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Re: [Pharo-users] running out of memory while processing a 220MB csv file with NeoCSVReader - tips?

by Alain Rastoul

ok, bad guess, sorry. my previous suggestion about interning data in this kind of processing is more reliable, and could help you reduce memory footprint by at least a factor 3 or more (depends if you have lots of integers or floats, and works very well with string and dates) and should be very easy to try (just few lines to change in the csv reading method). I used it several times and was always puzzled by that "statistical truth" about data. Le 16/11/2014 21:04, Paul DeBruicker a Ã©crit : > Hi Alain, > > Thanks for the link to the discussion. I attempted your suggestion for > changing the command line parameters and it had no effect. Adding the colon > prevented the image from starting, as did using a single hyphen. > > > Paul > > > > Alain Rastoul-2 wrote >> Ah, this reminded me an old thread about memory on windows about why the >> windows setting was 512 by default >> http://lists.pharo.org/pipermail/pharo-dev_lists.pharo.org/2011-April/04759… >> >> And about vm options, it reminded me too that on windows the option had >> a trailing ':' that didn't exist on mac IIRC >> (and no double '-' on mac I think). >> -memory: 1024 against -memory 1024 >> >> may be stupid, but perhaps you could try it ? >> > > > > > > -- > View this message in context: http://forum.world.st/running-out-of-memory-while-processing-a-220MB-csv-fi… > Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com. > >

Nov. 16, 2014

Re: [Pharo-users] running out of memory while processing a 220MB csv file with NeoCSVReader - tips?

by Paul DeBruicker

Hi Alain, Thanks for the link to the discussion. I attempted your suggestion for changing the command line parameters and it had no effect. Adding the colon prevented the image from starting, as did using a single hyphen. Paul Alain Rastoul-2 wrote > Ah, this reminded me an old thread about memory on windows about why the > windows setting was 512 by default > http://lists.pharo.org/pipermail/pharo-dev_lists.pharo.org/2011-April/04759… > > And about vm options, it reminded me too that on windows the option had > a trailing ':' that didn't exist on mac IIRC > (and no double '-' on mac I think). > -memory: 1024 against -memory 1024 > > may be stupid, but perhaps you could try it ? > -- View this message in context: http://forum.world.st/running-out-of-memory-while-processing-a-220MB-csv-fi… Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com.

Nov. 16, 2014

Re: [Pharo-users] running out of memory while processing a 220MB csv file with NeoCSVReader - tips?

by Alain Rastoul

Ah, this reminded me an old thread about memory on windows about why the windows setting was 512 by default http://lists.pharo.org/pipermail/pharo-dev_lists.pharo.org/2011-April/04759… And about vm options, it reminded me too that on windows the option had a trailing ':' that didn't exist on mac IIRC (and no double '-' on mac I think). -memory: 1024 against -memory 1024 may be stupid, but perhaps you could try it ? Le 16/11/2014 01:08, Paul DeBruicker a Ã©crit : > Hi Sven, > > I think you are right that I am mis-estimating how big these objects are, > especially lots of them. But I still think there's another problem with the > image not growing to the machine or VM limits. > > Eliot Miranda created a script to see how big a heap (using Spur) could grow > on different platforms (the email is here: > http://forum.world.st/New-Cog-VMs-available-td4764823.html#a4764840) I've > adapted it ever so slightly to run on Pharo 3: > > | them | > them := OrderedCollection new. > [[them addLast: (ByteArray new: 16000000). > Transcript cr; show: ((Smalltalk vm parameterAt: 3) / (1024*1024.0) > printShowingDecimalPlaces: 1); flush] repeat] > on: OutOfMemory > do: [:ex| 2 to: them size by: 2 do: [:i| them at: i put: nil. Smalltalk > garbageCollect]]. > Transcript cr; show: ((Smalltalk vm parameterAt: 3) / (1024*1024.0) > printShowingDecimalPlaces: 1); flush. > them := nil. > Smalltalk garbageCollect. > Transcript cr; show: ((Smalltalk vm parameterAt: 3) / (1024*1024.0) > printShowingDecimalPlaces: 1); flush > > When I run it in Pharo 3 (& Pharo 1.4) on my laptop this is the output: > > > 49.4 > 64.6 > 79.9 > 95.2 > 110.4 > 125.7 > 140.9 > 156.2 > 171.5 > 186.7 > 202.0 > 217.2 > 232.5 > 247.8 > 263.0 > 278.3 > 293.5 > 308.8 > 324.1 > 339.3 > 354.6 > 369.8 > 385.1 > 400.3 > 415.6 > 430.9 > 446.1 > 461.4 > 476.6 > 491.9 > 507.2 > 278.3 > 34.1 > > It shows that the heap grows to about 500MB and then an OutOfMemory error is > thrown. > > > It is my intuition that this test would make the image grow to either the > limit of the machine or the limit of the VM, whichever came first. > > Is there a setting I need to change to make the image grow to, say, 1GB for > this test? > > Starting the image with the '--memory 1000m' command line argument doesn't > change the test result. > > > Also - that weird stack with 'output file stack is full' was a result of > running the MessageTally profiler and hitting the issue that John McIntosh > described here: > http://forum.world.st/Squeak-hang-at-full-cpu-help-tp3006008p3007628.html > > > And for my immediate needs of processing the CSV files I ported everything > to GemStone and am all set in that regard. > > > > > > > Sven Van Caekenberghe-2 wrote >>> On 14 Nov 2014, at 23:14, Paul DeBruicker < > >> pdebruic@ > >> > wrote: >>> >>> Hi Sven >>> >>> Yes, like I said earlier, after your first email, that I think its not a >>> problem with NeoCSV as with what I'm doing and an out of memory >>> condition. >>> >>> Have you ever seen a stack after sending kill -SIGUSR1 that looks like >>> this: >>> >>> output file stack is full. >>> output file stack is full. >>> output file stack is full. >>> output file stack is full. >>> output file stack is full. >>> .... >>> >>> >>> What does that mean? >> >> I don't know, but I think that you are really out of memory. >> BTW, I think that setting no flags is better, memory will expand maximally >> then. >> I think the useful maximum is closer to 1GB than 2GB. >> >>> Answers to your questions below. >> >> It is difficult to follow what you are doing exactly, but I think that you >> underestimate how much memory a parsed, structured/nested object uses. >> Taking the second line of your example, the 20+ fields, with 3 >> DateAndTimes, easily cost between 512 and 1024 bytes per record. That >> would limit you to between 1M and 2M records. >> >> I tried this: >> >> Array streamContents: [ :data | >> 5e2 timesRepeat: [ >> data nextPut: (Array streamContents: [ :out | >> 20 timesRepeat: [ out nextPut: Character alphabet ]. >> 3 timesRepeat: [ out nextPut: DateAndTime now ] ]) ] ]. >> >> it worked to 5e5, but not for 5e6 - I didn't try numbers in between as it >> takes very long. >> >> Good luck, if you can solve this, please tell us how you did it. >> >>> Thanks again for helping me out >>> >>> >>> >>> Sven Van Caekenberghe-2 wrote >>>> OK then, you *can* read/process 300MB .csv files ;-) >>>> >>>> What does your CSV file look like, can you show a couple of lines ? >>>> >>>> here are 2 lines + a header: >>>> >>>> "provnum","Provname","address","city","state","zip","survey_date_output","SurveyType","defpref","tag","tag_desc","scope","defstat","statdate","cycle","standard","complaint","filedate" >>>> "015009","BURNS NURSING HOME, INC.","701 MONROE STREET >>>> NW","RUSSELLVILLE","AL","35653","2013-09-05","Health","F","0314","Give >>>> residents proper treatment to prevent new bed (pressure) sores or heal >>>> existing bed sores.","D","Deficient, Provider has date of >>>> correction","2013-10-10",1,"Y","N","2014-01-01" >>>> "015009","BURNS NURSING HOME, INC.","701 MONROE STREET >>>> NW","RUSSELLVILLE","AL","35653","2013-09-05","Health","F","0315","Ensure >>>> that each resident who enters the nursing home without a catheter is not >>>> given a catheter, unless medically necessary, and that incontinent >>>> patients receive proper services to prevent urinary tract infections and >>>> restore normal bladder functions.","D","Deficient, Provider has date of >>>> correction","2013-10-10",1,"Y","N","2014-01-01" >>>> >>>> >>>> You are using a custom record class of your own, what does that look >>>> like >>>> or do ? >>>> >>>> A custom record class. This is all publicly available data but I'm >>>> keeping track of the performance of US based health care providers >>>> during >>>> their annual inspections. So the records are notes of a deficiency >>>> during >>>> the inspection and I'm keeping those notes in a collection in an >>>> instance >>>> of the health care provider's class. The custom record class just >>>> converts the CSV record to objects (Integers, Strings, DateAndTime) and >>>> then gets stuffed in the health care provider's deficiency history >>>> OrderedCollection (which has about 100 items). Again I don't think >>>> its >>>> what I'm doing as much as the image isn't growing when it needs to. >>>> >>>> >>>> >>>> >>>> Maybe you can try using Array again ? >>>> >>>> I've attempted to do it where I parse and convert the entire CSV into >>>> domain objects then add them to the image and the parsing works fine, >>>> but >>>> the system runs out of resources during the update phase. >>>> >>>> >>>> What percentage of records read do you keep ? In my example it was very >>>> small. Have you tried calculating your memory usage ? >>>> >>>> >>>> I'm keeping some data from every record, but it doesn't load more than >>>> 500MB of the data before falling over. I am not attempting to load the >>>> 9GB of CSV files into one image. For 95% of the records in the CSV file >>>> 20 of the 22 columns of the data is the same from file to file, just a >>>> 'published date' and a 'time to expiration' date changes. Each file >>>> covers a month, with about 500k deficiencies. Each month some >>>> deficiencies are added to the file and some are resolved. So the total >>>> number of deficiencies in the image is about 500k. Of those records >>>> that >>>> don't expire in a given month I'm adding the published date to a >>>> collection of published dates for the record and also adding the "time >>>> to >>>> expiration" to a collection of those to record what was made public and >>>> letting the rest of the data get GC'd. I don't only load those two >>>> records because the other fields of the record in the CSV could change. >>>> >>>> I have not calculated the memory usage for the collection because I >>>> thought it would have no problem fitting in the 2GB of RAM I have on >>>> this >>>> machine. >>>> >>>> >>>> >>>>> On 14 Nov 2014, at 22:34, Paul DeBruicker < >>> >>>> pdebruic@ >>> >>>> > wrote: >>>>> >>>>> Yes. With the image & vm I'm having trouble with I get an array with >>>>> 9,942 >>>>> elements in it. So its works as you'd expect. >>>>> >>>>> While processing the CSV file the image stays at about 60MB in RAM. >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> Sven Van Caekenberghe-2 wrote >>>>>> Can you successfully run my example code ? >>>>>> >>>>>>> On 14 Nov 2014, at 22:03, Paul DeBruicker < >>>>> >>>>>> pdebruic@ >>>>> >>>>>> > wrote: >>>>>>> >>>>>>> Hi Sven, >>>>>>> >>>>>>> Thanks for taking a look and testing the NeoCSVReader portion for me. >>>>>>> You're right of course that there's something I'm doing that's slow. >>>>>>> But. >>>>>>> There is something I can't figure out yet. >>>>>>> >>>>>>> To provide a little more detail: >>>>>>> >>>>>>> When the 'csv reading' process completes successfully profiling shows >>>>>>> that >>>>>>> most of the time is spent in NeoCSVReader>>#peekChar and using >>>>>>> NeoCSVReader>>##addField: to convert a string to a DateAndTime. >>>>>>> Dropping >>>>>>> the DateAndTime conversion speeds things up but doesn't stop it from >>>>>>> running >>>>>>> out of memory. >>>>>>> >>>>>>> I start the image with >>>>>>> >>>>>>> ./pharo-ui --memory 1000m myimage.image >>>>>>> >>>>>>> Splitting the CSV file helps: >>>>>>> ~1.5MB 5,000 lines = 1.2 seconds. >>>>>>> ~15MB 50,000 lines = 8 seconds. >>>>>>> ~30MB 100,000 lines = 16 seconds. >>>>>>> ~60MB 200,000 lines = 45 seconds. >>>>>>> >>>>>>> >>>>>>> It seems that when the CSV file crosses ~70MB in size things start >>>>>>> going >>>>>>> haywire with performance, and leads to the out of memory condition. >>>>>>> The >>>>>>> processing never ends. Sending "kill -SIGUSR1" prints a stack >>>>>>> primarily >>>>>>> composed of: >>>>>>> >>>>>>> 0xbffc5d08 M OutOfMemory class(Exception class)>signal 0x1f7ac060: >>>>>>> a(n) >>>>>>> OutOfMemory class >>>>>>> 0xbffc5d20 M OutOfMemory class(Behavior)>basicNew 0x1f7ac060: a(n) >>>>>>> OutOfMemory class >>>>>>> 0xbffc5d38 M OutOfMemory class(Behavior)>new 0x1f7ac060: a(n) >>>>>>> OutOfMemory >>>>>>> class >>>>>>> 0xbffc5d50 M OutOfMemory class(Exception class)>signal 0x1f7ac060: >>>>>>> a(n) >>>>>>> OutOfMemory class >>>>>>> 0xbffc5d68 M OutOfMemory class(Behavior)>basicNew 0x1f7ac060: a(n) >>>>>>> OutOfMemory class >>>>>>> 0xbffc5d80 M OutOfMemory class(Behavior)>new 0x1f7ac060: a(n) >>>>>>> OutOfMemory >>>>>>> class >>>>>>> 0xbffc5d98 M OutOfMemory class(Exception class)>signal 0x1f7ac060: >>>>>>> a(n) >>>>>>> OutOfMemory class >>>>>>> >>>>>>> So it seems like its trying to signal that its out of memory after >>>>>>> its >>>>>>> out >>>>>>> of memory which triggers another OutOfMemory error. So that's why >>>>>>> progress >>>>>>> stops. >>>>>>> >>>>>>> >>>>>>> ** Aside - OutOfMemory should probably be refactored to be able to >>>>>>> signal >>>>>>> itself without taking up more memory, triggering itself infinitely. >>>>>>> Maybe >>>>>>> it & its signalling morph infrastructure would be good as a singleton >>>>>>> ** >>>>>>> >>>>>>> >>>>>>> >>>>>>> I'm confused about why it runs out of memory. According to htop the >>>>>>> image >>>>>>> only takes up about 520-540 MB of RAM when it reaches the >>>>>>> 'OutOfMemory' >>>>>>> condition. This Macbook Air laptop has 4GB, and has plenty of room >>>>>>> for >>>>>>> the >>>>>>> image to grow. Also I've specified a 1,000MB image size when >>>>>>> starting. >>>>>>> So >>>>>>> it should have plenty of room. Is there something I should check or >>>>>>> a >>>>>>> flag >>>>>>> somewhere that prevents it from growing on a Mac? This is the latest >>>>>>> Pharo30 VM. >>>>>>> >>>>>>> >>>>>>> Thanks for helping me get to the bottom of this >>>>>>> >>>>>>> Paul >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> Sven Van Caekenberghe-2 wrote >>>>>>>> Hi Paul, >>>>>>>> >>>>>>>> I think you must be doing something wrong with your class, the #do: >>>>>>>> is >>>>>>>> implemented as streaming over the record one by one, never holding >>>>>>>> more >>>>>>>> than one in memory. >>>>>>>> >>>>>>>> This is what I tried: >>>>>>>> >>>>>>>> 'paul.csv' asFileReference writeStreamDo: [ :file| >>>>>>>> ZnBufferedWriteStream on: file do: [ :out | >>>>>>>> (NeoCSVWriter on: out) in: [ :writer | >>>>>>>> writer writeHeader: { #Number. #Color. #Integer. #Boolean}. >>>>>>>> 1 to: 1e7 do: [ :each | >>>>>>>> writer nextPut: { each. #(Red Green Blue) atRandom. 1e6 >>>>>>>> atRandom. >>>>>>>> #(true false) atRandom } ] ] ] ]. >>>>>>>> >>>>>>>> This results in a 300Mb file: >>>>>>>> >>>>>>>> $ ls -lah paul.csv >>>>>>>> -rw-r--r--@ 1 sven staff 327M Nov 14 20:45 paul.csv >>>>>>>> $ wc paul.csv >>>>>>>> 10000001 10000001 342781577 paul.csv >>>>>>>> >>>>>>>> This is a selective read and collect (loads about 10K records): >>>>>>>> >>>>>>>> Array streamContents: [ :out | >>>>>>>> 'paul.csv' asFileReference readStreamDo: [ :in | >>>>>>>> (NeoCSVReader on: (ZnBufferedReadStream on: in)) in: [ :reader | >>>>>>>> reader skipHeader; addIntegerField; addSymbolField; >>>>>>>> addIntegerField; >>>>>>>> addFieldConverter: [ :x | x = #true ]. >>>>>>>> reader do: [ :each | each third < 1000 ifTrue: [ out nextPut: >>>>>>>> each >>>>>>>> ] >>>>>>>> ] ] ] ]. >>>>>>>> >>>>>>>> This worked fine on my MacBook Air, no memory problems. It takes a >>>>>>>> while >>>>>>>> to parse that much data, of course. >>>>>>>> >>>>>>>> Sven >>>>>>>> >>>>>>>>> On 14 Nov 2014, at 19:08, Paul DeBruicker < >>>>>>> >>>>>>>> pdebruic@ >>>>>>> >>>>>>>> > wrote: >>>>>>>>> >>>>>>>>> Hi - >>>>>>>>> >>>>>>>>> I'm processing a 9 GBs of CSV files (the biggest file is 220MB or >>>>>>>>> so). >>>>>>>>> I'm not sure if its because of the size of the files or the code >>>>>>>>> I've >>>>>>>>> written to keep track of the domain objects I'm interested in, but >>>>>>>>> I'm >>>>>>>>> getting out of memory errors & crashes in Pharo 3 on Mac with the >>>>>>>>> latest >>>>>>>>> VM. I haven't checked other vms. >>>>>>>>> >>>>>>>>> I'm going to profile my own code and attempt to split the files >>>>>>>>> manually >>>>>>>>> for now to see what else it could be. >>>>>>>>> >>>>>>>>> >>>>>>>>> Right now I'm doing something similar to >>>>>>>>> >>>>>>>>> |file reader| >>>>>>>>> file:= '/path/to/file/myfile.csv' asFileReference readStream. >>>>>>>>> reader: NeoCSVReader on: file >>>>>>>>> >>>>>>>>> reader >>>>>>>>> recordClass: MyClass; >>>>>>>>> skipHeader; >>>>>>>>> addField: #myField:; >>>>>>>>> .... >>>>>>>>> >>>>>>>>> >>>>>>>>> reader do:[:eachRecord | self >>>>>>>>> seeIfRecordIsInterestingAndIfSoKeepIt: >>>>>>>>> eachRecord]. >>>>>>>>> file close. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Is there a facility in NeoCSVReader to read a file in batches (e.g. >>>>>>>>> 1000 >>>>>>>>> lines at a time) or an easy way to do that ? >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> >>>>>>>>> Paul >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> View this message in context: >>>>>>> http://forum.world.st/running-out-of-memory-while-processing-a-220MB-csv-fi… >>>>>>> Sent from the Pharo Smalltalk Users mailing list archive at >>>>>>> Nabble.com. >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> View this message in context: >>>>> http://forum.world.st/running-out-of-memory-while-processing-a-220MB-csv-fi… >>>>> Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com. >>> >>> >>> >>> >>> >>> -- >>> View this message in context: >>> http://forum.world.st/running-out-of-memory-while-processing-a-220MB-csv-fi… >>> Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com. > > > > > > -- > View this message in context: http://forum.world.st/running-out-of-memory-while-processing-a-220MB-csv-fi… > Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com. > >

Nov. 16, 2014

Re: [Pharo-users] running out of memory while processing a 220MB csv file with NeoCSVReader - tips?

by Paul DeBruicker

Hi Sven, I think you are right that I am mis-estimating how big these objects are, especially lots of them. But I still think there's another problem with the image not growing to the machine or VM limits. Eliot Miranda created a script to see how big a heap (using Spur) could grow on different platforms (the email is here: http://forum.world.st/New-Cog-VMs-available-td4764823.html#a4764840) I've adapted it ever so slightly to run on Pharo 3: | them | them := OrderedCollection new. [[them addLast: (ByteArray new: 16000000). Transcript cr; show: ((Smalltalk vm parameterAt: 3) / (1024*1024.0) printShowingDecimalPlaces: 1); flush] repeat] on: OutOfMemory do: [:ex| 2 to: them size by: 2 do: [:i| them at: i put: nil. Smalltalk garbageCollect]]. Transcript cr; show: ((Smalltalk vm parameterAt: 3) / (1024*1024.0) printShowingDecimalPlaces: 1); flush. them := nil. Smalltalk garbageCollect. Transcript cr; show: ((Smalltalk vm parameterAt: 3) / (1024*1024.0) printShowingDecimalPlaces: 1); flush When I run it in Pharo 3 (& Pharo 1.4) on my laptop this is the output: 49.4 64.6 79.9 95.2 110.4 125.7 140.9 156.2 171.5 186.7 202.0 217.2 232.5 247.8 263.0 278.3 293.5 308.8 324.1 339.3 354.6 369.8 385.1 400.3 415.6 430.9 446.1 461.4 476.6 491.9 507.2 278.3 34.1 It shows that the heap grows to about 500MB and then an OutOfMemory error is thrown. It is my intuition that this test would make the image grow to either the limit of the machine or the limit of the VM, whichever came first. Is there a setting I need to change to make the image grow to, say, 1GB for this test? Starting the image with the '--memory 1000m' command line argument doesn't change the test result. Also - that weird stack with 'output file stack is full' was a result of running the MessageTally profiler and hitting the issue that John McIntosh described here: http://forum.world.st/Squeak-hang-at-full-cpu-help-tp3006008p3007628.html And for my immediate needs of processing the CSV files I ported everything to GemStone and am all set in that regard. Sven Van Caekenberghe-2 wrote >> On 14 Nov 2014, at 23:14, Paul DeBruicker < > pdebruic@ > > wrote: >> >> Hi Sven >> >> Yes, like I said earlier, after your first email, that I think its not a >> problem with NeoCSV as with what I'm doing and an out of memory >> condition. >> >> Have you ever seen a stack after sending kill -SIGUSR1 that looks like >> this: >> >> output file stack is full. >> output file stack is full. >> output file stack is full. >> output file stack is full. >> output file stack is full. >> .... >> >> >> What does that mean? > > I don't know, but I think that you are really out of memory. > BTW, I think that setting no flags is better, memory will expand maximally > then. > I think the useful maximum is closer to 1GB than 2GB. > >> Answers to your questions below. > > It is difficult to follow what you are doing exactly, but I think that you > underestimate how much memory a parsed, structured/nested object uses. > Taking the second line of your example, the 20+ fields, with 3 > DateAndTimes, easily cost between 512 and 1024 bytes per record. That > would limit you to between 1M and 2M records. > > I tried this: > > Array streamContents: [ :data | > 5e2 timesRepeat: [ > data nextPut: (Array streamContents: [ :out | > 20 timesRepeat: [ out nextPut: Character alphabet ]. > 3 timesRepeat: [ out nextPut: DateAndTime now ] ]) ] ]. > > it worked to 5e5, but not for 5e6 - I didn't try numbers in between as it > takes very long. > > Good luck, if you can solve this, please tell us how you did it. > >> Thanks again for helping me out >> >> >> >> Sven Van Caekenberghe-2 wrote >>> OK then, you *can* read/process 300MB .csv files ;-) >>> >>> What does your CSV file look like, can you show a couple of lines ? >>> >>> here are 2 lines + a header: >>> >>> "provnum","Provname","address","city","state","zip","survey_date_output","SurveyType","defpref","tag","tag_desc","scope","defstat","statdate","cycle","standard","complaint","filedate" >>> "015009","BURNS NURSING HOME, INC.","701 MONROE STREET >>> NW","RUSSELLVILLE","AL","35653","2013-09-05","Health","F","0314","Give >>> residents proper treatment to prevent new bed (pressure) sores or heal >>> existing bed sores.","D","Deficient, Provider has date of >>> correction","2013-10-10",1,"Y","N","2014-01-01" >>> "015009","BURNS NURSING HOME, INC.","701 MONROE STREET >>> NW","RUSSELLVILLE","AL","35653","2013-09-05","Health","F","0315","Ensure >>> that each resident who enters the nursing home without a catheter is not >>> given a catheter, unless medically necessary, and that incontinent >>> patients receive proper services to prevent urinary tract infections and >>> restore normal bladder functions.","D","Deficient, Provider has date of >>> correction","2013-10-10",1,"Y","N","2014-01-01" >>> >>> >>> You are using a custom record class of your own, what does that look >>> like >>> or do ? >>> >>> A custom record class. This is all publicly available data but I'm >>> keeping track of the performance of US based health care providers >>> during >>> their annual inspections. So the records are notes of a deficiency >>> during >>> the inspection and I'm keeping those notes in a collection in an >>> instance >>> of the health care provider's class. The custom record class just >>> converts the CSV record to objects (Integers, Strings, DateAndTime) and >>> then gets stuffed in the health care provider's deficiency history >>> OrderedCollection (which has about 100 items). Again I don't think >>> its >>> what I'm doing as much as the image isn't growing when it needs to. >>> >>> >>> >>> >>> Maybe you can try using Array again ? >>> >>> I've attempted to do it where I parse and convert the entire CSV into >>> domain objects then add them to the image and the parsing works fine, >>> but >>> the system runs out of resources during the update phase. >>> >>> >>> What percentage of records read do you keep ? In my example it was very >>> small. Have you tried calculating your memory usage ? >>> >>> >>> I'm keeping some data from every record, but it doesn't load more than >>> 500MB of the data before falling over. I am not attempting to load the >>> 9GB of CSV files into one image. For 95% of the records in the CSV file >>> 20 of the 22 columns of the data is the same from file to file, just a >>> 'published date' and a 'time to expiration' date changes. Each file >>> covers a month, with about 500k deficiencies. Each month some >>> deficiencies are added to the file and some are resolved. So the total >>> number of deficiencies in the image is about 500k. Of those records >>> that >>> don't expire in a given month I'm adding the published date to a >>> collection of published dates for the record and also adding the "time >>> to >>> expiration" to a collection of those to record what was made public and >>> letting the rest of the data get GC'd. I don't only load those two >>> records because the other fields of the record in the CSV could change. >>> >>> I have not calculated the memory usage for the collection because I >>> thought it would have no problem fitting in the 2GB of RAM I have on >>> this >>> machine. >>> >>> >>> >>>> On 14 Nov 2014, at 22:34, Paul DeBruicker < >> >>> pdebruic@ >> >>> > wrote: >>>> >>>> Yes. With the image & vm I'm having trouble with I get an array with >>>> 9,942 >>>> elements in it. So its works as you'd expect. >>>> >>>> While processing the CSV file the image stays at about 60MB in RAM. >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> Sven Van Caekenberghe-2 wrote >>>>> Can you successfully run my example code ? >>>>> >>>>>> On 14 Nov 2014, at 22:03, Paul DeBruicker < >>>> >>>>> pdebruic@ >>>> >>>>> > wrote: >>>>>> >>>>>> Hi Sven, >>>>>> >>>>>> Thanks for taking a look and testing the NeoCSVReader portion for me. >>>>>> You're right of course that there's something I'm doing that's slow. >>>>>> But. >>>>>> There is something I can't figure out yet. >>>>>> >>>>>> To provide a little more detail: >>>>>> >>>>>> When the 'csv reading' process completes successfully profiling shows >>>>>> that >>>>>> most of the time is spent in NeoCSVReader>>#peekChar and using >>>>>> NeoCSVReader>>##addField: to convert a string to a DateAndTime. >>>>>> Dropping >>>>>> the DateAndTime conversion speeds things up but doesn't stop it from >>>>>> running >>>>>> out of memory. >>>>>> >>>>>> I start the image with >>>>>> >>>>>> ./pharo-ui --memory 1000m myimage.image >>>>>> >>>>>> Splitting the CSV file helps: >>>>>> ~1.5MB 5,000 lines = 1.2 seconds. >>>>>> ~15MB 50,000 lines = 8 seconds. >>>>>> ~30MB 100,000 lines = 16 seconds. >>>>>> ~60MB 200,000 lines = 45 seconds. >>>>>> >>>>>> >>>>>> It seems that when the CSV file crosses ~70MB in size things start >>>>>> going >>>>>> haywire with performance, and leads to the out of memory condition. >>>>>> The >>>>>> processing never ends. Sending "kill -SIGUSR1" prints a stack >>>>>> primarily >>>>>> composed of: >>>>>> >>>>>> 0xbffc5d08 M OutOfMemory class(Exception class)>signal 0x1f7ac060: >>>>>> a(n) >>>>>> OutOfMemory class >>>>>> 0xbffc5d20 M OutOfMemory class(Behavior)>basicNew 0x1f7ac060: a(n) >>>>>> OutOfMemory class >>>>>> 0xbffc5d38 M OutOfMemory class(Behavior)>new 0x1f7ac060: a(n) >>>>>> OutOfMemory >>>>>> class >>>>>> 0xbffc5d50 M OutOfMemory class(Exception class)>signal 0x1f7ac060: >>>>>> a(n) >>>>>> OutOfMemory class >>>>>> 0xbffc5d68 M OutOfMemory class(Behavior)>basicNew 0x1f7ac060: a(n) >>>>>> OutOfMemory class >>>>>> 0xbffc5d80 M OutOfMemory class(Behavior)>new 0x1f7ac060: a(n) >>>>>> OutOfMemory >>>>>> class >>>>>> 0xbffc5d98 M OutOfMemory class(Exception class)>signal 0x1f7ac060: >>>>>> a(n) >>>>>> OutOfMemory class >>>>>> >>>>>> So it seems like its trying to signal that its out of memory after >>>>>> its >>>>>> out >>>>>> of memory which triggers another OutOfMemory error. So that's why >>>>>> progress >>>>>> stops. >>>>>> >>>>>> >>>>>> ** Aside - OutOfMemory should probably be refactored to be able to >>>>>> signal >>>>>> itself without taking up more memory, triggering itself infinitely. >>>>>> Maybe >>>>>> it & its signalling morph infrastructure would be good as a singleton >>>>>> ** >>>>>> >>>>>> >>>>>> >>>>>> I'm confused about why it runs out of memory. According to htop the >>>>>> image >>>>>> only takes up about 520-540 MB of RAM when it reaches the >>>>>> 'OutOfMemory' >>>>>> condition. This Macbook Air laptop has 4GB, and has plenty of room >>>>>> for >>>>>> the >>>>>> image to grow. Also I've specified a 1,000MB image size when >>>>>> starting. >>>>>> So >>>>>> it should have plenty of room. Is there something I should check or >>>>>> a >>>>>> flag >>>>>> somewhere that prevents it from growing on a Mac? This is the latest >>>>>> Pharo30 VM. >>>>>> >>>>>> >>>>>> Thanks for helping me get to the bottom of this >>>>>> >>>>>> Paul >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> Sven Van Caekenberghe-2 wrote >>>>>>> Hi Paul, >>>>>>> >>>>>>> I think you must be doing something wrong with your class, the #do: >>>>>>> is >>>>>>> implemented as streaming over the record one by one, never holding >>>>>>> more >>>>>>> than one in memory. >>>>>>> >>>>>>> This is what I tried: >>>>>>> >>>>>>> 'paul.csv' asFileReference writeStreamDo: [ :file| >>>>>>> ZnBufferedWriteStream on: file do: [ :out | >>>>>>> (NeoCSVWriter on: out) in: [ :writer | >>>>>>> writer writeHeader: { #Number. #Color. #Integer. #Boolean}. >>>>>>> 1 to: 1e7 do: [ :each | >>>>>>> writer nextPut: { each. #(Red Green Blue) atRandom. 1e6 >>>>>>> atRandom. >>>>>>> #(true false) atRandom } ] ] ] ]. >>>>>>> >>>>>>> This results in a 300Mb file: >>>>>>> >>>>>>> $ ls -lah paul.csv >>>>>>> -rw-r--r--@ 1 sven staff 327M Nov 14 20:45 paul.csv >>>>>>> $ wc paul.csv >>>>>>> 10000001 10000001 342781577 paul.csv >>>>>>> >>>>>>> This is a selective read and collect (loads about 10K records): >>>>>>> >>>>>>> Array streamContents: [ :out | >>>>>>> 'paul.csv' asFileReference readStreamDo: [ :in | >>>>>>> (NeoCSVReader on: (ZnBufferedReadStream on: in)) in: [ :reader | >>>>>>> reader skipHeader; addIntegerField; addSymbolField; >>>>>>> addIntegerField; >>>>>>> addFieldConverter: [ :x | x = #true ]. >>>>>>> reader do: [ :each | each third < 1000 ifTrue: [ out nextPut: >>>>>>> each >>>>>>> ] >>>>>>> ] ] ] ]. >>>>>>> >>>>>>> This worked fine on my MacBook Air, no memory problems. It takes a >>>>>>> while >>>>>>> to parse that much data, of course. >>>>>>> >>>>>>> Sven >>>>>>> >>>>>>>> On 14 Nov 2014, at 19:08, Paul DeBruicker < >>>>>> >>>>>>> pdebruic@ >>>>>> >>>>>>> > wrote: >>>>>>>> >>>>>>>> Hi - >>>>>>>> >>>>>>>> I'm processing a 9 GBs of CSV files (the biggest file is 220MB or >>>>>>>> so). >>>>>>>> I'm not sure if its because of the size of the files or the code >>>>>>>> I've >>>>>>>> written to keep track of the domain objects I'm interested in, but >>>>>>>> I'm >>>>>>>> getting out of memory errors & crashes in Pharo 3 on Mac with the >>>>>>>> latest >>>>>>>> VM. I haven't checked other vms. >>>>>>>> >>>>>>>> I'm going to profile my own code and attempt to split the files >>>>>>>> manually >>>>>>>> for now to see what else it could be. >>>>>>>> >>>>>>>> >>>>>>>> Right now I'm doing something similar to >>>>>>>> >>>>>>>> |file reader| >>>>>>>> file:= '/path/to/file/myfile.csv' asFileReference readStream. >>>>>>>> reader: NeoCSVReader on: file >>>>>>>> >>>>>>>> reader >>>>>>>> recordClass: MyClass; >>>>>>>> skipHeader; >>>>>>>> addField: #myField:; >>>>>>>> .... >>>>>>>> >>>>>>>> >>>>>>>> reader do:[:eachRecord | self >>>>>>>> seeIfRecordIsInterestingAndIfSoKeepIt: >>>>>>>> eachRecord]. >>>>>>>> file close. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Is there a facility in NeoCSVReader to read a file in batches (e.g. >>>>>>>> 1000 >>>>>>>> lines at a time) or an easy way to do that ? >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Thanks >>>>>>>> >>>>>>>> Paul >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> View this message in context: >>>>>> http://forum.world.st/running-out-of-memory-while-processing-a-220MB-csv-fi… >>>>>> Sent from the Pharo Smalltalk Users mailing list archive at >>>>>> Nabble.com. >>>> >>>> >>>> >>>> >>>> >>>> -- >>>> View this message in context: >>>> http://forum.world.st/running-out-of-memory-while-processing-a-220MB-csv-fi… >>>> Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com. >> >> >> >> >> >> -- >> View this message in context: >> http://forum.world.st/running-out-of-memory-while-processing-a-220MB-csv-fi… >> Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com. -- View this message in context: http://forum.world.st/running-out-of-memory-while-processing-a-220MB-csv-fi… Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com.

Nov. 16, 2014

Re: [Pharo-users] running out of memory while processing a 220MB csv file with NeoCSVReader - tips?

by Alain Rastoul

Hi Paul, These are some vm memory allocation issues that exists on windows vm too and are more related to your approach which is discutable than to a real vm problem. Suppose you have tomorrow to deal with all North American based health care providers including Canada or even add South America or the rate not being 95% , data won't fit in memory, even with 2G or 4G may be even with 16G. I saw the same approach and kind of problems in dotNet. Let say it's your current requirement, and you want to do it like that, a trick that may help you : during personal experiments about loading data in memory and statistics from databases, I found that most often 70 to 80 % of real data is the same. If you really need to load that in memory, you can intern all your data in a dictionary. Very simple to do: at the beginning or you processing. | internedData | internedData := Dictionary new. And for each field, before storing it in your array: field := internedData at: field ifAbsentPut:[field]. This will of course add some extra processing time but I guess it should be ok. :) Regards, Alain Le 14/11/2014 23:14, Paul DeBruicker a Ã©crit : > Hi Sven > > Yes, like I said earlier, after your first email, that I think its not a > problem with NeoCSV as with what I'm doing and an out of memory condition. > > Have you ever seen a stack after sending kill -SIGUSR1 that looks like this: > > output file stack is full. > output file stack is full. > output file stack is full. > output file stack is full. > output file stack is full. > .... > > > What does that mean? > > Answers to your questions below. > > Thanks again for helping me out > > > > Sven Van Caekenberghe-2 wrote >> OK then, you *can* read/process 300MB .csv files ;-) >> >> What does your CSV file look like, can you show a couple of lines ? >> >> here are 2 lines + a header: >> >> "provnum","Provname","address","city","state","zip","survey_date_output","SurveyType","defpref","tag","tag_desc","scope","defstat","statdate","cycle","standard","complaint","filedate" >> "015009","BURNS NURSING HOME, INC.","701 MONROE STREET >> NW","RUSSELLVILLE","AL","35653","2013-09-05","Health","F","0314","Give >> residents proper treatment to prevent new bed (pressure) sores or heal >> existing bed sores.","D","Deficient, Provider has date of >> correction","2013-10-10",1,"Y","N","2014-01-01" >> "015009","BURNS NURSING HOME, INC.","701 MONROE STREET >> NW","RUSSELLVILLE","AL","35653","2013-09-05","Health","F","0315","Ensure >> that each resident who enters the nursing home without a catheter is not >> given a catheter, unless medically necessary, and that incontinent >> patients receive proper services to prevent urinary tract infections and >> restore normal bladder functions.","D","Deficient, Provider has date of >> correction","2013-10-10",1,"Y","N","2014-01-01" >> >> >> You are using a custom record class of your own, what does that look like >> or do ? >> >> A custom record class. This is all publicly available data but I'm >> keeping track of the performance of US based health care providers during >> their annual inspections. So the records are notes of a deficiency during >> the inspection and I'm keeping those notes in a collection in an instance >> of the health care provider's class. The custom record class just >> converts the CSV record to objects (Integers, Strings, DateAndTime) and >> then gets stuffed in the health care provider's deficiency history >> OrderedCollection (which has about 100 items). Again I don't think its >> what I'm doing as much as the image isn't growing when it needs to. >> >> >> >> >> Maybe you can try using Array again ? >> >> I've attempted to do it where I parse and convert the entire CSV into >> domain objects then add them to the image and the parsing works fine, but >> the system runs out of resources during the update phase. >> >> >> What percentage of records read do you keep ? In my example it was very >> small. Have you tried calculating your memory usage ? >> >> >> I'm keeping some data from every record, but it doesn't load more than >> 500MB of the data before falling over. I am not attempting to load the >> 9GB of CSV files into one image. For 95% of the records in the CSV file >> 20 of the 22 columns of the data is the same from file to file, just a >> 'published date' and a 'time to expiration' date changes. Each file >> covers a month, with about 500k deficiencies. Each month some >> deficiencies are added to the file and some are resolved. So the total >> number of deficiencies in the image is about 500k. Of those records that >> don't expire in a given month I'm adding the published date to a >> collection of published dates for the record and also adding the "time to >> expiration" to a collection of those to record what was made public and >> letting the rest of the data get GC'd. I don't only load those two >> records because the other fields of the record in the CSV could change. >> >> I have not calculated the memory usage for the collection because I >> thought it would have no problem fitting in the 2GB of RAM I have on this >> machine. >> >> >> >>> On 14 Nov 2014, at 22:34, Paul DeBruicker < > >> pdebruic@ > >> > wrote: >>> >>> Yes. With the image & vm I'm having trouble with I get an array with >>> 9,942 >>> elements in it. So its works as you'd expect. >>> >>> While processing the CSV file the image stays at about 60MB in RAM. >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> Sven Van Caekenberghe-2 wrote >>>> Can you successfully run my example code ? >>>> >>>>> On 14 Nov 2014, at 22:03, Paul DeBruicker < >>> >>>> pdebruic@ >>> >>>> > wrote: >>>>> >>>>> Hi Sven, >>>>> >>>>> Thanks for taking a look and testing the NeoCSVReader portion for me. >>>>> You're right of course that there's something I'm doing that's slow. >>>>> But. >>>>> There is something I can't figure out yet. >>>>> >>>>> To provide a little more detail: >>>>> >>>>> When the 'csv reading' process completes successfully profiling shows >>>>> that >>>>> most of the time is spent in NeoCSVReader>>#peekChar and using >>>>> NeoCSVReader>>##addField: to convert a string to a DateAndTime. >>>>> Dropping >>>>> the DateAndTime conversion speeds things up but doesn't stop it from >>>>> running >>>>> out of memory. >>>>> >>>>> I start the image with >>>>> >>>>> ./pharo-ui --memory 1000m myimage.image >>>>> >>>>> Splitting the CSV file helps: >>>>> ~1.5MB 5,000 lines = 1.2 seconds. >>>>> ~15MB 50,000 lines = 8 seconds. >>>>> ~30MB 100,000 lines = 16 seconds. >>>>> ~60MB 200,000 lines = 45 seconds. >>>>> >>>>> >>>>> It seems that when the CSV file crosses ~70MB in size things start >>>>> going >>>>> haywire with performance, and leads to the out of memory condition. >>>>> The >>>>> processing never ends. Sending "kill -SIGUSR1" prints a stack >>>>> primarily >>>>> composed of: >>>>> >>>>> 0xbffc5d08 M OutOfMemory class(Exception class)>signal 0x1f7ac060: a(n) >>>>> OutOfMemory class >>>>> 0xbffc5d20 M OutOfMemory class(Behavior)>basicNew 0x1f7ac060: a(n) >>>>> OutOfMemory class >>>>> 0xbffc5d38 M OutOfMemory class(Behavior)>new 0x1f7ac060: a(n) >>>>> OutOfMemory >>>>> class >>>>> 0xbffc5d50 M OutOfMemory class(Exception class)>signal 0x1f7ac060: a(n) >>>>> OutOfMemory class >>>>> 0xbffc5d68 M OutOfMemory class(Behavior)>basicNew 0x1f7ac060: a(n) >>>>> OutOfMemory class >>>>> 0xbffc5d80 M OutOfMemory class(Behavior)>new 0x1f7ac060: a(n) >>>>> OutOfMemory >>>>> class >>>>> 0xbffc5d98 M OutOfMemory class(Exception class)>signal 0x1f7ac060: a(n) >>>>> OutOfMemory class >>>>> >>>>> So it seems like its trying to signal that its out of memory after its >>>>> out >>>>> of memory which triggers another OutOfMemory error. So that's why >>>>> progress >>>>> stops. >>>>> >>>>> >>>>> ** Aside - OutOfMemory should probably be refactored to be able to >>>>> signal >>>>> itself without taking up more memory, triggering itself infinitely. >>>>> Maybe >>>>> it & its signalling morph infrastructure would be good as a singleton >>>>> ** >>>>> >>>>> >>>>> >>>>> I'm confused about why it runs out of memory. According to htop the >>>>> image >>>>> only takes up about 520-540 MB of RAM when it reaches the 'OutOfMemory' >>>>> condition. This Macbook Air laptop has 4GB, and has plenty of room for >>>>> the >>>>> image to grow. Also I've specified a 1,000MB image size when starting. >>>>> So >>>>> it should have plenty of room. Is there something I should check or a >>>>> flag >>>>> somewhere that prevents it from growing on a Mac? This is the latest >>>>> Pharo30 VM. >>>>> >>>>> >>>>> Thanks for helping me get to the bottom of this >>>>> >>>>> Paul >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> Sven Van Caekenberghe-2 wrote >>>>>> Hi Paul, >>>>>> >>>>>> I think you must be doing something wrong with your class, the #do: is >>>>>> implemented as streaming over the record one by one, never holding >>>>>> more >>>>>> than one in memory. >>>>>> >>>>>> This is what I tried: >>>>>> >>>>>> 'paul.csv' asFileReference writeStreamDo: [ :file| >>>>>> ZnBufferedWriteStream on: file do: [ :out | >>>>>> (NeoCSVWriter on: out) in: [ :writer | >>>>>> writer writeHeader: { #Number. #Color. #Integer. #Boolean}. >>>>>> 1 to: 1e7 do: [ :each | >>>>>> writer nextPut: { each. #(Red Green Blue) atRandom. 1e6 >>>>>> atRandom. >>>>>> #(true false) atRandom } ] ] ] ]. >>>>>> >>>>>> This results in a 300Mb file: >>>>>> >>>>>> $ ls -lah paul.csv >>>>>> -rw-r--r--@ 1 sven staff 327M Nov 14 20:45 paul.csv >>>>>> $ wc paul.csv >>>>>> 10000001 10000001 342781577 paul.csv >>>>>> >>>>>> This is a selective read and collect (loads about 10K records): >>>>>> >>>>>> Array streamContents: [ :out | >>>>>> 'paul.csv' asFileReference readStreamDo: [ :in | >>>>>> (NeoCSVReader on: (ZnBufferedReadStream on: in)) in: [ :reader | >>>>>> reader skipHeader; addIntegerField; addSymbolField; >>>>>> addIntegerField; >>>>>> addFieldConverter: [ :x | x = #true ]. >>>>>> reader do: [ :each | each third < 1000 ifTrue: [ out nextPut: each >>>>>> ] >>>>>> ] ] ] ]. >>>>>> >>>>>> This worked fine on my MacBook Air, no memory problems. It takes a >>>>>> while >>>>>> to parse that much data, of course. >>>>>> >>>>>> Sven >>>>>> >>>>>>> On 14 Nov 2014, at 19:08, Paul DeBruicker < >>>>> >>>>>> pdebruic@ >>>>> >>>>>> > wrote: >>>>>>> >>>>>>> Hi - >>>>>>> >>>>>>> I'm processing a 9 GBs of CSV files (the biggest file is 220MB or >>>>>>> so). >>>>>>> I'm not sure if its because of the size of the files or the code I've >>>>>>> written to keep track of the domain objects I'm interested in, but >>>>>>> I'm >>>>>>> getting out of memory errors & crashes in Pharo 3 on Mac with the >>>>>>> latest >>>>>>> VM. I haven't checked other vms. >>>>>>> >>>>>>> I'm going to profile my own code and attempt to split the files >>>>>>> manually >>>>>>> for now to see what else it could be. >>>>>>> >>>>>>> >>>>>>> Right now I'm doing something similar to >>>>>>> >>>>>>> |file reader| >>>>>>> file:= '/path/to/file/myfile.csv' asFileReference readStream. >>>>>>> reader: NeoCSVReader on: file >>>>>>> >>>>>>> reader >>>>>>> recordClass: MyClass; >>>>>>> skipHeader; >>>>>>> addField: #myField:; >>>>>>> .... >>>>>>> >>>>>>> >>>>>>> reader do:[:eachRecord | self seeIfRecordIsInterestingAndIfSoKeepIt: >>>>>>> eachRecord]. >>>>>>> file close. >>>>>>> >>>>>>> >>>>>>> >>>>>>> Is there a facility in NeoCSVReader to read a file in batches (e.g. >>>>>>> 1000 >>>>>>> lines at a time) or an easy way to do that ? >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> Thanks >>>>>>> >>>>>>> Paul >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> View this message in context: >>>>> http://forum.world.st/running-out-of-memory-while-processing-a-220MB-csv-fi… >>>>> Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com. >>> >>> >>> >>> >>> >>> -- >>> View this message in context: >>> http://forum.world.st/running-out-of-memory-while-processing-a-220MB-csv-fi… >>> Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com. > > > > > > -- > View this message in context: http://forum.world.st/running-out-of-memory-while-processing-a-220MB-csv-fi… > Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com. > >

Nov. 15, 2014

Re: [Pharo-users] Has anyone tried compiling the Pharo VM into JS using Emscripten?

by stepharo

> Hi Alain, > Although I am really impressed with Dan's work, Emscripten seems to be very different. > > In theory - and my knowledge in this is very limited - it might allow the VM C files to be transpiled into a very tight subset of JS. On the face of it, this is a crazy idea, but they have achieved amazing performance with things like the QT library. This made me wonder whether a Js version of pharo is possible. We thought about it about one and half year ago but lack of resources.... you know the end of the story > > Just Idle conjecturing in. Friday night :-) > > > >> On 14 Nov 2014, at 18:09, pharo-users-request(a)lists.pharo.org wrote: >> >> Send Pharo-users mailing list submissions to >> pharo-users(a)lists.pharo.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://lists.pharo.org/mailman/listinfo/pharo-users_lists.pharo.org >> or, via email, send a message with subject or body 'help' to >> pharo-users-request(a)lists.pharo.org >> >> You can reach the person managing the list at >> pharo-users-owner(a)lists.pharo.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Pharo-users digest..." >> >> >> Today's Topics: >> >> 1. Re: running out of memory while processing a 220MB csv file >> with NeoCSVReader - tips? (Paul DeBruicker) >> 2. Re: running out of memory while processing a 220MB csv file >> with NeoCSVReader - tips? (Sven Van Caekenberghe) >> 3. Re: Has anyone tried compiling the Pharo VM into JS using >> Emscripten? (Alain Rastoul) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Fri, 14 Nov 2014 14:14:51 -0800 (PST) >> From: Paul DeBruicker <pdebruic(a)gmail.com> >> To: pharo-users(a)lists.pharo.org >> Subject: Re: [Pharo-users] running out of memory while processing a >> 220MB csv file with NeoCSVReader - tips? >> Message-ID: <1416003291281-4790341.post(a)n4.nabble.com> >> Content-Type: text/plain; charset=us-ascii >> >> Hi Sven >> >> Yes, like I said earlier, after your first email, that I think its not a >> problem with NeoCSV as with what I'm doing and an out of memory condition. >> >> Have you ever seen a stack after sending kill -SIGUSR1 that looks like this: >> >> output file stack is full. >> output file stack is full. >> output file stack is full. >> output file stack is full. >> output file stack is full. >> .... >> >> >> What does that mean? >> >> Answers to your questions below. >> >> Thanks again for helping me out >> >> >> >> Sven Van Caekenberghe-2 wrote >>> OK then, you *can* read/process 300MB .csv files ;-) >>> >>> What does your CSV file look like, can you show a couple of lines ? >>> >>> here are 2 lines + a header: >>> >>> "provnum","Provname","address","city","state","zip","survey_date_output","SurveyType","defpref","tag","tag_desc","scope","defstat","statdate","cycle","standard","complaint","filedate" >>> "015009","BURNS NURSING HOME, INC.","701 MONROE STREET >>> NW","RUSSELLVILLE","AL","35653","2013-09-05","Health","F","0314","Give >>> residents proper treatment to prevent new bed (pressure) sores or heal >>> existing bed sores.","D","Deficient, Provider has date of >>> correction","2013-10-10",1,"Y","N","2014-01-01" >>> "015009","BURNS NURSING HOME, INC.","701 MONROE STREET >>> NW","RUSSELLVILLE","AL","35653","2013-09-05","Health","F","0315","Ensure >>> that each resident who enters the nursing home without a catheter is not >>> given a catheter, unless medically necessary, and that incontinent >>> patients receive proper services to prevent urinary tract infections and >>> restore normal bladder functions.","D","Deficient, Provider has date of >>> correction","2013-10-10",1,"Y","N","2014-01-01" >>> >>> >>> You are using a custom record class of your own, what does that look like >>> or do ? >>> >>> A custom record class. This is all publicly available data but I'm >>> keeping track of the performance of US based health care providers during >>> their annual inspections. So the records are notes of a deficiency during >>> the inspection and I'm keeping those notes in a collection in an instance >>> of the health care provider's class. The custom record class just >>> converts the CSV record to objects (Integers, Strings, DateAndTime) and >>> then gets stuffed in the health care provider's deficiency history >>> OrderedCollection (which has about 100 items). Again I don't think its >>> what I'm doing as much as the image isn't growing when it needs to. >>> >>> >>> >>> >>> Maybe you can try using Array again ? >>> >>> I've attempted to do it where I parse and convert the entire CSV into >>> domain objects then add them to the image and the parsing works fine, but >>> the system runs out of resources during the update phase. >>> >>> >>> What percentage of records read do you keep ? In my example it was very >>> small. Have you tried calculating your memory usage ? >>> >>> >>> I'm keeping some data from every record, but it doesn't load more than >>> 500MB of the data before falling over. I am not attempting to load the >>> 9GB of CSV files into one image. For 95% of the records in the CSV file >>> 20 of the 22 columns of the data is the same from file to file, just a >>> 'published date' and a 'time to expiration' date changes. Each file >>> covers a month, with about 500k deficiencies. Each month some >>> deficiencies are added to the file and some are resolved. So the total >>> number of deficiencies in the image is about 500k. Of those records that >>> don't expire in a given month I'm adding the published date to a >>> collection of published dates for the record and also adding the "time to >>> expiration" to a collection of those to record what was made public and >>> letting the rest of the data get GC'd. I don't only load those two >>> records because the other fields of the record in the CSV could change. >>> >>> I have not calculated the memory usage for the collection because I >>> thought it would have no problem fitting in the 2GB of RAM I have on this >>> machine. >>> >>> >>> >>>> On 14 Nov 2014, at 22:34, Paul DeBruicker < >>> pdebruic@ >>> > wrote: >>>> Yes. With the image & vm I'm having trouble with I get an array with >>>> 9,942 >>>> elements in it. So its works as you'd expect. >>>> >>>> While processing the CSV file the image stays at about 60MB in RAM. >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> Sven Van Caekenberghe-2 wrote >>>>> Can you successfully run my example code ? >>>>> >>>>>> On 14 Nov 2014, at 22:03, Paul DeBruicker < >>>>> pdebruic@ >>>>> > wrote: >>>>>> Hi Sven, >>>>>> >>>>>> Thanks for taking a look and testing the NeoCSVReader portion for me. >>>>>> You're right of course that there's something I'm doing that's slow. >>>>>> But. >>>>>> There is something I can't figure out yet. >>>>>> >>>>>> To provide a little more detail: >>>>>> >>>>>> When the 'csv reading' process completes successfully profiling shows >>>>>> that >>>>>> most of the time is spent in NeoCSVReader>>#peekChar and using >>>>>> NeoCSVReader>>##addField: to convert a string to a DateAndTime. >>>>>> Dropping >>>>>> the DateAndTime conversion speeds things up but doesn't stop it from >>>>>> running >>>>>> out of memory. >>>>>> >>>>>> I start the image with >>>>>> >>>>>> ./pharo-ui --memory 1000m myimage.image >>>>>> >>>>>> Splitting the CSV file helps: >>>>>> ~1.5MB 5,000 lines = 1.2 seconds. >>>>>> ~15MB 50,000 lines = 8 seconds. >>>>>> ~30MB 100,000 lines = 16 seconds. >>>>>> ~60MB 200,000 lines = 45 seconds. >>>>>> >>>>>> >>>>>> It seems that when the CSV file crosses ~70MB in size things start >>>>>> going >>>>>> haywire with performance, and leads to the out of memory condition. >>>>>> The >>>>>> processing never ends. Sending "kill -SIGUSR1" prints a stack >>>>>> primarily >>>>>> composed of: >>>>>> >>>>>> 0xbffc5d08 M OutOfMemory class(Exception class)>signal 0x1f7ac060: a(n) >>>>>> OutOfMemory class >>>>>> 0xbffc5d20 M OutOfMemory class(Behavior)>basicNew 0x1f7ac060: a(n) >>>>>> OutOfMemory class >>>>>> 0xbffc5d38 M OutOfMemory class(Behavior)>new 0x1f7ac060: a(n) >>>>>> OutOfMemory >>>>>> class >>>>>> 0xbffc5d50 M OutOfMemory class(Exception class)>signal 0x1f7ac060: a(n) >>>>>> OutOfMemory class >>>>>> 0xbffc5d68 M OutOfMemory class(Behavior)>basicNew 0x1f7ac060: a(n) >>>>>> OutOfMemory class >>>>>> 0xbffc5d80 M OutOfMemory class(Behavior)>new 0x1f7ac060: a(n) >>>>>> OutOfMemory >>>>>> class >>>>>> 0xbffc5d98 M OutOfMemory class(Exception class)>signal 0x1f7ac060: a(n) >>>>>> OutOfMemory class >>>>>> >>>>>> So it seems like its trying to signal that its out of memory after its >>>>>> out >>>>>> of memory which triggers another OutOfMemory error. So that's why >>>>>> progress >>>>>> stops. >>>>>> >>>>>> >>>>>> ** Aside - OutOfMemory should probably be refactored to be able to >>>>>> signal >>>>>> itself without taking up more memory, triggering itself infinitely. >>>>>> Maybe >>>>>> it & its signalling morph infrastructure would be good as a singleton >>>>>> ** >>>>>> >>>>>> >>>>>> >>>>>> I'm confused about why it runs out of memory. According to htop the >>>>>> image >>>>>> only takes up about 520-540 MB of RAM when it reaches the 'OutOfMemory' >>>>>> condition. This Macbook Air laptop has 4GB, and has plenty of room for >>>>>> the >>>>>> image to grow. Also I've specified a 1,000MB image size when starting. >>>>>> So >>>>>> it should have plenty of room. Is there something I should check or a >>>>>> flag >>>>>> somewhere that prevents it from growing on a Mac? This is the latest >>>>>> Pharo30 VM. >>>>>> >>>>>> >>>>>> Thanks for helping me get to the bottom of this >>>>>> >>>>>> Paul >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> Sven Van Caekenberghe-2 wrote >>>>>>> Hi Paul, >>>>>>> >>>>>>> I think you must be doing something wrong with your class, the #do: is >>>>>>> implemented as streaming over the record one by one, never holding >>>>>>> more >>>>>>> than one in memory. >>>>>>> >>>>>>> This is what I tried: >>>>>>> >>>>>>> 'paul.csv' asFileReference writeStreamDo: [ :file| >>>>>>> ZnBufferedWriteStream on: file do: [ :out | >>>>>>> (NeoCSVWriter on: out) in: [ :writer | >>>>>>> writer writeHeader: { #Number. #Color. #Integer. #Boolean}. >>>>>>> 1 to: 1e7 do: [ :each | >>>>>>> writer nextPut: { each. #(Red Green Blue) atRandom. 1e6 >>>>>>> atRandom. >>>>>>> #(true false) atRandom } ] ] ] ]. >>>>>>> >>>>>>> This results in a 300Mb file: >>>>>>> >>>>>>> $ ls -lah paul.csv >>>>>>> -rw-r--r--@ 1 sven staff 327M Nov 14 20:45 paul.csv >>>>>>> $ wc paul.csv >>>>>>> 10000001 10000001 342781577 paul.csv >>>>>>> >>>>>>> This is a selective read and collect (loads about 10K records): >>>>>>> >>>>>>> Array streamContents: [ :out | >>>>>>> 'paul.csv' asFileReference readStreamDo: [ :in | >>>>>>> (NeoCSVReader on: (ZnBufferedReadStream on: in)) in: [ :reader | >>>>>>> reader skipHeader; addIntegerField; addSymbolField; >>>>>>> addIntegerField; >>>>>>> addFieldConverter: [ :x | x = #true ]. >>>>>>> reader do: [ :each | each third < 1000 ifTrue: [ out nextPut: each >>>>>>> ] >>>>>>> ] ] ] ]. >>>>>>> >>>>>>> This worked fine on my MacBook Air, no memory problems. It takes a >>>>>>> while >>>>>>> to parse that much data, of course. >>>>>>> >>>>>>> Sven >>>>>>> >>>>>>>> On 14 Nov 2014, at 19:08, Paul DeBruicker < >>>>>>> pdebruic@ >>>>>>> > wrote: >>>>>>>> Hi - >>>>>>>> >>>>>>>> I'm processing a 9 GBs of CSV files (the biggest file is 220MB or >>>>>>>> so). >>>>>>>> I'm not sure if its because of the size of the files or the code I've >>>>>>>> written to keep track of the domain objects I'm interested in, but >>>>>>>> I'm >>>>>>>> getting out of memory errors & crashes in Pharo 3 on Mac with the >>>>>>>> latest >>>>>>>> VM. I haven't checked other vms. >>>>>>>> >>>>>>>> I'm going to profile my own code and attempt to split the files >>>>>>>> manually >>>>>>>> for now to see what else it could be. >>>>>>>> >>>>>>>> >>>>>>>> Right now I'm doing something similar to >>>>>>>> >>>>>>>> |file reader| >>>>>>>> file:= '/path/to/file/myfile.csv' asFileReference readStream. >>>>>>>> reader: NeoCSVReader on: file >>>>>>>> >>>>>>>> reader >>>>>>>> recordClass: MyClass; >>>>>>>> skipHeader; >>>>>>>> addField: #myField:; >>>>>>>> .... >>>>>>>> >>>>>>>> >>>>>>>> reader do:[:eachRecord | self seeIfRecordIsInterestingAndIfSoKeepIt: >>>>>>>> eachRecord]. >>>>>>>> file close. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Is there a facility in NeoCSVReader to read a file in batches (e.g. >>>>>>>> 1000 >>>>>>>> lines at a time) or an easy way to do that ? >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Thanks >>>>>>>> >>>>>>>> Paul >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> View this message in context: >>>>>> http://forum.world.st/running-out-of-memory-while-processing-a-220MB-csv-fi… >>>>>> Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com. >>>> >>>> >>>> >>>> >>>> -- >>>> View this message in context: >>>> http://forum.world.st/running-out-of-memory-while-processing-a-220MB-csv-fi… >>>> Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com. >> >> >> >> >> -- >> View this message in context: http://forum.world.st/running-out-of-memory-while-processing-a-220MB-csv-fi… >> Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com. >> >> >> >> ------------------------------ >> >> Message: 2 >> Date: Sat, 15 Nov 2014 00:07:35 +0100 >> From: Sven Van Caekenberghe <sven(a)stfx.eu> >> To: Any question about pharo is welcome <pharo-users(a)lists.pharo.org> >> Subject: Re: [Pharo-users] running out of memory while processing a >> 220MB csv file with NeoCSVReader - tips? >> Message-ID: <4196B7D2-63C3-4E17-89DF-A0C7ACA919EF(a)stfx.eu> >> Content-Type: text/plain; charset=us-ascii >> >> >>> On 14 Nov 2014, at 23:14, Paul DeBruicker <pdebruic(a)gmail.com> wrote: >>> >>> Hi Sven >>> >>> Yes, like I said earlier, after your first email, that I think its not a >>> problem with NeoCSV as with what I'm doing and an out of memory condition. >>> >>> Have you ever seen a stack after sending kill -SIGUSR1 that looks like this: >>> >>> output file stack is full. >>> output file stack is full. >>> output file stack is full. >>> output file stack is full. >>> output file stack is full. >>> .... >>> >>> >>> What does that mean? >> I don't know, but I think that you are really out of memory. >> BTW, I think that setting no flags is better, memory will expand maximally then. >> I think the useful maximum is closer to 1GB than 2GB. >> >>> Answers to your questions below. >> It is difficult to follow what you are doing exactly, but I think that you underestimate how much memory a parsed, structured/nested object uses. Taking the second line of your example, the 20+ fields, with 3 DateAndTimes, easily cost between 512 and 1024 bytes per record. That would limit you to between 1M and 2M records. >> >> I tried this: >> >> Array streamContents: [ :data | >> 5e2 timesRepeat: [ >> data nextPut: (Array streamContents: [ :out | >> 20 timesRepeat: [ out nextPut: Character alphabet ]. >> 3 timesRepeat: [ out nextPut: DateAndTime now ] ]) ] ]. >> >> it worked to 5e5, but not for 5e6 - I didn't try numbers in between as it takes very long. >> >> Good luck, if you can solve this, please tell us how you did it. >> >>> Thanks again for helping me out >>> >>> >>> >>> Sven Van Caekenberghe-2 wrote >>>> OK then, you *can* read/process 300MB .csv files ;-) >>>> >>>> What does your CSV file look like, can you show a couple of lines ? >>>> >>>> here are 2 lines + a header: >>>> >>>> "provnum","Provname","address","city","state","zip","survey_date_output","SurveyType","defpref","tag","tag_desc","scope","defstat","statdate","cycle","standard","complaint","filedate" >>>> "015009","BURNS NURSING HOME, INC.","701 MONROE STREET >>>> NW","RUSSELLVILLE","AL","35653","2013-09-05","Health","F","0314","Give >>>> residents proper treatment to prevent new bed (pressure) sores or heal >>>> existing bed sores.","D","Deficient, Provider has date of >>>> correction","2013-10-10",1,"Y","N","2014-01-01" >>>> "015009","BURNS NURSING HOME, INC.","701 MONROE STREET >>>> NW","RUSSELLVILLE","AL","35653","2013-09-05","Health","F","0315","Ensure >>>> that each resident who enters the nursing home without a catheter is not >>>> given a catheter, unless medically necessary, and that incontinent >>>> patients receive proper services to prevent urinary tract infections and >>>> restore normal bladder functions.","D","Deficient, Provider has date of >>>> correction","2013-10-10",1,"Y","N","2014-01-01" >>>> >>>> >>>> You are using a custom record class of your own, what does that look like >>>> or do ? >>>> >>>> A custom record class. This is all publicly available data but I'm >>>> keeping track of the performance of US based health care providers during >>>> their annual inspections. So the records are notes of a deficiency during >>>> the inspection and I'm keeping those notes in a collection in an instance >>>> of the health care provider's class. The custom record class just >>>> converts the CSV record to objects (Integers, Strings, DateAndTime) and >>>> then gets stuffed in the health care provider's deficiency history >>>> OrderedCollection (which has about 100 items). Again I don't think its >>>> what I'm doing as much as the image isn't growing when it needs to. >>>> >>>> >>>> >>>> >>>> Maybe you can try using Array again ? >>>> >>>> I've attempted to do it where I parse and convert the entire CSV into >>>> domain objects then add them to the image and the parsing works fine, but >>>> the system runs out of resources during the update phase. >>>> >>>> >>>> What percentage of records read do you keep ? In my example it was very >>>> small. Have you tried calculating your memory usage ? >>>> >>>> >>>> I'm keeping some data from every record, but it doesn't load more than >>>> 500MB of the data before falling over. I am not attempting to load the >>>> 9GB of CSV files into one image. For 95% of the records in the CSV file >>>> 20 of the 22 columns of the data is the same from file to file, just a >>>> 'published date' and a 'time to expiration' date changes. Each file >>>> covers a month, with about 500k deficiencies. Each month some >>>> deficiencies are added to the file and some are resolved. So the total >>>> number of deficiencies in the image is about 500k. Of those records that >>>> don't expire in a given month I'm adding the published date to a >>>> collection of published dates for the record and also adding the "time to >>>> expiration" to a collection of those to record what was made public and >>>> letting the rest of the data get GC'd. I don't only load those two >>>> records because the other fields of the record in the CSV could change. >>>> >>>> I have not calculated the memory usage for the collection because I >>>> thought it would have no problem fitting in the 2GB of RAM I have on this >>>> machine. >>>> >>>> >>>> >>>>> On 14 Nov 2014, at 22:34, Paul DeBruicker < >>>> pdebruic@ >>>> > wrote: >>>>> Yes. With the image & vm I'm having trouble with I get an array with >>>>> 9,942 >>>>> elements in it. So its works as you'd expect. >>>>> >>>>> While processing the CSV file the image stays at about 60MB in RAM. >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> Sven Van Caekenberghe-2 wrote >>>>>> Can you successfully run my example code ? >>>>>> >>>>>>> On 14 Nov 2014, at 22:03, Paul DeBruicker < >>>>>> pdebruic@ >>>>>> > wrote: >>>>>>> Hi Sven, >>>>>>> >>>>>>> Thanks for taking a look and testing the NeoCSVReader portion for me. >>>>>>> You're right of course that there's something I'm doing that's slow. >>>>>>> But. >>>>>>> There is something I can't figure out yet. >>>>>>> >>>>>>> To provide a little more detail: >>>>>>> >>>>>>> When the 'csv reading' process completes successfully profiling shows >>>>>>> that >>>>>>> most of the time is spent in NeoCSVReader>>#peekChar and using >>>>>>> NeoCSVReader>>##addField: to convert a string to a DateAndTime. >>>>>>> Dropping >>>>>>> the DateAndTime conversion speeds things up but doesn't stop it from >>>>>>> running >>>>>>> out of memory. >>>>>>> >>>>>>> I start the image with >>>>>>> >>>>>>> ./pharo-ui --memory 1000m myimage.image >>>>>>> >>>>>>> Splitting the CSV file helps: >>>>>>> ~1.5MB 5,000 lines = 1.2 seconds. >>>>>>> ~15MB 50,000 lines = 8 seconds. >>>>>>> ~30MB 100,000 lines = 16 seconds. >>>>>>> ~60MB 200,000 lines = 45 seconds. >>>>>>> >>>>>>> >>>>>>> It seems that when the CSV file crosses ~70MB in size things start >>>>>>> going >>>>>>> haywire with performance, and leads to the out of memory condition. >>>>>>> The >>>>>>> processing never ends. Sending "kill -SIGUSR1" prints a stack >>>>>>> primarily >>>>>>> composed of: >>>>>>> >>>>>>> 0xbffc5d08 M OutOfMemory class(Exception class)>signal 0x1f7ac060: a(n) >>>>>>> OutOfMemory class >>>>>>> 0xbffc5d20 M OutOfMemory class(Behavior)>basicNew 0x1f7ac060: a(n) >>>>>>> OutOfMemory class >>>>>>> 0xbffc5d38 M OutOfMemory class(Behavior)>new 0x1f7ac060: a(n) >>>>>>> OutOfMemory >>>>>>> class >>>>>>> 0xbffc5d50 M OutOfMemory class(Exception class)>signal 0x1f7ac060: a(n) >>>>>>> OutOfMemory class >>>>>>> 0xbffc5d68 M OutOfMemory class(Behavior)>basicNew 0x1f7ac060: a(n) >>>>>>> OutOfMemory class >>>>>>> 0xbffc5d80 M OutOfMemory class(Behavior)>new 0x1f7ac060: a(n) >>>>>>> OutOfMemory >>>>>>> class >>>>>>> 0xbffc5d98 M OutOfMemory class(Exception class)>signal 0x1f7ac060: a(n) >>>>>>> OutOfMemory class >>>>>>> >>>>>>> So it seems like its trying to signal that its out of memory after its >>>>>>> out >>>>>>> of memory which triggers another OutOfMemory error. So that's why >>>>>>> progress >>>>>>> stops. >>>>>>> >>>>>>> >>>>>>> ** Aside - OutOfMemory should probably be refactored to be able to >>>>>>> signal >>>>>>> itself without taking up more memory, triggering itself infinitely. >>>>>>> Maybe >>>>>>> it & its signalling morph infrastructure would be good as a singleton >>>>>>> ** >>>>>>> >>>>>>> >>>>>>> >>>>>>> I'm confused about why it runs out of memory. According to htop the >>>>>>> image >>>>>>> only takes up about 520-540 MB of RAM when it reaches the 'OutOfMemory' >>>>>>> condition. This Macbook Air laptop has 4GB, and has plenty of room for >>>>>>> the >>>>>>> image to grow. Also I've specified a 1,000MB image size when starting. >>>>>>> So >>>>>>> it should have plenty of room. Is there something I should check or a >>>>>>> flag >>>>>>> somewhere that prevents it from growing on a Mac? This is the latest >>>>>>> Pharo30 VM. >>>>>>> >>>>>>> >>>>>>> Thanks for helping me get to the bottom of this >>>>>>> >>>>>>> Paul >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> Sven Van Caekenberghe-2 wrote >>>>>>>> Hi Paul, >>>>>>>> >>>>>>>> I think you must be doing something wrong with your class, the #do: is >>>>>>>> implemented as streaming over the record one by one, never holding >>>>>>>> more >>>>>>>> than one in memory. >>>>>>>> >>>>>>>> This is what I tried: >>>>>>>> >>>>>>>> 'paul.csv' asFileReference writeStreamDo: [ :file| >>>>>>>> ZnBufferedWriteStream on: file do: [ :out | >>>>>>>> (NeoCSVWriter on: out) in: [ :writer | >>>>>>>> writer writeHeader: { #Number. #Color. #Integer. #Boolean}. >>>>>>>> 1 to: 1e7 do: [ :each | >>>>>>>> writer nextPut: { each. #(Red Green Blue) atRandom. 1e6 >>>>>>>> atRandom. >>>>>>>> #(true false) atRandom } ] ] ] ]. >>>>>>>> >>>>>>>> This results in a 300Mb file: >>>>>>>> >>>>>>>> $ ls -lah paul.csv >>>>>>>> -rw-r--r--@ 1 sven staff 327M Nov 14 20:45 paul.csv >>>>>>>> $ wc paul.csv >>>>>>>> 10000001 10000001 342781577 paul.csv >>>>>>>> >>>>>>>> This is a selective read and collect (loads about 10K records): >>>>>>>> >>>>>>>> Array streamContents: [ :out | >>>>>>>> 'paul.csv' asFileReference readStreamDo: [ :in | >>>>>>>> (NeoCSVReader on: (ZnBufferedReadStream on: in)) in: [ :reader | >>>>>>>> reader skipHeader; addIntegerField; addSymbolField; >>>>>>>> addIntegerField; >>>>>>>> addFieldConverter: [ :x | x = #true ]. >>>>>>>> reader do: [ :each | each third < 1000 ifTrue: [ out nextPut: each >>>>>>>> ] >>>>>>>> ] ] ] ]. >>>>>>>> >>>>>>>> This worked fine on my MacBook Air, no memory problems. It takes a >>>>>>>> while >>>>>>>> to parse that much data, of course. >>>>>>>> >>>>>>>> Sven >>>>>>>> >>>>>>>>> On 14 Nov 2014, at 19:08, Paul DeBruicker < >>>>>>>> pdebruic@ >>>>>>>> > wrote: >>>>>>>>> Hi - >>>>>>>>> >>>>>>>>> I'm processing a 9 GBs of CSV files (the biggest file is 220MB or >>>>>>>>> so). >>>>>>>>> I'm not sure if its because of the size of the files or the code I've >>>>>>>>> written to keep track of the domain objects I'm interested in, but >>>>>>>>> I'm >>>>>>>>> getting out of memory errors & crashes in Pharo 3 on Mac with the >>>>>>>>> latest >>>>>>>>> VM. I haven't checked other vms. >>>>>>>>> >>>>>>>>> I'm going to profile my own code and attempt to split the files >>>>>>>>> manually >>>>>>>>> for now to see what else it could be. >>>>>>>>> >>>>>>>>> >>>>>>>>> Right now I'm doing something similar to >>>>>>>>> >>>>>>>>> |file reader| >>>>>>>>> file:= '/path/to/file/myfile.csv' asFileReference readStream. >>>>>>>>> reader: NeoCSVReader on: file >>>>>>>>> >>>>>>>>> reader >>>>>>>>> recordClass: MyClass; >>>>>>>>> skipHeader; >>>>>>>>> addField: #myField:; >>>>>>>>> .... >>>>>>>>> >>>>>>>>> >>>>>>>>> reader do:[:eachRecord | self seeIfRecordIsInterestingAndIfSoKeepIt: >>>>>>>>> eachRecord]. >>>>>>>>> file close. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Is there a facility in NeoCSVReader to read a file in batches (e.g. >>>>>>>>> 1000 >>>>>>>>> lines at a time) or an easy way to do that ? >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> >>>>>>>>> Paul >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> View this message in context: >>>>>>> http://forum.world.st/running-out-of-memory-while-processing-a-220MB-csv-fi… >>>>>>> Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com. >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> View this message in context: >>>>> http://forum.world.st/running-out-of-memory-while-processing-a-220MB-csv-fi… >>>>> Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com. >>> >>> >>> >>> >>> -- >>> View this message in context: http://forum.world.st/running-out-of-memory-while-processing-a-220MB-csv-fi… >>> Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com. >> >> >> >> ------------------------------ >> >> Message: 3 >> Date: Sat, 15 Nov 2014 00:09:48 +0100 >> From: Alain Rastoul <alf.mmm.cat(a)gmail.com> >> To: pharo-users(a)lists.pharo.org >> Subject: Re: [Pharo-users] Has anyone tried compiling the Pharo VM >> into JS using Emscripten? >> Message-ID: <m4623q$btk$1(a)ger.gmane.org> >> Content-Type: text/plain; charset=utf-8; format=flowed >> >> Hi Andy, >> >> If I understand your question, you want to remake Dan Ingall's lively >> kernel ? >> :) >> http://lively-web.org/welcome.html >> >> Cheers, >> Alain >> >> >> Le 14/11/2014 22:31, Andy Burnett a ?crit : >>> I just saw this implementation of SQLite as a JS system, via Emscripten, >>> and I was curious whether something similar would be even vaguely >>> possible for the VM. >>> >>> Cheers >>> Andy >>> ? >> >> >> >> >> ------------------------------ >> >> Subject: Digest Footer >> >> _______________________________________________ >> Pharo-users mailing list >> Pharo-users(a)lists.pharo.org >> http://lists.pharo.org/mailman/listinfo/pharo-users_lists.pharo.org >> >> >> ------------------------------ >> >> End of Pharo-users Digest, Vol 19, Issue 53 >> ******************************************* >

Nov. 15, 2014

Re: [Pharo-users] Has anyone tried compiling the Pharo VM into JS using Emscripten?

by stepharo

no This is if this is possible to run the vm over V8 Stef On 15/11/14 00:09, Alain Rastoul wrote: > Hi Andy, > > If I understand your question, you want to remake Dan Ingall's lively > kernel ? > :) > http://lively-web.org/welcome.html > > Cheers, > Alain > > > Le 14/11/2014 22:31, Andy Burnett a Ã©crit : >> I just saw this implementation of SQLite as a JS system, via Emscripten, >> and I was curious whether something similar would be even vaguely >> possible for the VM. >> >> Cheers >> Andy >> á§ > > > >

Nov. 15, 2014

Re: [Pharo-users] running out of memory while processing a 220MB csv file with NeoCSVReader - tips?

by stepharo

Thanks for this cool discussion. I will add this to the NepCSV chapter :) On 14/11/14 21:00, Sven Van Caekenberghe wrote: > This is what I tried: > > 'paul.csv' asFileReference writeStreamDo: [ :file| > ZnBufferedWriteStream on: file do: [ :out | > (NeoCSVWriter on: out) in: [ :writer | > writer writeHeader: { #Number. #Color. #Integer. #Boolean}. > 1 to: 1e7 do: [ :each | > writer nextPut: { each. #(Red Green Blue) atRandom. 1e6 atRandom. #(true false) atRandom } ] ] ] ]. > > This results in a 300Mb file: > > $ ls -lah paul.csv > -rw-r--r--@ 1 sven staff 327M Nov 14 20:45 paul.csv > $ wc paul.csv > 10000001 10000001 342781577 paul.csv > > This is a selective read and collect (loads about 10K records): > > Array streamContents: [ :out | > 'paul.csv' asFileReference readStreamDo: [ :in | > (NeoCSVReader on: (ZnBufferedReadStream on: in)) in: [ :reader | > reader skipHeader; addIntegerField; addSymbolField; addIntegerField; addFieldConverter: [ :x | x = #true ]. > reader do: [ :each | each third < 1000 ifTrue: [ out nextPut: each ] ] ] ] ].

Nov. 15, 2014

Re: [Pharo-users] Has anyone tried compiling the Pharo VM into JS using Emscripten?

by Alain Rastoul

Yes about the implementation you are right, but I was more talking about the idea and the fact that Dan Ingall is one of the smalltalk creators (see also my other answer about his potato vm). I agree it would be really cool :) Le 15/11/2014 09:38, kilon alios a Ã©crit : > > > "Hi Andy, > > If I understand your question, you want to remake Dan Ingall's lively > kernel ? > :) > http://lively-web.org/welcome.__html <http://lively-web.org/welcome.html> > > Cheers, > Alain" > > no these are two separate things. Compiling PharoVM with Emscripten > would be that you would still have the PharoVM but now running on top of > a browser since it will be pure javascript. While lively Kernel is not > related to Smalltalk at all, its just a gui on top of javascript meant > to be used as a javascript library. > > What Andy wants is something similar to SqueakJS but for Pharo. Would be > great to have something like that, but I fear this would be a quite > challenging project by itself since you would need to worry about things > like graphics and even handling inside the browser. Maybe someone could > take SqueakJS as a template and work on that. > > On Sat, Nov 15, 2014 at 1:09 AM, Alain Rastoul > <alf.mmm.cat(a)gmail.com > <mailto:alf.mmm.cat@gmail.com>> wrote: > > > > > Le 14/11/2014 22:31, Andy Burnett a Ã©crit : > > I just saw this implementation of SQLite as a JS system, via > Emscripten, > and I was curious whether something similar would be even vaguely > possible for the VM. > > Cheers > Andy > á§ > > > > >

Nov. 15, 2014

Re: [Pharo-users] Has anyone tried compiling the Pharo VM into JS using Emscripten?

by kilon alios

"Hi Andy, If I understand your question, you want to remake Dan Ingall's lively kernel ? :) http://lively-web.org/welcome.html Cheers, Alain" no these are two separate things. Compiling PharoVM with Emscripten would be that you would still have the PharoVM but now running on top of a browser since it will be pure javascript. While lively Kernel is not related to Smalltalk at all, its just a gui on top of javascript meant to be used as a javascript library. What Andy wants is something similar to SqueakJS but for Pharo. Would be great to have something like that, but I fear this would be a quite challenging project by itself since you would need to worry about things like graphics and even handling inside the browser. Maybe someone could take SqueakJS as a template and work on that. On Sat, Nov 15, 2014 at 1:09 AM, Alain Rastoul <alf.mmm.cat(a)gmail.com> wrote: > > > > Le 14/11/2014 22:31, Andy Burnett a Ã©crit : > >> I just saw this implementation of SQLite as a JS system, via Emscripten, >> and I was curious whether something similar would be even vaguely >> possible for the VM. >> >> Cheers >> Andy >> á§ >> > > > >

Nov. 15, 2014

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