Java Heap Space Increase Windows 10
Vida Hubbert
I am new to CellProfiler and am likely making a newbie mistake. I have been attempting to process a dataset of large images in CellProfiler 4.2.5. I keep getting the error message related to Java heap space, however I already increased my Java heap space manually through windows control panel. I increased it to a rather large size (10GB), but I still keep getting the same error. Is there anything else I can do? Please let me know if there are any other details I can provide.
and have allocated a max of 100 gb to java. However, even with only 1 image, as soon as I go into test mode, I get the above error. Any advice? (This workstation is running Windows 7 if that makes a difference!)
I am having the same issue with CP 4.2.6 on Windows 10 processing two 500MB images with a computer having 64GB RAM. The error is in the NamesAndTypes stage. Tried increasing memory in Java as others did and decreasing threads in preferences. Here is the error:
It is not working through command line and I also cannot find anything about Java memory in the CellProfiler preferences.
What is the correct way for CellProfiler 4 (I have version 4.0.7) to increase the Java heap space?
I have been using CCS Version: 7.1.0.00016 for half a year now without any problems of significance. The last week however, I have received with increasing intensity warnings about the Java heap space. I have increased the Xmx size in the eclipse.ini file first to 1024 then to 2048 without getting rid of the error messages. When I try to increase the size to above 1024 in ccs.ini, ccs won't start at all. Currently, I am not able to work with ccs as the warnings which also includes "An internal error occured during 'Computing Macro expansion'" results in a shutdown of ccs.
I am assuming that you are on Windows since the vast majority of these "out of memory" and heap space issues occur on CCS for Windows. This is because CCS for Windows is still a 32-bit application (we are planning have CCS be 64-bit starting with CCSv9) and hence runs into the 2GB limit on Windows.
Jan Gustav Heber said:I have increased the Xmx size in the eclipse.ini file first to 1024 then to 2048 without getting rid of the error messages. When I try to increase the size to above 1024 in ccs.ini, ccs won't start at all.
There is a "sweet spot" in regards to the max heap size for CCS. 768m to 1024m seems to be it. Any greater and you could run into the issues described above. The best value requires some experimentation. Looks like 1024m is it in your case. Note that it is ccstudio.ini that must be modified, not eclipse.ini.
Certain features in CCS can use up a lot of memory. When you get these warnings, what does you CCS environment look like? Are you in a debug session? And if so, for which target? Do you have many views open? If a program is loaded, how large is the executable file you loaded? Did you use the Stack Usage view? Any additional information about your environment will be helpful.
Once you execute a workflow that requires more than 512M RAM the JVM will automatically ask for more and increase the total value to at most the value provided by -Xmx. Just give it a try by using, e.g., a Data Generator node and increase the number of rows created to something big.
Btw. since we update with 4.0 the garbage collection algorithm resizing your heap-space is not as costly as it used to be anymore. However, please feel free to adapt Xms and Xmx according to your needs. If you are dealing with larger data increasing the maximum heap space can potentially save you a lot of execution time :).
In addition to failing to draw a graph of the whole dataset, SAS runs extremely slowly when asked to draw many graphs on subests of the data. I haven't had these problems on previous installations of SAS. The time taken to create 2128 graphs is:
The problem is, none of the methods of increasing heap space are working: I have tried a command prompt with increased jre options, AND I have also altered the config file, and yet SAS still only has 128 mb allocated.
One might also consider the actual SGPLOT code involved. How much of that 4.5 Gb dataset is actually used by Sgplot? What type of plot/plots are involved? Perhaps a different plot approach would reduce memory need.
I am trying to launch a staging client to test some edits, both on the server and my local development (non-gateway) PC, I am getting the per title error message when the staging client attempts to start.
I would infer that there is enough heap space available, and a normal (published) client starts fine, any known bugs with staging? As you can see we only rebooted 22 days ago, trying to avoid a reboot if possible.
Client heap != Gateway heap. Separate process, separate JVM, separate heap. If you can launch the designer, client heap is an option in the project properties. If you can't launch the designer, it's an option in the gateway settings.
Are you using the native client launcher? Is it using the embedded JRE, or the system runtime? It's possible, though unlikely, that you could be using a 32 bit runtime that can't dedicate sufficient heap, perhaps? Usually that just fails and disappears immediately rather than giving you a useful error message.
Okay, so I'll answer publicly just in case this comes up for anyone in the future, but basically, looking at the last line of the logs there's something like this:
Starting Java with the following parameters
And then a long command line string with a bunch of arguments. For your client launch, it looks like this (with anything sensitive redacted):
What you can do to capture the full logs from a client launch is to take the actual command line string from the logs and run it yourself, in a command prompt/windows terminal/powershell/etc window. It's probably also a good idea to pipe the output directly to a file, e.g. your actual command should be $theCommand > output.txt and thus all output from the launched process to stdout will be automatically logged to a new file output.txt. Then hopefully you should be able to get a useful stacktrace. You can also try manually increasing the memory (if your system has more available!) to get the client to launch, just as a curiosity.
Note it's only the staging that's failing to start (I was doing from Designer F9), all I added was a new main window with a few check boxes. As its such a small change I'm just going to pubish tomorrow anyway and ensure the published doesn't have heap issues.
I can't remember for sure (it's been a long time since I've been in the 7.9 codebase) but I want to say that the 'launch' options in the designer might have ignored the actual client memory options and simply launched at some hardcoded value for min/max memory. Those launches wouldn't show up in the client launcher logs you sent me; they're a special process launched from inside the designer itself. I don't know for sure, but I vaguely remember someone fixing that behavior somewhere in the 8.x line.
At this point, we have saved but unpublished resources. If you would like to see and test these changes before publishing them, you can open a staged Client from the Designer. Go to the menubar and select Tools > Launch Project > Windowed (Staging) . This will give you a Client with a blue banner at the top showing that you are running a Staging Client instead of a normal Client.
As per an earlier entry in this thread, I've attempted to increase the Java Heap via the Registry and Config Tool, and anything above 1 GB and restarting the SiteScope service on Windows... and... SiteScope UI doesn't come up. :(
1 Run the Configuration Tool, and select the Sizing option.
This tool increases JVM heap size to 1024 MB, desktop heap size to
2048 MB, and the number of file handles to 18,000. It also disables
pop-up warnings for SiteScope executables. For details, see "Running the
Configuration Tool on Windows Platforms".
Note: The Configuration Tool supports the default SiteScope service
name only. If you changed the service name, contact HP
By default, the Java heap space for SiteScope is set to 512 MB. This is
insufficient for the normal operation of large instances.
The heap space can be increased up to 1024 MB (this is the recommended
heap size for large loads) by modifying start-service and start-monitor
scripts in \bin directory
To fix the java.lang.OutOfMemoryError: Java heap space error, you can increase the maximum heap size allocated to the JVM. In your current configuration, you have set the initial heap size and maximum heap size to 5GB using the -Xms and -Xmx JVM options. However, this may not be sufficient for your application's memory requirements.
Keep in mind that setting the maximum heap size too high can also cause issues such as container OOM, so you need to find a balance between the memory requirements of your application and the available resources.
There are two types of memory stack memory and heap memory. All the dynamic allocations go into heap memory and the rest of the static allocations and variables allocations go into stack memory. Whenever a java program is executed in the java virtual machine it uses the heap memory to manage the data. Task Engine runs on JVM (Java Virtual Machine). Hierarchy is pictorially shown below.
A Java Virtual Machine implementation may provide the programmer or the user control over the initial size of the heap, as well as, if the heap can be dynamically expanded or contracted, control over the maximum and minimum heap size. The following exceptional condition is associated with the heap whenever a computation requires more heap than can be made available by the automatic storage management system, the Java Virtual Machine throws an OutOfMemoryError.
By default, the JVM heap size is 1GB, which is usually enough to accommodate the data used by Task Engine. However, larger heap size may be required under some circumstances, for example, when the average size of the parameters in a task is very large. Under these circumstances, the following log item is recorded in Task Engine log files. If this log item appears regularly, you need to increase the heap size.
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