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License: MIT License
mpi4py examples
License: MIT License
=== Dependencies === These programs depend on mpi4py (>= Version 1.0) The mpi4py documentation and installation instructions can be found at: http://mpi4py.scipy.org/ === How to run on a single (multi-core) host === Run it with mpirun -np 4 ./some-program where the number after "-np " is the number of parallel MPI processes to be started. === How to run on multiple hosts === If you want to run the program distributed over multiple hosts, you have to create a <hostfile> which looks like: -- hostfile -- host1 slots=4 host2 slots=4 host3 slots=4 -------------- Where "slots=" specifies the number of parallel processes that should be started on that host. Run it with mpirun --hostfile <hostfile> ./some-program === Run on a cluster with the Torque Job scheduling system === There are two possibilities: a) Run interactively: Request an interactive session and allocate a number of processors/nodes for your session: $ qsub -I X -l nodes=4:ppn=4 Where "-I" means you want to work interactively, "-X" requests grapical (X-Window) I/O -- (you can run arbitrary programs that open windows). The option "-l " specifies the resources you want to allocate. "-l nodes=4:ppn=4" requests four compute nodes with each having four processor cores [ppn =^ ProcessorsPerNode]. So in total you allocate 16 CPU cores. [The scheduler is free to run your job on two nodes having 8 CPU cores each] Once your interactive session is ready, you run $ mpirun ./your-program mpirun automatically knowns how many parallel processes have to be started and where they have to be started. b) Submit as non-interactive batch-job: Use $ qsub -l nodes=4:ppn=4 ./your-jobfile.job to submit jour job-file. Similar to the interactive case, "-l" again is used to request resources from the scheduling system. The job file usually is a simple shell script which specifies the commands to be run once your job starts. In addition, the jobfile can contain "#PBS <something>" statements which are used to specify additional options which could have been specified in the "qsub" commandline. Please see "man qsub" for details.
ModuleNotFoundError: No module named 'bernstein'
Where can I find bernstein
package?
Cheers
Thank you so much for preparing these examples. They helped me a lot in familiarizing with mpi4py
.
Would you be so kind to provide an open-source license for this project?
......
--------------------------------------------------------------------------
WARNING: Open MPI failed to TCP connect to a peer MPI process. This
should not happen.
Your Open MPI job may now fail.
Local host: pi02
PID: 24783
Message: connect() to 169.254.140.13:1026 failed
Error: Resource temporarily unavailable (11)
--------------------------------------------------------------------------
[pi01:28731] 3 more processes have sent help message help-mpi-btl-tcp.txt / dropped inbound connection
[pi01:28731] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
[pi01:28731] 3 more processes have sent help message help-mpi-btl-tcp.txt / client connect fail
My hostfile is:
$ cat ~/hostfile
192.168.1.253 slots=4
192.168.1.251 slots=4
192.168.1.249 slots=4
192.168.1.247 slots=4
Thanks for the very instructive examples of use of mpi4py.
I am actually trying to use mpi4py to gather processes of each node of a cluster [as explained on that StackExchange question]. My first idea was to directly use groups and intercommunications, but this post recommend to use the gather then split functions.
I am referring to you because you have a great experience with MPI using mpi4py and maybe one of your example could be simply adapted to achieve that. Also, It could be an interesting addition to your very good set of examples.
Hello, thanks for sharing such good examples which have much learning value.
I have a question on when I want to run the .py files of mpi4py, is there any configuration or setting I should do on the cluster?
Looking forward to your reply. Thanks so much!
10-task-pull-spawn.py should be run as Program should be started without argument. However,
pi@pi01:~/Downloads/mpi4py-examples $ python 10-task-pull-spawn.py
--------------------------------------------------------------------------
There are not enough slots available in the system to satisfy the 10 slots
that were requested by the application:
/usr/bin/python
Either request fewer slots for your application, or make more slots available
for use.
--------------------------------------------------------------------------
Traceback (most recent call last):
File "10-task-pull-spawn.py", line 38, in <module>
maxprocs=n_workers)
File "mpi4py/MPI/Comm.pyx", line 1534, in mpi4py.MPI.Intracomm.Spawn
mpi4py.MPI.Exception: MPI_ERR_SPAWN: could not spawn processes
If I run with mpirun, program hangs:
pi@pi01:~/Downloads/mpi4py-examples $ mpirun --hostfile ~/hostfile python 10-task-pull-spawn.py
--------------------------------------------------------------------------
All nodes which are allocated for this job are already filled.
--------------------------------------------------------------------------
Traceback (most recent call last):
File "10-task-pull-spawn.py", line 38, in <module>
maxprocs=n_workers)
File "mpi4py/MPI/Comm.pyx", line 1534, in mpi4py.MPI.Intracomm.Spawn
mpi4py.MPI.Exception: MPI_ERR_SPAWN: could not spawn processes
pi@pi01:~/Downloads/mpi4py-examples $ mpirun --hostfile ~/hostfile 03-scatter-gather
------------------------------------------------------------------------------
Running on 16 cores
------------------------------------------------------------------------------
After Scatter:
[0] [0. 1. 2. 3.]
[1] [4. 5. 6. 7.]
[pi01][[24145,1],0][btl_tcp_endpoint.c:626:mca_btl_tcp_endpoint_recv_connect_ack] received unexpected process identifier [[24145,1],3]
[2] [ 8. 9. 10. 11.]
[pi03][[24145,1],8][btl_tcp_endpoint.c:626:mca_btl_tcp_endpoint_recv_connect_ack] received unexpected process identifier [[24145,1],10]
pi@pi01:~/Downloads/mpi4py-examples $ mpirun --np 16 --hostfile ~/hostfile 05-pseudo-whitening
Traceback (most recent call last):
File "/home/pi/Downloads/mpi4py-examples/05-pseudo-whitening", line 26, in <module>
in_fname = sys.argv[-2]
IndexError: list index out of range
Traceback (most recent call last):
File "/home/pi/Downloads/mpi4py-examples/05-pseudo-whitening", line 26, in <module>
in_fname = sys.argv[-2]
IndexError: list index out of range
Traceback (most recent call last):
File "/home/pi/Downloads/mpi4py-examples/05-pseudo-whitening", line 26, in <module>
in_fname = sys.argv[-2]
IndexError: list index out of range
Traceback (most recent call last):
File "/home/pi/Downloads/mpi4py-examples/05-pseudo-whitening", line 26, in <module>
in_fname = sys.argv[-2]
IndexError: list index out of range
Traceback (most recent call last):
File "/home/pi/Downloads/mpi4py-examples/05-pseudo-whitening", line 26, in <module>
in_fname = sys.argv[-2]
IndexError: list index out of range
Traceback (most recent call last):
File "/home/pi/Downloads/mpi4py-examples/05-pseudo-whitening", line 26, in <module>
in_fname = sys.argv[-2]
IndexError: list index out of range
Traceback (most recent call last):
File "/home/pi/Downloads/mpi4py-examples/05-pseudo-whitening", line 26, in <module>
in_fname = sys.argv[-2]
IndexError: list index out of range
Traceback (most recent call last):
File "/home/pi/Downloads/mpi4py-examples/05-pseudo-whitening", line 26, in <module>
in_fname = sys.argv[-2]
IndexError: list index out of range
Traceback (most recent call last):
File "/home/pi/Downloads/mpi4py-examples/05-pseudo-whitening", line 26, in <module>
in_fname = sys.argv[-2]
IndexError: list index out of range
Traceback (most recent call last):
File "/home/pi/Downloads/mpi4py-examples/05-pseudo-whitening", line 26, in <module>
in_fname = sys.argv[-2]
IndexError: list index out of range
Traceback (most recent call last):
File "/home/pi/Downloads/mpi4py-examples/05-pseudo-whitening", line 26, in <module>
in_fname = sys.argv[-2]
IndexError: list index out of range
Traceback (most recent call last):
File "/home/pi/Downloads/mpi4py-examples/05-pseudo-whitening", line 26, in <module>
in_fname = sys.argv[-2]
IndexError: list index out of range
Traceback (most recent call last):
File "/home/pi/Downloads/mpi4py-examples/05-pseudo-whitening", line 26, in <module>
in_fname = sys.argv[-2]
IndexError: list index out of range
Traceback (most recent call last):
File "/home/pi/Downloads/mpi4py-examples/05-pseudo-whitening", line 26, in <module>
in_fname = sys.argv[-2]
IndexError: list index out of range
Traceback (most recent call last):
File "/home/pi/Downloads/mpi4py-examples/05-pseudo-whitening", line 26, in <module>
in_fname = sys.argv[-2]
IndexError: list index out of range
Traceback (most recent call last):
File "/home/pi/Downloads/mpi4py-examples/05-pseudo-whitening", line 26, in <module>
in_fname = sys.argv[-2]
IndexError: list index out of range
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[1099,1],7]
Exit code: 1
--------------------------------------------------------------------------
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