Re: Too many open files error, which gets resolved after some time
Hi. Thank for the advice, just to clarify: The upgrade of you speak of of cleaning the pipes/epolls more often, is regarding the issue discussed (HADOOP-4346, fixed in my distribution), or it's some other issue? If yes, does it has a ticket I can see, or it should be filled to Jira? Thanks! 2009/6/23 Brian Bockelman bbock...@cse.unl.edu Hey Stas, It sounds like it's technically possible, but it also sounds like a horrible hack: I'd avoid this at all expense. This is how cruft is born. The pipes/epolls are something that eventually get cleaned up - but they don't get cleaned up often enough for your cluster. I would recommend just increasing the limit on the node itself and then wait for an upgrade to solve this. Brian On Jun 23, 2009, at 3:31 AM, Stas Oskin wrote: Hi. Any idea if calling System.gc() periodically will help reducing the amount of pipes / epolls? Thanks for your opinion! 2009/6/22 Stas Oskin stas.os...@gmail.com Ok, seems this issue is already patched in the Hadoop distro I'm using (Cloudera). Any idea if I still should call GC manually/periodically to clean out all the stale pipes / epolls? 2009/6/22 Steve Loughran ste...@apache.org Stas Oskin wrote: Hi. So what would be the recommended approach to pre-0.20.x series? To insure each file is used only by one thread, and then it safe to close the handle in that thread? Regards. good question -I'm not sure. For anythiong you get with FileSystem.get(), its now dangerous to close, so try just setting the reference to null and hoping that GC will do the finalize() when needed
Re: Too many open files error, which gets resolved after some time
Stas Oskin wrote: Hi. Any idea if calling System.gc() periodically will help reducing the amount of pipes / epolls? since you have HADOOP-4346, you should not have excessive epoll/pipe fds open. First of all do you still have the problem? If yes, how many hadoop streams do you have at a time? System.gc() won't help if you have HADOOP-4346. Ragu. Thanks for your opinion! 2009/6/22 Stas Oskin stas.os...@gmail.com Ok, seems this issue is already patched in the Hadoop distro I'm using (Cloudera). Any idea if I still should call GC manually/periodically to clean out all the stale pipes / epolls? 2009/6/22 Steve Loughran ste...@apache.org Stas Oskin wrote: Hi. So what would be the recommended approach to pre-0.20.x series? To insure each file is used only by one thread, and then it safe to close the handle in that thread? Regards. good question -I'm not sure. For anythiong you get with FileSystem.get(), its now dangerous to close, so try just setting the reference to null and hoping that GC will do the finalize() when needed
Re: Too many open files error, which gets resolved after some time
To be more accurate, once you have HADOOP-4346, fds for epoll and pipes = 3 * threads blocked on Hadoop I/O Unless you have hundreds of threads at a time, you should not see hundreds of these. These fds stay up to 10sec even after the threads exit. I am a bit confused about your exact situation. Please check number of threads if you still facing the problem. Raghu. Raghu Angadi wrote: since you have HADOOP-4346, you should not have excessive epoll/pipe fds open. First of all do you still have the problem? If yes, how many hadoop streams do you have at a time? System.gc() won't help if you have HADOOP-4346. Ragu. Thanks for your opinion! 2009/6/22 Stas Oskin stas.os...@gmail.com Ok, seems this issue is already patched in the Hadoop distro I'm using (Cloudera). Any idea if I still should call GC manually/periodically to clean out all the stale pipes / epolls? 2009/6/22 Steve Loughran ste...@apache.org Stas Oskin wrote: Hi. So what would be the recommended approach to pre-0.20.x series? To insure each file is used only by one thread, and then it safe to close the handle in that thread? Regards. good question -I'm not sure. For anythiong you get with FileSystem.get(), its now dangerous to close, so try just setting the reference to null and hoping that GC will do the finalize() when needed
Re: Too many open files error, which gets resolved after some time
Hi. In my testings, I typically opened between 20 and 40 concurrent streams. Regards. 2009/6/23 Raghu Angadi rang...@yahoo-inc.com Stas Oskin wrote: Hi. Any idea if calling System.gc() periodically will help reducing the amount of pipes / epolls? since you have HADOOP-4346, you should not have excessive epoll/pipe fds open. First of all do you still have the problem? If yes, how many hadoop streams do you have at a time? System.gc() won't help if you have HADOOP-4346. Ragu. Thanks for your opinion! 2009/6/22 Stas Oskin stas.os...@gmail.com Ok, seems this issue is already patched in the Hadoop distro I'm using (Cloudera). Any idea if I still should call GC manually/periodically to clean out all the stale pipes / epolls? 2009/6/22 Steve Loughran ste...@apache.org Stas Oskin wrote: Hi. So what would be the recommended approach to pre-0.20.x series? To insure each file is used only by one thread, and then it safe to close the handle in that thread? Regards. good question -I'm not sure. For anythiong you get with FileSystem.get(), its now dangerous to close, so try just setting the reference to null and hoping that GC will do the finalize() when needed
Re: Too many open files error, which gets resolved after some time
how many threads do you have? Number of active threads is very important. Normally, #fds = (3 * #threads_blocked_on_io) + #streams 12 per stream is certainly way off. Raghu. Stas Oskin wrote: Hi. In my case it was actually ~ 12 fd's per stream, which included pipes and epolls. Could it be that HDFS opens 3 x 3 (input - output - epoll) fd's per each thread, which make it close to the number I mentioned? Or it always 3 at maximum per thread / stream? Up to 10 sec looks quite the correct number, it seems it gets freed arround this time indeed. Regards. 2009/6/23 Raghu Angadi rang...@yahoo-inc.com To be more accurate, once you have HADOOP-4346, fds for epoll and pipes = 3 * threads blocked on Hadoop I/O Unless you have hundreds of threads at a time, you should not see hundreds of these. These fds stay up to 10sec even after the threads exit. I am a bit confused about your exact situation. Please check number of threads if you still facing the problem. Raghu. Raghu Angadi wrote: since you have HADOOP-4346, you should not have excessive epoll/pipe fds open. First of all do you still have the problem? If yes, how many hadoop streams do you have at a time? System.gc() won't help if you have HADOOP-4346. Ragu. Thanks for your opinion! 2009/6/22 Stas Oskin stas.os...@gmail.com Ok, seems this issue is already patched in the Hadoop distro I'm using (Cloudera). Any idea if I still should call GC manually/periodically to clean out all the stale pipes / epolls? 2009/6/22 Steve Loughran ste...@apache.org Stas Oskin wrote: Hi. So what would be the recommended approach to pre-0.20.x series? To insure each file is used only by one thread, and then it safe to close the handle in that thread? Regards. good question -I'm not sure. For anythiong you get with FileSystem.get(), its now dangerous to close, so try just setting the reference to null and hoping that GC will do the finalize() when needed
Re: Too many open files error, which gets resolved after some time
Hi. So if I open one stream, it should be 4? 2009/6/23 Raghu Angadi rang...@yahoo-inc.com how many threads do you have? Number of active threads is very important. Normally, #fds = (3 * #threads_blocked_on_io) + #streams 12 per stream is certainly way off. Raghu. Stas Oskin wrote: Hi. In my case it was actually ~ 12 fd's per stream, which included pipes and epolls. Could it be that HDFS opens 3 x 3 (input - output - epoll) fd's per each thread, which make it close to the number I mentioned? Or it always 3 at maximum per thread / stream? Up to 10 sec looks quite the correct number, it seems it gets freed arround this time indeed. Regards. 2009/6/23 Raghu Angadi rang...@yahoo-inc.com To be more accurate, once you have HADOOP-4346, fds for epoll and pipes = 3 * threads blocked on Hadoop I/O Unless you have hundreds of threads at a time, you should not see hundreds of these. These fds stay up to 10sec even after the threads exit. I am a bit confused about your exact situation. Please check number of threads if you still facing the problem. Raghu. Raghu Angadi wrote: since you have HADOOP-4346, you should not have excessive epoll/pipe fds open. First of all do you still have the problem? If yes, how many hadoop streams do you have at a time? System.gc() won't help if you have HADOOP-4346. Ragu. Thanks for your opinion! 2009/6/22 Stas Oskin stas.os...@gmail.com Ok, seems this issue is already patched in the Hadoop distro I'm using (Cloudera). Any idea if I still should call GC manually/periodically to clean out all the stale pipes / epolls? 2009/6/22 Steve Loughran ste...@apache.org Stas Oskin wrote: Hi. So what would be the recommended approach to pre-0.20.x series? To insure each file is used only by one thread, and then it safe to close the handle in that thread? Regards. good question -I'm not sure. For anythiong you get with FileSystem.get(), its now dangerous to close, so try just setting the reference to null and hoping that GC will do the finalize() when needed
Re: Too many open files error, which gets resolved after some time
Is this before 0.20.0? Assuming you have closed these streams, it is mostly https://issues.apache.org/jira/browse/HADOOP-4346 It is the JDK internal implementation that depends on GC to free up its cache of selectors. HADOOP-4346 avoids this by using hadoop's own cache. Raghu. Stas Oskin wrote: Hi. After tracing some more with the lsof utility, and I managed to stop the growth on the DataNode process, but still have issues with my DFS client. It seems that my DFS client opens hundreds of pipes and eventpolls. Here is a small part of the lsof output: java10508 root 387w FIFO0,6 6142565 pipe java10508 root 388r FIFO0,6 6142565 pipe java10508 root 389u 0,100 6142566 eventpoll java10508 root 390u FIFO0,6 6135311 pipe java10508 root 391r FIFO0,6 6135311 pipe java10508 root 392u 0,100 6135312 eventpoll java10508 root 393r FIFO0,6 6148234 pipe java10508 root 394w FIFO0,6 6142570 pipe java10508 root 395r FIFO0,6 6135857 pipe java10508 root 396r FIFO0,6 6142570 pipe java10508 root 397r 0,100 6142571 eventpoll java10508 root 398u FIFO0,6 6135319 pipe java10508 root 399w FIFO0,6 6135319 pipe I'm using FSDataInputStream and FSDataOutputStream, so this might be related to pipes? So, my questions are: 1) What happens these pipes/epolls to appear? 2) More important, how I can prevent their accumation and growth? Thanks in advance! 2009/6/21 Stas Oskin stas.os...@gmail.com Hi. I have HDFS client and HDFS datanode running on same machine. When I'm trying to access a dozen of files at once from the client, several times in a row, I'm starting to receive the following errors on client, and HDFS browse function. HDFS Client: Could not get block locations. Aborting... HDFS browse: Too many open files I can increase the maximum number of files that can opened, as I have it set to the default 1024, but would like to first solve the problem, as larger value just means it would run out of files again later on. So my questions are: 1) Does the HDFS datanode keeps any files opened, even after the HDFS client have already closed them? 2) Is it possible to find out, who keeps the opened files - datanode or client (so I could pin-point the source of the problem). Thanks in advance!
Re: Too many open files error, which gets resolved after some time
Hi. I've started doing just that, and indeed the amount of fd's of the DataNode process have reduced significantly. My problem is that my own app, which works with DFS, still have dozens of pipes and epolls open. The usual level seems to be about 300-400 fd's, but when I access the DFS for accessing several files concurrently, this number easily climbs to 700-800. Moreover, the number sometimes seems to be stuck above 1000, and only shutting down the app, at it's start, brings this number back to 300-400. Any idea why this happens, and what else can be released to get it working? Also, every file I open seems to bump the fd count sometimes as high as by 12. Any idea why single file requires so many fd's? Thanks in advance. 2009/6/22 jason hadoop jason.had...@gmail.com Yes. Otherwise the file descriptors will flow away like water. I also strongly suggest having at least 64k file descriptors as the open file limit. On Sun, Jun 21, 2009 at 12:43 PM, Stas Oskin stas.os...@gmail.com wrote: Hi. Thanks for the advice. So you advice explicitly closing each and every file handle that I receive from HDFS? Regards. 2009/6/21 jason hadoop jason.had...@gmail.com Just to be clear, I second Brian's opinion. Relying on finalizes is a very good way to run out of file descriptors. On Sun, Jun 21, 2009 at 9:32 AM, brian.lev...@nokia.com wrote: IMHO, you should never rely on finalizers to release scarce resources since you don't know when the finalizer will get called, if ever. -brian -Original Message- From: ext jason hadoop [mailto:jason.had...@gmail.com] Sent: Sunday, June 21, 2009 11:19 AM To: core-user@hadoop.apache.org Subject: Re: Too many open files error, which gets resolved after some time HDFS/DFS client uses quite a few file descriptors for each open file. Many application developers (but not the hadoop core) rely on the JVM finalizer methods to close open files. This combination, expecially when many HDFS files are open can result in very large demands for file descriptors for Hadoop clients. We as a general rule never run a cluster with nofile less that 64k, and for larger clusters with demanding applications have had it set 10x higher. I also believe there was a set of JVM versions that leaked file descriptors used for NIO in the HDFS core. I do not recall the exact details. On Sun, Jun 21, 2009 at 5:27 AM, Stas Oskin stas.os...@gmail.com wrote: Hi. After tracing some more with the lsof utility, and I managed to stop the growth on the DataNode process, but still have issues with my DFS client. It seems that my DFS client opens hundreds of pipes and eventpolls. Here is a small part of the lsof output: java10508 root 387w FIFO0,6 6142565 pipe java10508 root 388r FIFO0,6 6142565 pipe java10508 root 389u 0,100 6142566 eventpoll java10508 root 390u FIFO0,6 6135311 pipe java10508 root 391r FIFO0,6 6135311 pipe java10508 root 392u 0,100 6135312 eventpoll java10508 root 393r FIFO0,6 6148234 pipe java10508 root 394w FIFO0,6 6142570 pipe java10508 root 395r FIFO0,6 6135857 pipe java10508 root 396r FIFO0,6 6142570 pipe java10508 root 397r 0,100 6142571 eventpoll java10508 root 398u FIFO0,6 6135319 pipe java10508 root 399w FIFO0,6 6135319 pipe I'm using FSDataInputStream and FSDataOutputStream, so this might be related to pipes? So, my questions are: 1) What happens these pipes/epolls to appear? 2) More important, how I can prevent their accumation and growth? Thanks in advance! 2009/6/21 Stas Oskin stas.os...@gmail.com Hi. I have HDFS client and HDFS datanode running on same machine. When I'm trying to access a dozen of files at once from the client, several times in a row, I'm starting to receive the following errors on client, and HDFS browse function. HDFS Client: Could not get block locations. Aborting... HDFS browse: Too many open files I can increase the maximum number of files that can opened, as I have it set to the default 1024, but would like to first solve the problem, as larger value just means it would run out of files again later on. So my questions
Re: Too many open files error, which gets resolved after some time
jason hadoop wrote: Yes. Otherwise the file descriptors will flow away like water. I also strongly suggest having at least 64k file descriptors as the open file limit. On Sun, Jun 21, 2009 at 12:43 PM, Stas Oskin stas.os...@gmail.com wrote: Hi. Thanks for the advice. So you advice explicitly closing each and every file handle that I receive from HDFS? Regards. I must disagree somewhat If you use FileSystem.get() to get your client filesystem class, then that is shared by all threads/classes that use it. Call close() on that and any other thread or class holding a reference is in trouble. You have to wait for the finalizers for them to get cleaned up. If you use FileSystem.newInstance() - which came in fairly recently (0.20? 0.21?) then you can call close() safely. So: it depends on how you get your handle. see: https://issues.apache.org/jira/browse/HADOOP-5933 Also: the too many open files problem can be caused in the NN -you need to set up the Kernel to have lots more file handles around. Lots.
Re: Too many open files error, which gets resolved after some time
Scott Carey wrote: Furthermore, if for some reason it is required to dispose of any objects after others are GC'd, weak references and a weak reference queue will perform significantly better in throughput and latency - orders of magnitude better - than finalizers. Good point. I would make sense for the FileSystem cache to be weak referenced, so that on long-lived processes the client references will get cleaned up without waiting for app termination
Re: Too many open files error, which gets resolved after some time
Raghu Angadi wrote: Is this before 0.20.0? Assuming you have closed these streams, it is mostly https://issues.apache.org/jira/browse/HADOOP-4346 It is the JDK internal implementation that depends on GC to free up its cache of selectors. HADOOP-4346 avoids this by using hadoop's own cache. yes, and it's that change that led to my stack traces :( http://jira.smartfrog.org/jira/browse/SFOS-1208
Re: Too many open files error, which gets resolved after some time
Hi. So what would be the recommended approach to pre-0.20.x series? To insure each file is used only by one thread, and then it safe to close the handle in that thread? Regards. 2009/6/22 Steve Loughran ste...@apache.org Raghu Angadi wrote: Is this before 0.20.0? Assuming you have closed these streams, it is mostly https://issues.apache.org/jira/browse/HADOOP-4346 It is the JDK internal implementation that depends on GC to free up its cache of selectors. HADOOP-4346 avoids this by using hadoop's own cache. yes, and it's that change that led to my stack traces :( http://jira.smartfrog.org/jira/browse/SFOS-1208
Re: Too many open files error, which gets resolved after some time
64k might help in the sense, you might hit GC before you hit the limit. Otherwise, your only options are to use the patch attached to HADOOP-4346 or run System.gc() occasionally. I think it should be committed to 0.18.4 Raghu. Stas Oskin wrote: Hi. Yes, it happens with 0.18.3. I'm closing now every FSData stream I receive from HDFS, so the number of open fd's in DataNode is reduced. Problem is that my own DFS client still have a high number of fd's open, mostly pipes and epolls. They sometimes quickly drop to the level of ~400 - 500, and sometimes just stuck at ~1000. I'm still trying to find out how well it behaves if I set the maximum fd number to 65K. Regards. 2009/6/22 Raghu Angadi rang...@yahoo-inc.com Is this before 0.20.0? Assuming you have closed these streams, it is mostly https://issues.apache.org/jira/browse/HADOOP-4346 It is the JDK internal implementation that depends on GC to free up its cache of selectors. HADOOP-4346 avoids this by using hadoop's own cache. Raghu. Stas Oskin wrote: Hi. After tracing some more with the lsof utility, and I managed to stop the growth on the DataNode process, but still have issues with my DFS client. It seems that my DFS client opens hundreds of pipes and eventpolls. Here is a small part of the lsof output: java10508 root 387w FIFO0,6 6142565 pipe java10508 root 388r FIFO0,6 6142565 pipe java10508 root 389u 0,100 6142566 eventpoll java10508 root 390u FIFO0,6 6135311 pipe java10508 root 391r FIFO0,6 6135311 pipe java10508 root 392u 0,100 6135312 eventpoll java10508 root 393r FIFO0,6 6148234 pipe java10508 root 394w FIFO0,6 6142570 pipe java10508 root 395r FIFO0,6 6135857 pipe java10508 root 396r FIFO0,6 6142570 pipe java10508 root 397r 0,100 6142571 eventpoll java10508 root 398u FIFO0,6 6135319 pipe java10508 root 399w FIFO0,6 6135319 pipe I'm using FSDataInputStream and FSDataOutputStream, so this might be related to pipes? So, my questions are: 1) What happens these pipes/epolls to appear? 2) More important, how I can prevent their accumation and growth? Thanks in advance! 2009/6/21 Stas Oskin stas.os...@gmail.com Hi. I have HDFS client and HDFS datanode running on same machine. When I'm trying to access a dozen of files at once from the client, several times in a row, I'm starting to receive the following errors on client, and HDFS browse function. HDFS Client: Could not get block locations. Aborting... HDFS browse: Too many open files I can increase the maximum number of files that can opened, as I have it set to the default 1024, but would like to first solve the problem, as larger value just means it would run out of files again later on. So my questions are: 1) Does the HDFS datanode keeps any files opened, even after the HDFS client have already closed them? 2) Is it possible to find out, who keeps the opened files - datanode or client (so I could pin-point the source of the problem). Thanks in advance!
Re: Too many open files error, which gets resolved after some time
Hi Rahid. A question - this issue does not influence Hadoop itself (DataNodes, etc...), but rather influence any application using DFS, correct? If so, without patching iI should either to increase fd limit (which might fill-up as well???), or periodically launch the GC? Regards. 2009/6/22 Raghu Angadi rang...@yahoo-inc.com 64k might help in the sense, you might hit GC before you hit the limit. Otherwise, your only options are to use the patch attached to HADOOP-4346 or run System.gc() occasionally. I think it should be committed to 0.18.4 Raghu. Stas Oskin wrote: Hi. Yes, it happens with 0.18.3. I'm closing now every FSData stream I receive from HDFS, so the number of open fd's in DataNode is reduced. Problem is that my own DFS client still have a high number of fd's open, mostly pipes and epolls. They sometimes quickly drop to the level of ~400 - 500, and sometimes just stuck at ~1000. I'm still trying to find out how well it behaves if I set the maximum fd number to 65K. Regards. 2009/6/22 Raghu Angadi rang...@yahoo-inc.com Is this before 0.20.0? Assuming you have closed these streams, it is mostly https://issues.apache.org/jira/browse/HADOOP-4346 It is the JDK internal implementation that depends on GC to free up its cache of selectors. HADOOP-4346 avoids this by using hadoop's own cache. Raghu. Stas Oskin wrote: Hi. After tracing some more with the lsof utility, and I managed to stop the growth on the DataNode process, but still have issues with my DFS client. It seems that my DFS client opens hundreds of pipes and eventpolls. Here is a small part of the lsof output: java10508 root 387w FIFO0,6 6142565 pipe java10508 root 388r FIFO0,6 6142565 pipe java10508 root 389u 0,100 6142566 eventpoll java10508 root 390u FIFO0,6 6135311 pipe java10508 root 391r FIFO0,6 6135311 pipe java10508 root 392u 0,100 6135312 eventpoll java10508 root 393r FIFO0,6 6148234 pipe java10508 root 394w FIFO0,6 6142570 pipe java10508 root 395r FIFO0,6 6135857 pipe java10508 root 396r FIFO0,6 6142570 pipe java10508 root 397r 0,100 6142571 eventpoll java10508 root 398u FIFO0,6 6135319 pipe java10508 root 399w FIFO0,6 6135319 pipe I'm using FSDataInputStream and FSDataOutputStream, so this might be related to pipes? So, my questions are: 1) What happens these pipes/epolls to appear? 2) More important, how I can prevent their accumation and growth? Thanks in advance! 2009/6/21 Stas Oskin stas.os...@gmail.com Hi. I have HDFS client and HDFS datanode running on same machine. When I'm trying to access a dozen of files at once from the client, several times in a row, I'm starting to receive the following errors on client, and HDFS browse function. HDFS Client: Could not get block locations. Aborting... HDFS browse: Too many open files I can increase the maximum number of files that can opened, as I have it set to the default 1024, but would like to first solve the problem, as larger value just means it would run out of files again later on. So my questions are: 1) Does the HDFS datanode keeps any files opened, even after the HDFS client have already closed them? 2) Is it possible to find out, who keeps the opened files - datanode or client (so I could pin-point the source of the problem). Thanks in advance!
Re: Too many open files error, which gets resolved after some time
Stas Oskin wrote: Hi. So what would be the recommended approach to pre-0.20.x series? To insure each file is used only by one thread, and then it safe to close the handle in that thread? Regards. good question -I'm not sure. For anythiong you get with FileSystem.get(), its now dangerous to close, so try just setting the reference to null and hoping that GC will do the finalize() when needed
Re: Too many open files error, which gets resolved after some time
Ok, seems this issue is already patched in the Hadoop distro I'm using (Cloudera). Any idea if I still should call GC manually/periodically to clean out all the stale pipes / epolls? 2009/6/22 Steve Loughran ste...@apache.org Stas Oskin wrote: Hi. So what would be the recommended approach to pre-0.20.x series? To insure each file is used only by one thread, and then it safe to close the handle in that thread? Regards. good question -I'm not sure. For anythiong you get with FileSystem.get(), its now dangerous to close, so try just setting the reference to null and hoping that GC will do the finalize() when needed
Re: Too many open files error, which gets resolved after some time
Hi. After tracing some more with the lsof utility, and I managed to stop the growth on the DataNode process, but still have issues with my DFS client. It seems that my DFS client opens hundreds of pipes and eventpolls. Here is a small part of the lsof output: java10508 root 387w FIFO0,6 6142565 pipe java10508 root 388r FIFO0,6 6142565 pipe java10508 root 389u 0,100 6142566 eventpoll java10508 root 390u FIFO0,6 6135311 pipe java10508 root 391r FIFO0,6 6135311 pipe java10508 root 392u 0,100 6135312 eventpoll java10508 root 393r FIFO0,6 6148234 pipe java10508 root 394w FIFO0,6 6142570 pipe java10508 root 395r FIFO0,6 6135857 pipe java10508 root 396r FIFO0,6 6142570 pipe java10508 root 397r 0,100 6142571 eventpoll java10508 root 398u FIFO0,6 6135319 pipe java10508 root 399w FIFO0,6 6135319 pipe I'm using FSDataInputStream and FSDataOutputStream, so this might be related to pipes? So, my questions are: 1) What happens these pipes/epolls to appear? 2) More important, how I can prevent their accumation and growth? Thanks in advance! 2009/6/21 Stas Oskin stas.os...@gmail.com Hi. I have HDFS client and HDFS datanode running on same machine. When I'm trying to access a dozen of files at once from the client, several times in a row, I'm starting to receive the following errors on client, and HDFS browse function. HDFS Client: Could not get block locations. Aborting... HDFS browse: Too many open files I can increase the maximum number of files that can opened, as I have it set to the default 1024, but would like to first solve the problem, as larger value just means it would run out of files again later on. So my questions are: 1) Does the HDFS datanode keeps any files opened, even after the HDFS client have already closed them? 2) Is it possible to find out, who keeps the opened files - datanode or client (so I could pin-point the source of the problem). Thanks in advance!
Re: Too many open files error, which gets resolved after some time
HDFS/DFS client uses quite a few file descriptors for each open file. Many application developers (but not the hadoop core) rely on the JVM finalizer methods to close open files. This combination, expecially when many HDFS files are open can result in very large demands for file descriptors for Hadoop clients. We as a general rule never run a cluster with nofile less that 64k, and for larger clusters with demanding applications have had it set 10x higher. I also believe there was a set of JVM versions that leaked file descriptors used for NIO in the HDFS core. I do not recall the exact details. On Sun, Jun 21, 2009 at 5:27 AM, Stas Oskin stas.os...@gmail.com wrote: Hi. After tracing some more with the lsof utility, and I managed to stop the growth on the DataNode process, but still have issues with my DFS client. It seems that my DFS client opens hundreds of pipes and eventpolls. Here is a small part of the lsof output: java10508 root 387w FIFO0,6 6142565 pipe java10508 root 388r FIFO0,6 6142565 pipe java10508 root 389u 0,100 6142566 eventpoll java10508 root 390u FIFO0,6 6135311 pipe java10508 root 391r FIFO0,6 6135311 pipe java10508 root 392u 0,100 6135312 eventpoll java10508 root 393r FIFO0,6 6148234 pipe java10508 root 394w FIFO0,6 6142570 pipe java10508 root 395r FIFO0,6 6135857 pipe java10508 root 396r FIFO0,6 6142570 pipe java10508 root 397r 0,100 6142571 eventpoll java10508 root 398u FIFO0,6 6135319 pipe java10508 root 399w FIFO0,6 6135319 pipe I'm using FSDataInputStream and FSDataOutputStream, so this might be related to pipes? So, my questions are: 1) What happens these pipes/epolls to appear? 2) More important, how I can prevent their accumation and growth? Thanks in advance! 2009/6/21 Stas Oskin stas.os...@gmail.com Hi. I have HDFS client and HDFS datanode running on same machine. When I'm trying to access a dozen of files at once from the client, several times in a row, I'm starting to receive the following errors on client, and HDFS browse function. HDFS Client: Could not get block locations. Aborting... HDFS browse: Too many open files I can increase the maximum number of files that can opened, as I have it set to the default 1024, but would like to first solve the problem, as larger value just means it would run out of files again later on. So my questions are: 1) Does the HDFS datanode keeps any files opened, even after the HDFS client have already closed them? 2) Is it possible to find out, who keeps the opened files - datanode or client (so I could pin-point the source of the problem). Thanks in advance! -- Pro Hadoop, a book to guide you from beginner to hadoop mastery, http://www.amazon.com/dp/1430219424?tag=jewlerymall www.prohadoopbook.com a community for Hadoop Professionals
RE: Too many open files error, which gets resolved after some time
IMHO, you should never rely on finalizers to release scarce resources since you don't know when the finalizer will get called, if ever. -brian -Original Message- From: ext jason hadoop [mailto:jason.had...@gmail.com] Sent: Sunday, June 21, 2009 11:19 AM To: core-user@hadoop.apache.org Subject: Re: Too many open files error, which gets resolved after some time HDFS/DFS client uses quite a few file descriptors for each open file. Many application developers (but not the hadoop core) rely on the JVM finalizer methods to close open files. This combination, expecially when many HDFS files are open can result in very large demands for file descriptors for Hadoop clients. We as a general rule never run a cluster with nofile less that 64k, and for larger clusters with demanding applications have had it set 10x higher. I also believe there was a set of JVM versions that leaked file descriptors used for NIO in the HDFS core. I do not recall the exact details. On Sun, Jun 21, 2009 at 5:27 AM, Stas Oskin stas.os...@gmail.com wrote: Hi. After tracing some more with the lsof utility, and I managed to stop the growth on the DataNode process, but still have issues with my DFS client. It seems that my DFS client opens hundreds of pipes and eventpolls. Here is a small part of the lsof output: java10508 root 387w FIFO0,6 6142565 pipe java10508 root 388r FIFO0,6 6142565 pipe java10508 root 389u 0,100 6142566 eventpoll java10508 root 390u FIFO0,6 6135311 pipe java10508 root 391r FIFO0,6 6135311 pipe java10508 root 392u 0,100 6135312 eventpoll java10508 root 393r FIFO0,6 6148234 pipe java10508 root 394w FIFO0,6 6142570 pipe java10508 root 395r FIFO0,6 6135857 pipe java10508 root 396r FIFO0,6 6142570 pipe java10508 root 397r 0,100 6142571 eventpoll java10508 root 398u FIFO0,6 6135319 pipe java10508 root 399w FIFO0,6 6135319 pipe I'm using FSDataInputStream and FSDataOutputStream, so this might be related to pipes? So, my questions are: 1) What happens these pipes/epolls to appear? 2) More important, how I can prevent their accumation and growth? Thanks in advance! 2009/6/21 Stas Oskin stas.os...@gmail.com Hi. I have HDFS client and HDFS datanode running on same machine. When I'm trying to access a dozen of files at once from the client, several times in a row, I'm starting to receive the following errors on client, and HDFS browse function. HDFS Client: Could not get block locations. Aborting... HDFS browse: Too many open files I can increase the maximum number of files that can opened, as I have it set to the default 1024, but would like to first solve the problem, as larger value just means it would run out of files again later on. So my questions are: 1) Does the HDFS datanode keeps any files opened, even after the HDFS client have already closed them? 2) Is it possible to find out, who keeps the opened files - datanode or client (so I could pin-point the source of the problem). Thanks in advance! -- Pro Hadoop, a book to guide you from beginner to hadoop mastery, http://www.amazon.com/dp/1430219424?tag=jewlerymall www.prohadoopbook.com a community for Hadoop Professionals
Re: Too many open files error, which gets resolved after some time
Just to be clear, I second Brian's opinion. Relying on finalizes is a very good way to run out of file descriptors. On Sun, Jun 21, 2009 at 9:32 AM, brian.lev...@nokia.com wrote: IMHO, you should never rely on finalizers to release scarce resources since you don't know when the finalizer will get called, if ever. -brian -Original Message- From: ext jason hadoop [mailto:jason.had...@gmail.com] Sent: Sunday, June 21, 2009 11:19 AM To: core-user@hadoop.apache.org Subject: Re: Too many open files error, which gets resolved after some time HDFS/DFS client uses quite a few file descriptors for each open file. Many application developers (but not the hadoop core) rely on the JVM finalizer methods to close open files. This combination, expecially when many HDFS files are open can result in very large demands for file descriptors for Hadoop clients. We as a general rule never run a cluster with nofile less that 64k, and for larger clusters with demanding applications have had it set 10x higher. I also believe there was a set of JVM versions that leaked file descriptors used for NIO in the HDFS core. I do not recall the exact details. On Sun, Jun 21, 2009 at 5:27 AM, Stas Oskin stas.os...@gmail.com wrote: Hi. After tracing some more with the lsof utility, and I managed to stop the growth on the DataNode process, but still have issues with my DFS client. It seems that my DFS client opens hundreds of pipes and eventpolls. Here is a small part of the lsof output: java10508 root 387w FIFO0,6 6142565 pipe java10508 root 388r FIFO0,6 6142565 pipe java10508 root 389u 0,100 6142566 eventpoll java10508 root 390u FIFO0,6 6135311 pipe java10508 root 391r FIFO0,6 6135311 pipe java10508 root 392u 0,100 6135312 eventpoll java10508 root 393r FIFO0,6 6148234 pipe java10508 root 394w FIFO0,6 6142570 pipe java10508 root 395r FIFO0,6 6135857 pipe java10508 root 396r FIFO0,6 6142570 pipe java10508 root 397r 0,100 6142571 eventpoll java10508 root 398u FIFO0,6 6135319 pipe java10508 root 399w FIFO0,6 6135319 pipe I'm using FSDataInputStream and FSDataOutputStream, so this might be related to pipes? So, my questions are: 1) What happens these pipes/epolls to appear? 2) More important, how I can prevent their accumation and growth? Thanks in advance! 2009/6/21 Stas Oskin stas.os...@gmail.com Hi. I have HDFS client and HDFS datanode running on same machine. When I'm trying to access a dozen of files at once from the client, several times in a row, I'm starting to receive the following errors on client, and HDFS browse function. HDFS Client: Could not get block locations. Aborting... HDFS browse: Too many open files I can increase the maximum number of files that can opened, as I have it set to the default 1024, but would like to first solve the problem, as larger value just means it would run out of files again later on. So my questions are: 1) Does the HDFS datanode keeps any files opened, even after the HDFS client have already closed them? 2) Is it possible to find out, who keeps the opened files - datanode or client (so I could pin-point the source of the problem). Thanks in advance! -- Pro Hadoop, a book to guide you from beginner to hadoop mastery, http://www.amazon.com/dp/1430219424?tag=jewlerymall www.prohadoopbook.com a community for Hadoop Professionals -- Pro Hadoop, a book to guide you from beginner to hadoop mastery, http://www.amazon.com/dp/1430219424?tag=jewlerymall www.prohadoopbook.com a community for Hadoop Professionals
Re: Too many open files error, which gets resolved after some time
Yes. Otherwise the file descriptors will flow away like water. I also strongly suggest having at least 64k file descriptors as the open file limit. On Sun, Jun 21, 2009 at 12:43 PM, Stas Oskin stas.os...@gmail.com wrote: Hi. Thanks for the advice. So you advice explicitly closing each and every file handle that I receive from HDFS? Regards. 2009/6/21 jason hadoop jason.had...@gmail.com Just to be clear, I second Brian's opinion. Relying on finalizes is a very good way to run out of file descriptors. On Sun, Jun 21, 2009 at 9:32 AM, brian.lev...@nokia.com wrote: IMHO, you should never rely on finalizers to release scarce resources since you don't know when the finalizer will get called, if ever. -brian -Original Message- From: ext jason hadoop [mailto:jason.had...@gmail.com] Sent: Sunday, June 21, 2009 11:19 AM To: core-user@hadoop.apache.org Subject: Re: Too many open files error, which gets resolved after some time HDFS/DFS client uses quite a few file descriptors for each open file. Many application developers (but not the hadoop core) rely on the JVM finalizer methods to close open files. This combination, expecially when many HDFS files are open can result in very large demands for file descriptors for Hadoop clients. We as a general rule never run a cluster with nofile less that 64k, and for larger clusters with demanding applications have had it set 10x higher. I also believe there was a set of JVM versions that leaked file descriptors used for NIO in the HDFS core. I do not recall the exact details. On Sun, Jun 21, 2009 at 5:27 AM, Stas Oskin stas.os...@gmail.com wrote: Hi. After tracing some more with the lsof utility, and I managed to stop the growth on the DataNode process, but still have issues with my DFS client. It seems that my DFS client opens hundreds of pipes and eventpolls. Here is a small part of the lsof output: java10508 root 387w FIFO0,6 6142565 pipe java10508 root 388r FIFO0,6 6142565 pipe java10508 root 389u 0,100 6142566 eventpoll java10508 root 390u FIFO0,6 6135311 pipe java10508 root 391r FIFO0,6 6135311 pipe java10508 root 392u 0,100 6135312 eventpoll java10508 root 393r FIFO0,6 6148234 pipe java10508 root 394w FIFO0,6 6142570 pipe java10508 root 395r FIFO0,6 6135857 pipe java10508 root 396r FIFO0,6 6142570 pipe java10508 root 397r 0,100 6142571 eventpoll java10508 root 398u FIFO0,6 6135319 pipe java10508 root 399w FIFO0,6 6135319 pipe I'm using FSDataInputStream and FSDataOutputStream, so this might be related to pipes? So, my questions are: 1) What happens these pipes/epolls to appear? 2) More important, how I can prevent their accumation and growth? Thanks in advance! 2009/6/21 Stas Oskin stas.os...@gmail.com Hi. I have HDFS client and HDFS datanode running on same machine. When I'm trying to access a dozen of files at once from the client, several times in a row, I'm starting to receive the following errors on client, and HDFS browse function. HDFS Client: Could not get block locations. Aborting... HDFS browse: Too many open files I can increase the maximum number of files that can opened, as I have it set to the default 1024, but would like to first solve the problem, as larger value just means it would run out of files again later on. So my questions are: 1) Does the HDFS datanode keeps any files opened, even after the HDFS client have already closed them? 2) Is it possible to find out, who keeps the opened files - datanode or client (so I could pin-point the source of the problem). Thanks in advance! -- Pro Hadoop, a book to guide you from beginner to hadoop mastery, http://www.amazon.com/dp/1430219424?tag=jewlerymall www.prohadoopbook.com a community for Hadoop Professionals -- Pro Hadoop, a book to guide you from beginner to hadoop mastery, http://www.amazon.com/dp/1430219424?tag=jewlerymall www.prohadoopbook.com a community for Hadoop Professionals -- Pro Hadoop, a book to guide you from beginner to hadoop mastery, http://www.amazon.com/dp/1430219424?tag=jewlerymall www.prohadoopbook.com a community for Hadoop Professionals
Re: Too many open files error, which gets resolved after some time
Furthermore, if for some reason it is required to dispose of any objects after others are GC'd, weak references and a weak reference queue will perform significantly better in throughput and latency - orders of magnitude better - than finalizers. On 6/21/09 9:32 AM, brian.lev...@nokia.com brian.lev...@nokia.com wrote: IMHO, you should never rely on finalizers to release scarce resources since you don't know when the finalizer will get called, if ever. -brian -Original Message- From: ext jason hadoop [mailto:jason.had...@gmail.com] Sent: Sunday, June 21, 2009 11:19 AM To: core-user@hadoop.apache.org Subject: Re: Too many open files error, which gets resolved after some time HDFS/DFS client uses quite a few file descriptors for each open file. Many application developers (but not the hadoop core) rely on the JVM finalizer methods to close open files. This combination, expecially when many HDFS files are open can result in very large demands for file descriptors for Hadoop clients. We as a general rule never run a cluster with nofile less that 64k, and for larger clusters with demanding applications have had it set 10x higher. I also believe there was a set of JVM versions that leaked file descriptors used for NIO in the HDFS core. I do not recall the exact details. On Sun, Jun 21, 2009 at 5:27 AM, Stas Oskin stas.os...@gmail.com wrote: Hi. After tracing some more with the lsof utility, and I managed to stop the growth on the DataNode process, but still have issues with my DFS client. It seems that my DFS client opens hundreds of pipes and eventpolls. Here is a small part of the lsof output: java10508 root 387w FIFO0,6 6142565 pipe java10508 root 388r FIFO0,6 6142565 pipe java10508 root 389u 0,100 6142566 eventpoll java10508 root 390u FIFO0,6 6135311 pipe java10508 root 391r FIFO0,6 6135311 pipe java10508 root 392u 0,100 6135312 eventpoll java10508 root 393r FIFO0,6 6148234 pipe java10508 root 394w FIFO0,6 6142570 pipe java10508 root 395r FIFO0,6 6135857 pipe java10508 root 396r FIFO0,6 6142570 pipe java10508 root 397r 0,100 6142571 eventpoll java10508 root 398u FIFO0,6 6135319 pipe java10508 root 399w FIFO0,6 6135319 pipe I'm using FSDataInputStream and FSDataOutputStream, so this might be related to pipes? So, my questions are: 1) What happens these pipes/epolls to appear? 2) More important, how I can prevent their accumation and growth? Thanks in advance! 2009/6/21 Stas Oskin stas.os...@gmail.com Hi. I have HDFS client and HDFS datanode running on same machine. When I'm trying to access a dozen of files at once from the client, several times in a row, I'm starting to receive the following errors on client, and HDFS browse function. HDFS Client: Could not get block locations. Aborting... HDFS browse: Too many open files I can increase the maximum number of files that can opened, as I have it set to the default 1024, but would like to first solve the problem, as larger value just means it would run out of files again later on. So my questions are: 1) Does the HDFS datanode keeps any files opened, even after the HDFS client have already closed them? 2) Is it possible to find out, who keeps the opened files - datanode or client (so I could pin-point the source of the problem). Thanks in advance! -- Pro Hadoop, a book to guide you from beginner to hadoop mastery, http://www.amazon.com/dp/1430219424?tag=jewlerymall www.prohadoopbook.com a community for Hadoop Professionals
