daleroberts / pypar Goto Github PK

Efficient and scalable parallelism using the message passing interface (MPI) to handle big data and highly computational problems.

License: GNU General Public License v3.0

C 26.55% Python 73.45%

big-data map-reduce mpi python

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pypar's Issues

Error on import pypar

I recently installed fresh ubuntu14.04.
Then I installed mpich2.
I forgot whether i have installed openmpi also or not.

I create virtual environment.
Install numpy as required by pypar 2.0 using pip
Then install pypar using

python setup.py install

I checked using pip freeze and pypar is really installed

I tried pypar in python intrepeter

import pypar

Then i got this error.

[pangrango:02488] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_paffinity_hwloc: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)
[pangrango:02488] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_carto_auto_detect: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)
[pangrango:02488] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_carto_file: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)
[pangrango:02488] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_shmem_mmap: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)
[pangrango:02488] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_shmem_posix: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)
[pangrango:02488] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_shmem_sysv: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)
--------------------------------------------------------------------------
Sorry!  You were supposed to get help about:
    opal_init:startup:internal-failure
But I couldn't open the help file:
    /usr/share/openmpi/help-opal-runtime.txt: No such file or directory.  Sorry!
--------------------------------------------------------------------------
[pangrango:02488] [[INVALID],INVALID] ORTE_ERROR_LOG: Error in file runtime/orte_init.c at line 79
--------------------------------------------------------------------------
Sorry!  You were supposed to get help about:
    mpi_init:startup:internal-failure
But I couldn't open the help file:
    /usr/share/openmpi/help-mpi-runtime: No such file or directory.  Sorry!
--------------------------------------------------------------------------
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL: your MPI job will now abort
[pangrango:2488] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed!

I try:

mpirun -np 4 pwd

and it worked/

I tried restart the computer, and I still got the same error.
Any idea what might have happened?
Thanks.

Python 2 discontinued

Is there any chance this library will be upgraded to python 3?

global name string.split does not exist in line 51 in setup.py

Hello!Please edit setup.py.I added the string object in get_mpi_flags().

Allow 'gather' to handle values (instead of requiring a numpy array)

In certain cases, it makes sense to gather single values (on clients) to an array (on master). See the examples/pi.py

Segfault after Control+C; OpenMPI

Hi,

For quite a while I'm observing that after importing pypar python segfaults on Control+C. In the same time when for example using mpi4py, nothing like this happens. That suggest to me that maybe it is not the issue with the mpi library itself.
Here is the test program which segfaults on me:

import os
# import mpi4py
import pypar
os.kill(os.getpid(),2)

My OS is RHEL 6.6 on x86_64 with OpenMPI 1.8.1. Python version 2.7.6
I've been observing this issue for last year/couple of years.

ImportError: No module named tblib

I installed pypar on a cluster I use at work, but when I went to run it, I got this:

> python
Python 2.7.8 (default, Oct  9 2014, 13:11:01) 
[GCC 4.7.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import pypar
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "PATH/packages/lib/python2.7/site-packages/pypar/__init__.py", line 9, in <module>
    import test
  File "PATH/packages/lib/python2.7/site-packages/pypar/test.py", line 15, in <module>
    from tblib import pickling_support
ImportError: No module named tblib

As the trace states, __init__.py imports test.py, which in turn imports tblib. There's no mention anywhere (that I can find) that tblib is a dependency of pypar.

Why is test.py imported in __init__.py? If I just comment out the import, pypar seems to work just fine without me needing to install tblib.

Merge in MPI_Isend changes from ANUGA

Take care of differences between OpenMPI and MPICH.

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