I am trying to run a Java tool in Linux Ubuntu system and I keep getting the following error after the program imports 12% of the data:
Fata Error:
Exception in thread 'Thread-l" java.lang.OutOfMemoryError: java heap space
I tried to set the heap size using
java -Xms8G -Xmx16G -jar Haploview.jar
but the error appears again exactly at same point after just using less than 500M Of the allocated Ram.
Using the command 'free -m' I can see that there are lots of free RAM memory left but I don't know why Java do not use it
According to the specification Haploview allocates 512 MB of memory by default. You can increase the memory up to 2000 MB via java -jar Haploview.jar -memory 2000.
For details see https://www.broadinstitute.org/haploview/frequent-questions
But a memory larger than 2 GB is most likely not possible because Haploview seems to be a 32-bit application which is limited to a memory
of 2 GB independent of the underlying OS (32 Bit or 64 Bit).
See https://haploview.software.informer.com/download/
and Memory limit to a 32-bit process running on a 64-bit Linux OS
Related
My Jenkins build is running out of memory because of JUnits. When I try to give it (the JUnits) more than 4GB it errors out. I am using Linux as my build machine.
Invalid maximum heap size: -Xmx4096m
I am just wondering, is there a upper limit to how much heap size JUnits can use?
"For a 32-bit process model, the maximum virtual address size of the process is typically 4 GB, though some operating systems limit this to 2 GB or 3 GB. The maximum heap size is typically -Xmx3800m (1600m) for 2 GB limits), though the actual limitation is application dependent. For 64-bit process models, the maximum is essentially unlimited."
Found a pretty good answer here:
Java maximum memory on Windows XP
Memory is allocated to JVM not JUnit or any other class.
and there is limit on 32-bit system to assign max of 4Gb but if you requires more memory then move to 64 bit machine as there is no limit of max memory allocation .
i would guess you are using a 32 bit jvm ..
check this post:
Maximum Java heap size of a 32-bit JVM on a 64-bit OS
It's not JUnit but JVM. 4GB heap is too much for 32-bit JVMs.
There is insufficient memory for the Java Runtime Environment to continue.
Native memory allocation (malloc) failed to allocate 180992 bytes for Chunk::new
Possible reasons:
The system is out of physical RAM or swap space
In 32 bit mode, the process size limit was hit
Possible solutions:
Reduce memory load on the system
Increase physical memory or swap space
Check if swap backing store is full
Use 64 bit Java on a 64 bit OS
Decrease Java heap size (-Xmx/-Xms)
Decrease number of Java threads
Decrease Java thread stack sizes (-Xss)
Set larger code cache with -XX:ReservedCodeCacheSize=
This output file may be truncated or incomplete.
Out of Memory Error (allocation.cpp:328), pid=71060, tid=71956
Im getting the above error when i run my game server on a small vps (only 1gb of ram)
Im not sure what could be the cause i have installed 64 bit java as its 64 bit
im using java -Xmx768m
Check your -Xms attribute also.
Sorry for asking the question, should have searched a bit more.
Im running weka with a rather large dataset and a memory intesive algoithm. I need all the heap space I cant get!
This works:
java -jar -Xmx2048m weka.jar &
But this does not
java -jar -Xmx4096m weka.jar &
I get:
Error occurred during initialization of VM Could not reserve enough
space for object heap Could not create the Java virtual machine.
By some quick searching I found that this is the upper limit
java -jar -Xmx2594m weka.jar &
I have 4GB ram but a 32 bit machine. Why can't I use 2^32 bytes = 4096MB of memory?
For the future I am wondering if I can run java with e.g. hundreds of GB of heap space if I have the correct hardware and OS?
I have both 1.6 and 1.7 JVM installed:
$java -showversion
java version "1.6.0_24"
OpenJDK Runtime Environment (IcedTea6 1.11.4) (6b24-1.11.4-1ubuntu0.12.04.1)
OpenJDK Server VM (build 20.0-b12, mixed mode)
I have 4GB ram but a 32 bit machine. Why can't I use 2^32 bytes = 4096MB of memory?
For the future I am wondering if I can run java with e.g. hundreds of GB of heap space if I have the correct hardware and OS?
For 4 GB I suggest you use a 64-bit OS and possibly a 64-bit JVM as the limit for the heap size can be as small as 1.2 GB (on Windows XP)
If you want larger JVMs I suggest making sure you have 64-bit OS and JVM and you have more memory than the size of the JVM. e.g. if you want a 40 GB heap you need something like 48 GB or 64 GB of memory.
Use the 64-bit version of Java which allows you to use more memory. This is the limit of the 32-bit Java virtual machine.
If you have 4GB of RAM how can you expect that all will be available to your JVM? What about the OS the JVM is running in, this will also require memory. The way it works is that even though you can address all 4GB generally an OS will limit the amount available per process.
You are not able to have an allocation of 4096m because. It tries to get a single block of 4096m. Which is not possible at any given point of time. So you can use some smaller values between
3000-4000. or make sure your RAM is not used by any of the processes
I am running a server with the following attributes:
Windows Server 2008 R2 Standard - 64bit
4gb RAM
I am trying to set the heap size to 3gb for an application. I am using the flags -Xmx3G -Xms3G. Running with the flags results in the following error:
Error occurred during initialization of VM
Could not reserve enough space for object heap
Could not create the Java virtual machine.
I have been playing with the setting to see what my ceiling is and found that 1568 is my ceiling. What am I missing?
How much physical memory is available on your system (out of the original 4 GB)? It sounds like your system doesn't have 3GB of physical memory available when the vm starts up.
Remember that the JVM needs more memory than is allocated to the heap -- there are other data structures as well (thread stacks, etc) that also need memory. So the settings you are providing attempt to use more than 3GB of memory.
Also, are you using a 64-bit jvm? The practical limit for heap size on a 32-bit vm is 1.4 to 1.6 gigabytes according to this document.
Java requires continuous virtual memory on startup. On windows, 32-bit application run in an 32-bit emulated environment so you don't get much more continuous memory than you would in a 32-bit OS. c.f. on Solaris you get over 3 GB virtual memory for 32-bit Java.
I suggest you use the 64-bit version of Java as this will make use of all the memory you have. You still need to have free memory but the larger address space doesn't suffer from fragmentation.
BTW: The heap space is only part of the memory used, you need memory for shared libraries, direct memory, GUI components etc.
It seems you don't have 3G of physical mememory available. Here is an interesting article on Java heap size settings errors. Java heap size setting errors
I run a Java code with the following command:
$ java -Xms4G -Xmx4G myjavacode
My cpu's RAM capacity is 6GB.
However it always fail to execute giving me this
error message:
Invalid initial heap size: -Xms5G
The specified size exceeds the maximum representable size.
Could not create the Java virtual machine
Is there any way to set up Java option so that we can
execute the code?
You've exceeded the maximum heap size of your JVM. This is both JVM and OS dependent. In most 32-bit systems the maximum value will be 2Gb, regardless of the physical memory available.
By default Java will run in 32 bit mode. Be sure to give it the -d64 option to put it into 64 bit mode. Once in 64-bit mode, you shouldn't have any trouble allocating a 6GB JVM.
Actually, the maximum memory size on 32-bit systems can vary, being anything up to 4 GB, but 2 GB is a common value. It's often possible to re-link your kernel to increase this to 3 or 3.5 GB. The issue, of course, is that you just don't have the address space to map more memory. Have you tried a 64-bit machine?
Also, remember to set your ulimit higher before you do this.