We had a similar issue before with Secondary Namenode failing with
2008-10-09 02:00:58,288 ERROR org.apache.hadoop.dfs.NameNode.Secondary: java.io.IOException: javax.security.auth.login.LoginException: Login failed: Cannot run program "whoami": java.io.IOException: error=12, Cannot allocate memory In our case, simply increasing the swap space fixed our problem. http://hudson.gotdns.com/wiki/display/HUDSON/IOException+Not+enough+spac e When checking with strace, it was failing at [pid 7927] clone(child_stack=0, flags=CLONE_CHILD_CLEARTID|CLONE_CHILD_SETTID|SIGCHLD, child_tidptr=0x4133c9f0) = -1 ENOMEM (Cannot allocate memory) Without CLONE_VM. In the clone man page, "If CLONE_VM is not set, the child process runs in a separate copy of the memory space of the calling process at the time of clone. Memory writes or file mappings/unmappings performed by one of the processes do not affect the other, as with fork(2). " Koji -----Original Message----- From: Brian Bockelman [mailto:[EMAIL PROTECTED] Sent: Tuesday, November 18, 2008 3:12 PM To: [email protected] Subject: Re: Cannot run program "bash": java.io.IOException: error=12, Cannot allocate memory Hey Xavier, Don't forget, the Linux kernel reserves the memory; current heap space is disregarded. How much heap space does your data node and tasktracker get? (PS: overcommit ratio is disregarded if overcommit_memory=2). You also have to remember that there is some overhead from the OS, the Java code cache, and a bit from running the JVM. Add at least 64 MB per JVM for code cache and running, and we get 400MB of memory left for the OS and any other process running. You're definitely running out of memory. Either allow overcommitting (which will mean Java is no longer locked out of swap) or reduce memory consumption. Brian On Nov 18, 2008, at 4:57 PM, Xavier Stevens wrote: > 1) It doesn't look like I'm out of memory but it is coming really > close. > 2) overcommit_memory is set to 2, overcommit_ratio = 100 > > As for the JVM, I am using Java 1.6. > > **Note of Interest**: The virtual memory I see allocated in top for > each > task is more than what I am specifying in the hadoop job/site configs. > > Currently each physical box has 16 GB of memory. I see the datanode > and > tasktracker using: > > RES VIRT > Datanode 145m 1408m > Tasktracker 206m 1439m > > When idle. > > So taking that into account I do 16000 MB - (1408+1439) MB which would > leave me with 13200 MB. In my old settings I was using 8 map tasks > so > 13200 / 8 = 1650 MB. > > My mapred.child.java.opts is -Xmx1536m which should leave me a little > head room. > > When running though I see some tasks reporting 1900m. > > > -Xavier > > > -----Original Message----- > From: Brian Bockelman [mailto:[EMAIL PROTECTED] > Sent: Tuesday, November 18, 2008 2:42 PM > To: [email protected] > Subject: Re: Cannot run program "bash": java.io.IOException: error=12, > Cannot allocate memory > > Hey Xavier, > > 1) Are you out of memory (dumb question, but doesn't hurt to ask...)? > What does Ganglia tell you about the node? > 2) Do you have /proc/sys/vm/overcommit_memory set to 2? > > Telling Linux not to overcommit memory on Java 1.5 JVMs can be very > problematic. Java 1.5 asks for min heap size + 1 GB of reserved, non- > swap memory on Linux systems by default. The 1GB of reserved, non- > swap > memory is used for the JIT to compile code; this bug wasn't fixed > until > later Java 1.5 updates. > > Brian > > On Nov 18, 2008, at 4:32 PM, Xavier Stevens wrote: > >> I'm still seeing this problem on a cluster using Hadoop 0.18.2. I >> tried >> dropping the max number of map tasks per node from 8 to 7. I still >> get >> the error although it's less frequent. But I don't get the error at >> all >> when using Hadoop 0.17.2. >> >> Anyone have any suggestions? >> >> >> -Xavier >> >> -----Original Message----- >> From: [EMAIL PROTECTED] On Behalf Of Edward J. Yoon >> Sent: Thursday, October 09, 2008 2:07 AM >> To: [email protected] >> Subject: Re: Cannot run program "bash": java.io.IOException: >> error=12, >> Cannot allocate memory >> >> Thanks Alexander!! >> >> On Thu, Oct 9, 2008 at 4:49 PM, Alexander Aristov >> <[EMAIL PROTECTED]> wrote: >>> I received such errors when I overloaded data nodes. You may >>> increase >>> swap space or run less tasks. >>> >>> Alexander >>> >>> 2008/10/9 Edward J. Yoon <[EMAIL PROTECTED]> >>> >>>> Hi, >>>> >>>> I received below message. Can anyone explain this? >>>> >>>> 08/10/09 11:53:33 INFO mapred.JobClient: Task Id : >>>> task_200810081842_0004_m_000000_0, Status : FAILED >>>> java.io.IOException: Cannot run program "bash": >>>> java.io.IOException: >>>> error=12, Cannot allocate memory >>>> at java.lang.ProcessBuilder.start(ProcessBuilder.java:459) >>>> at org.apache.hadoop.util.Shell.runCommand(Shell.java:149) >>>> at org.apache.hadoop.util.Shell.run(Shell.java:134) >>>> at org.apache.hadoop.fs.DF.getAvailable(DF.java:73) >>>> at >>>> >> org.apache.hadoop.fs.LocalDirAllocator >> $AllocatorPerContext.getLocalPathF >> orWrite(LocalDirAllocator.java:296) >>>> at >>>> >> org >> .apache.hadoop.fs.LocalDirAllocator.getLocalPathForWrite(LocalDirAllo >> cator.java:124) >>>> at >>>> >> org >> .apache.hadoop.mapred.MapOutputFile.getSpillFileForWrite(MapOutputFil >> e.java:107) >>>> at >>>> >> org.apache.hadoop.mapred.MapTask >> $MapOutputBuffer.sortAndSpill(MapTask.ja >> va:734) >>>> at >>>> >> org.apache.hadoop.mapred.MapTask$MapOutputBuffer.flush(MapTask.java: >> 694) >>>> at org.apache.hadoop.mapred.MapTask.run(MapTask.java:220) >>>> at >>>> org.apache.hadoop.mapred.TaskTracker$Child.main(TaskTracker.java: >>>> 2124 >>>> ) Caused by: java.io.IOException: java.io.IOException: error=12, >>>> Cannot allocate memory >>>> at java.lang.UNIXProcess.<init>(UNIXProcess.java:148) >>>> at java.lang.ProcessImpl.start(ProcessImpl.java:65) >>>> at java.lang.ProcessBuilder.start(ProcessBuilder.java:452) >>>> ... 10 more >>>> >>>> -- >>>> Best regards, Edward J. Yoon >>>> [EMAIL PROTECTED] >>>> http://blog.udanax.org >>>> >>> >>> >>> >>> -- >>> Best Regards >>> Alexander Aristov >>> >> >> >> >> -- >> Best regards, Edward J. Yoon >> [EMAIL PROTECTED] >> http://blog.udanax.org >> > >
