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POWhat is the fastest way to get multiple copies of a tree in python?
 

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  1. POWhat is the fastest way to get multiple copies of a tree in python?
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    <p>In my python program I need multiple copies of a tree. Initially, I use deepcopy from the copy module, which turns out to be very slow. Then I write my own code to copy a tree, the code traverses the tree being copied and create a new node at each node being visited. Then I call this subroutines multiple times to get multiple copies. This solution is much faster (~40 times faster) than deepcopy. </p> <p>Solution 2: Then I think, traversing a tree needs time T, make n copies, the time required is nT; but if I create n new nodes for each node being copied, I only need to traverse the tree being copied once, although at each node, you copy multiple nodes. Will this be faster? The result turns out to be: not much.</p> <p>Still the copy operation is the bottleneck of my program. Is there any faster way to do that? Thanks! Stats -- using custom copy_tree function;</p> <pre><code> ncalls tottime percall cumtime percall filename:lineno(function) 1 0.000 0.000 10.406 10.406 &lt;string&gt;:1(&lt;module&gt;) 1 0.002 0.002 10.406 10.406 C:\Python27\sdk.py:1431(algorithm1) 26 0.005 0.000 4.602 0.177 C:\Python27\sdk.py:1310(engage) 1342 0.005 0.000 4.208 0.003 C:\Python27\lib\idlelib\rpc.py:594(__call__) 1342 0.007 0.000 4.203 0.003 C:\Python27\lib\idlelib\rpc.py:208(remotecall) 1342 0.017 0.000 3.992 0.003 C:\Python27\lib\idlelib\rpc.py:238(asyncreturn) 1342 0.005 0.000 3.972 0.003 C:\Python27\lib\idlelib\rpc.py:279(getresponse) 1342 0.033 0.000 3.961 0.003 C:\Python27\lib\idlelib\rpc.py:295(_getresponse) 411/26 0.202 0.000 3.930 0.151 C:\Python27\sdk.py:1227(NodeEngage) 1338 0.014 0.000 3.909 0.003 C:\Python27\lib\threading.py:235(wait) 5356 3.877 0.001 3.877 0.001 {method 'acquire' of 'thread.lock' objects} 27 0.001 0.000 3.798 0.141 C:\Python27\sdk.py:888(pick_best_group) 378 0.003 0.000 3.797 0.010 C:\Python27\sdk.py:862(group_info) 46947/378 0.155 0.000 3.786 0.010 C:\Python27\sdk.py:833(core_possibilities) 27490 0.114 0.000 3.547 0.000 C:\Python27\sdk.py:779(find_cores) 46569 1.046 0.000 3.424 0.000 C:\Python27\sdk.py:798(find_a_true_core) 280274 0.873 0.000 1.464 0.000 C:\Python27\sdk.py:213(next) 27 0.002 0.000 1.393 0.052 C:\Python27\sdk.py:1008(s) 28196 0.016 0.000 1.070 0.000 C:\Python27\sdk.py:1000(copy_tree) </code></pre> <p>.............................Compare with deepcopy approach</p> <pre><code> ncalls tottime percall cumtime percall filename:lineno(function) 1 0.000 0.000 191.193 191.193 &lt;string&gt;:1(&lt;module&gt;) 1 0.002 0.002 191.193 191.193 C:\Python27\sdk.py:1431(algorithm1) 26 0.006 0.000 185.611 7.139 C:\Python27\sdk.py:1310(engage) 411/26 1.200 0.003 185.013 7.116 C:\Python27\sdk.py:1227(NodeEngage) 30033397/28196 56.608 0.000 177.885 0.006 C:\Python27\lib\copy.py:145(deepcopy) 3340177/28196 15.354 0.000 177.741 0.006 C:\Python27\lib\copy.py:283(_deepcopy_inst) 6680354/28196 23.276 0.000 177.261 0.006 C:\Python27\lib\copy.py:253(_deepcopy_dict) 3340177/150307 22.345 0.000 171.525 0.001 C:\Python27\lib\copy.py:234(_deepcopy_tuple) 13360708 23.793 0.000 23.793 0.000 {hasattr} 13614747 12.483 0.000 15.349 0.000 C:\Python27\lib\copy.py:267(_keep_alive) 1342 0.005 0.000 7.281 0.005 C:\Python27\lib\idlelib\rpc.py:594(__call__) 1342 0.008 0.000 7.276 0.005 C:\Python27\lib\idlelib\rpc.py:208(remotecall) 1342 0.019 0.000 7.039 0.005 C:\Python27\lib\idlelib\rpc.py:238(asyncreturn) 1342 0.005 0.000 7.018 0.005 C:\Python27\lib\idlelib\rpc.py:279(getresponse) 1342 0.035 0.000 7.006 0.005 C:\Python27\lib\idlelib\rpc.py:295(_getresponse) 43649486 6.971 0.000 6.971 0.000 {method 'get' of 'dict' objects} 1341 0.015 0.000 6.950 0.005 C:\Python27\lib\threading.py:235(wait) 5365 6.917 0.001 6.917 0.001 {method 'acquire' of 'thread.lock' objects} 6680354 5.325 0.000 5.325 0.000 {method 'iteritems' of 'dict' objects} 57037048 4.854 0.000 4.854 0.000 {id} </code></pre> <p>@ThomasH: this is the copy function, which is very simple and custom. See my comment to Ross for the content of tree nodes</p> <pre><code>def r_copy_tree(node_to_copy, dad_info): new_node = node(dad_info) for (a,son_to_copy) in node_to_copy.sons.items(): new_node.sons[a]=r_copy_tree(son_to_copy,(new_node,a)) return new_node def copy_tree(root): return r_copy_tree(root,(None,None)) </code></pre>
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      1. POWhat is the fastest way to get multiple copies of a tree in python?
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    1. COWhy do you need multiple copies of a tree, by the way?
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      1. POWhat is the fastest way to get multiple copies of a tree in python?
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    2. COThey will be mounted on a bigger tree.
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      1. POWhat is the fastest way to get multiple copies of a tree in python?
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    3. CO+1 Very good topic, thanks for bringing it up. - Why do you think copying is still the bottleneck, even with your custom copy_tree? Your stats show it at about 10% of the overall run time. Can you show the implementation of copy_tree?
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      1. POWhat is the fastest way to get multiple copies of a tree in python?
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