numpy - Parallelism in (I)Python with large blocks of data -


i've been toiling threads , processes while try speed parallel job in ipython. i'm not sure how detail function i'm calling useful, here's bash ask if need more.

my function's call signature looks like

def intersplit_array(ob,er,nl,m,mi,t,ti,dmax,n0=6,steps=50):

basically, ob, er , nl parameters observed values , m,mi,t,ti , dmax parameters represent models against observations compared. (n0 , steps fixed numerical parameters function.) function loops through models in m and, using associated information in mi, t, ti , dmax, calculates probability model matches. note m quite big: it's list of 700 000 22x3 numpy arrays. mi , dmax of similar sizes. if releant, normal ipython instance uses 25% of system memory in top: 4gb of 16gb of ram.

i've tried parallelize in 2 ways. first, tried use parallel_map function given on at scipy cookbook. made call

p = parallel_map(lambda i: intersplit_array(ob,er,nl,m[i+1],mi[i:i+2],t[i+1],ti[i:i+2],dmax[i+1],range(1,len(m)-1))

which runs, , provides correct answer. without parallel_ part, result of applying function 1 one each element. slower using single core. guess related global interpreter lock?

second, tried use pool multiprocessing. initialized pool with

p = multiprocessing.pool(6)

and tried call function with

p = p.map(lambda i: intersplit_array(ob,er,nl,m[i+1],mi[i:i+2],t[i+1],ti[i:i+2],dmax[i+1],range(1,len(m)-1))

first, error.

exception in thread thread-3: traceback (most recent call last):   file "/usr/lib64/python2.7/threading.py", line 551, in __bootstrap_inner     self.run()   file "/usr/lib64/python2.7/threading.py", line 504, in run     self.__target(*self.__args, **self.__kwargs)   file "/usr/lib64/python2.7/multiprocessing/pool.py", line 319, in _handle_tasks     put(task) picklingerror: can't pickle <type 'function'>: attribute lookup __builtin__.function failed

having in top, see ipython processes, each of apparently taking 25% of ram (which can't so, because i've still got 4gb free) , using 0% cpu. presume isn't doing anything. can't use ipython, either. tried ctrl-c while, gave once got passed 300th pool worker.

does work not interactively?

multiprocessing doesn't play interactively, because of way splits processes. why had trouble killing because spawned many processes. have keep track of master process cancel it.

from the documentation:

note
functionality within package requires __main__ module importable children. covered in programming guidelines worth pointing out here. means examples, such multiprocessing.pool examples not work in interactive interpreter.
...
if try output full tracebacks interleaved in semi-random fashion, , may have stop master process somehow.

the best solution run script command line. alternatively, ipython has own system parallel computing, i've never used it.


Comments

Post a Comment

Popular posts from this blog

php - cannot display multiple markers in google maps v3 from traceroute result -

i'm newbie in php mysql , google maps v3. have problems in google maps v3. made traceroute web based , map traceroute's result in google maps v3 final project of college education. have try many tutorials didn't work. have tried tutorials in forum nothing worked. problem cannot display multiple markers got location data database. maybe because i'm newbie , not know how do. confuse looping show markers. here code <?php error_reporting(e_all ^ (e_notice)); ini_set('max_execution_time', 360); $enable_log_user = false; global $ip, $host_name, $host_ip; $host = @$_post['host']; $trace = @$_post['trace']; $self = $_server['php_self']; include("phpsqlajax_dbinfo.php"); $connection = mysql_connect ('127.0.0.1', $username, $password); if (!$connection) { die('not connected : ' . mysql_error());} $db_selected = mysql_select_db($database, $connection); if (!$db_selected) { die ('can\'t use db :
Read more

c# - DetailsView in ASP.Net - How to add another column on the side/add a control in each row? -

i have detailsview control on page used edit various fields of record, works in respect. i looking way add 1 column (and if works, why not more) right, absolutely read-only, show same fields of record comparison purposes. i aware there no obvious way such thing out of box detailsview . have looked other controls (transposed gridview , recommended formview , listview ), nothing satisfies. have special data binding setup using detailsview , can't out of without losing features. anyone on how "hack in" additional columns (for display only) on detailsview ? the solution have now, use second detailsview , visible set false in aspx. in code, make sure databind hidden detailsview hosts data third column first, initial detailsview named itemdetails . and in item created event, pass third column html rendering of hidden controls (in last code block) : protected void itemdetails_itemcreated(object sender, eventargs e) { if (dataite
Read more

javascript - firefox memory leak -

i have following script (i use raphaeljs also) draws circle, waits 1 second, draws circle again, etc (you can copy paste - functional, need include raphael raphaeljs.com): <div id="holder"> </div> <script src="raphael.js" type="text/javascript"></script> <script> var paper = raphael(10, 50, 320, 200); var rad = math.pi / 180; var finangle = 0; function sector(cx, cy, r, startangle, endangle, params) { var x1 = cx + r * math.cos(-startangle * rad), x2 = cx + r * math.cos(-endangle * rad), y1 = cy + r * math.sin(-startangle * rad), y2 = cy + r * math.sin(-endangle * rad); return ["m", cx, cy, "l", x1, y1, "a", r, r, 0, +(endangle - startangle > 180), 0, x2, y2]; } var path = sector(100,100,50,0,180); var arc = paper.path(path); function draw() { path = sector(100,100,50,0,finangle);
Read more