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Re: [Pytables-users] Pytables-users Digest, Vol 81, Issue 11
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From: Anthony S. <sc...@gm...> - 2013-02-27 20:06:49
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Hi David, Sorry about the delay. I have mostly forgotten what exactly this issue was. I am pretty swamped this week so I could throw out some WAGs but I don't think I'll be able to do any real work myself on it. Be Well Anthony On Mon, Feb 25, 2013 at 2:15 PM, David Reed <dav...@gm...> wrote: > Anthony, > > I've had a chance recently to revisit this problem and am not getting > anywhere. I was hoping I might be able to get more support in getting this > working. If you have some ideas, through them out and I can do the leg > work and see what I can come up with. > > -David > > > On Mon, Feb 4, 2013 at 3:44 PM, < > pyt...@li...> wrote: > >> Send Pytables-users mailing list submissions to >> pyt...@li... >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://lists.sourceforge.net/lists/listinfo/pytables-users >> or, via email, send a message with subject or body 'help' to >> pyt...@li... >> >> You can reach the person managing the list at >> pyt...@li... >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Pytables-users digest..." >> >> >> Today's Topics: >> >> 1. Re: Pytables-users Digest, Vol 81, Issue 9 (Anthony Scopatz) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Mon, 4 Feb 2013 14:43:37 -0600 >> From: Anthony Scopatz <sc...@gm...> >> Subject: Re: [Pytables-users] Pytables-users Digest, Vol 81, Issue 9 >> To: Discussion list for PyTables >> <pyt...@li...> >> Message-ID: >> < >> CAP...@ma...> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Hey David, >> >> I am getting the following error now: >> >> scopatz@ares ~ $ python t.py >> 10669890 Comparisons >> Traceback (most recent call last): >> File "t.py", line 61, in <module> >> get_hd() >> File "t.py", line 54, in get_hd >> for (t1, m1, ii), (t2, m2, jj) in combinations(izip(templates, masks, >> range(N_irises)), 2): >> File "/home/scopatz/.local/lib/python2.7/site-packages/tables/table.py", >> line 3308, in __iter__ >> out=buf_slice) >> File "/home/scopatz/.local/lib/python2.7/site-packages/tables/table.py", >> line 1807, in read >> arr = self._read(start, stop, step, field, out) >> File "/home/scopatz/.local/lib/python2.7/site-packages/tables/table.py", >> line 1732, in _read >> bytes_required)) >> ValueError: output array size invalid, got 4620 bytes, need 753984000 >> bytes >> >> And I had to change the phasors line to ths following: >> >> r['phasors'] = np.empty((17, 20*240), complex) >> >> Thanks. >> Be Well >> Anthony >> >> >> >> On Mon, Feb 4, 2013 at 1:41 PM, David Reed <dav...@gm...> >> wrote: >> >> > I didn't have any luck. I replaced that __iter__ function which led to >> me >> > replacing the read function which lead to me replaceing the _read >> function >> > and I eventually got another error. >> > >> > Below are 2 functions and my HDF5 Table class declaration. They should >> be >> > self explanatory. I wasn't sure if attachments would go through and >> this >> > is pretty small, so I figured it would be ok just to post. I apologize >> if >> > this is a bit cluttered. I would also appreciate any comments on how I >> > assign the results to the matrix D, this does not seem very pythonic at >> all >> > and could use some advice there if its easy. (the ii*jj is just a place >> > holder for a more sophisticated measure). Thanks again! >> > >> > import numpy as np >> > import tables as tb >> > >> > class Iris(tb.IsDescription): >> > subject_id = tb.IntCol() >> > iris_id = tb.IntCol() >> > database = tb.StringCol(5) >> > is_left = tb.BoolCol() >> > is_flipped = tb.BoolCol() >> > templates = tb.BoolCol(shape=(17, 20*480)) >> > masks1 = tb.BoolCol(shape=(17, 20*480)) >> > phasors = tb.ComplexCol(itemsize=8, shape=(17, 20*240)) >> > masks2 = tb.BoolCol(shape=(17, 20*240)) >> > >> > >> > def create_hdf5(): >> > """ >> > """ >> > with tb.openFile('test.h5', 'w') as f: >> > >> > # Create and fill the table of irises", >> > irises = f.createTable(f.root, 'irises', Iris, 'Irises', >> > filters=tb.Filters(1)) >> > for ii in range(4620): >> > >> > r = irises.row >> > r['subject_id'] = ii >> > r['iris_id'] = 0 >> > r['database'] = 'test' >> > r['is_left'] = True >> > r['is_flipped'] = False >> > r['templates'] = np.empty((17, 20*480), np.bool8) >> > r['masks1'] = np.empty((17, 20*480), np.bool8) >> > r['phasors'] = np.empty((17, 20*240)) + 1j*np.empty((17, 20*240)) >> > r['masks2'] = np.empty((17, 20*240), np.bool8) >> > r.append() >> > >> > irises.flush() >> > >> > def get_hd(): >> > """ >> > """ >> > from itertools import combinations, izip >> > with tb.openFile('test.h5') as f: >> > irises = f.root.irises >> > >> > templates = f.root.irises.cols.templates >> > masks = f.root.irises.cols.masks1 >> > >> > N_irises = len(irises) >> > >> > print '%i Comparisons' % (N_irises*(N_irises - 1)/2) >> > D = np.empty((N_irises, N_irises)) >> > for (t1, m1, ii), (t2, m2, jj) in combinations(izip(templates, masks, >> > range(N_irises)), 2): >> > D[ii, jj] = ii*jj >> > >> > np.save('test', D) >> > >> > >> > >> > >> > On Mon, Feb 4, 2013 at 11:16 AM, < >> > pyt...@li...> wrote: >> > >> >> Send Pytables-users mailing list submissions to >> >> pyt...@li... >> >> >> >> To subscribe or unsubscribe via the World Wide Web, visit >> >> https://lists.sourceforge.net/lists/listinfo/pytables-users >> >> or, via email, send a message with subject or body 'help' to >> >> pyt...@li... >> >> >> >> You can reach the person managing the list at >> >> pyt...@li... >> >> >> >> When replying, please edit your Subject line so it is more specific >> >> than "Re: Contents of Pytables-users digest..." >> >> >> >> >> >> Today's Topics: >> >> >> >> 1. Re: Pytables-users Digest, Vol 81, Issue 7 (Anthony Scopatz) >> >> >> >> >> >> ---------------------------------------------------------------------- >> >> >> >> Message: 1 >> >> Date: Mon, 4 Feb 2013 10:16:24 -0600 >> >> From: Anthony Scopatz <sc...@gm...> >> >> Subject: Re: [Pytables-users] Pytables-users Digest, Vol 81, Issue 7 >> >> To: Discussion list for PyTables >> >> <pyt...@li...> >> >> Message-ID: >> >> < >> >> CAP...@ma...> >> >> Content-Type: text/plain; charset="iso-8859-1" >> >> >> >> On Mon, Feb 4, 2013 at 9:53 AM, David Reed <dav...@gm...> >> >> wrote: >> >> >> >> > Hi Josh, >> >> > >> >> > Here is my __iter__ code: >> >> > >> >> > def __iter__(self): >> >> > table = self.table >> >> > itemsize = self.dtype.itemsize >> >> > nrowsinbuf = table._v_file.params['IO_BUFFER_SIZE'] // >> itemsize >> >> > max_row = len(self) >> >> > for start_row in xrange(0, len(self), nrowsinbuf): >> >> > end_row = min([start_row + nrowsinbuf, max_row]) >> >> > buf = table.read(start_row, end_row, 1, >> field=self.pathname) >> >> > for row in buf: >> >> > yield row >> >> > >> >> > It does look different, I will try swapping in the code from github >> and >> >> > see what happens. >> >> > >> >> >> >> Yes, please let us know how that goes! Otherwise send the list both >> the >> >> test data generator script and the script that fails. >> >> >> >> Be Well >> >> Anthony >> >> >> >> >> >> > >> >> > >> >> > On Mon, Feb 4, 2013 at 9:59 AM, < >> >> > pyt...@li...> wrote: >> >> > >> >> >> Send Pytables-users mailing list submissions to >> >> >> pyt...@li... >> >> >> >> >> >> To subscribe or unsubscribe via the World Wide Web, visit >> >> >> https://lists.sourceforge.net/lists/listinfo/pytables-users >> >> >> or, via email, send a message with subject or body 'help' to >> >> >> pyt...@li... >> >> >> >> >> >> You can reach the person managing the list at >> >> >> pyt...@li... >> >> >> >> >> >> When replying, please edit your Subject line so it is more specific >> >> >> than "Re: Contents of Pytables-users digest..." >> >> >> >> >> >> >> >> >> Today's Topics: >> >> >> >> >> >> 1. Re: Pytables-users Digest, Vol 81, Issue 4 (Josh Ayers) >> >> >> 2. Re: Pytables-users Digest, Vol 81, Issue 6 (David Reed) >> >> >> >> >> >> >> >> >> >> ---------------------------------------------------------------------- >> >> >> >> >> >> Message: 1 >> >> >> Date: Fri, 1 Feb 2013 14:08:47 -0800 >> >> >> From: Josh Ayers <jos...@gm...> >> >> >> Subject: Re: [Pytables-users] Pytables-users Digest, Vol 81, Issue 4 >> >> >> To: Discussion list for PyTables >> >> >> <pyt...@li...> >> >> >> Message-ID: >> >> >> <CACOB4aPG4NZ6b2a3v= >> >> >> 1Ue...@ma...> >> >> >> Content-Type: text/plain; charset="iso-8859-1" >> >> >> >> >> >> David, >> >> >> >> >> >> You added a custom version of table.Column.__iter__, correct? Could >> >> you >> >> >> also include that along with the script to reproduce the error? >> >> >> >> >> >> It seems like the problem may be in the 'nrowsinbuf' calculation - >> see >> >> >> [1]. Each of your rows is 17 x 9600 = 163200 bytes. If you're >> using >> >> the >> >> >> default 1MB value for IO_BUFFER_SIZE, it should be reading in rows >> of 6 >> >> >> chunks. Instead, it's reading the entire table. >> >> >> >> >> >> [1]: >> >> >> >> >> >> https://github.com/PyTables/PyTables/blob/develop/tables/table.py#L3296 >> >> >> >> >> >> >> >> >> >> >> >> On Fri, Feb 1, 2013 at 1:50 PM, Anthony Scopatz <sc...@gm...> >> >> >> wrote: >> >> >> >> >> >> > >> >> >> > >> >> >> > On Fri, Feb 1, 2013 at 3:27 PM, David Reed < >> dav...@gm...> >> >> >> wrote: >> >> >> > >> >> >> >> at the error: >> >> >> >> >> >> >> >> result = numpy.empty(shape=nrows, dtype=dtypeField) >> >> >> >> >> >> >> >> nrows = 4620 and dtypeField is ('bool', (17, 9600)) >> >> >> >> >> >> >> >> I'm not sure what that means as a dtype, but thats what it is. >> >> >> >> >> >> >> >> Forgive me if I'm being totally naive, but I thought the whole >> >> point of >> >> >> >> __iter__ with pyttables was to do iteration on the fly, so there >> is >> >> no >> >> >> >> preallocation. >> >> >> >> >> >> >> > >> >> >> > Nope you are not being naive at all. That is the point. >> >> >> > >> >> >> > >> >> >> >> If you have any ideas on this I'm all ears. >> >> >> >> >> >> >> > >> >> >> > If you could send a minimal script which reproduces this error, >> that >> >> >> would >> >> >> > help a lot. >> >> >> > >> >> >> > Be Well >> >> >> > Anthony >> >> >> > >> >> >> > >> >> >> >> >> >> >> >> >> >> >> >> Thanks again. >> >> >> >> >> >> >> >> Dave >> >> >> >> >> >> >> >> >> >> >> >> On Fri, Feb 1, 2013 at 3:45 PM, < >> >> >> >> pyt...@li...> wrote: >> >> >> >> >> >> >> >>> Send Pytables-users mailing list submissions to >> >> >> >>> pyt...@li... >> >> >> >>> >> >> >> >>> To subscribe or unsubscribe via the World Wide Web, visit >> >> >> >>> >> >> https://lists.sourceforge.net/lists/listinfo/pytables-users >> >> >> >>> or, via email, send a message with subject or body 'help' to >> >> >> >>> pyt...@li... >> >> >> >>> >> >> >> >>> You can reach the person managing the list at >> >> >> >>> pyt...@li... >> >> >> >>> >> >> >> >>> When replying, please edit your Subject line so it is more >> specific >> >> >> >>> than "Re: Contents of Pytables-users digest..." >> >> >> >>> >> >> >> >>> >> >> >> >>> Today's Topics: >> >> >> >>> >> >> >> >>> 1. Re: Pytables-users Digest, Vol 81, Issue 2 (Anthony >> Scopatz) >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> ---------------------------------------------------------------------- >> >> >> >>> >> >> >> >>> Message: 1 >> >> >> >>> Date: Fri, 1 Feb 2013 14:44:40 -0600 >> >> >> >>> From: Anthony Scopatz <sc...@gm...> >> >> >> >>> Subject: Re: [Pytables-users] Pytables-users Digest, Vol 81, >> Issue >> >> 2 >> >> >> >>> To: Discussion list for PyTables >> >> >> >>> <pyt...@li...> >> >> >> >>> Message-ID: >> >> >> >>> < >> >> >> >>> >> CAP...@ma... >> >> > >> >> >> >>> Content-Type: text/plain; charset="iso-8859-1" >> >> >> >>> >> >> >> >>> On Fri, Feb 1, 2013 at 12:43 PM, David Reed < >> >> dav...@gm...> >> >> >> >>> wrote: >> >> >> >>> >> >> >> >>> > Hi Anthony, >> >> >> >>> > >> >> >> >>> > Thanks for the reply. >> >> >> >>> > >> >> >> >>> > I honestly don't know how to monitor my Python memory usage, >> but >> >> I'm >> >> >> >>> sure >> >> >> >>> > that its caused by out of memory. >> >> >> >>> > >> >> >> >>> >> >> >> >>> Well, I would just run top or process monitor or something while >> >> >> running >> >> >> >>> the python script to see what happens to memory usage as the >> script >> >> >> chugs >> >> >> >>> along... >> >> >> >>> >> >> >> >>> >> >> >> >>> > I'm just trying to find out how to fix it. My HDF5 table has >> >> 4620 >> >> >> >>> rows >> >> >> >>> > and the column I'm iterating over is a 17x9600 boolean matrix. >> >> The >> >> >> >>> > __iter__ method is preallocating an array that is this size >> which >> >> >> >>> appears >> >> >> >>> > to be root of the error. I was hoping there is a fix >> somewhere >> >> in >> >> >> >>> here to >> >> >> >>> > not have to do this preallocation. >> >> >> >>> > >> >> >> >>> >> >> >> >>> So a 17x9600 boolean matrix should only be 0.155 MB in space. >> >> 4620 of >> >> >> >>> these is ~760 MB. If you have 2 GB of memory and you are >> iterating >> >> >> over >> >> >> >>> 2 >> >> >> >>> of these (templates & masks) it is conceivable that you are just >> >> >> running >> >> >> >>> out of memory. Maybe there is a way that __iter__ could not >> >> >> preallocate >> >> >> >>> something that is basically a temporary. What is the dtype of >> the >> >> >> >>> templates array? >> >> >> >>> >> >> >> >>> Be Well >> >> >> >>> Anthony >> >> >> >>> >> >> >> >>> >> >> >> >>> > >> >> >> >>> > Thanks again. >> >> >> >>> >> >> >> >>> >> >> >> -------------- next part -------------- >> >> >> An HTML attachment was scrubbed... >> >> >> >> >> >> ------------------------------ >> >> >> >> >> >> Message: 2 >> >> >> Date: Mon, 4 Feb 2013 09:58:53 -0500 >> >> >> From: David Reed <dav...@gm...> >> >> >> Subject: Re: [Pytables-users] Pytables-users Digest, Vol 81, Issue 6 >> >> >> To: pyt...@li... >> >> >> Message-ID: >> >> >> <CAM6XA7= >> >> >> h50...@ma...> >> >> >> Content-Type: text/plain; charset="iso-8859-1" >> >> >> >> >> >> Hi Anthony, >> >> >> >> >> >> Sorry to just get back to you. I can send a script, should I send a >> >> script >> >> >> that creates some fake data as well? >> >> >> >> >> >> -Dave >> >> >> >> >> >> >> >> >> On Fri, Feb 1, 2013 at 4:50 PM, < >> >> >> pyt...@li...> wrote: >> >> >> >> >> >> > Send Pytables-users mailing list submissions to >> >> >> > pyt...@li... >> >> >> > >> >> >> > To subscribe or unsubscribe via the World Wide Web, visit >> >> >> > >> https://lists.sourceforge.net/lists/listinfo/pytables-users >> >> >> > or, via email, send a message with subject or body 'help' to >> >> >> > pyt...@li... >> >> >> > >> >> >> > You can reach the person managing the list at >> >> >> > pyt...@li... >> >> >> > >> >> >> > When replying, please edit your Subject line so it is more >> specific >> >> >> > than "Re: Contents of Pytables-users digest..." >> >> >> > >> >> >> > >> >> >> > Today's Topics: >> >> >> > >> >> >> > 1. Re: Pytables-users Digest, Vol 81, Issue 4 (Anthony Scopatz) >> >> >> > >> >> >> > >> >> >> > >> >> ---------------------------------------------------------------------- >> >> >> > >> >> >> > Message: 1 >> >> >> > Date: Fri, 1 Feb 2013 15:50:11 -0600 >> >> >> > From: Anthony Scopatz <sc...@gm...> >> >> >> > Subject: Re: [Pytables-users] Pytables-users Digest, Vol 81, >> Issue 4 >> >> >> > To: Discussion list for PyTables >> >> >> > <pyt...@li...> >> >> >> > Message-ID: >> >> >> > < >> >> >> > >> CAP...@ma...> >> >> >> > Content-Type: text/plain; charset="iso-8859-1" >> >> >> > >> >> >> > On Fri, Feb 1, 2013 at 3:27 PM, David Reed < >> dav...@gm...> >> >> >> wrote: >> >> >> > >> >> >> > > at the error: >> >> >> > > >> >> >> > > result = numpy.empty(shape=nrows, dtype=dtypeField) >> >> >> > > >> >> >> > > nrows = 4620 and dtypeField is ('bool', (17, 9600)) >> >> >> > > >> >> >> > > I'm not sure what that means as a dtype, but thats what it is. >> >> >> > > >> >> >> > > Forgive me if I'm being totally naive, but I thought the whole >> >> point >> >> >> of >> >> >> > > __iter__ with pyttables was to do iteration on the fly, so there >> >> is no >> >> >> > > preallocation. >> >> >> > > >> >> >> > >> >> >> > Nope you are not being naive at all. That is the point. >> >> >> > >> >> >> > >> >> >> > > If you have any ideas on this I'm all ears. >> >> >> > > >> >> >> > >> >> >> > If you could send a minimal script which reproduces this error, >> that >> >> >> would >> >> >> > help a lot. >> >> >> > >> >> >> > Be Well >> >> >> > Anthony >> >> >> > >> >> >> > >> >> >> > > >> >> >> > > >> >> >> > > Thanks again. >> >> >> > > >> >> >> > > Dave >> >> >> > > >> >> >> > > >> >> >> > > On Fri, Feb 1, 2013 at 3:45 PM, < >> >> >> > > pyt...@li...> wrote: >> >> >> > > >> >> >> > >> Send Pytables-users mailing list submissions to >> >> >> > >> pyt...@li... >> >> >> > >> >> >> >> > >> To subscribe or unsubscribe via the World Wide Web, visit >> >> >> > >> >> >> https://lists.sourceforge.net/lists/listinfo/pytables-users >> >> >> > >> or, via email, send a message with subject or body 'help' to >> >> >> > >> pyt...@li... >> >> >> > >> >> >> >> > >> You can reach the person managing the list at >> >> >> > >> pyt...@li... >> >> >> > >> >> >> >> > >> When replying, please edit your Subject line so it is more >> >> specific >> >> >> > >> than "Re: Contents of Pytables-users digest..." >> >> >> > >> >> >> >> > >> >> >> >> > >> Today's Topics: >> >> >> > >> >> >> >> > >> 1. Re: Pytables-users Digest, Vol 81, Issue 2 (Anthony >> Scopatz) >> >> >> > >> >> >> >> > >> >> >> >> > >> >> >> >> >> ---------------------------------------------------------------------- >> >> >> > >> >> >> >> > >> Message: 1 >> >> >> > >> Date: Fri, 1 Feb 2013 14:44:40 -0600 >> >> >> > >> From: Anthony Scopatz <sc...@gm...> >> >> >> > >> Subject: Re: [Pytables-users] Pytables-users Digest, Vol 81, >> >> Issue 2 >> >> >> > >> To: Discussion list for PyTables >> >> >> > >> <pyt...@li...> >> >> >> > >> Message-ID: >> >> >> > >> < >> >> >> > >> >> >> CAP...@ma...> >> >> >> > >> Content-Type: text/plain; charset="iso-8859-1" >> >> >> > >> >> >> >> > >> On Fri, Feb 1, 2013 at 12:43 PM, David Reed < >> >> dav...@gm...> >> >> >> > >> wrote: >> >> >> > >> >> >> >> > >> > Hi Anthony, >> >> >> > >> > >> >> >> > >> > Thanks for the reply. >> >> >> > >> > >> >> >> > >> > I honestly don't know how to monitor my Python memory usage, >> but >> >> >> I'm >> >> >> > >> sure >> >> >> > >> > that its caused by out of memory. >> >> >> > >> > >> >> >> > >> >> >> >> > >> Well, I would just run top or process monitor or something >> while >> >> >> running >> >> >> > >> the python script to see what happens to memory usage as the >> >> script >> >> >> > chugs >> >> >> > >> along... >> >> >> > >> >> >> >> > >> >> >> >> > >> > I'm just trying to find out how to fix it. My HDF5 table >> has >> >> 4620 >> >> >> > rows >> >> >> > >> > and the column I'm iterating over is a 17x9600 boolean >> matrix. >> >> The >> >> >> > >> > __iter__ method is preallocating an array that is this size >> >> which >> >> >> > >> appears >> >> >> > >> > to be root of the error. I was hoping there is a fix >> somewhere >> >> in >> >> >> > here >> >> >> > >> to >> >> >> > >> > not have to do this preallocation. >> >> >> > >> > >> >> >> > >> >> >> >> > >> So a 17x9600 boolean matrix should only be 0.155 MB in space. >> >> 4620 >> >> >> of >> >> >> > >> these is ~760 MB. If you have 2 GB of memory and you are >> >> iterating >> >> >> > over 2 >> >> >> > >> of these (templates & masks) it is conceivable that you are >> just >> >> >> running >> >> >> > >> out of memory. Maybe there is a way that __iter__ could not >> >> >> preallocate >> >> >> > >> something that is basically a temporary. What is the dtype of >> the >> >> >> > >> templates array? >> >> >> > >> >> >> >> > >> Be Well >> >> >> > >> Anthony >> >> >> > >> >> >> >> > >> >> >> >> > >> > >> >> >> > >> > Thanks again. >> >> >> > >> > >> >> >> > >> > >> >> >> > >> > >> >> >> > >> > >> >> >> > >> > On Fri, Feb 1, 2013 at 11:12 AM, < >> >> >> > >> > pyt...@li...> wrote: >> >> >> > >> > >> >> >> > >> >> Send Pytables-users mailing list submissions to >> >> >> > >> >> pyt...@li... >> >> >> > >> >> >> >> >> > >> >> To subscribe or unsubscribe via the World Wide Web, visit >> >> >> > >> >> >> >> >> https://lists.sourceforge.net/lists/listinfo/pytables-users >> >> >> > >> >> or, via email, send a message with subject or body 'help' to >> >> >> > >> >> pyt...@li... >> >> >> > >> >> >> >> >> > >> >> You can reach the person managing the list at >> >> >> > >> >> pyt...@li... >> >> >> > >> >> >> >> >> > >> >> When replying, please edit your Subject line so it is more >> >> >> specific >> >> >> > >> >> than "Re: Contents of Pytables-users digest..." >> >> >> > >> >> >> >> >> > >> >> >> >> >> > >> >> Today's Topics: >> >> >> > >> >> >> >> >> > >> >> 1. Re: Pytables-users Digest, Vol 80, Issue 9 (Anthony >> >> Scopatz) >> >> >> > >> >> >> >> >> > >> >> >> >> >> > >> >> >> >> >> > >> >> ---------------------------------------------------------------------- >> >> >> > >> >> >> >> >> > >> >> Message: 1 >> >> >> > >> >> Date: Fri, 1 Feb 2013 10:11:47 -0600 >> >> >> > >> >> From: Anthony Scopatz <sc...@gm...> >> >> >> > >> >> Subject: Re: [Pytables-users] Pytables-users Digest, Vol 80, >> >> >> Issue 9 >> >> >> > >> >> To: Discussion list for PyTables >> >> >> > >> >> <pyt...@li...> >> >> >> > >> >> Message-ID: >> >> >> > >> >> < >> >> >> > >> >> >> >> >> CAP...@ma...> >> >> >> > >> >> Content-Type: text/plain; charset="iso-8859-1" >> >> >> > >> >> >> >> >> > >> >> Hi David, >> >> >> > >> >> >> >> >> > >> >> Sorry, I haven't had a ton of time recently. You seem to be >> >> >> getting >> >> >> > a >> >> >> > >> >> memory error on creating a numpy array. This kind of thing >> >> >> typically >> >> >> > >> >> happens when you are out of memory. Does this seem to be >> the >> >> case >> >> >> > with >> >> >> > >> >> you? When this dies, is your memory usage at 100%? If so, >> >> this >> >> >> > >> algorithm >> >> >> > >> >> might require a little tweaking... >> >> >> > >> >> >> >> >> > >> >> Be Well >> >> >> > >> >> Anthony >> >> >> > >> >> >> >> >> > >> >> >> >> >> > >> >> On Fri, Feb 1, 2013 at 6:15 AM, David Reed < >> >> >> dav...@gm...> >> >> >> > >> >> wrote: >> >> >> > >> >> >> >> >> > >> >> > I'm still having problems with this one. I can't tell if >> >> this >> >> >> > >> something >> >> >> > >> >> > dumb Im doing with itertools, or if its something in >> >> pytables. >> >> >> > >> >> > >> >> >> > >> >> > Would appreciate any help. >> >> >> > >> >> > >> >> >> > >> >> > Thanks >> >> >> > >> >> > >> >> >> > >> >> > >> >> >> > >> >> > On Wed, Jan 30, 2013 at 5:00 PM, David Reed < >> >> >> > dav...@gm... >> >> >> > >> >> >wrote: >> >> >> > >> >> > >> >> >> > >> >> >> I think I have to reopen this issue. I have been running >> >> fine >> >> >> for >> >> >> > >> >> awhile >> >> >> > >> >> >> using the combinations method from itertools, but have >> >> recently >> >> >> > run >> >> >> > >> >> into a >> >> >> > >> >> >> memory since I have recently quadrupled the size of the >> hdf >> >> >> file. >> >> >> > >> >> >> >> >> >> > >> >> >> Here is my code again: >> >> >> > >> >> >> >> >> >> > >> >> >> from itertools import combinations, izip >> >> >> > >> >> >> with tb.openFile(h5_all, 'r') as f: >> >> >> > >> >> >> irises = f.root.irises >> >> >> > >> >> >> >> >> >> > >> >> >> templates = f.root.irises.cols.templates >> >> >> > >> >> >> masks = f.root.irises.cols.masks1 >> >> >> > >> >> >> >> >> >> > >> >> >> N_irises = len(irises) >> >> >> > >> >> >> index = np.ones((20 * 480), np.bool) >> >> >> > >> >> >> >> >> >> > >> >> >> print '%i Comparisons' % (N_irises*(N_irises - 1)/2) >> >> >> > >> >> >> D = np.empty((N_irises, N_irises)) >> >> >> > >> >> >> for (t1, m1, ii), (t2, m2, jj) in >> >> combinations(izip(templates, >> >> >> > >> masks, >> >> >> > >> >> >> range(N_irises)), 2): >> >> >> > >> >> >> # print ii >> >> >> > >> >> >> D[ii, jj] = ham_dist( >> >> >> > >> >> >> t1[8, index], >> >> >> > >> >> >> t2[:, index], >> >> >> > >> >> >> m1[8, index], >> >> >> > >> >> >> m2[:, index], >> >> >> > >> >> >> ) >> >> >> > >> >> >> >> >> >> > >> >> >> And here is the error: >> >> >> > >> >> >> >> >> >> > >> >> >> In [10]: get_hd3() >> >> >> > >> >> >> 10669890 Comparisons >> >> >> > >> >> >> >> >> >> > >> >> >> >> >> >> > >> >> >> >> >> > >> >> >> >> > >> >> >> >> >> >> --------------------------------------------------------------------------- >> >> >> > >> >> >> MemoryError Traceback (most >> >> >> recent >> >> >> > >> call >> >> >> > >> >> >> last) >> >> >> > >> >> >> <ipython-input-10-cfb255ce7bd1> in <module>() >> >> >> > >> >> >> ----> 1 get_hd3() >> >> >> > >> >> >> >> >> >> > >> >> >> >> >> >> > >> >> >> 118 print '%i Comparisons' % >> >> >> > >> (N_irises*(N_irises - >> >> >> > >> >> >> 1)/2) >> >> >> > >> >> >> 119 D = np.empty((N_irises, >> N_irises)) >> >> >> > >> >> >> --> 120 for (t1, m1, ii), (t2, m2, jj) in >> >> >> > >> >> >> combinations(izip(temp >> >> >> > >> >> >> lates, masks, range(N_irises)), 2): >> >> >> > >> >> >> 121 # print ii >> >> >> > >> >> >> 122 D[ii, jj] = ham_dist( >> >> >> > >> >> >> >> >> >> > >> >> >> c:\python27\lib\site-packages\tables\table.pyc in >> >> >> __iter__(self) >> >> >> > >> >> >> 3274 for start_row in xrange(0, len(self), >> >> >> nrowsinbuf): >> >> >> > >> >> >> 3275 end_row = min([start_row + >> nrowsinbuf, >> >> >> > max_row]) >> >> >> > >> >> >> -> 3276 buf = table.read(start_row, end_row, >> 1, >> >> >> > >> >> >> field=self.pathname) >> >> >> > >> >> >> >> >> >> > >> >> >> 3277 for row in buf: >> >> >> > >> >> >> 3278 yield row >> >> >> > >> >> >> >> >> >> > >> >> >> c:\python27\lib\site-packages\tables\table.pyc in >> read(self, >> >> >> > start, >> >> >> > >> >> stop, >> >> >> > >> >> >> step, >> >> >> > >> >> >> field) >> >> >> > >> >> >> 1772 (start, stop, step) = >> >> >> > self._processRangeRead(start, >> >> >> > >> >> stop, >> >> >> > >> >> >> step) >> >> >> > >> >> >> 1773 >> >> >> > >> >> >> -> 1774 arr = self._read(start, stop, step, >> field) >> >> >> > >> >> >> 1775 return internal_to_flavor(arr, >> self.flavor) >> >> >> > >> >> >> 1776 >> >> >> > >> >> >> >> >> >> > >> >> >> c:\python27\lib\site-packages\tables\table.pyc in >> >> _read(self, >> >> >> > start, >> >> >> > >> >> >> stop, step, >> >> >> > >> >> >> field) >> >> >> > >> >> >> 1719 if field: >> >> >> > >> >> >> 1720 # Create a container for the results >> >> >> > >> >> >> -> 1721 result = numpy.empty(shape=nrows, >> >> >> > >> dtype=dtypeField) >> >> >> > >> >> >> 1722 else: >> >> >> > >> >> >> 1723 # Recarray case >> >> >> > >> >> >> >> >> >> > >> >> >> MemoryError: >> >> >> > >> >> >> > >> c:\python27\lib\site-packages\tables\table.py(1721)_read() >> >> >> > >> >> >> 1720 # Create a container for the results >> >> >> > >> >> >> -> 1721 result = numpy.empty(shape=nrows, >> >> >> > >> dtype=dtypeField) >> >> >> > >> >> >> 1722 else: >> >> >> > >> >> >> >> >> >> > >> >> >> Also, if you guys see any performance problems in my >> code, >> >> >> please >> >> >> > >> let >> >> >> > >> >> me >> >> >> > >> >> >> know. >> >> >> > >> >> >> >> >> >> > >> >> >> Thank you so much for the help. >> >> >> > >> >> >> >> >> >> > >> >> >> -Dave >> >> >> > >> >> >> >> >> >> > >> >> >> >> >> >> > >> >> >> On Fri, Jan 4, 2013 at 8:57 AM, < >> >> >> > >> >> >> pyt...@li...> wrote: >> >> >> > >> >> >> >> >> >> > >> >> >>> Send Pytables-users mailing list submissions to >> >> >> > >> >> >>> pyt...@li... >> >> >> > >> >> >>> >> >> >> > >> >> >>> To subscribe or unsubscribe via the World Wide Web, >> visit >> >> >> > >> >> >>> >> >> >> > >> https://lists.sourceforge.net/lists/listinfo/pytables-users >> >> >> > >> >> >>> or, via email, send a message with subject or body >> 'help' >> >> to >> >> >> > >> >> >>> pyt...@li... >> >> >> > >> >> >>> >> >> >> > >> >> >>> You can reach the person managing the list at >> >> >> > >> >> >>> pyt...@li... >> >> >> > >> >> >>> >> >> >> > >> >> >>> When replying, please edit your Subject line so it is >> more >> >> >> > specific >> >> >> > >> >> >>> than "Re: Contents of Pytables-users digest..." >> >> >> > >> >> >>> >> >> >> > >> >> >>> >> >> >> > >> >> >>> Today's Topics: >> >> >> > >> >> >>> >> >> >> > >> >> >>> 1. Re: Pytables-users Digest, Vol 80, Issue 8 (David >> >> Reed) >> >> >> > >> >> >>> >> >> >> > >> >> >>> >> >> >> > >> >> >>> >> >> >> > >> >> >> >> >> ---------------------------------------------------------------------- >> >> >> > >> >> >>> >> >> >> > >> >> >>> Message: 1 >> >> >> > >> >> >>> Date: Fri, 4 Jan 2013 08:56:28 -0500 >> >> >> > >> >> >>> From: David Reed <dav...@gm...> >> >> >> > >> >> >>> Subject: Re: [Pytables-users] Pytables-users Digest, Vol >> >> 80, >> >> >> > Issue >> >> >> > >> 8 >> >> >> > >> >> >>> To: pyt...@li... >> >> >> > >> >> >>> Message-ID: >> >> >> > >> >> >>> < >> >> >> > >> >> >>> >> >> >> > >> CAM...@ma... >> >> >> > >> > >> >> >> > >> >> >>> Content-Type: text/plain; charset="iso-8859-1" >> >> >> > >> >> >>> >> >> >> > >> >> >>> I can't thank you guys enough for the help. I was able >> to >> >> add >> >> >> > the >> >> >> > >> >> >>> __iter__ >> >> >> > >> >> >>> function to the table.py file and everything seems to be >> >> >> working >> >> >> > >> >> great! >> >> >> > >> >> >>> I'm not quite as fast as I was with iterating right of >> a >> >> >> matrix >> >> >> > >> but >> >> >> > >> >> >>> pretty >> >> >> > >> >> >>> close. I was at 555 comparisons per second, and now im >> at >> >> >> 420. >> >> >> > >> >> >>> >> >> >> > >> >> >>> I handled the problem I mentioned earlier by doing this, >> >> and >> >> >> it >> >> >> > >> seems >> >> >> > >> >> to >> >> >> > >> >> >>> work great: >> >> >> > >> >> >>> >> >> >> > >> >> >>> A = f.root.data.cols.A >> >> >> > >> >> >>> B = f.root.data.cols.B >> >> >> > >> >> >>> >> >> >> > >> >> >>> D = np.empty((len(A), len(A)) >> >> >> > >> >> >>> for (a1, b1, ii), (a2, b2, jj) in combinations(izip(A, >> B, >> >> >> > >> >> range(len(A))), >> >> >> > >> >> >>> 2): >> >> >> > >> >> >>> D[ii, jj] = compare(a1, a2, b1, b2) >> >> >> > >> >> >>> >> >> >> > >> >> >>> Again, thanks a lot. >> >> >> > >> >> >>> >> >> >> > >> >> >>> -Dave >> >> >> > >> >> >>> >> >> >> > >> >> >>> >> >> >> > >> >> >>> On Thu, Jan 3, 2013 at 6:31 PM, < >> >> >> > >> >> >>> pyt...@li...> wrote: >> >> >> > >> >> >>> >> >> >> > >> >> >>> > Send Pytables-users mailing list submissions to >> >> >> > >> >> >>> > pyt...@li... >> >> >> > >> >> >>> > >> >> >> > >> >> >>> > To subscribe or unsubscribe via the World Wide Web, >> visit >> >> >> > >> >> >>> > >> >> >> > >> https://lists.sourceforge.net/lists/listinfo/pytables-users >> >> >> > >> >> >>> > or, via email, send a message with subject or body >> >> 'help' to >> >> >> > >> >> >>> > pyt...@li... >> >> >> > >> >> >>> > >> >> >> > >> >> >>> > You can reach the person managing the list at >> >> >> > >> >> >>> > pyt...@li... >> >> >> > >> >> >>> > >> >> >> > >> >> >>> > When replying, please edit your Subject line so it is >> >> more >> >> >> > >> specific >> >> >> > >> >> >>> > than "Re: Contents of Pytables-users digest..." >> >> >> > >> >> >>> > >> >> >> > >> >> >>> > >> >> >> > >> >> >>> > Today's Topics: >> >> >> > >> >> >>> > >> >> >> > >> >> >>> > 1. Re: Pytables-users Digest, Vol 80, Issue 3 >> (Anthony >> >> >> > >> Scopatz) >> >> >> > >> >> >>> > 2. Re: Pytables-users Digest, Vol 80, Issue 4 >> (Anthony >> >> >> > >> Scopatz) >> >> >> > >> >> >>> > >> >> >> > >> >> >>> > >> >> >> > >> >> >>> > >> >> >> > >> >> >> >> >> > >> >> ---------------------------------------------------------------------- >> >> >> > >> >> >>> > >> >> >> > >> >> >>> > Message: 1 >> >> >> > >> >> >>> > Date: Thu, 3 Jan 2013 17:26:55 -0600 >> >> >> > >> >> >>> > From: Anthony Scopatz <sc...@gm...> >> >> >> > >> >> >>> > Subject: Re: [Pytables-users] Pytables-users Digest, >> Vol >> >> 80, >> >> >> > >> Issue 3 >> >> >> > >> >> >>> > To: Discussion list for PyTables >> >> >> > >> >> >>> > <pyt...@li...> >> >> >> > >> >> >>> > Message-ID: >> >> >> > >> >> >>> > <CAPk-6T6sz=J5ay_a9YGLPe_yBLGa9c+XgxG0CRNs6fJ= >> >> >> > >> >> >>> > Gz...@ma...> >> >> >> > >> >> >>> > Content-Type: text/plain; charset="iso-8859-1" >> >> >> > >> >> >>> > >> >> >> > >> >> >>> > On Thu, Jan 3, 2013 at 2:17 PM, David Reed < >> >> >> > >> dav...@gm...> >> >> >> > >> >> >>> wrote: >> >> >> > >> >> >>> > >> >> >> > >> >> >>> > > Thanks a lot for the help so far guys! >> >> >> > >> >> >>> > > >> >> >> > >> >> >>> > > Looking at itertools, I found what I believe to be >> the >> >> >> > perfect >> >> >> > >> >> >>> function >> >> >> > >> >> >>> > > for what I need, itertools.combinations. This >> appears >> >> to >> >> >> be a >> >> >> > >> >> valid >> >> >> > >> >> >>> > > replacement to the method proposed. >> >> >> > >> >> >>> > > >> >> >> > >> >> >>> > >> >> >> > >> >> >>> > Yes, combinations is awesome! >> >> >> > >> >> >>> > >> >> >> > >> >> >>> > >> >> >> > >> >> >>> > > >> >> >> > >> >> >>> > > There is a small problem that I didn't mention is >> that >> >> my >> >> >> > >> compare >> >> >> > >> >> >>> > function >> >> >> > >> >> >>> > > actually takes as inputs 2 columns from the table. >> Like >> >> >> so: >> >> >> > >> >> >>> > > >> >> >> > >> >> >>> > > D = np.empty((N_irises, N_irises)) >> >> >> > >> >> >>> > > for ii in xrange(N_elements): >> >> >> > >> >> >>> > > for jj in xrange(ii+1, N_elements): >> >> >> > >> >> >>> > > D[ii, jj] = compare(data['element1'][ii], >> >> >> > >> >> >>> > data['element1'][jj],data['element2'][ii], >> >> >> > >> >> >>> > > data['element2'][jj]) >> >> >> > >> >> >>> > > >> >> >> > >> >> >>> > > Is there an efficient way of using itertools with >> this >> >> >> > >> structure? >> >> >> > >> >> >>> > > >> >> >> > >> >> >>> > >> >> >> > >> >> >>> > You can always make two other iterators for each >> column. >> >> >> Since >> >> >> > >> you >> >> >> > >> >> >>> have >> >> >> > >> >> >>> > two columns you would have 4 iterators. I am not sure >> >> how >> >> >> fast >> >> >> > >> >> this is >> >> >> > >> >> >>> > going to be but I am confident that there is >> definitely a >> >> >> way >> >> >> > to >> >> >> > >> do >> >> >> > >> >> >>> this in >> >> >> > >> >> >>> > one for-loop, which is going to be way faster than >> nested >> >> >> > loops. >> >> >> > >> >> >>> > >> >> >> > >> >> >>> > Be Well >> >> >> > >> >> >>> > Anthony >> >> >> > >> >> >>> > >> >> >> > >> >> >>> > >> >> >> > >> >> >>> > > >> >> >> > >> >> >>> > > >> >> >> > >> >> >>> > > On Thu, Jan 3, 2013 at 1:29 PM, < >> >> >> > >> >> >>> > > pyt...@li...> >> wrote: >> >> >> > >> >> >>> > > >> >> >> > >> >> >>> > >> Send Pytables-users mailing list submissions to >> >> >> > >> >> >>> > >> pyt...@li... >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> To subscribe or unsubscribe via the World Wide Web, >> >> visit >> >> >> > >> >> >>> > >> >> >> >> > >> >> https://lists.sourceforge.net/lists/listinfo/pytables-users >> >> >> > >> >> >>> > >> or, via email, send a message with subject or body >> >> >> 'help' to >> >> >> > >> >> >>> > >> >> pyt...@li... >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> You can reach the person managing the list at >> >> >> > >> >> >>> > >> pyt...@li... >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> When replying, please edit your Subject line so it >> is >> >> >> more >> >> >> > >> >> specific >> >> >> > >> >> >>> > >> than "Re: Contents of Pytables-users digest..." >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> Today's Topics: >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> 1. Re: Nested Iteration of HDF5 using PyTables >> >> (Josh >> >> >> > Ayers) >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> >> >> >> > >> >> >> >> >> ---------------------------------------------------------------------- >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> Message: 1 >> >> >> > >> >> >>> > >> Date: Thu, 3 Jan 2013 10:29:33 -0800 >> >> >> > >> >> >>> > >> From: Josh Ayers <jos...@gm...> >> >> >> > >> >> >>> > >> Subject: Re: [Pytables-users] Nested Iteration of >> HDF5 >> >> >> using >> >> >> > >> >> >>> PyTables >> >> >> > >> >> >>> > >> To: Discussion list for PyTables >> >> >> > >> >> >>> > >> <pyt...@li...> >> >> >> > >> >> >>> > >> Message-ID: >> >> >> > >> >> >>> > >> < >> >> >> > >> >> >>> > >> >> >> >> > >> >> >> >> >> CAC...@ma...> >> >> >> > >> >> >>> > >> Content-Type: text/plain; charset="iso-8859-1" >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> David, >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> The change in issue 27 was only for iteration over >> a >> >> >> > >> >> tables.Column >> >> >> > >> >> >>> > >> instance. To use it, tweak Anthony's code as >> follows. >> >> >> This >> >> >> > >> will >> >> >> > >> >> >>> > iterate >> >> >> > >> >> >>> > >> over the "element" column, as in your original >> >> example. >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> Note also that this will only work with the >> >> development >> >> >> > >> version >> >> >> > >> >> of >> >> >> > >> >> >>> > >> PyTables >> >> >> > >> >> >>> > >> available on github. It will be very slow using >> the >> >> >> > released >> >> >> > >> >> >>> v2.4.0. >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> from itertools import izip >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> with tb.openFile(...) as f: >> >> >> > >> >> >>> > >> data = f.root.data.cols.element >> >> >> > >> >> >>> > >> data_i = iter(data) >> >> >> > >> >> >>> > >> data_j = iter(data) >> >> >> > >> >> >>> > >> data_i.next() # throw the first value away >> >> >> > >> >> >>> > >> for i, j in izip(data_i, data_j): >> >> >> > >> >> >>> > >> compare(i, j) >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> Hope that helps, >> >> >> > >> >> >>> > >> Josh >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> On Thu, Jan 3, 2013 at 9:11 AM, Anthony Scopatz < >> >> >> > >> >> sc...@gm...> >> >> >> > >> >> >>> > >> wrote: >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> > HI David, >> >> >> > >> >> >>> > >> > >> >> >> > >> >> >>> > >> > Tables and table column iteration have been >> >> overhauled >> >> >> > >> fairly >> >> >> > >> >> >>> recently >> >> >> > >> >> >>> > >> > [1]. So you might try creating two iterators, >> >> offset >> >> >> by >> >> >> > >> one, >> >> >> > >> >> and >> >> >> > >> >> >>> then >> >> >> > >> >> >>> > >> > doing the comparison. I am hacking this out >> super >> >> >> quick >> >> >> > so >> >> >> > >> >> please >> >> >> > >> >> >>> > >> forgive >> >> >> > >> >> >>> > >> > me: >> >> >> > >> >> >>> > >> > >> >> >> > >> >> >>> > >> > from itertools import izip >> >> >> > >> >> >>> > >> > >> >> >> > >> >> >>> > >> > with tb.openFile(...) as f: >> >> >> > >> >> >>> > >> > data = f.root.data >> >> >> > >> >> >>> > >> > data_i = iter(data) >> >> >> > >> >> >>> > >> > data_j = iter(data) >> >> >> > >> >> >>> > >> > data_i.next() # throw the first value away >> >> >> > >> >> >>> > >> > for i, j in izip(data_i, data_j): >> >> >> > >> >> >>> > >> > compare(i, j) >> >> >> > >> >> >>> > >> > >> >> >> > >> >> >>> > >> > You get the idea ;) >> >> >> > >> >> >>> > >> > >> >> >> > >> >> >>> > >> > Be Well >> >> >> > >> >> >>> > >> > Anthony >> >> >> > >> >> >>> > >> > >> >> >> > >> >> >>> > >> > 1. >> https://github.com/PyTables/PyTables/issues/27 >> >> >> > >> >> >>> > >> > >> >> >> > >> >> >>> > >> > >> >> >> > >> >> >>> > >> > On Thu, Jan 3, 2013 at 9:25 AM, David Reed < >> >> >> > >> >> >>> dav...@gm...> >> >> >> > >> >> >>> > >> wrote: >> >> >> > >> >> >>> > >> > >> >> >> > >> >> >>> > >> >> I was hoping someone could help me out here. >> >> >> > >> >> >>> > >> >> >> >> >> > >> >> >>> > >> >> This is from a post I put up on StackOverflow, >> >> >> > >> >> >>> > >> >> >> >> >> > >> >> >>> > >> >> I am have a fairly large dataset that I store in >> >> HDF5 >> >> >> and >> >> >> > >> >> access >> >> >> > >> >> >>> > using >> >> >> > >> >> >>> > >> >> PyTables. One operation I need to do on this >> >> dataset >> >> >> are >> >> >> > >> >> pairwise >> >> >> > >> >> >>> > >> >> comparisons between each of the elements. This >> >> >> requires 2 >> >> >> > >> >> loops, >> >> >> > >> >> >>> one >> >> >> > >> >> >>> > to >> >> >> > >> >> >>> > >> >> iterate over each element, and an inner loop to >> >> >> iterate >> >> >> > >> over >> >> >> > >> >> >>> every >> >> >> > >> >> >>> > >> other >> >> >> > >> >> >>> > >> >> element. This operation thus looks at N(N-1)/2 >> >> >> > comparisons. >> >> >> > >> >> >>> > >> >> >> >> >> > >> >> >>> > >> >> For fairly small sets I found it to be faster to >> >> dump >> >> >> the >> >> >> > >> >> >>> contents >> >> >> > >> >> >>> > >> into a >> >> >> > >> >> >>> > >> >> multdimensional numpy array and then do my >> >> iteration. >> >> >> I >> >> >> > run >> >> >> > >> >> into >> >> >> > >> >> >>> > >> problems >> >> >> > >> >> >>> > >> >> with large sets because of memory issues and >> need >> >> to >> >> >> > access >> >> >> > >> >> each >> >> >> > >> >> >>> > >> element of >> >> >> > >> >> >>> > >> >> the dataset at run time. >> >> >> > >> >> >>> > >> >> >> >> >> > >> >> >>> > >> >> Putting the elements into an array gives me >> about >> >> 600 >> >> >> > >> >> >>> comparisons per >> >> >> > >> >> >>> > >> >> second, while operating on hdf5 data itself >> gives >> >> me >> >> >> > about >> >> >> > >> 300 >> >> >> > >> >> >>> > >> comparisons >> >> >> > >> >> >>> > >> >> per second. >> >> >> > >> >> >>> > >> >> >> >> >> > >> >> >>> > >> >> Is there a way to speed this process up? >> >> >> > >> >> >>> > >> >> >> >> >> > >> >> >>> > >> >> Example follows (this is not my real code, just >> an >> >> >> > >> example): >> >> >> > >> >> >>> > >> >> >> >> >> > >> >> >>> > >> >> *Small Set*: >> >> >> > >> >> >>> > >> >> >> >> >> > >> >> >>> > >> >> >> >> >> > >> >> >>> > >> >> with tb.openFile(h5_file, 'r') as f: >> >> >> > >> >> >>> > >> >> data = f.root.data >> >> >> > >> >> >>> > >> >> >> >> >> > >> >> >>> > >> >> N_elements = len(data) >> >> >> > >> >> >>> > >> >> elements = np.empty((N_irises, 1e5)) >> >> >> > >> >> >>> > >> >> >> >> >> > >> >> >>> > >> >> for ii, d in enumerate(data): >> >> >> > >> >> >>> > >> >> elements[ii] = data['element'] >> >> >> > >> >> >>> > >> >> >> >> >> > >> >> >>> > >> >> D = np.empty((N_irises, N_irises)) for ii in >> >> >> > >> >> xrange(N_elements): >> >> >> > >> >> >>> > >> >> for jj in xrange(ii+1, N_elements): >> >> >> > >> >> >>> > >> >> D[ii, jj] = compare(elements[ii], >> >> >> elements[jj]) >> >> >> > >> >> >>> > >> >> >> >> >> > >> >> >>> > >> >> *Large Set*: >> >> >> > >> >> >>> > >> >> >> >> >> > >> >> >>> > >> >> >> >> >> > >> >> >>> > >> >> with tb.openFile(h5_file, 'r') as f: >> >> >> > >> >> >>> > >> >> data = f.root.data >> >> >> > >> >> >>> > >> >> >> >> >> > >> >> >>> > >> >> N_elements = len(data) >> >> >> > >> >> >>> > >> >> >> >> >> > >> >> >>> > >> >> D = np.empty((N_irises, N_irises)) >> >> >> > >> >> >>> > >> >> for ii in xrange(N_elements): >> >> >> > >> >> >>> > >> >> for jj in xrange(ii+1, N_elements): >> >> >> > >> >> >>> > >> >> D[ii, jj] = >> >> compare(data['element'][ii], >> >> >> > >> >> >>> > >> data['element'][jj]) >> >> >> > >> >> >>> > >> >> >> >> >> > >> >> >>> > >> >> >> >> >> > >> >> >>> > >> >> >> >> >> > >> >> >>> > >> >> >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> >> >> > >> >> >>> >> >> >> > >> >> >> >> >> > >> >> >> >> > >> >> >> >> >> >> ------------------------------------------------------------------------------ >> >> >> > >> >> >>> > >> >> Master Visual Studio, SharePoint, SQL, ASP.NET, >> C# >> >> >> 2012, >> >> >> > >> >> HTML5, >> >> >> > >> >> >>> CSS, >> >> >> > >> >> >>> > >> >> MVC, Windows 8 Apps, JavaScript and much more. >> Keep >> >> >> your >> >> >> > >> >> skills >> >> >> > >> >> >>> > current >> >> >> > >> >> >>> > >> >> with LearnDevNow - 3,200 step-by-step video >> >> tutorials >> >> >> by >> >> >> > >> >> >>> Microsoft >> >> >> > >> >> >>> > >> >> MVPs and experts. ON SALE this month only -- >> learn >> >> >> more >> >> >> > at: >> >> >> > >> >> >>> > >> >> http://p.sf.net/sfu/learnmore_122712 >> >> >> > >> >> >>> > >> >> _______________________________________________ >> >> >> > >> >> >>> > >> >> Pytables-users mailing list >> >> >> > >> >> >>> > >> >> Pyt...@li... >> >> >> > >> >> >>> > >> >> >> >> >> > >> https://lists.sourceforge.net/lists/listinfo/pytables-users >> >> >> > >> >> >>> > >> >> >> >> >> > >> >> >>> > >> >> >> >> >> > >> >> >>> > >> > >> >> >> > >> >> >>> > >> > >> >> >> > >> >> >>> > >> > >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> >> >> > >> >> >>> >> >> >> > >> >> >> >> >> > >> >> >> >> > >> >> >> >> >> >> ------------------------------------------------------------------------------ >> >> >> > >> >> >>> > >> > Master Visual Studio, SharePoint, SQL, ASP.NET, >> C# >> >> >> 2012, >> >> >> > >> >> HTML5, >> >> >> > >> >> >>> CSS, >> >> >> > >> >> >>> > >> > MVC, Windows 8 Apps, JavaScript and much more. >> Keep >> >> >> your >> >> >> > >> skills >> >> >> > >> >> >>> > current >> >> >> > >> >> >>> > >> > with LearnDevNow - 3,200 step-by-step video >> >> tutorials >> >> >> by >> >> >> > >> >> Microsoft >> >> >> > >> >> >>> > >> > MVPs and experts. ON SALE this month only -- >> learn >> >> more >> >> >> > at: >> >> >> > >> >> >>> > >> > http://p.sf.net/sfu/learnmore_122712 >> >> >> > >> >> >>> > >> > _______________________________________________ >> >> >> > >> >> >>> > >> > Pytables-users mailing list >> >> >> > >> >> >>> > >> > Pyt...@li... >> >> >> > >> >> >>> > >> > >> >> >> > https://lists.sourceforge.net/lists/listinfo/pytables-users >> >> >> > >> >> >>> > >> > >> >> >> > >> >> >>> > >> > >> >> >> > >> >> >>> > >> -------------- next part -------------- >> >> >> > >> >> >>> > >> An HTML attachment was scrubbed... >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> ------------------------------ >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> >> >> > >> >> >>> >> >> >> > >> >> >> >> >> > >> >> >> >> > >> >> >> >> >> >> ------------------------------------------------------------------------------ >> >> >> > >> >> >>> > >> Master Visual Studio, SharePoint, SQL, ASP.NET, C# >> >> 2012, >> >> >> > >> HTML5, >> >> >> > >> >> >>> CSS, >> >> >> > >> >> >>> > >> MVC, Windows 8 Apps, JavaScript and much more. Keep >> >> your >> >> >> > >> skills >> >> >> > >> >> >>> current >> >> >> > >> >> >>> > >> with LearnDevNow - 3,200 step-by-step video >> tutorials >> >> by >> >> >> > >> >> Microsoft >> >> >> > >> >> >>> > >> MVPs and experts. ON SALE this month only -- learn >> >> more >> >> >> at: >> >> >> > >> >> >>> > >> http://p.sf.net/sfu/learnmore_122712 >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> ------------------------------ >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> _______________________________________________ >> >> >> > >> >> >>> > >> Pytables-users mailing list >> >> >> > >> >> >>> > >> Pyt...@li... >> >> >> > >> >> >>> > >> >> >> >> https://lists.sourceforge.net/lists/listinfo/pytables-users >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> End of Pytables-users Digest, Vol 80, Issue 3 >> >> >> > >> >> >>> > >> ********************************************* >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > > >> >> >> > >> >> >>> > > >> >> >> > >> >> >>> > > >> >> >> > >> >> >>> > > >> >> >> > >> >> >>> > >> >> >> > >> >> >>> >> >> >> > >> >> >> >> >> > >> >> >> >> > >> >> >> >> >> >> ------------------------------------------------------------------------------ >> >> >> > >> >> >>> > > Master Visual Studio, SharePoint, SQL, ASP.NET, C# >> >> 2012, >> >> >> > >> HTML5, >> >> >> > >> >> CSS, >> >> >> > >> >> >>> > > MVC, Windows 8 Apps, JavaScript and much more. Keep >> >> your >> >> >> > skills >> >> >> > >> >> >>> current >> >> >> > >> >> >>> > > with LearnDevNow - 3,200 step-by-step video >> tutorials >> >> by >> >> >> > >> Microsoft >> >> >> > >> >> >>> > > MVPs and experts. ON SALE this month only -- learn >> more >> >> >> at: >> >> >> > >> >> >>> > > http://p.sf.net/sfu/learnmore_122712 >> >> >> > >> >> >>> > > _______________________________________________ >> >> >> > >> >> >>> > > Pytables-users mailing list >> >> >> > >> >> >>> > > Pyt...@li... >> >> >> > >> >> >>> > > >> >> >> https://lists.sourceforge.net/lists/listinfo/pytables-users >> >> >> > >> >> >>> > > >> >> >> > >> >> >>> > > >> >> >> > >> >> >>> > -------------- next part -------------- >> >> >> > >> >> >>> > An HTML attachment was scrubbed... >> >> >> > >> >> >>> > >> >> >> > >> >> >>> > ------------------------------ >> >> >> > >> >> >>> > >> >> >> > >> >> >>> > Message: 2 >> >> >> > >> >> >>> > Date: Thu, 3 Jan 2013 17:30:59 -0600 >> >> >> > >> >> >>> > From: Anthony Scopatz <sc...@gm...> >> >> >> > >> >> >>> > Subject: Re: [Pytables-users] Pytables-users Digest, >> Vol >> >> 80, >> >> >> > >> Issue 4 >> >> >> > >> >> >>> > To: Discussion list for PyTables >> >> >> > >> >> >>> > <pyt...@li...> >> >> >> > >> >> >>> > Message-ID: >> >> >> > >> >> >>> > < >> >> >> > >> >> >>> > >> >> >> > >> >> >> CAP...@ma...> >> >> >> > >> >> >>> > Content-Type: text/plain; charset="iso-8859-1" >> >> >> > >> >> >>> > >> >> >> > >> >> >>> > Josh is right that you can just edit the code by hand >> >> (which >> >> >> > >> works >> >> >> > >> >> but >> >> >> > >> >> >>> > sucks). >> >> >> > >> >> >>> > >> >> >> > >> >> >>> > However, on Windows -- on the rare occasion when I >> also >> >> >> have to >> >> >> > >> >> >>> develop on >> >> >> > >> >> >>> > it -- I typically use a distribution that includes a >> >> >> compiler, >> >> >> > >> >> cython, >> >> >> > >> >> >>> > hdf5, and pytables already and then I install my >> >> development >> >> >> > >> version >> >> >> > >> >> >>> from >> >> >> > >> >> >>> > github OVER this. I recommend either EPD or Anaconda, >> >> >> though >> >> >> > >> other >> >> >> > >> >> >>> > distributions listed here [1] might also work. >> >> >> > >> >> >>> > >> >> >> > >> >> >>> > Be well >> >> >> > >> >> >>> > Anthony >> >> >> > >> >> >>> > >> >> >> > >> >> >>> > 1. >> >> http://numfocus.org/projects-2/software-distributions/ >> >> >> > >> >> >>> > >> >> >> > >> >> >>> > >> >> >> > >> >> >>> > On Thu, Jan 3, 2013 at 3:46 PM, Josh Ayers < >> >> >> > jos...@gm... >> >> >> > >> > >> >> >> > >> >> >>> wrote: >> >> >> > >> >> >>> > >> >> >> > >> >> >>> > > The change was in pure Python code, so you should be >> >> able >> >> >> to >> >> >> > >> just >> >> >> > >> >> >>> paste >> >> >> > >> >> >>> > in >> >> >> > >> >> >>> > > the changes to your local copy. Start with the >> >> >> > >> >> table.Column.__iter__ >> >> >> > >> >> >>> > > method (lines 3296-3310) here. >> >> >> > >> >> >>> > > >> >> >> > >> >> >>> > > >> >> >> > >> >> >>> > > >> >> >> > >> >> >>> > >> >> >> > >> >> >>> >> >> >> > >> >> >> >> >> > >> >> >> >> > >> >> >> >> >> >> https://github.com/PyTables/PyTables/blob/b479ed025f4636f7f4744ac83a89bc947808907c/tables/table.py >> >> >> > >> >> >>> > > >> >> >> > >> >> >>> > > It needs to be modified slightly because it uses >> some >> >> >> > >> additional >> >> >> > >> >> >>> features >> >> >> > >> >> >>> > > that aren't available in the released version (the >> >> >> > >> out=buf_slice >> >> >> > >> >> >>> argument >> >> >> > >> >> >>> > > to table.read). The following should work. >> >> >> > >> >> >>> > > >> >> >> > >> >> >>> > > def __iter__(self): >> >> >> > >> >> >>> > > table = self.table >> >> >> > >> >> >>> > > itemsize = self.dtype.itemsize >> >> >> > >> >> >>> > > nrowsinbuf = >> >> >> table._v_file.params['IO_BUFFER_SIZE'] >> >> >> > // >> >> >> > >> >> >>> itemsize >> >> >> > >> >> >>> > > max_row = len(self) >> >> >> > >> >> >>> > > for start_row in xrange(0, len(self), >> >> nrowsinbuf): >> >> >> > >> >> >>> > > end_row = min([start_row + nrowsinbuf, >> >> >> max_row]) >> >> >> > >> >> >>> > > buf = table.read(start_row, end_row, 1, >> >> >> > >> >> >>> field=self.pathname) >> >> >> > >> >> >>> > > for row in buf: >> >> >> > >> >> >>> > > yield row >> >> >> > >> >> >>> > > >> >> >> > >> >> >>> > > >> >> >> > >> >> >>> > > I haven't tested this, but I think it will work. >> >> >> > >> >> >>> > > >> >> >> > >> >> >>> > > Josh >> >> >> > >> >> >>> > > >> >> >> > >> >> >>> > > >> >> >> > >> >> >>> > > >> >> >> > >> >> >>> > > On Thu, Jan 3, 2013 at 1:25 PM, David Reed < >> >> >> > >> >> dav...@gm...> >> >> >> > >> >> >>> > wrote: >> >> >> > >> >> >>> > > >> >> >> > >> >> >>> > >> I apologize if I'm starting to sound helpless, but >> I'm >> >> >> > forced >> >> >> > >> to >> >> >> > >> >> >>> work on >> >> >> > >> >> >>> > >> Windows 7 at work and have never had luck compiling >> >> >> python >> >> >> > >> source >> >> >> > >> >> >>> > >> successfully. I have had to rely on precompiled >> >> binaries >> >> >> > and >> >> >> > >> now >> >> >> > >> >> >>> its >> >> >> > >> >> >>> > >> biting me in the butt. >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> Is there any quick fix I can do to improve this >> >> iteration >> >> >> > >> using >> >> >> > >> >> >>> v2.4.0? >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >> On Thu, Jan 3, 2013 at 3:17 PM, < >> >> >> > >> >> >>> > >> pyt...@li...> >> wrote: >> >> >> > >> >> >>> > >> >> >> >> > >> >> >>> > >>> Send Pytables-users mailing list submissions to >> >> >> > >> >> >>> > >>> pyt...@li... >> >> >> > >> >> >>> > >>> >> >> >> > >> >> >>> > >>> To subscribe or unsubscribe via the World Wide >> Web, >> >> >> visit >> >> >> > >> >> >>> > >>> >> >> >> > >> >> >>> >> >> https://lists.sourceforge.net/lists/listinfo/pytables-users >> >> >> > >> >> >>> > >>> or, via email, send a message with subject or body >> >> >> 'help' >> >> >> > to >> >> >> > >> >> >>> > >>> >> pyt...@li... >> >> >> > >> >> >>> > >>> >> >> >> > >> >> >>> > >>> You can reach the person managing the list at >> >> >> > >> >> >>> > >>> >> pyt...@li... >> >> >> > >> >> >>> > >>> >> >> >> > >> >> >>> > >>> When replying, please edit your Subject line so >> it is >> >> >> more >> >> >> > >> >> specific >> >> >> > >> >> >>> > >>> than "Re: Contents of Pytables-users digest..." >> >> >> > >> >> >>> > >>> >> >> >> > >> >> >>> > >>> >> >> >> > >> >> >>> > >>> Today's Topics: >> >> >> > >> >> >>> > >>> >> >> >> > >> >> >>> > >>> 1. Re: Pytables-users Digest, Vol 80, Issue 2 >> >> (David >> >> >> > Reed) >> >> >> > >> >> >>> > >>> 2. Re: Pytables-users Digest, Vol 80, Issue 3 >> >> (David >> >> >> > Reed) >> >> >> > >> >> >>> > >>> >> >> >> > >> >> >>> > >>> >> >> >> > >> >> >>> > >>> >> >> >> > >> >> >>> >> >> >> > >> >> >> >> >> ---------------------------------------------------------------------- >> >> >> > >> >> >>> > >>> >> >> >> > >> >> >>> > >>> Message: 1 >> >> >> > >> >> >>> > >>> Date: Thu, 3 Jan 2013 13:44:29 -0500 >> >> >> > >> >> >>> > >>> From: David Reed <dav...@gm...> >> >> >> > >> >> >>> > >>> Subject: Re: [Pytables-users] Pytables-users >> Digest, >> >> Vol >> >> >> > 80, >> >> >> > >> >> Issue >> >> >> > >> >> >>> 2 >> >> >> > >> >> >>> > >>> To: pyt...@li... >> >> >> > >> >> >>> > >>> Message-ID: >> >> >> > >> >> >>> > >>> >> >> <CAM6XA7=8ocg5WPD4KLSvLhSw-3BCvq5u7MRxq3Ajd6ha= >> >> >> > >> >> >>> > >>> ev...@ma...> >> >> >> > >> >> >>> > >>> Content-Type: text/plain; charset="iso-8859-1" >> >> >> > >> >> >>> > >>> >> >> >> > >> >> >>> > >>> Thanks Anthony, but unless Im missing something I >> >> don't >> >> >> > think >> >> >> > >> >> that >> >> >> > >> >> >>> > method >> >> >> > >> >> >>> > >>> will work since this will only be comparing the >> ith >> >> >> element >> >> >> > >> with >> >> >> > >> >> >>> ith+1 >> >> >> > >> >> >>> > >>> element. I still need 2 for loops right? >> >> >> > >> >> >>> > >>> >> >> >> > >> >> >>> > >>> Using itertools might speed things up though, I've >> >> never >> >> >> > used >> >> >> > >> >> them >> >> >> > >> >> >>> so I >> >> >> > >> >> >>> > >>> will give it a shot and let you know how it goes. >> >> Looks >> >> >> > >> like I >> >> >> > >> >> >>> need to >> >> >> > >> >> >>> > >>> download the latest release before I do that too. >> >> >> Thanks >> >> >> > for >> >> >> > >> >> the >> >> >> > >> >> >>> help. >> >> >> > >> >> >>> > >>> >> >> >> > >> >> >>> > >>> -Dave >> >> >> > >> >> >>> > >>> >> >> >> > >> >> >>> > >>> >> >> >> > >> >> >>> > >>> >> >> >> > >> >> >>> > >>> On Thu, Jan 3, 2013 at 12:12 PM, < >> >> >> > >> >> >>> > >>> pyt...@li...> >> wrote: >> >> >> > >> >> >>> > >>> >> >> >> > >> >> >>> > >>> > Send Pytables-users mailing list submissions to >> >> >> > >> >> >>> > >>> > pyt...@li... >> >> >> > >> >> >>> > >>> > >> >> >> > >> >> >>> > >>> > To subscribe or unsubscribe via the World Wide >> Web, >> >> >> visit >> >> >> > >> >> >>> > >>> > >> >> >> > >> >> >>> >> >> https://lists.sourceforge.net/lists/listin... 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