We Keep Coding

Very slow performance with DotSpatial shapefile

I'm trying to read all of the feature data from particular shapefile. In this case, I'm using DotSpatial to open the file, and I'm iterating through the features. This particular shapefile is only 9mb in size, and the dbf file is 14mb. There is roughly 75k features to loop through.
Note, this is all programmatically through a console app, so there is no rendering or anything involved.
When loading the shape file, I reproject, then I'm iterating. The loading an reprojecting is super quick. However, as soon as the code reaches my foreach block, it takes nearly 2 full minutes to load the data, and uses roughly 2GB of memory when debugging in VisualStudio. This seems very, very excessive for what's a reasonably small data file.
I've ran the same code outside of Visual Studio, from the command line, however the time is still roughly 2 full minutes, and about 1.3GB of memory for the process.
Is there anyway to speed this up at all?
Below is my code:
// Load the shape file and project to GDA94
Shapefile indexMapFile = Shapefile.OpenFile(shapeFilePath);
indexMapFile.Reproject(KnownCoordinateSystems.Geographic.Australia.GeocentricDatumofAustralia1994);
// Get's slow here and takes forever to get to the first item
foreach(IFeature feature in indexMapFile.Features)
{
// Once inside the loop, it's blazingly quick.
}
Interestingly, when I use the VS immediate window, it's super super fast, no delay at all...

I've managed to figure this out...
For some reason, calling foreach on the features is painfully slow.
However, as these files have a 1-1 mapping with features - data rows (each feature has a relevant data row), I've modified it slightly to the following. It's now very quick.. less than a second to start the iterations.
// Load the shape file and project to GDA94
Shapefile indexMapFile = Shapefile.OpenFile(shapeFilePath);
indexMapFile.Reproject(KnownCoordinateSystems.Geographic.Australia.GeocentricDatumofAustralia1994);
// Get the map index from the Feature data
for(int i = 0; i < indexMapFile.DataTable.Rows.Count; i++)
{
// Get the feature
IFeature feature = indexMapFile.Features.ElementAt(i);
// Now it's very quick to iterate through and work with the feature.
}
I wonder why this would be. I think I need to look at the iterator on the IFeatureList implementation.
Cheers,
Justin

This has the same problem for very large files (1.2 millions of features), populating .Features collections never ends.
But if you ask for the feature you do not have memory or delay overheads.
int lRows = fs.NumRows();
for (int i = 0; i < lRows; i++)
{
// Get the feature
IFeature pFeat = fs.GetFeature(i);
StringBuilder sb = new StringBuilder();
{
sb.Append(Guid.NewGuid().ToString());
sb.Append("|");
sb.Append(pFeat.DataRow["MAPA"]);
sb.Append("|");
sb.Append(pFeat.BasicGeometry.ToString());
}
pLinesList.Add(sb.ToString());
lCnt++;
if (lCnt % 10 == 0)
{
pOld = Console.ForegroundColor;
Console.ForegroundColor = ConsoleColor.DarkGreen;
Console.Write("\r{0} de {1} ({2}%)", lCnt.ToString(), lRows.ToString(), (100.0 * ((float)lCnt / (float)lRows)).ToString());
Console.ForegroundColor = pOld;
}
}
Look for the GetFeature method.

TextWriter/StreamWriter high memory usage

I have a console app that reads in a large text file with 40k+ lines, each line is a key that I use in a search for which the results are written to a output file. Issue is I leave this console app running for a while until it just suddenly closes and I realize that the process memory usage was really high was sitting at 1.6gb when I last saw it crash.
I looked around and didn't find many answers I did try to use the gcAllowVeryLargeObjects but that seems like I'm just dodging the problem.
Below is a snippet from my main() of where I write out to the file. I can't seem to understand why the memory usage gets so high. I flush the writer after every write (could it be because I'm keeping the file open for such a long period of time?).
TextWriter writer = new StreamWriter("output.csv", false));
foreach (var item in list)
{
Console.WriteLine("{0}/{1}", count, numofitem);
var result = TableServiceContext.Read(p.id);
if (result != null)
{
writer.WriteLine(String.Join(",", result.id,
result.code,
result.hash));
}
count++;
writer.Flush();
}
writer.Close();
Edit: I have 32gb of ram on my computer so I am sure it's not running out of memory because I don't have enough ram.
Edit2: changed the name of the repository as that was misleading.

If the average line length is 1KB then 40K lines is 40MB, and it nothing. That's why, I'm pretty sure problem is in your repository class. If it is EF repository, try to recreate DbContext for each line.
If you want to tune up your program, then, you can use the following method: Try to put timestamps to Console output, you can use Stopwatch class, and try to recreate your repository each 10 or 100 or N lines. Then, looking at timestamps, you can find optimal N to use.
var timer = Stopwatch.StartNew();
...
Console.WriteLine(timer.ElapsedMilliseconds);

From looking at the code I think the problem isN't the Streamwriter but some memory leak in your repository. Suggestions to check:
replace the repository by some dummy e.g. class dummy_repository with just the three properties id, value, hash.
likewise create a long "list" e.g. 40k small entries.
run your program and see if it still consumes memory (I am pretty sure it will not)
then step by step add back your original parts. See what step causes the memory leak.

Can I convert while(true) loop to EventWaitHandle?

I'm trying to process large amount of text files via Parallel.ForEach adding processed data to BlockingCollection.
The problem is that I want the Task taskWriteMergedFile to consume the collection and write them to result file at least every 800000 lines.
I guess that I can't test the collection size within the iteration because it is paralleled so I created the Task.
Can I convert while(true) loop in the task to EventWaitHandle in this case?
const int MAX_SIZE = 1000000;
static BlockingCollection<string> mergeData;
mergeData = new BlockingCollection<string>(new ConcurrentBag<string>(), MAX_SIZE);
string[] FilePaths = Directory.GetFiles("somepath");
var taskWriteMergedFile = new Task(() =>
{
while ( true )
{
if ( mergeData.Count > 800000)
{
String.Join(System.Environment.NewLine, mergeData.GetConsumingEnumerable());
//Write to file
}
Thread.Sleep(10000);
}
}, TaskCreationOptions.LongRunning);
taskWriteMergedFile.Start();
Parallel.ForEach(FilePaths, FilePath => AddToDataPool(FilePath));
mergeData.CompleteAdding();

You probably don't want to do it that way. Instead, have your task write each line to the file as it's received. If you want to limit the file size to 80,000 lines, then after the 80,000th line is written, close the current file and open a new one.
Come to think of it, what you have can't work because GetConsumingEnumerable() won't stop until the collection is marked as complete for adding. What would happen is that the thing would go through the sleep loop until there were 80,000 items in the queue, and then it would block on the String.Join until the main thread calls CompleteAdding. With enough data, you'd run out of memory.
Also, unless you have a very good reason, you shouldn't use ConcurrentBag here. Just use the default for BlockingCollection, which is ConcurrentQueue. ConcurrentBag is a rather special purpose data structure that won't perform as well as ConcurrentQueue.
So your task becomes:
var taskWriteMergedFile = new Task(() =>
{
int recordCount = 0;
foreach (var line in mergeData.GetConsumingEnumerable())
{
outputFile.WriteLine(line);
++recordCount;
if (recordCount == 80,000)
{
// If you want to do something after 80,000 lines, do it here
// and then reset the record count
recordCount = 0;
}
}
}, TaskCreationOptions.LongRunning);
That assumes, of course, that you've opened the output file somewhere else. It's probably better to open the output at the start of the task, and close it after the foreach has exited.
On another note, you probably don't want your producer loop to be parallel. You have:
Parallel.ForEach(FilePaths, FilePath => AddToDataPool(FilePath));
I don't know for sure what AddToDataPool is doing, but if it's reading a file and writing the data to the collection, you have a couple of problems. First, the disk drive can only do one thing at a time, so it ends up reading part of one file, then part of another, then part of another, etc. In order to read each chunk of the next file, it has to seek the head to the proper position. Disk head seeks are incredibly expensive--5 milliseconds or more. An eternity in CPU time. Unless you're doing heavy duty processing that takes much longer than reading the file, you're almost always better off processing one file at a time. Unless you can guarantee that the input files are on separate physical disks . . .
The second potential problem is that with multiple threads running, you can't guarantee the order in which things are written to the collection. That might not be a problem, of course, but if you expect all of the data from a single file to be grouped together in the output, that's not going to happen with multiple threads each writing multiple lines to the collection.
Just something to keep in mind.

C# Parallel.foreach - Making variables thread safe

I have been rewriting some process intensive looping to use TPL to increase speed. This is the first time I have tried threading, so want to check what I am doing is the correct way to do it.
The results are good - processing the data from 1000 Rows in a DataTable has reduced processing time from 34 minutes to 9 minutes when moving from a standard foreach loop into a Parallel.ForEach loop. For this test, I removed non thread safe operations, such as writing data to a log file and incrementing a counter.
I still need to write back into a log file and increment a counter, so i tried implementing a lock which encases the streamwriter/increment code block.
FileStream filestream = new FileStream("path_to_file.txt", FileMode.Create);
StreamWriter streamwriter = new StreamWriter(filestream);
streamwriter.AutoFlush = true;
try
{
object locker = new object();
// Lets assume we have a DataTable containing 1000 rows of data.
DataTable datatable_results;
if (datatable_results.Rows.Count > 0)
{
int row_counter = 0;
Parallel.ForEach(datatable_results.AsEnumerable(), data_row =>
{
// Process data_row as normal.
// When ready to write to log, do so.
lock (locker)
{
row_counter++;
streamwriter.WriteLine("Processing row: {0}", row_counter);
// Write any data we want to log.
}
});
}
}
catch (Exception e)
{
// Catch the exception.
}
streamwriter.Close();
The above seems to work as expected, with minimal performance costs (still 9 minutes execution time). Granted, the actions contained in the lock are hardly significant themselves - I assume that as the time taken to process code within the lock increases, the longer the thread is locked for, the more it affects processing time.
My question: is the above an efficient way of doing this or is there a different way of achieving the above that is either faster or safer?
Also, lets say our original DataTable actually contains 30000 rows. Is there anything to be gained by splitting this DataTable into chunks of 1000 rows each and then processing them in the Parallel.ForEach, instead of processing all 300000 rows in one go?

Writing to the file is expensive, you're holding a exclusive lock while writing to the file, that's bad. It's going to introduce contention.
You could add it in a buffer, then write to the file all at once. That should remove contention and provide way to scale.
if (datatable_results.Rows.Count > 0)
{
ConcurrentQueue<string> buffer = new ConcurrentQueue<string>();
Parallel.ForEach(datatable_results.AsEnumerable(), (data_row, state, index) =>
{
// Process data_row as normal.
// When ready to write to log, do so.
buffer.Enqueue(string.Format( "Processing row: {0}", index));
});
streamwriter.AutoFlush = false;
string line;
while (buffer.TryDequeue(out line))
{
streamwriter.WriteLine(line);
}
streamwriter.Flush();//Flush once when needed
}
Note that you don't need to maintain a loop counter,
Parallel.ForEach provides you one. Difference is that it is not
the counter but index. If I've changed the expected behavior you can
still add the counter back and use Interlocked.Increment to
increment it.
I see that you're using streamwriter.AutoFlush = true, that will hurt performance, you can set it to false and flush it once you're done writing all the data.
If possible, wrap the StreamWriter in using statement, so that you don't even need to flush the stream(you get it for free).
Alternatively, you could look at the logging frameworks which does their job pretty well. Example: NLog, Log4net etc.

You may try to improve this, if you avoid logging, or log into only thread specific log file (not sure if that makes sense to you)
TPL start as many threads as many cores you have Does Parallel.ForEach limits the number of active threads?.
So what you can do is:
1) Get numbers of core on target machine
2) Create a list of counters, with as many elements inside as many cores you have
3) Update counter for every core
4) Sum all them up after parallel execution terminates.
So, in practice :
//KEY(THREAD ID, VALUE: THREAD LOCAL COUNTER)
Dictionary<int,int> counters = new Dictionary<int, int>(NUMBER_OF_CORES);
....
Parallel.ForEach(datatable_results.AsEnumerable(), data_row =>
{
// Process data_row as normal.
// When ready to write to log, do so.
//lock (locker) //NO NEED FOR LOCK, EVERY THREAD UPDATES ITS _OWN_ COUNTER
//{
//row_counter++;
counters[Thread.CurrentThread.ManagedThreadId].Value +=1;
//NO WRITING< OR WRITING THREAD SPECIFIC FILE ONLY
//streamwriter.WriteLine("Processing row: {0}", row_counter);
//}
});
....
//AFTER EXECUTION OF PARALLEL LOOP SUM ALL COUNTERS AND GET TOTAL OF ALL THREADS.
The benefit of this that no locking envolved at all, which will drammatically improve performance. When you use .net concurent collections, they are always use some kind of locking inside.
This is naturally a basic idea, may not work as it expected if you copy paste. We are talking about multi threading , which is always a hard topic. But, hopefully, it provides to you some ideas to relay on.

First of all, it takes about 2 seconds to process a row in your table and perhaps a few milliseconds to increment the counter and write to the log file. With the actual processing being 1000x more than the part you need to serialize, the method doesn't matter too much.
Furthermore, the way you have implemented it is perfectly solid. There are ways to optimize it, but none that are worth implementing in your situation.
One useful way to avoid locking on the increment is to use Interlocked.Increment. It is a bit slower than x++ but much faster than lock {x++;}. In your case, though, it doesn't matter.
As for the file output, remember that the output is going to be serialized anyway, so at best you can minimize the amount of time spent in the lock. You can do this by buffering all of your output before entering the lock, then just perform the write operation inside the lock. You probably want to do async writes to avoid unnecessary blocking on I/O.

You can transfer the parallel code in new method. For example :
// Class scope
private string GetLogRecord(int rowCounter, DataRow row)
{
return string.Format("Processing row: {0}", rowCounter); // Write any data we want to log.
}
//....
Parallel.ForEach(datatable_results.AsEnumerable(), data_row =>
{
// Process data_row as normal.
// When ready to write to log, do so.
lock (locker)
row_counter++;
var logRecord = GetLogRecord(row_counter, data_row);
lock (locker)
streamwriter.WriteLine(logRecord);
});

This is my code that uses a parallel for. The concept is similar, and perhaps easier for you to implement. FYI, for debugging, I keep a regular for loop in the code and conditionally compile the parallel code. Hope this helps. The value of i in this scenario isn't the same as the number of records processed, however. You could create a counter and use a lock and add values for that. For my other code where I do have a counter, I didn't use a lock and just allowed the value to be potentially off to avoid the slower code. I have a status mechanism to indicate number of records processed. For my implementation, the slight chance that the count is not an issue - at the end of the loop I put out a message saying all the records have been processed.
#if DEBUG
for (int i = 0; i < stend.PBBIBuckets.Count; i++)
{
//int serverIndex = 0;
#else
ParallelOptions options = new ParallelOptions();
options.MaxDegreeOfParallelism = m_maxThreads;
Parallel.For(0, stend.PBBIBuckets.Count, options, (i) =>
{
#endif
g1client.Message request;
DataTable requestTable;
request = new g1client.Message();
requestTable = request.GetDataTable();
requestTable.Columns.AddRange(
Locations.Columns.Cast<DataColumn>().Select(x => new DataColumn(x.ColumnName, x.DataType)).ToArray
());
FillPBBIRequestTables(requestTable, request, stend.PBBIBuckets[i], stend.BucketLen[i], stend.Hierarchies);
#if DEBUG
}
#else
});
#endif

Parallel.For loop freezes

I'm trying to add to a DataTable some information in Parallel but if the the loop is to long it freezes or just takes a lot of time, more time then an usual for loop, this is my code for the Parallel.For loop:
Parallel.For(1, linii.Length, index =>
{
DataRow drRow = dtResult.NewRow();
alResult = CSVParser(linii[index], txtDelimiter, txtQualifier);
for (int i = 0; i < alResult.Count; i++)
{
drRow[i] = alResult[i];
}
dtResult.Rows.Add(drRow);
}
);
What's wrong? this Parallel.For loop takes much more time than a normal one, what is wrong?
Thanks!

You can't mutate a DataTable from 2 different threads; it will error. DataTable makes no attempt to be thread-safe. So: don't do that. Just do this from one thread. Most likely you are limited by IO, so you should just do it on a single thread as a stream. It looks like you're processing text data. You seem to have a string[] for lines, perhaps File.ReadAllLines() ? Well, that is very bad here:
it forces it all to load into memory
you have to wait for it all to load into memory
CSV is a multi-line format; it is not guaranteed that 1 line == 1 row
What you should do is use something like the CsvReader from code project, but even if you want to just use one line at a time, use a StreamReader:
using(var file = File.OpenText(path)) {
string line;
while((line = file.ReadLine()) != null) {
// process this line
alResult = CSVParser(line, txtDelimiter, txtQualifier);
for (int i = 0; i < alResult.Count; i++)
{
drRow[i] = alResult[i];
}
dtResult.Rows.Add(drRow);
}
}
This will not be faster using Parallel, so I have not attempted to do so. IO is your bottleneck here. Locking would be an option, but it isn't going to help you massively.
As an unrelated aside, I notice that alResult is not declared inside the loop. That means that in your original code alResult is a captured variable that is shared between all the loop iterations - which means you are already overwriting each row horribly.
Edit: illustration of why Parallel is not relevant for reading 1,000,000 lines from a file:
Approach 1: use ReadAllLines to load the lines, then use Parallel to process them; this costs [fixed time] for the physical file IO, and then we parallelise. The CPU work is minimal, and we've basically spent [fixed time]. However, we've added a lot of threading overhead and memory overhead, and we couldn't even start until all the file was loaded.
Approach 2: use a streaming API; read each one line by line - processing each line and adding it. The cost here is basically again: [fixed time] for the actual IO bandwidth to load the file. But; we now have no threading overhead, no sync conflicts, no huge memory to allocate, and we start filling the table right away.
Approach 3: If you really wanted, a third approach would be a reader/writer queue, with one dedicated thread processing file IO and enqueueing the lines, and a second that does the DataTable. Frankly, it is a lot more moving parts, and the second thread will spend 95% of its time waiting for data from the file; stick to Approach 2!

Parallel.For(1, linii.Length, index =>
{
alResult = CSVParser(linii[index], txtDelimiter, txtQualifier);
lock (dtResult)
{
DataRow drRow = dtResult.NewRow();
for (int i = 0; i < alResult.Count; i++)
{
drRow[i] = alResult[i];
}
dtResult.Rows.Add(drRow);
}
});