Simple UserGuide for MPICH2
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| - | = | + | =MPICH2 on ifp-32= |
| + | Version and configure information: | ||
| - | = | + | [pineking@ifp-32 mpich2]$ mpich2version |
| + | MPICH2 Version: 1.2.1 | ||
| + | MPICH2 Release date: Unknown, built on Sun Jan 10 18:06:02 CST 2010 | ||
| + | MPICH2 Device: ch3:nemesis | ||
| + | MPICH2 configure: --prefix=/cworkspace/ifp-32-2/hasegawa/pineking/programs/mpich2/ --enable-cxx --enable-threads=multiple | ||
| + | MPICH2 CC: gcc -O2 | ||
| + | MPICH2 CXX: g++ -O2 | ||
| + | MPICH2 F77: gfortran -O2 | ||
| + | MPICH2 F90: f95 -O2 | ||
| + | |||
| + | Parallel environment on SGE: | ||
| + | |||
| + | [pineking@ifp-32 test]$ qconf -sp mpich | ||
| + | pe_name mpich | ||
| + | slots 9999 | ||
| + | user_lists NONE | ||
| + | xuser_lists NONE | ||
| + | start_proc_args /opt/gridengine/mpi/startmpi.sh -catch_rsh $pe_hostfile | ||
| + | stop_proc_args /opt/gridengine/mpi/stopmpi.sh | ||
| + | allocation_rule $fill_up | ||
| + | control_slaves TRUE | ||
| + | job_is_first_task FALSE | ||
| + | urgency_slots min | ||
| + | accounting_summary TRUE | ||
| + | |||
| + | =Users= | ||
| + | |||
| + | |||
| + | * '''add MPICH2 binary path to your PATH''' | ||
| + | export PATH=/cworkspace/ifp-32-2/hasegawa/pineking/programs/mpich2/bin:$PATH | ||
| + | Check we can find them: | ||
| + | which mpd | ||
| + | which mpiexec | ||
| + | which mpirun | ||
| + | |||
| + | |||
| + | * '''.mpd.conf''' | ||
| + | MPI expects the configuration file in your home directory named ~/.mpd.conf (/etc/mpd.conf if root). It should contain one line: | ||
| + | secretword=<secretword> | ||
| + | |||
| + | where <secretword> is a password, that should not be your user password. Make it readable/writable only by you: | ||
| + | chmod 600 .mpd.conf | ||
| + | |||
| + | * '''check mpd daemon''' | ||
| + | [pineking@ifp-32 test]$ mpdtrace | ||
| + | ifp-32 | ||
| + | compute-1-14 | ||
| + | compute-1-13 | ||
| + | compute-1-11 | ||
| + | compute-1-8 | ||
| + | compute-1-12 | ||
| + | compute-1-2 | ||
| + | compute-1-16 | ||
| + | compute-1-15 | ||
| + | compute-1-7 | ||
| + | compute-1-6 | ||
| + | compute-1-1 | ||
| + | compute-1-10 | ||
| + | compute-1-9 | ||
| + | compute-1-3 | ||
| + | compute-1-5 | ||
| + | compute-1-4 | ||
| + | |||
| + | The information above show that mpd daemon is already run on each node. | ||
| + | |||
| + | * '''run a MPI program to check the parallel environment''' | ||
| + | |||
| + | [pineking@ifp-32 test]$ mpiexec -l -n 4 ./cpi | ||
| + | 0: Process 0 on ifp-32.ifp.uiuc.edu | ||
| + | 1: Process 1 on compute-1-14.local | ||
| + | 2: Process 2 on compute-1-13.local | ||
| + | 3: Process 3 on compute-1-11.local | ||
| + | 0: pi is approximately 3.1416009869231249, Error is 0.0000083333333318 | ||
| + | 0: wall clock time = 0.005698 | ||
=Using MPI with qsub on ifp-32= | =Using MPI with qsub on ifp-32= | ||
| + | * '''Create a bash file''', such as: | ||
| + | #!/bin/bash | ||
| + | #$ -cwd | ||
| + | #$ -pe mpich 4 | ||
| + | |||
| + | /cworkspace/ifp-32-2/hasegawa/pineking/programs/mpich2/bin/mpiexec -n 3 ./cpi | ||
| + | |||
| + | and submit: | ||
| + | |||
| + | [pineking@ifp-32 test]$ qsub test.sh | ||
| + | Your job 283054 ("test.sh") has been submitted | ||
| + | [pineking@ifp-32 test]$ qstat -u pineking | ||
| + | job-ID prior name user state submit/start at queue slots ja-task-ID | ||
| + | ----------------------------------------------------------------------------------------------------------------- | ||
| + | 283054 0.60167 test.sh pineking r 05/02/2010 19:23:10 all.q@compute-1-7.local 4 | ||
| + | |||
| + | some log files are generated: | ||
| + | |||
| + | [pineking@ifp-32 test]$ ll test.sh.* | ||
| + | -rw-r--r-- 1 pineking hasegawa 93 May 2 19:23 test.sh.e283054 | ||
| + | -rw-r--r-- 1 pineking hasegawa 179 May 2 19:23 test.sh.o283054 | ||
| + | -rw-r--r-- 1 pineking hasegawa 0 May 2 19:23 test.sh.pe283054 | ||
| + | -rw-r--r-- 1 pineking hasegawa 134 May 2 19:23 test.sh.po283054 | ||
| + | |||
| + | =Administrators= | ||
| + | |||
| + | * '''MPI host file: mpd.hosts''' | ||
| + | Create a host file named "mpd.hosts" in your home directory ~/mpd.hosts , it contains the hosts list, such as: | ||
| + | compute-1-1 | ||
| + | compute-1-2 | ||
| + | compute-1-3 | ||
| + | compute-1-4 | ||
| + | compute-1-5 | ||
| + | compute-1-6 | ||
| + | compute-1-7 | ||
| + | compute-1-8 | ||
| + | compute-1-9 | ||
| + | compute-1-10 | ||
| + | compute-1-11 | ||
| + | compute-1-12 | ||
| + | compute-1-13 | ||
| + | compute-1-14 | ||
| + | compute-1-15 | ||
| + | compute-1-16 | ||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| - | = | + | =Reference= |
| + | # [http://www.mcs.anl.gov/research/projects/mpich2/ MPICH2 website] | ||
| + | # [http://www.mcs.anl.gov/research/projects/mpich2/documentation/files/mpich2-1.2.1-installguide.pdf MPICH2 Installer's Guide] | ||
| + | # [http://www.mcs.anl.gov/research/projects/mpich2/documentation/files/mpich2-1.2.1-userguide.pdf MPICH2 User's Guide] | ||
| + | # [http://gridengine.sunsource.net/howto/mpich2-integration/mpich2-integration.html http://gridengine.sunsource.net/howto/mpich2-integration/mpich2-integration.html] | ||
Latest revision as of 00:31, 3 May 2010
Contents |
MPICH2 on ifp-32
Version and configure information:
[pineking@ifp-32 mpich2]$ mpich2version MPICH2 Version: 1.2.1 MPICH2 Release date: Unknown, built on Sun Jan 10 18:06:02 CST 2010 MPICH2 Device: ch3:nemesis MPICH2 configure: --prefix=/cworkspace/ifp-32-2/hasegawa/pineking/programs/mpich2/ --enable-cxx --enable-threads=multiple MPICH2 CC: gcc -O2 MPICH2 CXX: g++ -O2 MPICH2 F77: gfortran -O2 MPICH2 F90: f95 -O2
Parallel environment on SGE:
[pineking@ifp-32 test]$ qconf -sp mpich pe_name mpich slots 9999 user_lists NONE xuser_lists NONE start_proc_args /opt/gridengine/mpi/startmpi.sh -catch_rsh $pe_hostfile stop_proc_args /opt/gridengine/mpi/stopmpi.sh allocation_rule $fill_up control_slaves TRUE job_is_first_task FALSE urgency_slots min accounting_summary TRUE
Users
- add MPICH2 binary path to your PATH
export PATH=/cworkspace/ifp-32-2/hasegawa/pineking/programs/mpich2/bin:$PATH
Check we can find them:
which mpd which mpiexec which mpirun
- .mpd.conf
MPI expects the configuration file in your home directory named ~/.mpd.conf (/etc/mpd.conf if root). It should contain one line:
secretword=<secretword>
where <secretword> is a password, that should not be your user password. Make it readable/writable only by you:
chmod 600 .mpd.conf
- check mpd daemon
[pineking@ifp-32 test]$ mpdtrace
ifp-32 compute-1-14 compute-1-13 compute-1-11 compute-1-8 compute-1-12 compute-1-2 compute-1-16 compute-1-15 compute-1-7 compute-1-6 compute-1-1 compute-1-10 compute-1-9 compute-1-3 compute-1-5 compute-1-4
The information above show that mpd daemon is already run on each node.
- run a MPI program to check the parallel environment
[pineking@ifp-32 test]$ mpiexec -l -n 4 ./cpi 0: Process 0 on ifp-32.ifp.uiuc.edu 1: Process 1 on compute-1-14.local 2: Process 2 on compute-1-13.local 3: Process 3 on compute-1-11.local 0: pi is approximately 3.1416009869231249, Error is 0.0000083333333318 0: wall clock time = 0.005698
Using MPI with qsub on ifp-32
- Create a bash file, such as:
#!/bin/bash #$ -cwd #$ -pe mpich 4 /cworkspace/ifp-32-2/hasegawa/pineking/programs/mpich2/bin/mpiexec -n 3 ./cpi
and submit:
[pineking@ifp-32 test]$ qsub test.sh
Your job 283054 ("test.sh") has been submitted
[pineking@ifp-32 test]$ qstat -u pineking
job-ID prior name user state submit/start at queue slots ja-task-ID
-----------------------------------------------------------------------------------------------------------------
283054 0.60167 test.sh pineking r 05/02/2010 19:23:10 all.q@compute-1-7.local 4
some log files are generated:
[pineking@ifp-32 test]$ ll test.sh.* -rw-r--r-- 1 pineking hasegawa 93 May 2 19:23 test.sh.e283054 -rw-r--r-- 1 pineking hasegawa 179 May 2 19:23 test.sh.o283054 -rw-r--r-- 1 pineking hasegawa 0 May 2 19:23 test.sh.pe283054 -rw-r--r-- 1 pineking hasegawa 134 May 2 19:23 test.sh.po283054
Administrators
- MPI host file: mpd.hosts
Create a host file named "mpd.hosts" in your home directory ~/mpd.hosts , it contains the hosts list, such as:
compute-1-1 compute-1-2 compute-1-3 compute-1-4 compute-1-5 compute-1-6 compute-1-7 compute-1-8 compute-1-9 compute-1-10 compute-1-11 compute-1-12 compute-1-13 compute-1-14 compute-1-15 compute-1-16
