Re: [Pytables-users] Row.append() performance

2013-04-15 Thread Anthony Scopatz
Hello Shyam, Can you please post the full traceback? In any event, I am fairly certain that this error is coming from the np.fromiter step. The problem here is that you are trying to read yur entire SQL query into a single numpy array in memory. This is impossible because you don't have enough

Re: [Pytables-users] Row.append() performance

2013-04-15 Thread Shyam Parimal Katti
Hello Anthony, Thank you for your suggestions. When I mentioned that I am reading the data from database, I meant a DB2 database, not a HDF5 database/file. I followed your suggestions, so the code looks as follows: def createHDF5File(): h5File= tables.openFile(, mode="a")

Re: [Pytables-users] Row.append() performance

2013-04-11 Thread Anthony Scopatz
On Thu, Apr 11, 2013 at 5:16 PM, Shyam Parimal Katti wrote: > Hello Anthony, > > Thank you for replying back with suggestions. > > In response to your suggestions, I am *not reading the data from a file > in the first step, but instead a database*. > Hello Shyam, To put too fine a point on it,

Re: [Pytables-users] Row.append() performance

2013-04-11 Thread Shyam Parimal Katti
Hello Anthony, Thank you for replying back with suggestions. In response to your suggestions, I am *not reading the data from a file in the first step, but instead a database*. I did try out your 1st suggestion of doing a table.append(list of tuples), which took a little more than the executed ti

Re: [Pytables-users] Row.append() performance

2013-04-11 Thread Anthony Scopatz
Hi Shyam, The pattern that you are using to write to a table is basically one for writing Python data to HDF5. However, your data is already in a machine / HDF5 native format. Thus what you are doing here is an excessive amount of work: read data from file -> convert to Python data structures -