallel job may be allocated more CPUs than it requested, depending on its resource request;
the srun or mpirun -srun launch commands within the job still honor the original CPU
1-6 Overview o f the User Environment
- HP XC System Software 1
- Contents 3
- 3 Developing Applications 4
- 4 Debugging Applications 5
- 5 Tuning Applications 5
- 6UsingSLURM 5
- 8UsingHP-MPI 6
- 7 Using LSF 6
- 9UsingHPMLIB 7
- 10 Advanced Topics 8
- AExamples 8
- About This Document 11
- HP XC Inform ation 12
- For M ore Information 13
- Supplementary Information 13
- Manpages 14
- Related Information 15
- Typographical Conventions 16
- HP Encourages Your Comments 17
- 1.1 System Architecture 19
- 1.1.3 Storage and I/O 20
- 1.1.4 File System 20
- 1.2 User Environment 22
- 1.3.1 Parallel Applications 23
- 1.3.2 Serial Applications 23
- 1.4 Run-Time E nvironment 24
- 1.4.4 HP-MPI 25
- Using the System 27
- 2.2.1 Notes on Modulefiles 28
- 2.2.2 Supplied Modulefiles 29
- 2.2.6 Loading a Modulefile 30
- 2.2.7 Unloading a M odulefile 31
- 2.2.8 Modulefile Conflicts 31
- 2.2.9 Creating a Mod u lefile 32
- 2.3.1 Introduction 33
- 2.3.5 Launching Jobs 34
- $ man sinfo 39
- $ man -k keyword 39
- Using the System 2-13 39
- Developing Applications 41
- 3.2 Using Compilers 42
- 3.4 Interrupting a Job 43
- 3-4 Developing Applications 44
- Developing Applications 3-5 45
- 3-6 Developing Applications 46
- Developing Applications 3-7 47
- $ module load mpi 48
- $ mpicc -o mycode hello.c 48
- $ mpif90 -o mycode hello.f 48
- 3-8 Developing Applications 48
- 3.8 Developing Libraries 49
- 3.9 Advanced To pics 50
- 3-14 Deve loping Applications 54
- Developing Applications 3-15 55
- Debugging Applications 57
- 4-2 D ebugging Applications 58
- $ totalview 60
- 4-4 D ebugging Applications 60
- Debugging Applications 4-5 61
- 4-6 D ebugging Applications 62
- -verbosity %V %F" 63
- Debugging Applications 4-7 63
- 4-8 D ebugging Applications 64
- Etnus TotalView Version# 65
- Debugging Applications 4-9 65
- $ mpirun -srun -n2 Psimple 66
- 4-10 Debugging Applications 66
- $ squeue 67
- $ scancel --user username 67
- Debugging Applications 4-11 67
- Tuning Applications 69
- Using SLURM 71
- $ srun -N 16 -b myscript.sh 73
- $ srun -A -N 4 myscript.sh 73
- $ srun -a 6543 -j 73
- Using SLURM 6-3 73
- 6.4.2 srun Signal Handling 74
- 6.4.3 srun Run-Mode Options 74
- Using SLURM 6-5 75
- 6-6 Using SLURM 76
- 6.4.5 srun Control Options 77
- 6.4.6 srun I/O Options 78
- Using SLURM 6-9 79
- 6.4.7 srun Constraint Options 80
- Using SLURM 6-11 81
- 6.4.9 Using srun with HP-MPI 82
- 6.4.10 Using srun with LSF 82
- 6.8 Job Accounting 84
- 6.9 Fault Tolerance 84
- 6.10 Security 84
- Using LSF 85
- 7.1.2 Topology Support 86
- 7.1.3 Notes on LSF-HPC 87
- SLURM_JOBID=53 89
- SLURM_NPROCS=4 89
- 7-6 Using LSF 90
- 7.3.1 Getting Status of LSF 91
- $ bhosts 92
- 7-8 Using LSF 92
- 7.4 Submitting Jobs 93
- 7.4.3 Submitting a Serial Job 97
- Using LSF 7-17 101
- 7-18 Using LSF 102
- Using HP-MPI 111
- 8.3.3 Using srun with HP-MPI 114
- 8.3.4 Using LSF and HP-MPI 116
- 8.3.5 MPI Versioning 117
- 8.6 Truncated Messages 118
- 8.5 32-Bit B uilds on XC4000 118
- Using HP-MPI 8-9 119
- 8.9 Environment Variables 120
- 8.9.5 MPI_PIN_PERCENTAGE 121
- 8.9.6 MPI_PAGE_ALIGN_MEM 121
- 8.9.7 MPI_MAX_WINDOW 121
- 8.9.8 MPI_ELANLOCK 121
- 8.9.9 MPI_USE_LIBELAN 121
- 8.9.10 MPI_USE_LIBELAN_SUB 122
- Work-arounds 124
- Using HP MLIB 125
- 9.1.2 MLIB and Module Files 126
- 9.2.1 Platform Sup port 126
- 9.2.2 Library Support 126
- 9.2.3 MPI Parallelism 126
- 9.2.4 Modulefiles and MLIB 127
- 9.2.6 Compiling and Linking 127
- 9.2.7 Licensing 128
- 9.2.8 MLIB Man pages 128
- 9.3.1 Platform Sup port 128
- 9.3.2 Library Support 128
- 9.3.3 MPI Parallelism 129
- 9.3.4 Modulefiles and MLIB 129
- 9.3.5 Compiling and Linking 129
- 9.3.6 Licensing 130
- 9.3.7 MLIB Man pages 130
- Advanced Topics 131
- Examples 135
- $ lshosts 140
- Show the environment: 142
- Run the job: 142
- View the running job: 142
- View the finished job: 142
- Examples A-9 143
- Glossary 145
- Glossary-2 146
- Glossary-3 147
- Glossary-4 148
- Glossary-5 149
- Glossary-6 150
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