[datatable-help] Fwd: fread on very large file
Matthew Dowle
mdowle at mdowle.plus.com
Fri May 3 11:51:47 CEST 2013
Hi Paul,
Thanks for all this!
> The problem arises when the file
reaches 4GB, in this case between 8,030,000 and 8,040,000 rows:
Ahah.
Are you using a 32bit or 64bit Windows machine?
Thanks, Matthew
On
02.05.2013 10:19, Paul Harding wrote:
> Some supplementary
information, here is the portion of the file (with row numbers, +1 for
header) around where fread thinks the file ends.
>
> $ nl
spd_all_fixed.csv | head -n 9186300 |tail
> 9186291
204029,2617097,20110803,0,0,0.3014501,0,0,0
> 9186292
204030,2617097,20110803,0,0,0.52049100000000004,0,0,0
> 9186293
204034,2617097,20110803,0,0,0.86560269999999995,0.86560269999999995,2,13
> 9186294 204038,2617097,20110803,0,0,0.49455500000000002,0,0,0
>
9186295 204039,2617097,20110803,0,0,0.24952240000000001,0,0,0
> 9186296
204041,2617097,20110803,1,0,1.0032293000000001,0,0,0
> 9186297
204042,2617097,20110803,0,0,0.1375876,0,0,0
> 9186298
204043,2617097,20110803,0,0,0.53391279999999997,0,0,0
> 9186299
204044,2617097,20110803,0,0,0.16047169999999999,0,0,0
> 9186300
204045,2617097,20110803,1,0,0.78766970000000003,0,0,0
> 9186294 (row
9186293 excl header) is where fread thinks the file ends, mid-line by
the look of it!
> I've experimented by truncating the file. The error
varies, either it reads too few records or gives the error I reported,
presumably determined by whether the last perceived line is entire.
>
The problem arises when the file reaches 4GB, in this case between
8,030,000 and 8,040,000 rows:
>
> -rw-r--r--+ 1 Paul.Harding Domain
Users 4.0G May 1 12:02 spd_all_trunc_8030k.csv
> -rw-r--r--+ 1
Paul.Harding Domain Users 4.1G May 1 12:06 spd_all_trunc_8040k.csv
>
>> dt<-fread("data/spd_all_trunc_8030k.csv", sep=",",verbose=T)
>
>
Detected eol as rn (CRLF) in that order, the Windows standard.
>
Looking for supplied sep ',' on line 30 (the last non blank line in the
first 30) ... found
> Found 9 columns
> First row with 9 fields occurs
on line 1 (either column names or first row of data)
> All the fields
on line 1 are character fields. Treating as the column names.
> Count
of eol after first data row: 80300000
> Subtracted 1 for last eol and
any trailing empty lines, leaving 80299999 data rows
>
> Type codes:
000002000 (first 5 rows)
> Type codes: 000002000 (+middle 5 rows)
>
Type codes: 000002000 (+last 5 rows)
> 0%Bumping column 7 from INT to
INT64 on data row 9, field contains '0.42634430000000001'
> Bumping
column 7 from INT64 to REAL on data row 9, field contains
'0.42634430000000001'
> 0.000s ( 0%) Memory map (rerun may be quicker)
> 0.000s ( 0%) Sep and header detection
> 0.000s ( 0%) Count rows (wc
-l)
> 0.000s ( 0%) Colmn type detection (first, middle and last 5 rows)
> 0.000s ( 0%) Allocation of 80299999x9 result (xMB) in RAM
> 171.188s
( 65%) Reading data
> 1365231.809s (518439%) Allocation for type bumps
(if any), including gc time if triggered
> -1365231.809s (-518439%)
Coercing data already read in type bumps (if any)
> 0.000s ( 0%)
Changing na.strings to NA
> 0.000s Total
>>
dt<-fread("data/spd_all_trunc_8040k.csv", sep=",",verbose=T)
>
>
Detected eol as rn (CRLF) in that order, the Windows standard.
>
Looking for supplied sep ',' on line 30 (the last non blank line in the
first 30) ... found
> Found 9 columns
> First row with 9 fields occurs
on line 1 (either column names or first row of data)
> All the fields
on line 1 are character fields. Treating as the column names.
> Count
of eol after first data row: 18913
> Subtracted 0 for last eol and any
trailing empty lines, leaving 18913 data rows
>
> Type codes:
000002000 (first 5 rows)
> Type codes: 000002000 (+middle 5 rows)
>
Error in fread("data/spd_all_trunc_8040k.csv", sep = ",", verbose = T) :
> Expected sep (',') but ',' ends field 2 on line 6 when detecting
types: 204650,724540,
> Regards,
> Paul
>
> On 1 May 2013 10:28,
Paul Harding <p.harding at paniscus.com [2]> wrote:
>
>> Here is the
verbose output:
>>
>>> dt<-fread("data/spd_all_fixed.csv",
sep=",",verbose=T)
>> Detected eol as rn (CRLF) in that order, the
Windows standard.
>> Looking for supplied sep ',' on line 30 (the last
non blank line in the first 30) ... found
>> Found 9 columns
>> First
row with 9 fields occurs on line 1 (either column names or first row of
data)
>> All the fields on line 1 are character fields. Treating as the
column names.
>> Count of eol after first data row: 9186293
>>
Subtracted 0 for last eol and any trailing empty lines, leaving 9186293
data rows
>> Type codes: 000002000 (first 5 rows)
>> Type codes:
000002200 (+middle 5 rows)
>> Error in fread("data/spd_all_fixed.csv",
sep = ",", verbose = T) :
>>
>> Expected sep (',') but '0' ends field
5 on line 6 when detecting types: 204038,2617097,20110803,0,0
>> But
here is the wc output (via cygwin; newline, word (whitespace delim so
each word one 'line' here), byte)@
>>
>> $ wc spd_all_fixed.csv
>>
168997637 168997638 9078155125 spd_all_fixed.csv
>> [So fread 9M, wc
168M rows].
>> Regards
>> Paul
>>
>> On 30 April 2013 18:52, Matthew
Dowle <mdowle at mdowle.plus.com [1]> wrote:
>>
>>> Hi,
>>>
>>> Thanks
for reporting this. Please set verbose=TRUE and let us know the output.
>>>
>>> Thanks, Matthew
>>>
>>> On 30.04.2013 18:01, Paul Harding
wrote:
>>>
>>>> Problem with fread on a large file The file is 8GB,
just short of 200,000 lines, produced as SQLoutput and modified by
cygwin/perl to remove the second line.
>>>>
>>>> Using data.table 1.8.8
on R3.0.0 I get an fread error
>>>>
>>>>
fread("data/spd_all_fixed.csv",sep=",")
>>>> Error in
fread("data/spd_all_fixed.csv", sep = ",") :
>>>> Expected sep (',')
but '0' ends field 5 on line 6 when detecting types:
204038,2617097,20110803,0,0
>>>> Looking for the offending line,with
line numbers in output so I'm guessing this is line 6 of the mid-file
chunk examined,
>>>>
>>>> $ grep -n '204038,2617097,201108'
spd_all_fixed.csv
>>>>
8316105:204038,2617097,20110801,0,0,0.64220529999999998,0,0,0
>>>>
8751106:204038,2617097,20110802,1,0,0.65744469999999999,0,0,0
>>>>
9186294:204038,2617097,20110803,0,0,0.49455500000000002,0,0,0
>>>>
9621619:204038,2617097,20110804,0,0,0.3461342,0,0,0
>>>>
10057189:204038,2617097,20110805,0,0,0.34128710000000001,0,0,0
>>>> and
comparing to surrounding lines and the first ten lines
>>>>
>>>> $
head spd_all_fixed.csv
>>>> s_key,i_key,p_key,q,pq,d,l,epi,class
>>>>
203974,1107181,20110713,0,0,0.13700080000000001,0,0,0
>>>>
203975,1107181,20110713,0,0,5.8352899999999999E-2,0,0,0
>>>>
203976,1107181,20110713,0,0,7.1298999999999998E-3,0,0,0
>>>>
203978,1107181,20110713,0,0,0.78346819999999995,0,0,0
>>>>
203979,1107181,20110713,0,0,0.61627779999999999,0,0,0
>>>>
203981,1107181,20110713,1,0,0.38610509999999998,0,0,0
>>>>
203982,1107181,20110713,0,0,4.0657899999999997E-2,0,0,0
>>>>
203983,1107181,20110713,2,0,0.71278109999999995,0,0,0
>>>>
203984,1107181,20110713,0,0,0.42634430000000001,0.42634430000000001,2,13
>>>> I can't see any difference. I wonder if this is a bug? I have no
problems on a small test data set run through an identical process and
using the same fread command.
>>>> Regards
>>>> Paul
Links:
------
[1] mailto:mdowle at mdowle.plus.com
[2]
mailto:p.harding at paniscus.com
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