A fatal error has been detected by the Java Runtime Environment: SIGSEGV, libjvm

Question

Hi and thanks for reading,

I have the following error while running my program and can't figure out what the solution would be. I also looked at all the topics with a similar error here, but could not resolve my issue. Here the error:

# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007f0b024734cd, pid=21947, tid=139676677560592
#
# JRE version: 6.0_15-b03
# Java VM: Java HotSpot(TM) 64-Bit Server VM (14.1-b02 mixed mode linux-amd64 )
# Problematic frame:
# V  [libjvm.so+0x5df4cd]

My program takes some serialized objects and deserializes them, this is where the problem occurs. The strange thing however is, that the same code with the same objects to deserialize works perfectly fine on other machines with the same hardware, OS, etc. (I'm not sure if this might be hardware related, but I guess its not).

Here is the code, that I'm executing in Java:

        FileInputStream f_in = new FileInputStream(path+"/"+docNum+"/"+docNum+"Part.data");
        ObjectInputStream obj_in = new ObjectInputStream (f_in);
        Object obj = obj_in.readObject();
    //ERROR
        FileInputStream f_in5 = new FileInputStream(path+"/"+docNum+"/"+docNum+"Part_clustIdx_pairClustIdxs_.data");
        ObjectInputStream obj_in5 = new ObjectInputStream (f_in5);      
        Object clustIdx_pairClustIdxs = obj_in5.readObject();

        FileInputStream f_in4 = new FileInputStream(path+"/"+docNum+"/"+docNum+"Part_pairClustIdxs_pairPartRootNodeIds_.data");
        ObjectInputStream obj_in4 = new ObjectInputStream (f_in4);      
        Object pairClustIdxs_pairPartRootNodeIds = obj_in4.readObject();

        FileInputStream f_in3 = new FileInputStream(path+"/"+docNum+"/"+docNum+"Part_clustIdx_partRootNodeIds_.data");
        ObjectInputStream obj_in3 = new ObjectInputStream (f_in3);      
        Object clustIdx_partRootNodeIds = obj_in3.readObject();

        FileInputStream f_in2 = new FileInputStream(path+"/"+docNum+"/"+docNum+"Part_rootNodeId_Part.data");
        ObjectInputStream obj_in2 = new ObjectInputStream (f_in2);
        Object rootNodeId_Part = obj_in2.readObject();  

        Part part = (Part) obj;
        part.rootNodeId_part_ = (Map<String, Part>) rootNodeId_Part;
        part.clustIdx_partRootNodeIds_ = (Map<Integer,TreeSet<String>> ) clustIdx_partRootNodeIds;
        part.pairClustIdxs_pairPartRootNodeIds_ = (Map<Pair<Integer,Integer>,Set<Pair<String,String>>> ) pairClustIdxs_pairPartRootNodeIds;
        part.clustIdx_pairClustIdxs_ = (Map<Integer,Set<Pair<Integer,Integer>>> ) clustIdx_pairClustIdxs;   

The error occurs after the first deserialization block. However, if I interchange it with any of the following blocks, the error is still in the second deserialization block. Again, the same code, with the same data works just fine on other machines. I tried reinstalling and updating Java, but it didn't help.

Here the logfile of the error:

#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007f0b024734cd, pid=21947, tid=139676677560592
#
# JRE version: 6.0_15-b03
# Java VM: Java HotSpot(TM) 64-Bit Server VM (14.1-b02 mixed mode linux-amd64 )
# Problematic frame:
# V  [libjvm.so+0x5df4cd]
#
# If you would like to submit a bug report, please visit:
#   http://java.sun.com/webapps/bugreport/crash.jsp
#

---------------  T H R E A D  ---------------

Current thread (0x00000000408c9000):  GCTaskThread [stack: 0x00007f0902afd000,0x00007f0902bfe000] [id=21951]

siginfo:si_signo=SIGSEGV: si_errno=0, si_code=128 (), si_addr=0x0000000000000000

Registers:
RAX=0x0000000000000001, RBX=0x00007f09184091a8, RCX=0x00007f0b02748cb0, RDX=0x000600007f090486
RSP=0x00007f0902bfce00, RBP=0x00007f0902bfce70, RSI=0x00007f0a808d4ed2, RDI=0x000600007f090496
R8 =0x0000000000000001, R9 =0x00000000aa10002f, R10=0x00007f09184091a8, R11=0x00007f09027a8218
R12=0x0708000000000000, R13=0x0000000000000000, R14=0x00007f0a808d4ed2, R15=0x0000000040914ef0
RIP=0x00007f0b024734cd, EFL=0x0000000000010246, CSGSFS=0x0000000000000033, ERR=0x0000000000000000
  TRAPNO=0x000000000000000d

Top of Stack: (sp=0x00007f0902bfce00)
0x00007f0902bfce00:   0000000000000400 00000000408c06a0
0x00007f0902bfce10:   0000000000000005 01007f090c6663b8
0x00007f0902bfce20:   00007f0902bfce50 00007f0b024741d0
0x00007f0902bfce30:   00007f0918408028 0000000000257071
0x00007f0902bfce40:   000000000025703f 00007f09184091a8
0x00007f0902bfce50:   0000000040914fa0 0000000000000000
0x00007f0902bfce60:   0000000000000001 00007f0902bfcefc
0x00007f0902bfce70:   00007f0902bfce90 00007f0b02473f50
0x00007f0902bfce80:   0000000000000001 0000000040914ef0
0x00007f0902bfce90:   00007f0902bfced0 00007f0b02473092
0x00007f0902bfcea0:   000000004095dc20 00007f09184091a8
0x00007f0902bfceb0:   0000000040914ef0 0000000000000002
0x00007f0902bfcec0:   00007f0b0275d4e0 000000004095dc20
0x00007f0902bfced0:   00007f0902bfcf30 00007f0b0247672d
0x00007f0902bfcee0:   00007f0902bfcef0 00007f0902bfcf00
0x00007f0902bfcef0:   00007f0902bfcf30 6cfb9568021cd407
0x00007f0902bfcf00:   00007f0ab4e04578 00007f0b027492a4
0x00007f0902bfcf10:   000000004095dc20 00000000408c9000
0x00007f0902bfcf20:   00007f0b025b0506 0000000000000000
0x00007f0902bfcf30:   00007f0902bfd030 00007f0b021ce67a
0x00007f0902bfcf40:   00007f0902bfcf80 00007f0902bfcf58
0x00007f0902bfcf50:   00007f0b02760f40 0000000000000000
0x00007f0902bfcf60:   00000000408c91e0 00000000408c9210
0x00007f0902bfcf70:   00000000408c9220 00000000408c95f8
0x00007f0902bfcf80:   00000000408c9000 00000000408c9600
0x00007f0902bfcf90:   00000000408c9630 00000000408c9640
0x00007f0902bfcfa0:   00000000408c9a18 00007f0902bfcfd0
0x00007f0902bfcfb0:   00000000408c91e0 00000000408c9210
0x00007f0902bfcfc0:   00000000408c9220 00000000408c95f8
0x00007f0902bfcfd0:   00000000408c9000 00000000408c9600
0x00007f0902bfcfe0:   00000000408c9630 00000000408c9640
0x00007f0902bfcff0:   00000000408c9a18 00000000408c9a20 

Instructions: (pc=0x00007f0b024734cd)
0x00007f0b024734bd:   00 48 8d 14 f5 00 00 00 00 48 03 13 48 8d 7a 10
0x00007f0b024734cd:   8b 5f 08 89 d8 c1 f8 03 85 db 0f 8e cb 05 00 00 

Stack: [0x00007f0902afd000,0x00007f0902bfe000],  sp=0x00007f0902bfce00,  free space=1023k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
V  [libjvm.so+0x5df4cd]
V  [libjvm.so+0x5dff50]
V  [libjvm.so+0x5df092]
V  [libjvm.so+0x5e272d]
V  [libjvm.so+0x33a67a]
V  [libjvm.so+0x5971af]


---------------  P R O C E S S  ---------------

Java Threads: ( => current thread )
  0x0000000040946800 JavaThread "Low Memory Detector" daemon [_thread_blocked, id=21959, stack(0x00007f0902020000,0x00007f0902121000)]
  0x0000000040942800 JavaThread "CompilerThread1" daemon [_thread_blocked, id=21958, stack(0x00007f0902121000,0x00007f0902222000)]
  0x0000000040940000 JavaThread "CompilerThread0" daemon [_thread_blocked, id=21957, stack(0x00007f0902222000,0x00007f0902323000)]
  0x000000004093d800 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=21956, stack(0x00007f0902323000,0x00007f0902424000)]
  0x000000004091f800 JavaThread "Finalizer" daemon [_thread_blocked, id=21955, stack(0x00007f0902463000,0x00007f0902564000)]
  0x000000004091d800 JavaThread "Reference Handler" daemon [_thread_blocked, id=21954, stack(0x00007f0902564000,0x00007f0902665000)]
  0x00000000408bb000 JavaThread "main" [_thread_blocked, id=21948, stack(0x00007f0b01b0f000,0x00007f0b01c10000)]

Other Threads:
  0x0000000040917000 VMThread [stack: 0x00007f0902665000,0x00007f0902766000] [id=21953]
  0x0000000040949000 WatcherThread [stack: 0x00007f0901f1f000,0x00007f0902020000] [id=21960]

=>0x00000000408c9000 (exited) GCTaskThread [stack: 0x00007f0902afd000,0x00007f0902bfe000] [id=21951]

VM state:at safepoint (normal execution)

VM Mutex/Monitor currently owned by a thread:  ([mutex/lock_event])
[0x00000000408b7c90] Threads_lock - owner thread: 0x0000000040917000
[0x00000000408b8190] Heap_lock - owner thread: 0x00000000408bb000

Heap
 PSYoungGen      total 1792000K, used 1536000K [0x00007f0a571c0000, 0x00007f0ad41c0000, 0x00007f0afdc60000)
  eden space 1536000K, 100% used [0x00007f0a571c0000,0x00007f0ab4dc0000,0x00007f0ab4dc0000)
  from space 256000K, 0% used [0x00007f0ac47c0000,0x00007f0ac47c0000,0x00007f0ad41c0000)
  to   space 256000K, 99% used [0x00007f0ab4dc0000,0x00007f0ac47b8068,0x00007f0ac47c0000)
 PSOldGen        total 4096000K, used 237896K [0x00007f0909c60000, 0x00007f0a03c60000, 0x00007f0a571c0000)
  object space 4096000K, 5% used [0x00007f0909c60000,0x00007f09184b2028,0x00007f0a03c60000)
 PSPermGen       total 21248K, used 3845K [0x00007f0904860000, 0x00007f0905d20000, 0x00007f0909c60000)
  object space 21248K, 18% used [0x00007f0904860000,0x00007f0904c21718,0x00007f0905d20000)

Dynamic libraries:
40000000-40009000 r-xp 00000000 08:01 859892                             /usr/lib/jvm/java-6-sun-1.6.0.15/jre/bin/java
40108000-4010a000 rwxp 00008000 08:01 859892                             /usr/lib/jvm/java-6-sun-1.6.0.15/jre/bin/java
408b2000-40d42000 rwxp 00000000 00:00 0                                  [heap]
7f08fc000000-7f08fc4aa000 rwxp 00000000 00:00 0 
7f08fc4aa000-7f0900000000 ---p 00000000 00:00 0 
7f0901f1f000-7f0901f20000 ---p 00000000 00:00 0 
7f0901f20000-7f0902020000 rwxp 00000000 00:00 0 
7f0902020000-7f0902023000 ---p 00000000 00:00 0 
7f0902023000-7f0902121000 rwxp 00000000 00:00 0 
7f0902121000-7f0902124000 ---p 00000000 00:00 0 
7f0902124000-7f0902222000 rwxp 00000000 00:00 0 
7f0902222000-7f0902225000 ---p 00000000 00:00 0 
7f0902225000-7f0902323000 rwxp 00000000 00:00 0 
7f0902323000-7f0902326000 ---p 00000000 00:00 0 
7f0902326000-7f0902424000 rwxp 00000000 00:00 0 
7f0902424000-7f0902463000 r-xp 00000000 08:01 688275                     /usr/lib/locale/en_US.utf8/LC_CTYPE
7f0902463000-7f0902466000 ---p 00000000 00:00 0 
7f0902466000-7f0902564000 rwxp 00000000 00:00 0 
7f0902564000-7f0902567000 ---p 00000000 00:00 0 
7f0902567000-7f0902665000 rwxp 00000000 00:00 0 
7f0902665000-7f0902666000 ---p 00000000 00:00 0 
7f0902666000-7f090283e000 rwxp 00000000 00:00 0 
7f090283e000-7f09029d4000 r-xs 02fb3000 08:01 803613                     /usr/lib/jvm/java-6-sun-1.6.0.15/jre/lib/rt.jar
7f09029d4000-7f09029fc000 rwxp 00000000 00:00 0 
7f09029fc000-7f09029fd000 ---p 00000000 00:00 0 
7f09029fd000-7f0902afd000 rwxp 00000000 00:00 0 
7f0902afd000-7f0902afe000 ---p 00000000 00:00 0 
7f0902afe000-7f0902bfe000 rwxp 00000000 00:00 0 
7f0902bfe000-7f0902bff000 ---p 00000000 00:00 0 
7f0902bff000-7f0902cff000 rwxp 00000000 00:00 0 
7f0902cff000-7f0902d00000 ---p 00000000 00:00 0 
7f0902d00000-7f0902e0b000 rwxp 00000000 00:00 0 
7f0902e0b000-7f0902e2a000 rwxp 00000000 00:00 0 
7f0902e2a000-7f09035fa000 rwxp 00000000 00:00 0 
7f09035fa000-7f0903895000 rwxp 00000000 00:00 0 
7f0903895000-7f09038a0000 rwxp 00000000 00:00 0 
7f09038a0000-7f09038bf000 rwxp 00000000 00:00 0 
7f09038bf000-7f090408f000 rwxp 00000000 00:00 0 
7f090408f000-7f0904329000 rwxp 00000000 00:00 0 
7f0904329000-7f0904712000 rwxp 00000000 00:00 0 
7f0904712000-7f090485f000 rwxp 00000000 00:00 0 
7f090485f000-7f0905d20000 rwxp 00000000 00:00 0 
7f0905d20000-7f0909c60000 rwxp 00000000 00:00 0 
7f0909c60000-7f0a03c60000 rwxp 00000000 00:00 0 
7f0a03c60000-7f0a571c0000 rwxp 00000000 00:00 0 
7f0a571c0000-7f0ad41c0000 rwxp 00000000 00:00 0 
7f0ad41c0000-7f0afdc60000 rwxp 00000000 00:00 0 
7f0afdc6f000-7f0afdedf000 rwxp 00000000 00:00 0 
7f0afdedf000-7f0b00c6f000 rwxp 00000000 00:00 0 
7f0b00c6f000-7f0b00c7d000 r-xp 00000000 08:01 860090                     /usr/lib/jvm/java-6-sun-1.6.0.15/jre/lib/amd64/libzip.so
7f0b00c7d000-7f0b00d7f000 ---p 0000e000 08:01 860090                     /usr/lib/jvm/java-6-sun-1.6.0.15/jre/lib/amd64/libzip.so
7f0b00d7f000-7f0b00d82000 rwxp 00010000 08:01 860090                     /usr/lib/jvm/java-6-sun-1.6.0.15/jre/lib/amd64/libzip.so
7f0b00d82000-7f0b00d83000 rwxp 00000000 00:00 0 
7f0b00d83000-7f0b00d8f000 r-xp 00000000 08:01 1251026                    /lib/libnss_files-2.10.1.so
7f0b00d8f000-7f0b00f8e000 ---p 0000c000 08:01 1251026                    /lib/libnss_files-2.10.1.so
7f0b00f8e000-7f0b00f8f000 r-xp 0000b000 08:01 1251026                    /lib/libnss_files-2.10.1.so
7f0b00f8f000-7f0b00f90000 rwxp 0000c000 08:01 1251026                    /lib/libnss_files-2.10.1.so
7f0b00f90000-7f0b00f9a000 r-xp 00000000 08:01 1251036                    /lib/libnss_nis-2.10.1.so
7f0b00f9a000-7f0b01199000 ---p 0000a000 08:01 1251036                    /lib/libnss_nis-2.10.1.so
7f0b01199000-7f0b0119a000 r-xp 00009000 08:01 1251036                    /lib/libnss_nis-2.10.1.so
7f0b0119a000-7f0b0119b000 rwxp 0000a000 08:01 1251036                    /lib/libnss_nis-2.10.1.so
7f0b0119b000-7f0b011a2000 r-xp 00000000 08:01 1251022                    /lib/libnss_compat-2.10.1.so
7f0b011a2000-7f0b013a2000 ---p 00007000 08:01 1251022                    /lib/libnss_compat-2.10.1.so
7f0b013a2000-7f0b013a3000 r-xp 00007000 08:01 1251022                    /lib/libnss_compat-2.10.1.so
7f0b013a3000-7f0b013a4000 rwxp 00008000 08:01 1251022                    /lib/libnss_compat-2.10.1.so
7f0b013a4000-7f0b013ab000 r-xp 00000000 08:01 860092                     /usr/lib/jvm/java-6-sun-1.6.0.15/jre/lib/amd64/native_threads/libhpi.so
7f0b013ab000-7f0b014ac000 ---p 00007000 08:01 860092                     /usr/lib/jvm/java-6-sun-1.6.0.15/jre/lib/amd64/native_threads/libhpi.so
7f0b014ac000-7f0b014ae000 rwxp 00008000 08:01 860092                     /usr/lib/jvm/java-6-sun-1.6.0.15/jre/lib/amd64/native_threads/libhpi.so
7f0b014ae000-7f0b014af000 rwxp 00000000 00:00 0 
7f0b014af000-7f0b014c5000 r-xp 00000000 08:01 1251020                    /lib/libnsl-2.10.1.so
7f0b014c5000-7f0b016c5000 ---p 00016000 08:01 1251020                    /lib/libnsl-2.10.1.so
7f0b016c5000-7f0b016c6000 r-xp 00016000 08:01 1251020                    /lib/libnsl-2.10.1.so
7f0b016c6000-7f0b016c7000 rwxp 00017000 08:01 1251020                    /lib/libnsl-2.10.1.so
7f0b016c7000-7f0b016c9000 rwxp 00000000 00:00 0 
7f0b016c9000-7f0b016f2000 r-xp 00000000 08:01 860157                     /usr/lib/jvm/java-6-sun-1.6.0.15/jre/lib/amd64/libjava.so
7f0b016f2000-7f0b017f1000 ---p 00029000 08:01 860157                     /usr/lib/jvm/java-6-sun-1.6.0.15/jre/lib/amd64/libjava.so
7f0b017f1000-7f0b017f8000 rwxp 00028000 08:01 860157                     /usr/lib/jvm/java-6-sun-1.6.0.15/jre/lib/amd64/libjava.so
7f0b017f8000-7f0b01805000 r-xp 00000000 08:01 860082                     /usr/lib/jvm/java-6-sun-1.6.0.15/jre/lib/amd64/libverify.so
7f0b01805000-7f0b01904000 ---p 0000d000 08:01 860082                     /usr/lib/jvm/java-6-sun-1.6.0.15/jre/lib/amd64/libverify.so
7f0b01904000-7f0b01907000 rwxp 0000c000 08:01 860082                     /usr/lib/jvm/java-6-sun-1.6.0.15/jre/lib/amd64/libverify.so
7f0b01907000-7f0b0190e000 r-xp 00000000 08:01 1251065                    /lib/librt-2.10.1.so
7f0b0190e000-7f0b01b0d000 ---p 00007000 08:01 1251065                    /lib/librt-2.10.1.so
7f0b01b0d000-7f0b01b0e000 r-xp 00006000 08:01 1251065                    /lib/librt-2.10.1.so
7f0b01b0e000-7f0b01b0f000 rwxp 00007000 08:01 1251065                    /lib/librt-2.10.1.so
7f0b01b0f000-7f0b01b12000 ---p 00000000 00:00 0 
7f0b01b12000-7f0b01c10000 rwxp 00000000 00:00 0 
7f0b01c10000-7f0b01c92000 r-xp 00000000 08:01 1251013                    /lib/libm-2.10.1.so
7f0b01c92000-7f0b01e92000 ---p 00082000 08:01 1251013                    /lib/libm-2.10.1.so
7f0b01e92000-7f0b01e93000 r-xp 00082000 08:01 1251013                    /lib/libm-2.10.1.so
7f0b01e93000-7f0b01e94000 rwxp 00083000 08:01 1251013                    /lib/libm-2.10.1.so
7f0b01e94000-7f0b025f2000 r-xp 00000000 08:01 860164                     /usr/lib/jvm/java-6-sun-1.6.0.15/jre/lib/amd64/server/libjvm.so
7f0b025f2000-7f0b026f1000 ---p 0075e000 08:01 860164                     /usr/lib/jvm/java-6-sun-1.6.0.15/jre/lib/amd64/server/libjvm.so
7f0b026f1000-7f0b02869000 rwxp 0075d000 08:01 860164                     /usr/lib/jvm/java-6-sun-1.6.0.15/jre/lib/amd64/server/libjvm.so
7f0b02869000-7f0b028a7000 rwxp 00000000 00:00 0 
7f0b028a7000-7f0b02a0d000 r-xp 00000000 08:01 1250971                    /lib/libc-2.10.1.so
7f0b02a0d000-7f0b02c0c000 ---p 00166000 08:01 1250971                    /lib/libc-2.10.1.so
7f0b02c0c000-7f0b02c10000 r-xp 00165000 08:01 1250971                    /lib/libc-2.10.1.so
7f0b02c10000-7f0b02c11000 rwxp 00169000 08:01 1250971                    /lib/libc-2.10.1.so
7f0b02c11000-7f0b02c16000 rwxp 00000000 00:00 0 
7f0b02c16000-7f0b02c18000 r-xp 00000000 08:01 1250985                    /lib/libdl-2.10.1.so
7f0b02c18000-7f0b02e18000 ---p 00002000 08:01 1250985                    /lib/libdl-2.10.1.so
7f0b02e18000-7f0b02e19000 r-xp 00002000 08:01 1250985                    /lib/libdl-2.10.1.so
7f0b02e19000-7f0b02e1a000 rwxp 00003000 08:01 1250985                    /lib/libdl-2.10.1.so
7f0b02e1a000-7f0b02e31000 r-xp 00000000 08:01 1251058                    /lib/libpthread-2.10.1.so
7f0b02e31000-7f0b03030000 ---p 00017000 08:01 1251058                    /lib/libpthread-2.10.1.so
7f0b03030000-7f0b03031000 r-xp 00016000 08:01 1251058                    /lib/libpthread-2.10.1.so
7f0b03031000-7f0b03032000 rwxp 00017000 08:01 1251058                    /lib/libpthread-2.10.1.so
7f0b03032000-7f0b03036000 rwxp 00000000 00:00 0 
7f0b03036000-7f0b03055000 r-xp 00000000 08:01 1250947                    /lib/ld-2.10.1.so
7f0b03069000-7f0b03073000 rwxp 00000000 00:00 0 
7f0b03073000-7f0b03129000 rwxp 00000000 00:00 0 
7f0b03129000-7f0b0312b000 rwxp 00000000 00:00 0 
7f0b0312b000-7f0b03132000 r-xp 00000000 08:01 860069                     /usr/lib/jvm/java-6-sun-1.6.0.15/jre/lib/amd64/jli/libjli.so
7f0b03132000-7f0b03233000 ---p 00007000 08:01 860069                     /usr/lib/jvm/java-6-sun-1.6.0.15/jre/lib/amd64/jli/libjli.so
7f0b03233000-7f0b03235000 rwxp 00008000 08:01 860069                     /usr/lib/jvm/java-6-sun-1.6.0.15/jre/lib/amd64/jli/libjli.so
7f0b03235000-7f0b03236000 rwxp 00000000 00:00 0 
7f0b0323d000-7f0b03240000 r-xs 00033000 08:06 23371793                   /data/evgeny/usp/jars/pusp08.jar
7f0b03240000-7f0b03247000 r-xs 00000000 08:01 956835                     /usr/lib/gconv/gconv-modules.cache
7f0b03247000-7f0b0324f000 rwxs 00000000 08:01 531447                     /tmp/hsperfdata_evgeny/21947
7f0b0324f000-7f0b03250000 rwxp 00000000 00:00 0 
7f0b03250000-7f0b03251000 ---p 00000000 00:00 0 
7f0b03251000-7f0b03254000 rwxp 00000000 00:00 0 
7f0b03254000-7f0b03255000 r-xp 0001e000 08:01 1250947                    /lib/ld-2.10.1.so
7f0b03255000-7f0b03256000 rwxp 0001f000 08:01 1250947                    /lib/ld-2.10.1.so
7fffb0ea5000-7fffb0eba000 rwxp 00000000 00:00 0                          [stack]
7fffb0f10000-7fffb0f11000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]

VM Arguments:
jvm_args: -Xms6000m -Xmx8000m -Dfile.encoding=UTF8 -verbose:gc 
java_command: usp.semantic.ParseCreateAgenda /data/evgeny/usp/serialized/pusp_abstracts /data/evgeny/usp/logs 3200 13 16 8 200 5 1
Launcher Type: SUN_STANDARD

Environment Variables:
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
LD_LIBRARY_PATH=/usr/lib/jvm/java-6-sun-1.6.0.15/jre/lib/amd64/server:/usr/lib/jvm/java-6-sun-1.6.0.15/jre/lib/amd64:/usr/lib/jvm/java-6-sun-1.6.0.15/jre/../lib/amd64
SHELL=/bin/sh

Signal Handlers:
SIGSEGV: [libjvm.so+0x6bdd00], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGBUS: [libjvm.so+0x6bdd00], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGFPE: [libjvm.so+0x594ed0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGPIPE: [libjvm.so+0x594ed0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGXFSZ: [libjvm.so+0x594ed0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGILL: [libjvm.so+0x594ed0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGUSR1: SIG_DFL, sa_mask[0]=0x00000000, sa_flags=0x00000000
SIGUSR2: [libjvm.so+0x597690], sa_mask[0]=0x00000000, sa_flags=0x10000004
SIGHUP: [libjvm.so+0x5973e0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGINT: [libjvm.so+0x5973e0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGTERM: [libjvm.so+0x5973e0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGQUIT: [libjvm.so+0x5973e0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004


---------------  S Y S T E M  ---------------

OS:squeeze/sid

uname:Linux 2.6.31-14-generic #48-Ubuntu SMP Fri Oct 16 14:05:01 UTC 2009 x86_64
libc:glibc 2.10.1 NPTL 2.10.1 
rlimit: STACK 8192k, CORE 0k, NPROC infinity, NOFILE 1024, AS infinity
load average:0.76 0.19 0.06

CPU:total 4 (4 cores per cpu, 1 threads per core) family 6 model 23 stepping 10, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1

Memory: 4k page, physical 8194680k(4274500k free), swap 9767480k(9755964k free)

vm_info: Java HotSpot(TM) 64-Bit Server VM (14.1-b02) for linux-amd64 JRE (1.6.0_15-b03), built on Jul  2 2009 15:26:16 by "java_re" with gcc 3.2.2 (SuSE Linux)

time: Wed Jun 22 10:52:33 2011
elapsed time: 17 seconds

Thanks for your help!

As suggested by the posters, it does sound like a hardware problem. I have changed the memory parameters of java and after some changes the program stops at different parts. I will investigate the diagnostics proposed below. I'll give an update as soon as I've done that.

@egridasov, I tried JRE 1.6.0_26, but get the same problem:

#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007f51c12048e1, pid=29200, tid=139989005547792
#
# JRE version: 6.0_26-b03
# Java VM: Java HotSpot(TM) 64-Bit Server VM (20.1-b02 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# V  [libjvm.so+0x7608e1]  PSPromotionManager::copy_to_survivor_space(oopDesc*)+0x1f1
#
# If you would like to submit a bug report, please visit:
#   http://java.sun.com/webapps/bugreport/crash.jsp
#

---------------  T H R E A D  ---------------

Current thread (0x00000000418da800):  GCTaskThread [stack: 0x00007f51bae2b000,0x00007f51baf2c000] [id=29202]

siginfo:si_signo=SIGSEGV: si_errno=0, si_code=128 (), si_addr=0x0000000000000000
Register to memory mapping:

RAX=0x0000000000000001 is an unknown value
RBX=0x0000000606e01eb8 is an oop
[[I 
 - klass: 'java/lang/Object'[]
 - length: 2
RCX=0x0000000000000003 is an unknown value
RDX=0x000000060ff12000 is an oop

[error occurred during error reporting (printing register info), id 0xb]

Stack: [0x00007f51bae2b000,0x00007f51baf2c000],  sp=0x00007f51baf2ae90,  free space=1023k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
V  [libjvm.so+0x7608e1]  PSPromotionManager::copy_to_survivor_space(oopDesc*)+0x1f1
V  [libjvm.so+0x76114d]  void PSScavenge::copy_and_push_safe_barrier<unsigned>(PSPromotionManager*, unsigned*)+0xcd
V  [libjvm.so+0x7605bf]  PSPromotionManager::drain_stacks_depth(bool)+0xdf
V  [libjvm.so+0x76382e]  StealTask::do_it(GCTaskManager*, unsigned)+0x2e
V  [libjvm.so+0x466efa]  GCTaskThread::run()+0x16a
V  [libjvm.so+0x710adf]  java_start(Thread*)+0x13f


---------------  P R O C E S S  ---------------

Java Threads: ( => current thread )
  0x00007f51b406f800 JavaThread "Low Memory Detector" daemon [_thread_blocked, id=29212, stack(0x00007f51b9ce9000,0x00007f51b9dea000)]
  0x00007f51b406d000 JavaThread "C2 CompilerThread1" daemon [_thread_blocked, id=29211, stack(0x00007f51b9dea000,0x00007f51b9eeb000)]
  0x00007f51b406a000 JavaThread "C2 CompilerThread0" daemon [_thread_blocked, id=29210, stack(0x00007f51b9eeb000,0x00007f51b9fec000)]
  0x00007f51b4068000 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=29209, stack(0x00007f51b9fec000,0x00007f51ba0ed000)]
  0x00007f51b404c800 JavaThread "Finalizer" daemon [_thread_blocked, id=29208, stack(0x00007f51ba12c000,0x00007f51ba22d000)]
  0x00007f51b404a800 JavaThread "Reference Handler" daemon [_thread_blocked, id=29207, stack(0x00007f51ba22d000,0x00007f51ba32e000)]
  0x00000000418c7800 JavaThread "main" [_thread_blocked, id=29201, stack(0x00007f51c071f000,0x00007f51c0820000)]

Other Threads:
  0x00007f51b4044000 VMThread [stack: 0x00007f51ba32e000,0x00007f51ba42f000] [id=29206]
  0x00007f51b407a800 WatcherThread [stack: 0x00007f51b9be8000,0x00007f51b9ce9000] [id=29213]

=>0x00000000418da800 (exited) GCTaskThread [stack: 0x00007f51bae2b000,0x00007f51baf2c000] [id=29202]

VM state:at safepoint (normal execution)

VM Mutex/Monitor currently owned by a thread:  ([mutex/lock_event])
[0x00000000418c4530] Threads_lock - owner thread: 0x00007f51b4044000
[0x00000000418c4a30] Heap_lock - owner thread: 0x00000000418c7800

Answer 1

1.Set the following Environment Property on your active Shell. - open bash terminal and type in:

  $ export LD_BIND_NOW=1

2. Re-Run the Jar or Java File

Note: for superuser in bash type su and press enter

Answer 2

Generally if something works on various computers but fails on only one computer, then there's something wrong with that computer. Here are a few things to check:
(1) Are you running the same stuff on that computer -- OS including patches, etc.
(2) Does the computer report problems? Where to look depends on the OS, but it looks like you're using linux, so check syslog
(3) Run hardware diagnostics, e.g. the ones recommended here. Start with memory and disk checks in particular.

If you can't turn up any issues, then search for a similar issue in the bug parade for whichever VM you're using. Unfortunately if you're already on the latest version of the VM, then you won't necessarily find a fix.

Finally, one more option is simply to try another VM -- e.g. OpenJDK or JRockit, instead of Oracle's standard.

Answer 3

Here is your relief for the problem :

I have a problem of running different versions of STS this morning, the application crash with the similar way as the question did.

Excerpt of my log file.

A fatal error has been detected by the Java Runtime Environment:
#a
#  SIGSEGV (0xb) at pc=0x00007f459db082a1, pid=4577, tid=139939015632640
#
# JRE version: 6.0_30-b12
# Java VM: Java HotSpot(TM) 64-Bit Server VM 
(20.5-b03 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# C  [libsoup-2.4.so.1+0x6c2a1]  short+0x11

note that exception occured at # C [libsoup-2.4.so.1+0x6c2a1] short+0x11

Okay then little below the line:

R9 =0x00007f461829e550: <offset 0xa85550> in /usr/share/java/jdk1.6.0_30/jre/lib/amd64/server/libjvm.so at 0x00007f4617819000
R10=0x00007f461750f7c0 is pointing into the stack for thread: 0x00007f4610008000
R11=0x00007f459db08290: soup_session_feature_detach+0 in /usr/lib/x86_64-linux-gnu/libsoup-2.4.so.1 at 0x00007f459da9c000
R12=0x0000000000000000 is an unknown value
R13=0x000000074404c840 is an oop
{method} 

This line tells you where the actual bug or crash is to investigate more on this crash issue please use below links to see more, but let's continue the crash investigation and how I resolved it and the novelty of this bug :)

links are :

a fATAL ERROR JAVA THIS ONE IS GREAT LOTS OF USER!

a fATAL ERROR JAVA 2

Okay, after that here's what I found out to casue this case and why it happens as general advise.

1. Most of the time, check that if you have installed, updated recently on Ubunu and Windows there are libraries like libsoup in linux which were the casuse of my crash.

2. Check also for a new hardware problem and try to investigate the Logfile which STS or Java generated and also syslog in linux by

   tail - f /var/lib/messages or some other file
   

Then by carfully looking at those files the one you have the crash log for ... you can really solve the issue as follows:

sudo unlink /usr/lib/i386-linux-gnu/libsoup-2.4.so.1

or

sudo unlink /usr/lib/x86_64-linux-gnu/libsoup-2.4.so.1

Done !! Cheers!!