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then \
echo "Making $$i ..."; \
(cd $$i; make); \
echo ""; \
fi; \
done
clean:
@ \
for i in ${HYPRE_DIRS}; \
do \
if [ -d $$i ]; \
then \
echo "Cleaning $$i ..."; \
(cd $$i; make clean); \
fi; \
done
veryclean:
@ \
for i in ${HYPRE_DIRS}; \
do \
if [ -d $$i ]; \
then \
echo "Very-cleaning $$i ..."; \
(cd $$i; make veryclean); \
fi; \
done
11.3.1 Example Procedure 1
Go through the directories serially and have the make procedure within each directory be parallel.
For the purpose of this exercise we are only parallelizing the “make all” component. The “clean”
and “veryclean” components can be parallelized in a similar fashion.
Modified Makefile:
all:
@ \
for i ${HYPRE_DIRS}; \
do \
if [ -d $$i ]; \
then \
echo "Making $$i ..."; \
echo $(PREFIX) $(MAKE) $(MAKE_J) -C $$i; \
$(PREFIX) $(MAKE) $(MAKE_J) -C $$i; \
fi; \
done
By modifying the Makefile to reflect the changes illustrated above, we will now be processing
each directory serially and parallelize the individual makes within each directory. The modified
Makefile is invoked as follows:
$ make PREFIX=’srun –n1 –N1 MAKE_J='-j4'
11.3.2 Example Procedure 2
Go through the directories in parallel and have the make procedure within each directory be
serial.
For the purpose of this exercise we are only parallelizing the “make all” component. The “clean”
and “veryclean” components can be parallelized in a similar fashion.
Modified Makefile:
all:
11.3 Using the GNU Parallel Make Capability 121
- 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
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