VM isseue
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edae...@umn.edu
May 9, 2018, 4:14:58 PM5/9/18
to TASSEL - Trait Analysis by Association, Evolution and Linkage
Hi there,
I was trying to run Tassel5 GBSv2 GBSSeqToTagDBPlugin () with Memory Settings: -Xms100G -Xmx200G.
Any idea to solve the following error.
Error occurred during initialization of VM
Could not reserve enough space for object heap
Thanks,
Erena.
Terry Casstevens
May 9, 2018, 4:18:43 PM5/9/18
to Tassel User Group
If you're on a 32-bit machine or have a 32-bit version of Java
installed, you probably can't set the head that large. If you machine
is 64-bit, I would check that your Java installation is also 64-bit
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installed, you probably can't set the head that large. If you machine
is 64-bit, I would check that your Java installation is also 64-bit
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Erena Edae
May 9, 2018, 4:32:07 PM5/9/18
to tas...@googlegroups.com
Thank you for your response. I have java 8 (64-bits) installed on the machine.
On Wed, May 9, 2018 at 3:18 PM, Terry Casstevens <tm...@cornell.edu> wrote:
If you're on a 32-bit machine or have a 32-bit version of Java
installed, you probably can't set the head that large. If you machine
is 64-bit, I would check that your Java installation is also 64-bit
On Wed, May 9, 2018 at 4:13 PM, <edae...@umn.edu> wrote:
>
> Hi there,
>
> I was trying to run Tassel5 GBSv2 GBSSeqToTagDBPlugin () with Memory
> Settings: -Xms100G -Xmx200G.
>
> Any idea to solve the following error.
>
> Error occurred during initialization of VM
> Could not reserve enough space for object heap
>
> Thanks,
> Erena.
>
>
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Terry Casstevens
May 9, 2018, 4:38:04 PM5/9/18
to Tassel User Group
Can you send the results of this command?
java -version
And the full command and logging that you are running?
On Wed, May 9, 2018 at 4:32 PM, Erena Edae <edae...@umn.edu> wrote:
> Thank you for your response. I have java 8 (64-bits) installed on the
> machine.
>
> Erena.
>
> On Wed, May 9, 2018 at 3:18 PM, Terry Casstevens <tm...@cornell.edu> wrote:
>>
>> If you're on a 32-bit machine or have a 32-bit version of Java
>> installed, you probably can't set the head that large. If you machine
>> is 64-bit, I would check that your Java installation is also 64-bit
>>
>> On Wed, May 9, 2018 at 4:13 PM, <edae...@umn.edu> wrote:
>> >
>> > Hi there,
>> >
>> > I was trying to run Tassel5 GBSv2 GBSSeqToTagDBPlugin () with Memory
>> > Settings: -Xms100G -Xmx200G.
>> >
>> > Any idea to solve the following error.
>> >
>> > Error occurred during initialization of VM
>> > Could not reserve enough space for object heap
>> >
>> > Thanks,
>> > Erena.
>> >
>> >
>> > --
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>> > "TASSEL - Trait Analysis by Association, Evolution and Linkage" group.
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>> > an
>> > email to tassel+un...@googlegroups.com.
java -version
And the full command and logging that you are running?
On Wed, May 9, 2018 at 4:32 PM, Erena Edae <edae...@umn.edu> wrote:
> Thank you for your response. I have java 8 (64-bits) installed on the
> machine.
>
> Erena.
>
> On Wed, May 9, 2018 at 3:18 PM, Terry Casstevens <tm...@cornell.edu> wrote:
>>
>> If you're on a 32-bit machine or have a 32-bit version of Java
>> installed, you probably can't set the head that large. If you machine
>> is 64-bit, I would check that your Java installation is also 64-bit
>>
>> On Wed, May 9, 2018 at 4:13 PM, <edae...@umn.edu> wrote:
>> >
>> > Hi there,
>> >
>> > I was trying to run Tassel5 GBSv2 GBSSeqToTagDBPlugin () with Memory
>> > Settings: -Xms100G -Xmx200G.
>> >
>> > Any idea to solve the following error.
>> >
>> > Error occurred during initialization of VM
>> > Could not reserve enough space for object heap
>> >
>> > Thanks,
>> > Erena.
>> >
>> >
>> > --
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>> > "TASSEL - Trait Analysis by Association, Evolution and Linkage" group.
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>>
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Erena Edae
May 11, 2018, 1:19:08 PM5/11/18
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Hi Terry,
Here the results of the command.
/home/rousem/edaex002/tassel-5-standalone/lib/ahocorasick-0.2.4.jar:/home/rousem/edaex002/tassel-5-standalone/lib/biojava-alignment-4.0.0.jar:/home/rousem/edaex002/tassel-5-standalone/lib/biojava-core-4.0.0.jar:/home/rousem/edaex002/tassel-5-standalone/lib/biojava-phylo-4.0.0.jar:/home/rousem/edaex002/tassel-5-standalone/lib/colt-1.2.0.jar:/home/rousem/edaex002/tassel-5-standalone/lib/commons-codec-1.10.jar:/home/rousem/edaex002/tassel-5-standalone/lib/commons-math3-3.4.1.jar:/home/rousem/edaex002/tassel-5-standalone/lib/ejml-0.23.jar:/home/rousem/edaex002/tassel-5-standalone/lib/forester-1.038.jar:/home/rousem/edaex002/tassel-5-standalone/lib/guava-22.0.jar:/home/rousem/edaex002/tassel-5-standalone/lib/htsjdk-2.14.0.jar:/home/rousem/edaex002/tassel-5-standalone/lib/itextpdf-5.1.0.jar:/home/rousem/edaex002/tassel-5-standalone/lib/javax.json-1.0.4.jar:/home/rousem/edaex002/tassel-5-standalone/lib/jcommon-1.0.23.jar:/home/rousem/edaex002/tassel-5-standalone/lib/jfreechart-1.0.19.jar:/home/rousem/edaex002/tassel-5-standalone/lib/jfreesvg-3.2.jar:/home/rousem/edaex002/tassel-5-standalone/lib/jhdf5-14.12.5.jar:/home/rousem/edaex002/tassel-5-standalone/lib/json-simple-1.1.1.jar:/home/rousem/edaex002/tassel-5-standalone/lib/junit-4.10.jar:/home/rousem/edaex002/tassel-5-standalone/lib/log4j-1.2.13.jar:/home/rousem/edaex002/tassel-5-standalone/lib/mail-1.4.jar:/home/rousem/edaex002/tassel-5-standalone/lib/postgresql-9.4-1201.jdbc41.jar:/home/rousem/edaex002/tassel-5-standalone/lib/slf4j-api-1.7.10.jar:/home/rousem/edaex002/tassel-5-standalone/lib/slf4j-simple-1.7.10.jar:/home/rousem/edaex002/tassel-5-standalone/lib/snappy-java-1.1.1.6.jar:/home/rousem/edaex002/tassel-5-standalone/lib/sqlite-jdbc-3.8.5-pre1.jar:/home/rousem/edaex002/tassel-5-standalone/lib/trove-3.0.3.jar:/home/rousem/edaex002/tassel-5-standalone/sTASSEL.jar
Memory Settings: -Xms100G -Xmx200G
Tassel Pipeline Arguments: -fork1 -GBSSeqToTagDBPlugin -e PstI-MspI -i /home/rousem/edaex002/sequence/AM_TCAP -db AMTCAP_GBS.db -k Key_DNA_AmspringPanel_TCAPf.txt -kmerLength 64 -minKmerL 20 -mnQS 20 -mxKmerNum 500000000 -endPlugin -runfork1
Memory Settings: -Xms100G -Xmx200G
Tassel Pipeline Arguments: -fork1 -GBSSeqToTagDBPlugin -e PstI-MspI -i /home/rousem/edaex002/sequence/AM_TCAP -db AMTCAP_GBS.db -k Key_DNA_AmspringPanel_TCAPf.txt -kmerLength 64 -minKmerL 20 -mnQS 20 -mxKmerNum 500000000 -endPlugin -runfork1
Error occurred during initialization of VM
Could not reserve enough space for object heap
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Terry Casstevens
May 12, 2018, 8:35:06 AM5/12/18
to Tassel User Group
Can you send the results of this command?
java -version
java -version
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Erena Edae
May 12, 2018, 1:32:10 PM5/12/18
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He Terry,
This was the result in the output file, and the error file was empty (nothing in it)
Erena.
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Erena Edae
May 12, 2018, 1:44:29 PM5/12/18
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Hi Terry,
With memory setting -Xms512m -Xmx10G, I got the following error.
Exception in thread "main" java.lang.UnsupportedClassVersionError: net/maizegenetics/pipeline/TasselPipeline : Unsupported major.minor version 52.0
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:648)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:272)
at java.net.URLClassLoader.access$000(URLClassLoader.java:68)
at java.net.URLClassLoader$1.run(URLClassLoader.java:207)
at java.net.URLClassLoader$1.run(URLClassLoader.java:201)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:200)
at java.lang.ClassLoader.loadClass(ClassLoader.java:325)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:296)
at java.lang.ClassLoader.loadClass(ClassLoader.java:270)
at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:406)
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:648)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:272)
at java.net.URLClassLoader.access$000(URLClassLoader.java:68)
at java.net.URLClassLoader$1.run(URLClassLoader.java:207)
at java.net.URLClassLoader$1.run(URLClassLoader.java:201)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:200)
at java.lang.ClassLoader.loadClass(ClassLoader.java:325)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:296)
at java.lang.ClassLoader.loadClass(ClassLoader.java:270)
at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:406)
Erena Edae
May 12, 2018, 11:27:06 PM5/12/18
to tas...@googlegroups.com
Hi Terry,
It worked after when after I changed java version form 1.8.0_14
to 1.8.0_45 on the server side.
Thanks,
Erena.
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