I'm getting OutOfMemory error in Apache Lucene.
Here is the problem code:
DirectoryReader oldReader = directoryReader;
DirectoryReader newReader = DirectoryReader.openIfChanged(directoryReader);
if ((newReader != null) & (oldReader != newReader)) {
directoryReader = newReader;
}
Here is the log:
Caused by: java.lang.OutOfMemoryError: Java Heap Space
at java.lang.Class.getMethodImpl(Native Method)
at java.lang.Class.getMethod(Class.java:917)
at org.apache.lucene.store.MMapDirectory$MMapIndexInput$1.run(MMapDirectory.java:244)
at org.apache.lucene.store.MMapDirectory$MMapIndexInput$1.run(MMapDirectory.java:241)
at java.security.AccessController.doPrivileged(AccessController.java:327)
at org.apache.lucene.store.MMapDirectory$MMapIndexInput.freeBuffer(MMapDirectory.java:241)
at org.apache.lucene.store.ByteBufferIndexInput.close(ByteBufferIndexInput.java:295)
at org.apache.lucene.index.SegmentInfos$FindSegmentsFile.run(SegmentInfos.java:788)
at org.apache.lucene.index.SegmentInfos$FindSegmentsFile.run(SegmentInfos.java:694)
at org.apache.lucene.index.SegmentInfos.read(SegmentInfos.java:400)
at org.apache.lucene.index.StandardDirectoryReader.isCurrent(StandardDirectoryReader.java:349)
at org.apache.lucene.index.StandardDirectoryReader.doOpenNoWriter(StandardDirectoryReader.java:303)
at org.apache.lucene.index.StandardDirectoryReader.doOpenIfChanged(StandardDirectoryReader.java:266)
at org.apache.lucene.index.StandardDirectoryReader.doOpenIfChanged(StandardDirectoryReader.java:254)
at org.apache.lucene.index.DirectoryReader.openIfChanged(DirectoryReader.java:170)
Any idea, what can be the problem?
Since you're using MMapDirectory, you should be aware, that:
NOTE: memory mapping uses up a portion of the virtual memory address
space in your process equal to the size of the file being mapped.
Before using this class, be sure your have plenty of virtual address
space, e.g. by using a 64 bit JRE, or a 32 bit JRE with indexes that
are guaranteed to fit within the address space. On 32 bit platforms
also consult MMapDirectory(Path, LockFactory, int) if you have
problems with mmap failing because of fragmented address space. If you
get an OutOfMemoryException, it is recommended to reduce the chunk
size, until it works.
MMapDirectory uses memory-mapped IO when reading. This is a good
choice if you have plenty of virtual memory relative to your index
size, eg if you are running on a 64 bit JRE, or you are running on a
32 bit JRE but your index sizes are small enough to fit into the
virtual memory space
So, consider tuning your chunk size or choose other implementation of the Directory, like NIOFSDirectory or SimpleFSDirectory
Related
I was reading through the MMapDirectoryFactory and how to set it as DirectoryFactory to use for indexes in my core's solrconfig.xml.
<directoryFactory name="DirectoryFactory"
class="solr.MMapDirectoryFactory">
<bool name="preload">true</bool>
</directoryFactory>
I am not able to understand nor able to find any example about how to set the maxChunkSize.
references:
https://solr.apache.org/guide/8_5/datadir-and-directoryfactory-in-solrconfig.html-
https://solr.apache.org/docs/8_5_0/solr-core/org/apache/solr/core/MMapDirectoryFactory.html
<directoryFactory name="DirectoryFactory"
class="${solr.directoryFactory:solr.MMapDirectoryFactory}">
<int name="maxChunkSize">1073741824</int>
<bool name="preload">true</bool>
</directoryFactory>
I hope you are looking for this.
Please note there is a validation in place for chunk size.
public MMapDirectory(Path path, LockFactory lockFactory, int maxChunkSize) throws IOException {
...
this.chunkSizePower = 31 - Integer.numberOfLeadingZeros(maxChunkSize);
assert this.chunkSizePower >= 0 && this.chunkSizePower <= 30;
}
However, that said, you ideally would not be required to modify this param for modern production systems (as they would usually be 64-bit already) per the java doc.
Create a new MMapDirectory for the named location, specifying the maximum chunk size used for memory mapping. The directory is created at the named location if it does not yet exist.
Especially on 32 bit platform, the address space can be very fragmented, so large index files cannot be mapped. Using a lower chunk size makes the directory implementation a little bit slower (as the correct chunk may be resolved on lots of seeks) but the chance is higher that mmap does not fail. On 64 bit Java platforms, this parameter should always be 1 << 30, as the address space is big enough.
Older, now deprecated, macOS file system APIs provided flags to read a file unbuffered.
I seek a modern way to accomplish the same, so that I can read a file's data into memory without it being cached needlessly somewhere else in memory (such as the volume cache).
Reading with fread and first calling setvbuf (fp, NULL, _IONBF, 0) is not having the desired effect in my tests, for example. I am seeking other low-level functions that let me read into a prepared memory buffer and that let me avoid buffering of the whole data.
Background
I am writing a file search program. It reads large amounts of file content (many GBs) that isn't and won't be used by the user otherwise. It would be a waste to have all this data cached in the volume cache as it'll soon get purged by further reads again, anyway. It'll also likely lead to purging file data that's actually in use by the user or system, causing more cache misses.
Therefore, I should be able to tell the system that I do not need the file data cached. The little caching needed for cluster boundaries is not an issue. It's the many large chunks that I read briefly into memory to search it that is not needed to be cached.
Two suggestions:
Use the read() system call instead of stdio.
Disable data caching with the F_NOCACHE option for fcntl().
In Swift that would be something like (error checking omitted for brevity):
import Foundation
let path = "/path/to/file"
let fd = open(path, O_RDONLY)
fcntl(fd, F_NOCACHE, 1)
var buffer = Data(count: 1024 * 1024)
buffer.withUnsafeMutableBytes { ptr in
let amount = read(fd, ptr.baseAddress, ptr.count)
}
close(fd)
I'm using GraphDb Free 8.6.1 in research project, I'm running it with default configuration on linux server having 4GB memory.
However, it has started to throw exceptions pointing to insufficient memory:
Caused by: org.eclipse.rdf4j.repository.RepositoryException: Query evaluation error: Insufficient free Heap Memory 238Mb for group by and distinct, threshold:250Mb, reached 0Mb (HTTP status 500)
at org.eclipse.rdf4j.http.client.SPARQLProtocolSession.execute(SPARQLProtocolSession.java:1143)
at org.eclipse.rdf4j.http.client.SPARQLProtocolSession.executeOK(SPARQLProtocolSession.java:1066)
at org.eclipse.rdf4j.http.client.SPARQLProtocolSession.sendTupleQueryViaHttp(SPARQLProtocolSession.java:834)
at org.eclipse.rdf4j.http.client.SPARQLProtocolSession.getTupleQueryResult(SPARQLProtocolSession.java:763)
at org.eclipse.rdf4j.http.client.SPARQLProtocolSession.sendTupleQuery(SPARQLProtocolSession.java:391)
at org.eclipse.rdf4j.repository.http.HTTPTupleQuery.evaluate(HTTPTupleQuery.java:69)
Please, can you help me to identify the problem?
How can I properly configure GraphDB?
The behavior you observe is part of memory optimization of distinct/group by operations. The error message itself is related to the default threshold of 250 mb and it's there to let you know you need to adjust your memory. When the free heap memory became less than the threshold, a QueryEvaluationException is thrown so to avoid running out of memory due to hungry distinct/group by operation. You can adjust the threshold to minimize those errors, by reducing it with with passing the following argument when starting GraphDB "-Ddefaut.min.distinct.threshold=XXX" (which could be set to the amount of memory in bytes for the threshold).
Insufficient free Heap Memory 238Mb for group by and distinct, threshold:250Mb, reached 0Mb
238Mb = free heap space reported by the JVM
250Mb = the default threshold below which the protection should raise an exception to prevent OME
0Mb = the current buffer used for distinct and group by
I suspect another operation takes most of your RAM and once you run any DISTINCT/GROUP BY query it immediately stop because of the OME protection.
This answer would have helped me.
Example, if your machine has 32 GB RAM:
/opt/graphdb-free/app/graphdb-free.cfg (cutout)
[JVMOptions]
-Xms20G
-Xmx20G
-XX:PermSize=4G
-XX:MaxPermSize=4G
-Dfile.encoding=UTF-8
-Djava.net.preferIPv4Stack=true
--add-exports
jdk.management.agent/jdk.internal.agent=ALL-UNNAMED
--add-opens
java.base/java.lang=ALL-UNNAMED
Via GUI and Settings:
graphdb.page.cache.size 10G
Is there anyway to get information about how many Garbage collection been performed for different generations from a dump file. When I try to run some psscor4 commands I get following.
0:003> !GCUsage
The garbage collector data structures are not in a valid state for traversal.
It is either in the "plan phase," where objects are being moved around, or
we are at the initialization or shutdown of the gc heap. Commands related to
displaying, finding or traversing objects as well as gc heap segments may not
work properly. !dumpheap and !verifyheap may incorrectly complain of heap
consistency errors.
Error: Requesting GC Heap data
0:003> !CLRUsage
The garbage collector data structures are not in a valid state for traversal.
It is either in the "plan phase," where objects are being moved around, or
we are at the initialization or shutdown of the gc heap. Commands related to
displaying, finding or traversing objects as well as gc heap segments may not
work properly. !dumpheap and !verifyheap may incorrectly complain of heap
consistency errors.
Error: Requesting GC Heap data
I can get output from eehpeap though, but it does not give me what I am looking for.
0:003> !EEHeap -gc
Number of GC Heaps: 1
generation 0 starts at 0x0000000002c81030
generation 1 starts at 0x0000000002c81018
generation 2 starts at 0x0000000002c81000
ephemeral segment allocation context: none
segment begin allocated size
0000000002c80000 0000000002c81000 0000000002c87fe8 0x6fe8(28648)
Large object heap starts at 0x0000000012c81000
segment begin allocated size
0000000012c80000 0000000012c81000 0000000012c9e358 0x1d358(119640)
Total Size: Size: 0x24340 (148288) bytes.
------------------------------
GC Heap Size: Size: 0x24340 (148288) bytes.
Dumps
You can see the number of garbage collections in performance monitor. However, the way performance counters work makes me believe that this information is not available in a dump file and probably even not available during live debugging.
Think of Debug.WriteLine(): once the text was written to the debug output, it is gone. If you didn't have DebugView running at the time, the information is lost. And that's good, otherwise it would look like a memory leak.
Performance counters (as I understand them) work in a similar fashion. Various "pings" are sent out for someone else (the performance monitor) to be recorded. If noone does, the ping with all its information is gone.
Live debugging
As already mentioned, you can try performance monitor. If you prefer WinDbg, you can use sxe clrn to see garbage collections happen.
PSSCOR
The commands you mentioned, do not show information about garbage collection count:
0:016> !gcusage
Number of GC Heaps: 1
------------------------------
GC Heap Size 0x36d498(3,593,368)
Total Commit Size 0000000000384000 (3 MB)
Total Reserved Size 0000000017c7c000 (380 MB)
0:016> !clrusage
Number of GC Heaps: 1
------------------------------
GC Heap Size 0x36d498(3,593,368)
Total Commit Size 0000000000384000 (3 MB)
Total Reserved Size 0000000017c7c000 (380 MB)
Note: I'm using PSSCOR2 here, since I have the same .NET 4.5 issue on this machine. But I expect the output of PSSCOR4 to be similar.
I'm trying to understand the apc.shm_strings_buffer setting in apc.ini. After restarting PHP, the pie chart in the APC admin shows 8MB of cache is already used, even though there are no cached entries (except for apc.php, of course). I've found this relates to the apc.shm_strings_buffer setting.
Can someone help me understand what the setting means? The config file notes that this is the "shared memory size reserved for strings, with M/G suffixe", but I fail to comprehend.
I'm using APC with PHP-FPM.
The easy part to explain is "with M/G suffixe" which means that if you set it to 8M, then 8 megabytes would be allocated, or 1G would allocated 1 gigabyte of memory.
The more difficult bit to explain is that it's a cache for storing strings that are used internally by APC when it's compiling and caching opcode.
The config value was introduced in this change and the bulk of the change was to add apc_string.c to the APC project. The main function that is defined in that C file is apc_new_interned_string which is then used in apc_string_pmemcpy in apc_compile.c. the rest of the APC module to store strings.
For example in apc_compile.c
/* private members are stored inside property_info as a mangled
* string of the form:
* \0<classname>\0<membername>\0
*/
CHECK((dst->name = apc_string_pmemcpy((char *)src->name, src->name_length+1, pool TSRMLS_CC)));
When APC goes to store a string, the function apc_new_interned_string looks to see if it that string is already saved in memory by doing a hash on the string, and if it is already stored in memory, it returns the previous instance of the stored string.
Only if that string is not already stored in the cache does a new piece of memory get allocated to store the string.
If you're running PHP with PHP-FPM, I'm 90% confident that the cache of stored strings is shared amongst all the workers in a single pool, but am still double-checking that.
The whole size allocated to storing shared strings is allocated when PHP starts up - it's not allocated dynamically. So it's to be expected that APC shows the 8MB used for the string cache, even though hardly any strings have actually been cached yet.
Edit
Although this answers what it does, I have no idea how to see how much of the shared string buffer is being used, so there's no way of knowing what it should be set to.