ggiecold-zz/concurrent_ap

A scalable and concurrent programming implementation of Affinity Propagation clustering.

concurrent_ap's Issues

Need help with HDF5 issue on running in anaconda virutal env on Windows

(new_env) E:\cca\test>Concurrent_AP iris_data.tsv
Traceback (most recent call last):
File "c:\users\ramotlan\appdata\local\continuum\anaconda3\envs\new_env\lib\runpy.py", line 174, in _run_module_as_main
"main", fname, loader, pkg_name)
File "c:\users\ramotlan\appdata\local\continuum\anaconda3\envs\new_env\lib\runpy.py", line 72, in run_code
exec code in run_globals
File "C:\Users\ramotlan\AppData\Local\Continuum\anaconda3\envs\new_env\Scripts\Concurrent_AP.exe_main.py", line 9, in
File "c:\users\ramotlan\appdata\local\continuum\anaconda3\envs\new_env\lib\site-packages\Concurrent_AP.py", line 1337, in main
check_HDF5_arrays(hdf5_file, N, opts.convergence_iter)
File "c:\users\ramotlan\appdata\local\continuum\anaconda3\envs\new_env\lib\site-packages\Concurrent_AP.py", line 304, in check_HDF5_arrays
with tables.open_file(hdf5_file, 'r+') as fileh:
File "c:\users\ramotlan\appdata\local\continuum\anaconda3\envs\new_env\lib\site-packages\tables\file.py", line 320, in open_file
return File(filename, mode, title, root_uep, filters, **kwargs)
File "c:\users\ramotlan\appdata\local\continuum\anaconda3\envs\new_env\lib\site-packages\tables\file.py", line 784, in init
self._g_new(filename, mode, **params)
File "tables\hdf5extension.pyx", line 489, in tables.hdf5extension.File._g_new
tables.exceptions.HDF5ExtError: HDF5 error back trace
File "C:\ci\hdf5_1525883526020\work\src\H5F.c", line 511, in H5Fopen
unable to open file
File "C:\ci\hdf5_1525883526020\work\src\H5Fint.c", line 1450, in H5F_open
unable to open file: time = Sat Sep 01 15:50:52 2018
, name = 'E:\cca\test\tmpkjpotn.h5', tent_flags = 1
File "C:\ci\hdf5_1525883526020\work\src\H5FD.c", line 733, in H5FD_open
open failed
File "C:\ci\hdf5_1525883526020\work\src\H5FDsec2.c", line 346, in H5FD_sec2_open
unable to open file: name = 'E:\cca\test\tmpkjpotn.h5', errno = 13, error message = 'Permission denied', flags = 1, o_flags = 2
End of HDF5 error back trace
Unable to open/create file 'E:\cca\test\tmpkjpotn.h5'

Hey @GGiecold
I trying to run Concurrent_AP in Anaconda virtual env on Windows 10.
Although i know you have mentioned you've not mentioned Windows in your tested OS, but looking at this error, would you be able to find out how can i get your code running?
It will be really helpful!!
Thanks in Advance! :)

cannot parallel

Hi, Gregory Giecold, thank you for your great work. It helps us a lot to solve the memory issue when using affinity propagation. Thanks.

However, I encountered a problem that it only parallelly runs just for a while (at the beginning). Then, it only uses 1 thread to run continually. Do you have any idea what's going wrong? Thanks.
(As in the picture, you can see, only the No70 runs the program. PS. I am the admin of the server, so probably it's not permission problems)

Best way to run on a cluster with qsub?

This is a very useful package. I am now assessing what would be the best way to run it on a cluster with qsub (open MPI, etc.)? Any suggestion would be great.

Its unable to read a CSV file and getting error 'xrange' is not defined?

When i run this command on my dataset, dataset without index and header as per requirement, i get an error.

command = Concurrent_AP --preference -5.47 --v test1.csv
ValueError: could not convert string to float: '-3.1327,-10.187999999999999,-1.0488,-3.0399,-0.43163,-0.061478,-2.9783,-0.4948,-0.81215,21.24,42.72,15.42'

while on command = Concurrent_AP --preference -5.47 --v iris_data.tsv
for i in xrange(N_processes):
NameError: name 'xrange' is not defined

UnboundLocalError: local variable 'labels' referenced before assignment

Hi,
I am having an issue running your code on mac osx :

Traceback (most recent call last):
File "/usr/local/bin/concurrent_AP", line 9, in
load_entry_point('Concurrent-AP==1.4', 'console_scripts', 'Concurrent_AP')()
File "/Library/Python/2.7/site-packages/Concurrent_AP.py", line 1416, in main
output_clusters(labels, cluster_centers_indices)
UnboundLocalError: local variable 'labels' referenced before assignment

Any hint ?