Hi,
New SCIFIO I/O system in Fiji/IJ2 automatically detects wether virtual
stack is needed according to system memory available and image size
(if I understood correctly).
Virtual stack is fine but it always better to work without when you
can. For example working with timelapse stacks, sliding time is much
faster when image is not a virtual stack (and it makes sense since RAM
memory access is much faster than hard drive memory access...).
Saying that I noticed something: when I close a big image (no virtual
stack because moving time slider is fast), java does not release
memory to system (and it's a normal behaviour according to this
http://stackoverflow.com/questions/22912063/automatically-release-unused-memory-in-imagej-fiji).
Now when I load the same kind of image (same size), the JVM should use
the free memory released by the previously closed image isn't it ? I
have the feeling that it does not because, when I move the time slider
on the second image, it's very slow....
Some numbers:
- image size : 4.6GB
- Fiji memory after start : 0.3GB
- Fiji memory after loading first image: 6.9GiB
- Fiji memory after closing first image: 6.9GiB
- Fiji memory after loading second image: 6.9GiB
My hypothesis is that when loading an image, Fiji/SCIFIO look at free
memory in the system but not in the JVM. Is that possible ? Did you
already noticed that ?
PS: I have attached to this mail some properties of my system.
Best,
--
Hadrien Mary
Ph.D student in Biology
Tournier-Gachet Team
CNRS - LBCMCP - UMR 5088
Université de Toulouse - Bât. 4R3B1
118, route de Narbonne - 31062 Toulouse
java.version: 1.7.0_65
java.vendor: Oracle Corporation
os.name: Linux
os.version: 3.16.7-031607-generic
os.arch: amd64
file.separator: /
path.separator: :
line.separator: <lf>
user.name: hadim
user.home: /home/hadim
user.dir: /home/hadim
user.country: US
file.encoding: UTF-8
java.home: /usr/lib/jvm/java-7-openjdk-amd64/jre
java.class.path: /home/hadim/local/Fiji.app/jars/imagej-launcher-3.1.6.jar
java.ext.dirs:
/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/ext:/usr/java/packages/lib/ext
java.io.tmpdir: /tmp
IJ.getVersion: 2.0.0-rc-23/1.49m
IJ.getFullVersion: 1.49m99
IJ.isJava2: true
IJ.isJava15: true
IJ.isJava16: true
IJ.isLinux: true
IJ.isMacintosh: false
IJ.isMacOSX: false
IJ.isWindows: false
IJ.is64Bit: true
IJ.getDirectory("imagej"): /home/hadim/local/Fiji.app/
IJ.getDirectory("home"): /home/hadim/
IJ.getDirectory("plugins"): /home/hadim/local/Fiji.app/plugins/
IJ.getDirectory("macros"): /home/hadim/local/Fiji.app/macros/
IJ.getDirectory("luts"): /home/hadim/local/Fiji.app/luts/
IJ.getDirectory("current"): /home/hadim/
IJ.getDirectory("temp"): /tmp/
IJ.getDirectory("default"): /home/hadim/
IJ.getDirectory("image"): null
Menus.getPlugInsPath: /home/hadim/local/Fiji.app/plugins/
Menus.getMacrosPath: /home/hadim/local/Fiji.app/macros/
Prefs.getImageJDir: /home/hadim/local/Fiji.app/
Prefs.getThreads: 16 (16 cores)
Prefs.open100Percent: false
Prefs.blackBackground: false
Prefs.useJFileChooser: false
Prefs.weightedColor: false
Prefs.blackCanvas: false
Prefs.pointAutoMeasure: false
Prefs.pointAutoNextSlice: false
Prefs.requireControlKey: false
Prefs.useInvertingLut: false
Prefs.antialiasedTools: true
Prefs.useInvertingLut: false
Prefs.intelByteOrder: false
Prefs.doubleBuffer: true
Prefs.noPointLabels: false
Prefs.disableUndo: false
Prefs dir: /home/hadim/.imagej
Current dir: /home/hadim/
Sample images dir: http://imagej.nih.gov/ij/images/
Memory in use: 4475MB of 9585MB (46%)
Screen size: 1600x1200
Max window bounds: x=0,y=0,width=1600,height=1200
Union of bounds: x=0,y=0,width=2880,height=1200
Monitor1: x=0,y=0,width=1600,height=1200
Monitor2: x=1600,y=0,width=1280,height=1024
All Java Properties
ij.dir: /home/hadim/local/Fiji.app
java.runtime.name: OpenJDK Runtime Environment
fiji.dir: /home/hadim/local/Fiji.app
imagej.dir: /home/hadim/local/Fiji.app
sun.boot.library.path: /usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64
java.vm.version: 24.65-b04
fiji.defaultLibPath: lib/amd64/server/libjvm.so
java.vm.vendor: Oracle Corporation
java.vendor.url: http://java.oracle.com/
path.separator: :
java.vm.name: OpenJDK 64-Bit Server VM
file.encoding.pkg: sun.io
user.country: US
sun.os.patch.level: unknown
java.vm.specification.name: Java Virtual Machine Specification
user.dir: /home/hadim
java.runtime.version: 1.7.0_65-b32
java.awt.graphicsenv: sun.awt.X11GraphicsEnvironment
java.endorsed.dirs: /usr/lib/jvm/java-7-openjdk-amd64/jre/lib/endorsed
os.arch: amd64
java.io.tmpdir: /tmp
line.separator:
java.vm.specification.vendor: Oracle Corporation
os.name: Linux
sun.jnu.encoding: UTF-8
java.library.path:
/home/hadim/local/Fiji.app/lib/linux64:/home/hadim/local/Fiji.app/mm/linux64
sun.awt.enableExtraMouseButtons: true
java.specification.name: Java Platform API Specification
java.class.version: 51.0
sun.management.compiler: HotSpot 64-Bit Tiered Compilers
os.version: 3.16.7-031607-generic
user.home: /home/hadim
user.timezone: Europe/Paris
java.awt.printerjob: sun.print.PSPrinterJob
file.encoding: UTF-8
java.specification.version: 1.7
plugins.dir: /home/hadim/local/Fiji.app
java.class.path: /home/hadim/local/Fiji.app/jars/imagej-launcher-3.1.6.jar
user.name: hadim
java.vm.specification.version: 1.7
java.home: /usr/lib/jvm/java-7-openjdk-amd64/jre
sun.arch.data.model: 64
user.language: en
java.specification.vendor: Oracle Corporation
awt.toolkit: sun.awt.X11.XToolkit
java.vm.info: mixed mode
java.version: 1.7.0_65
java.ext.dirs:
/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/ext:/usr/java/packages/lib/ext
sun.boot.class.path:
/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/resources.jar:/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/rt.jar:/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/sunrsasign.jar:/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/jsse.jar:/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/jce.jar:/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/charsets.jar:/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/rhino.jar:/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/jfr.jar:/usr/lib/jvm/java-7-openjdk-amd64/jre/classes
java.vendor: Oracle Corporation
ij.executable: /home/hadim/local/Fiji.app/ImageJ-linux64
python.cachedir.skip: true
file.separator: /
java.vendor.url.bug: http://bugreport.sun.com/bugreport/
sun.font.fontmanager: sun.awt.X11FontManager
sun.io.unicode.encoding: UnicodeLittle
sun.cpu.endian: little
sun.desktop: gnome
fiji.executable: /home/hadim/local/Fiji.app/ImageJ-linux64
sun.cpu.isalist:
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