I have a netlogo model, for which a run takes about 15 minutes, but goes through a lot of ticks. This is because per tick, not much happens. I want to do quite a few runs in an experiment in behaviorspace. The output (only table output) will be all the output and input variables per tick. However, not all this data is relevant: it's only relevant once a day (day is variable, a run lasts 1095 days).
The result is that the model gets so slow running experiments via behaviorspace. Not only would it be nicer to have output data with just 1095 rows, it perhaps also causes the experiment to slow down tremendously.
How to fix this?
It is possible to write your own output file in a BehaviorSpace experiment. Program your code to create and open an output file that contains only the results you want.
The problem is to keep BehaviorSpace from trying to open the same output file from different model runs running on different processors, which causes a runtime error. I have tried two solutions.
Tell BehaviorSpace to only use one processor for the experiment. Then you can use the same output file for all model runs. If you want the output lines to include which model run it's on, use the primitive behaviorspace-run-number.
Have each model run create its own output file with a unique name. Open the file using something like:
file-open (word "Output-for-run-" behaviorspace-run-number ".csv")
so the output files will be named Output-for-run-1.csv etc.
(If you are not familiar with it, the CSV extension is very useful for writing output files. You can put everything you want to output on a big list, and then when the model finishes write the list into a CSV file with:
csv:to-file (word "Output-for-run-" behaviorspace-run-number ".csv") the-big-list
)
Related
Im trying to make a game on Scratch that will use a feature to generate a special code, and when that code is input into a certain area it will load the stats that were there when the code was generated. I've run into a problem however, I don't know how to make it and I couldn't find a clear cut answer for how to make it.
I would prefer that the solution be:
Able to save information for as long as needed (from 1 second to however long until it's input again.)
Doesn't take too many blocks to make, so that the project won't take forever to load it.
Of course i'm willing to take any solution in order to get my game up and running, those are just preferences.
You can put all of the programs in a custom block with "Run without screen refresh" on so that the program runs instantly.
If you save the stats using variables, you could combine those variable values into one string divided by /s. i.e. join([highscore]) (join("/") (join([kills]) (/))
NOTE: Don't add any "/" in your stats, you can probably guess why.
Now "bear" (pun) with me, this is going to take a while to read
Then you need the variables:
[read] for reading the inputted code
[input] for storing the numbers
Then you could make another function that reads the code like so: letter ([read]) of (code) and stores that information to the [input] variable like this: set [input] to (letter ([read]) of (code)). Then change [read] by (1) so the function can read the next character of the code. Once it letter ([read]) of (code) equals "/", this tells the program to set [*stat variable*] to (input) (in our example, this would be [highscore] since it was the first variable we saved) and set [input] to (0), and repeat again until all of the stats variables are filled (In this case, it repeats 2 times because we saved two variables: [highscore] and [kills]).
This is the least amount of code that it takes. Jumbling it up takes more code. I will later edit this answer with a screenshot showcasing whatever I just said before, hopefully clearing up the mess of words above.
The technique you mentioned is used in many scratch games but there is two option for you when making the save/load system. You can either do it the simpler way which makes the code SUPER long(not joking). The other way is most scratchers use, encoding the data into a string as short as possible so it's easy to transfer.
If you want to do the second way, you can have a look at griffpatch's video on the mario platformer remake where he used a encode system to save levels.https://www.youtube.com/watch?v=IRtlrBnX-dY The tips is to encode your data (maybe score/items name/progress) into numbers and letters for example converting repeated letters to a shorter string which the game can still decode and read without errors
If you are worried it took too long to load, I am pretty sure it won't be a problem unless you really save a big load of data. The common compress method used by everyone works pretty well. If you want more data stored you may have to think of some other method. There is not an actual way to do that as different data have different unique methods for things working the best. Good luck.
I'm reaching you hoping to find answers about Pentaho data integrator limitation.
I'm currentlty working on a 1 to 1 data source integration and would like to make it n to 1-n. This requires dynamic jobs creation and would like to know if any of came across such issue. My 1 to 1 is working perfectly, it integration form differents data source types (CSV, databases "Mysql, Oracle ...) to same date destination and need to make it n to 1-n.
There is a Metadata Injection Step just for that.
A use case similar to yours is described by Diethard here.
Because it seams that you have a lot of different source format, it may be a good investment to read the use case of Jens, the author of the step, here, which (apart for the automation) is precisely your case.
AFAIK in Pentaho DI, it is not possible to create dynamic transformations for any random data sources. PDI looks for the input columns to be available in the input stream before it loads the data to the target database. For example, if you are using 1 data source (in MySQL) and loading the same to the csv output, the csv output step is expecting the presence of input columns in the data source step (Table input). If you are trying to load any n random data sources you need to define input columns/fields for each of them individually.
Alternatively there are few things which you can explore:
1. Fast Dump in Text File Output step:
There is an option to fast data dump the data set in Text file output step. Here you don't need to define any output column. The input fields will be automatically dumped without formatting as it is. You can use this to map all of the input sources to a csv format and then load it to their targets.
2. Extending Java and Kettle together to build a solution:
PDI allows you to create custom JAVA codes on top of kettle. You can check this blog for more. You can use this idea to create custom code to pass n data sources fields to the kettle as a parameter and execute them. {note: i haven't tried this step, just thinking out loud here}
Hope this helps :)
I'm trying to retrieve the alignment score of two sequences compared using emboss in biopython. The only way that I know is to retrieve it from an output text file produced by emboss. The problem is that there will be hundreds of these files to iterate over. Is there an easier/cleaner method to retrieve the alignment score, without resorting to that? This is the main part of the code that I'm using.
From Bio.Emboss.Applications import StretcherCommandline
needle_cline = StretcherCommandline(asequence=,bsequence=,gapopen=,gapextend=,outfile=)
stdout, stderr = needle_cline()
I had the same problem and after some time spent on searching for a neat solution I popped up a white flag.
However, to speed up significantly the processing of output files I did the following things:
1) I used re python module for handling regular expressions to extract all data needed.
2) I created a ramdisk space for the output files. The use of a ramdisk here allowed for processing and exchanging all the data in RAM memory (much faster than writing and reading the output files from a hard drive, not to mention it saves your hdd in case of processing massive number of alignments).
I don't know if there is one specifically for your command.
For Primer3CommandLine, there is Primer3. Make your life much easier with something like:
from Bio.Emboss import Primer3
inputFile = "./wherever/your/outputfileis.out"
with open(inputFile) as fileHandle:
record = Primer3.parse(fileHandle)
# XXX check is len>0
primers = record.next().primers
numPrimers = len(primers)
# you should have access to each primer, using a for loop
# to check how to access the data you care about. For example:
I would also check http://biopython.org/wiki/SeqIO#Sequence_Input
I had an pre-interview task, which I have completed and the solution works, however I was marked down and did not get an interview due to having used a TADODataset. I basically imported a CSV file which populated the dataset, the data had to be processed in a specific way, so I used Filtering and Sorting of the dataset to make sure that the data was ordered in the way I wanted it and then I did the logic processing in a while loop. The feedback that was received said that this was bad as it would be very slow for large files.
My main question here is if using an in memory dataset is slow for processing large files, what would have been better way to access the information from the csv file. Should I have used String Lists or something like that?
It really depends on how "big" and the available resources(in this case RAM) for the task.
"The feedback that was received said that this was bad as it would be very slow for large files."
CSV files are usually used for moving data around(in most cases that I've encountered files are ~1MB+ up to ~10MB, but that's not to say that others would not dump more data in CSV format) without worrying too much(if at all) about import/export since it is extremely simplistic.
Suppose you have a 80MB CSV file, now that's a file you want to process in chunks, otherwise(depending on your processing) you can eat hundreds of MB of RAM, in this case what I would do is:
while dataToProcess do begin
// step1
read <X> lines from file, where <X> is the max number of lines
you read in one go, if there are less lines(i.e. you're down to 50 lines and X is 100)
to process, then you read those
// step2
process information
// step3
generate output, database inserts, etc.
end;
In the above case, you're not loading 80MB of data into RAM, but only a few hundred KB, and the rest you use for processing, i.e. linked lists, dynamic insert queries(batch insert), etc.
"...however I was marked down and did not get an interview due to having used a TADODataset."
I'm not surprised, they were probably looking to see if you're capable of creating algorithm(s) and provide simple solutions on the spot, but without using "ready-made" solutions.
They were probably thinking of seeing you use dynamic arrays and creating one(or more) sorting algorithm(s).
"Should I have used String Lists or something like that?"
The response might have been the same, again, I think they wanted to see how you "work".
The interviewer was quite right.
The correct, scalable and fastest solution on any medium file upwards is to use an 'external sort'.
An 'External Sort' is a 2 stage process, the first stage being to split each file into manageable and sorted smaller files. The second stage is to merge these files back into a single sorted file which can then be processed line by line.
It is extremely efficient on any CSV file with over say 200,000 lines. The amount of memory the process runs in can be controlled and thus dangers of running out of memory can be eliminated.
I have implemented many such sort processes and in Delphi would recommend a combination of TStringList, TList and TQueue classes.
Good Luck
I'm trying to do the following in hadoop map/reduce( written in java, linux kernel OS)
Text files 'rules-1' and 'rules-2' (total 3GB in size) contains some rules, each rule are separated by endline character, so the files can be read using readLine() function.
These files 'rules-1' and 'rules-2' needs to be imported as a whole from hdfs in every map function in my cluster i.e. these file are not splittable across different map function.
Input to the mapper's map function is a text file called 'record' (each line is terminated by endline character), so from the 'record' file we get the (key, value) pair. The file is splittable and can be given as input to different map function used in the whole map/reduce process.
What needs to be done is compare each value(i.e. lines from record file) with the rules inside 'rules-1' and 'rules-2'
Problem is, if I pull out each line of rules-1 and rules-2 files to a static arraylist only once, so that each mapper can share the same arraylint and try to compare elements in the arraylist with the each input value from the record file, I get a memory overflow error, since 3GB cannot be stored at a time in the arraylist.
Alternatively, if I import only few lines from the rules-1 and rules-2 files at a time and compare them to each value, map/reduce is taking a lot time to finish its job.
Could you guys provide me any other alternative ideas how can this be done without the memory overflow error? Will it help if I put those file-1 and file-2 inside a hdfs supporting database or something? I'm going out of ideas actually.Would really appreciate if some of you guys could provide me your valuable suggestions.
Iif you input files are small - you can load them into static variables and use rules as an input.
If above is not a case I can suggest the following ways:
a) To give rule-1 and rule-2 high replication factor close to the number of nodes you have. Then you can read from HDFS rule=1 and rule-2 for each record in the input relatively efficient - because it will be sequential read from the local datanode.
b) If you can consider some hash function which, when applied to the rule and to the input string will predict without false negatives that they can match - then you can emit this hash for rules, input record and resolve all possible matches in the reducer. It will be very similar to the way how a join is done using MR
c) I would consider some other optimization techniques like building search trees, or sorting since otherwise the problem looks computationally expensive and will took forever...
On this page find Real-World Cluster Configurations
it will cover file size configuration
You could use the param "mapred.child.java.opts" in conf/mapred-site.xml to increase the memory for your mappers. You might not be able to run as many map slots per server but with more servers in your cluster you could still parallelize your job.
Read the content text file from the MapReduce function and read the keyword text file from the mapper function (for reading your HDFS) and split using StringTokenizer value.toString reading from MapReduce and in your mapper function write HDFS read text file code it will read line-by-line so use two while loops here you compare. Whenever you want data send it to reducer.
Split the 3gb text file into several text files and apply that all text files as usual MapReduce your previous program.
For splitting text file I written Java program and you decide how many lines you want write in each text file.