ShowJ: export of large SetOfParticles fails

[pconesa]

No description provided.

[pconesa]

This happens when exporting an .xmd from the ShowJ.

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

SIGSEGV (0xb) at pc=0x00007f6a175f2c69, pid=76694, tid=140092772443904

JRE version: OpenJDK Runtime Environment (7.0_79-b14) (build 1.7.0_79-b14)
Java VM: OpenJDK 64-Bit Server VM (24.79-b02 mixed mode linux-amd64 compressed oops)
Derivative: IcedTea 2.5.6
Distribution: Debian GNU/Linux 8.1 (jessie), package 7u79-2.5.6-1~deb8u1
Problematic frame:
C [libsqlite3.so.0+0x2ac69] sqlite3VdbeIntValue+0x10

Failed to write core dump. Core dumps have been disabled. To enable co

Inside the ~/ScipionUserData/projects/TestXmippWorkflow/hs_err_pid76694.log(stack section):

Stack: [0x00007f69e3dfe000,0x00007f69e3eff000], sp=0x00007f69e3efa0e0, free space=1008k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
C [libsqlite3.so.0+0x2ac69] sqlite3VdbeIntValue+0x10
C [libsqlite3.so.0+0x30c88] sqlite3_value_int+0x18
C [libsqlite3.so.0+0x31c11] sqlite3_column_int+0x28
C [libXmippData.so+0x2585bf] MDSql::extractValue(sqlite3_stmt_, int, MDObject&)+0xc3
C [libXmippData.so+0x250e8f] MDSql::getObjectValue(int, MDObject&)+0x20f
C [libXmippData.so+0x20d0a7] MetaData::getValue(MDObject&, unsigned long) const+0x127
C [libXmippJNI.so+0xab336] bool MetaData::getValue(MDLabel, int&, unsigned long) const+0x40
C [libXmippJNI.so+0xaf2ac] Java_xmipp_jni_MetaData_getValueInt+0xa8
j xmipp.jni.MetaData.getValueInt(IJ)I+0
j xmipp.jni.MetaData.getEnabled(J)Z+17
j xmipp.viewer.models.GalleryData.isEnabled(I)Z+19
j xmipp.viewer.models.ImageGalleryTableModel$ImageItem.isEnabled()Z+11
j xmipp.viewer.ImageItemRenderer.getTableCellRendererComponent(Ljavax/swing/JTable;Ljava/lang/Object;ZZII)Ljava/awt/Component;+97
j javax.swing.JTable.prepareRenderer(Ljavax/swing/table/TableCellRenderer;II)Ljava/awt/Component;+108
j javax.swing.plaf.basic.BasicTableUI.paintCell(Ljava/awt/Graphics;Ljava/awt/Rectangle;II)V+77
j javax.swing.plaf.basic.BasicTableUI.paintCells(Ljava/awt/Graphics;IIII)V+133
j javax.swing.plaf.basic.BasicTableUI.paint(Ljava/awt/Graphics;Ljavax/swing/JComponent;)V+249
j javax.swing.plaf.ComponentUI.update(Ljava/awt/Graphics;Ljavax/swing/JComponent;)V+32
j javax.swing.JComponent.paintComponent(Ljava/awt/Graphics;)V+26
j javax.swing.JComponent.paint(Ljava/awt/Graphics;)V+286
j javax.swing.JComponent.paintChildren(Ljava/awt/Graphics;)V+501
j javax.swing.JComponent.paint(Ljava/awt/Graphics;)V+318
j javax.swing.JViewport.paint(Ljava/awt/Graphics;)V+205
j javax.swing.JComponent.paintChildren(Ljava/awt/Graphics;)V+501
j javax.swing.JComponent.paint(Ljava/awt/Graphics;)V+318
j javax.swing.JComponent.paintChildren(Ljava/awt/Graphics;)V+501
j javax.swing.JComponent.paint(Ljava/awt/Graphics;)V+318
j javax.swing.JComponent.paintChildren(Ljava/awt/Graphics;)V+501
j javax.swing.JComponent.paint(Ljava/awt/Graphics;)V+318
j javax.swing.JComponent.paintChildren(Ljava/awt/Graphics;)V+501
j javax.swing.JComponent.paint(Ljava/awt/Graphics;)V+318
j javax.swing.JLayeredPane.paint(Ljava/awt/Graphics;)V+73
j javax.swing.JComponent.paintChildren(Ljava/awt/Graphics;)V+501
j javax.swing.JComponent.paint(Ljava/awt/Graphics;)V+318
j javax.swing.JComponent.paintToOffscreen(Ljava/awt/Graphics;IIIIII)V+41
j javax.swing.BufferStrategyPaintManager.paint(Ljavax/swing/JComponent;Ljavax/swing/JComponent;Ljava/awt/Graphics;IIII)Z+157
j javax.swing.RepaintManager.paint(Ljavax/swing/JComponent;Ljavax/swing/JComponent;Ljava/awt/Graphics;IIII)V+52
j javax.swing.JComponent.paintImmediately(IIII)V+683
j javax.swing.JComponent.paintImmediately(IIII)V+138
j javax.swing.RepaintManager$3.run()Ljava/lang/Void;+75
j javax.swing.RepaintManager$3.run()Ljava/lang/Object;+1
v ~StubRoutines::call_stub
V [libjvm.so+0x5fac34] JavaCalls::call_helper(JavaValue, methodHandle_, JavaCallArguments_, Thread_)+0x354
V [libjvm.so+0x5fa6a8] JavaCalls::call(JavaValue_, methodHandle, JavaCallArguments_, Thread_)+0x28
V [libjvm.so+0x63a735] JVM_DoPrivileged+0x255
j java.security.AccessController.doPrivileged(Ljava/security/PrivilegedAction;Ljava/security/AccessControlContext;)Ljava/lang/Object;+0
j java.security.ProtectionDomain$1.doIntersectionPrivilege(Ljava/security/PrivilegedAction;Ljava/security/AccessControlContext;Ljava/security/AccessControlContext;)Ljava/lang/Object;+28
j javax.swing.RepaintManager.paintDirtyRegions(Ljava/util/Map;)V+154
j javax.swing.RepaintManager.paintDirtyRegions()V+46
j javax.swing.RepaintManager.prePaintDirtyRegions()V+73
j javax.swing.RepaintManager.access$1100(Ljavax/swing/RepaintManager;)V+1
j javax.swing.RepaintManager$ProcessingRunnable.run()V+37
j java.awt.event.InvocationEvent.dispatch()V+47
j java.awt.EventQueue.dispatchEventImpl(Ljava/awt/AWTEvent;Ljava/lang/Object;)V+21
j java.awt.EventQueue.access$300(Ljava/awt/EventQueue;Ljava/awt/AWTEvent;Ljava/lang/Object;)V+3
j java.awt.EventQueue$3.run()Ljava/lang/Void;+12
j java.awt.EventQueue$3.run()Ljava/lang/Object;+1
v ~StubRoutines::call_stub
V [libjvm.so+0x5fac34] JavaCalls::call_helper(JavaValue_, methodHandle_, JavaCallArguments_, Thread_)+0x354
V [libjvm.so+0x5fa6a8] JavaCalls::call(JavaValue_, methodHandle, JavaCallArguments_, Thread_)+0x28
V [libjvm.so+0x63a735] JVM_DoPrivileged+0x255
j java.security.AccessController.doPrivileged(Ljava/security/PrivilegedAction;Ljava/security/AccessControlContext;)Ljava/lang/Object;+0
j java.security.ProtectionDomain$1.doIntersectionPrivilege(Ljava/security/PrivilegedAction;Ljava/security/AccessControlContext;Ljava/security/AccessControlContext;)Ljava/lang/Object;+28
j java.awt.EventQueue.dispatchEvent(Ljava/awt/AWTEvent;)V+46
j java.awt.EventDispatchThread.pumpOneEventForFilters(I)V+245
j java.awt.EventDispatchThread.pumpEventsForFilter(ILjava/awt/Conditional;Ljava/awt/EventFilter;)V+35
j java.awt.EventDispatchThread.pumpEventsForHierarchy(ILjava/awt/Conditional;Ljava/awt/Component;)V+11
j java.awt.EventDispatchThread.pumpEvents(ILjava/awt/Conditional;)V+4
j java.awt.EventDispatchThread.pumpEvents(Ljava/awt/Conditional;)V+3
j java.awt.EventDispatchThread.run()V+9
v ~StubRoutines::call_stub
V [libjvm.so+0x5fac34] JavaCalls::call_helper(JavaValue_, methodHandle_, JavaCallArguments_, Thread_)+0x354
V [libjvm.so+0x5f995e] JavaCalls::call_virtual(JavaValue_, Handle, KlassHandle, Symbol_, Symbol_, Thread_)+0x21e
V [libjvm.so+0x63702f] thread_entry(JavaThread_, Thread_)+0xdf
V [libjvm.so+0x92dde8] JavaThread::thread_main_inner()+0x118
V [libjvm.so+0x92e071] JavaThread::run()+0x231
V [libjvm.so+0x7f05a2] java_start(Thread_)+0xf2

[pconesa]

Excluded from V1.1, sadly.