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Sofia Robb
Hi Nathan,

I have all my annotations loaded up, now my annotation track just has the spinning wheel in it. i can do other things, like add users, switch organims, etc, but my annotation won't load. Though right now it says Loading... and I can't do anything.

I thought that maybe it might be a memory problem, but here are my settings.

tomcat     1378      1  1 Jun16 ?        00:49:21 /usr/lib/jvm/jre/bin/java -Xms1g -Xmx2g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -classpath /usr/share/tomcat/bin/bootstrap.jar:/usr/share/tomcat/bin/tomcat-juli.jar:/usr/share/java/commons-daemon.jar -Dcatalina.base=/usr/share/tomcat -Dcatalina.home=/usr/share/tomcat -Djava.endorsed.dirs= -Djava.io.tmpdir=/var/cache/tomcat/temp -Djava.util.logging.config.file=/usr/share/tomcat/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager org.apache.catalina.startup.Bootstrap start


Any ideas?

Thank you again!!
Sofia






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Re: Loading....

Sofia Robb
I just got this error for the first time. 

Inline image 1

On Mon, Jun 19, 2017 at 10:54 AM, Sofia Robb <[hidden email]> wrote:
Hi Nathan,

I have all my annotations loaded up, now my annotation track just has the spinning wheel in it. i can do other things, like add users, switch organims, etc, but my annotation won't load. Though right now it says Loading... and I can't do anything.

I thought that maybe it might be a memory problem, but here are my settings.

tomcat     1378      1  1 Jun16 ?        00:49:21 /usr/lib/jvm/jre/bin/java -Xms1g -Xmx2g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -classpath /usr/share/tomcat/bin/bootstrap.jar:/usr/share/tomcat/bin/tomcat-juli.jar:/usr/share/java/commons-daemon.jar -Dcatalina.base=/usr/share/tomcat -Dcatalina.home=/usr/share/tomcat -Djava.endorsed.dirs= -Djava.io.tmpdir=/var/cache/tomcat/temp -Djava.util.logging.config.file=/usr/share/tomcat/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager org.apache.catalina.startup.Bootstrap start


Any ideas?

Thank you again!!
Sofia







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Re: Loading....

nathandunn

You consistently get this when reloading? 

You can try wiping the preference table and see if that helps (i.e., delete from preference).   This may be especially useful going from 2.0.5 to master.

Are you getting any other errors in the catalana.out (tomcat log)? 

Nathan


On Jun 19, 2017, at 9:58 AM, Sofia Robb <[hidden email]> wrote:

I just got this error for the first time. 

<Screen Shot 2017-06-19 at 10.57.16 AM.png>

On Mon, Jun 19, 2017 at 10:54 AM, Sofia Robb <[hidden email]> wrote:
Hi Nathan,

I have all my annotations loaded up, now my annotation track just has the spinning wheel in it. i can do other things, like add users, switch organims, etc, but my annotation won't load. Though right now it says Loading... and I can't do anything.

I thought that maybe it might be a memory problem, but here are my settings.

tomcat     1378      1  1 Jun16 ?        00:49:21 /usr/lib/jvm/jre/bin/java -Xms1g -Xmx2g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -classpath /usr/share/tomcat/bin/bootstrap.jar:/usr/share/tomcat/bin/tomcat-juli.jar:/usr/share/java/commons-daemon.jar -Dcatalina.base=/usr/share/tomcat -Dcatalina.home=/usr/share/tomcat -Djava.endorsed.dirs= -Djava.io.tmpdir=/var/cache/tomcat/temp -Djava.util.logging.config.file=/usr/share/tomcat/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager org.apache.catalina.startup.Bootstrap start


Any ideas?

Thank you again!!
Sofia






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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Re: Loading....

Sofia Robb
No, I am not getting that error consistently, but it consistently will not load.

Nothing in my catatina.log file

Deleting from preference helped for my dev server, i tried in my production server, but it is doing the same thing as before. Hmm. Strange. The dbs are slightly different, the dev has multiple copies of some of the annotations, since i reloaded, and reloaded some of the test data. I stoped and restarted tomcat, maybe the machine needs a restart.



On Mon, Jun 19, 2017 at 11:02 AM, Nathan Dunn <[hidden email]> wrote:

You consistently get this when reloading? 

You can try wiping the preference table and see if that helps (i.e., delete from preference).   This may be especially useful going from 2.0.5 to master.

Are you getting any other errors in the catalana.out (tomcat log)? 

Nathan


On Jun 19, 2017, at 9:58 AM, Sofia Robb <[hidden email]> wrote:

I just got this error for the first time. 

<Screen Shot 2017-06-19 at 10.57.16 AM.png>

On Mon, Jun 19, 2017 at 10:54 AM, Sofia Robb <[hidden email]> wrote:
Hi Nathan,

I have all my annotations loaded up, now my annotation track just has the spinning wheel in it. i can do other things, like add users, switch organims, etc, but my annotation won't load. Though right now it says Loading... and I can't do anything.

I thought that maybe it might be a memory problem, but here are my settings.

tomcat     1378      1  1 Jun16 ?        00:49:21 /usr/lib/jvm/jre/bin/java -Xms1g -Xmx2g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -classpath /usr/share/tomcat/bin/bootstrap.jar:/usr/share/tomcat/bin/tomcat-juli.jar:/usr/share/java/commons-daemon.jar -Dcatalina.base=/usr/share/tomcat -Dcatalina.home=/usr/share/tomcat -Djava.endorsed.dirs= -Djava.io.tmpdir=/var/cache/tomcat/temp -Djava.util.logging.config.file=/usr/share/tomcat/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager org.apache.catalina.startup.Bootstrap start


Any ideas?

Thank you again!!
Sofia






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







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Re: Loading....

nathandunn

Well, a restart can’t hurt.  I would:

- bring down the server
- remove entries from the preference table
- bring it back up

If that doesn’t work, if you could send me a dump, that might be helpful.

Thanks,

Nathan

On Jun 19, 2017, at 10:19 AM, Sofia Robb <[hidden email]> wrote:

No, I am not getting that error consistently, but it consistently will not load.

Nothing in my catatina.log file

Deleting from preference helped for my dev server, i tried in my production server, but it is doing the same thing as before. Hmm. Strange. The dbs are slightly different, the dev has multiple copies of some of the annotations, since i reloaded, and reloaded some of the test data. I stoped and restarted tomcat, maybe the machine needs a restart.



On Mon, Jun 19, 2017 at 11:02 AM, Nathan Dunn <[hidden email]> wrote:

You consistently get this when reloading? 

You can try wiping the preference table and see if that helps (i.e., delete from preference).   This may be especially useful going from 2.0.5 to master.

Are you getting any other errors in the catalana.out (tomcat log)? 

Nathan


On Jun 19, 2017, at 9:58 AM, Sofia Robb <[hidden email]> wrote:

I just got this error for the first time. 

<Screen Shot 2017-06-19 at 10.57.16 AM.png>

On Mon, Jun 19, 2017 at 10:54 AM, Sofia Robb <[hidden email]> wrote:
Hi Nathan,

I have all my annotations loaded up, now my annotation track just has the spinning wheel in it. i can do other things, like add users, switch organims, etc, but my annotation won't load. Though right now it says Loading... and I can't do anything.

I thought that maybe it might be a memory problem, but here are my settings.

tomcat     1378      1  1 Jun16 ?        00:49:21 /usr/lib/jvm/jre/bin/java -Xms1g -Xmx2g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -classpath /usr/share/tomcat/bin/bootstrap.jar:/usr/share/tomcat/bin/tomcat-juli.jar:/usr/share/java/commons-daemon.jar -Dcatalina.base=/usr/share/tomcat -Dcatalina.home=/usr/share/tomcat -Djava.endorsed.dirs= -Djava.io.tmpdir=/var/cache/tomcat/temp -Djava.util.logging.config.file=/usr/share/tomcat/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager org.apache.catalina.startup.Bootstrap start


Any ideas?

Thank you again!!
Sofia






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: Loading....

Sofia Robb
It did not work. I am trying a reload on my dev sever to see if it will work again there. If it works, i will probably just load a dump from my dev on my production.,

I am doing a dump of my production server and will send to you. 

Thanks!



On Mon, Jun 19, 2017 at 12:15 PM, Nathan Dunn <[hidden email]> wrote:

Well, a restart can’t hurt.  I would:

- bring down the server
- remove entries from the preference table
- bring it back up

If that doesn’t work, if you could send me a dump, that might be helpful.

Thanks,

Nathan

On Jun 19, 2017, at 10:19 AM, Sofia Robb <[hidden email]> wrote:

No, I am not getting that error consistently, but it consistently will not load.

Nothing in my catatina.log file

Deleting from preference helped for my dev server, i tried in my production server, but it is doing the same thing as before. Hmm. Strange. The dbs are slightly different, the dev has multiple copies of some of the annotations, since i reloaded, and reloaded some of the test data. I stoped and restarted tomcat, maybe the machine needs a restart.



On Mon, Jun 19, 2017 at 11:02 AM, Nathan Dunn <[hidden email]> wrote:

You consistently get this when reloading? 

You can try wiping the preference table and see if that helps (i.e., delete from preference).   This may be especially useful going from 2.0.5 to master.

Are you getting any other errors in the catalana.out (tomcat log)? 

Nathan


On Jun 19, 2017, at 9:58 AM, Sofia Robb <[hidden email]> wrote:

I just got this error for the first time. 

<Screen Shot 2017-06-19 at 10.57.16 AM.png>

On Mon, Jun 19, 2017 at 10:54 AM, Sofia Robb <[hidden email]> wrote:
Hi Nathan,

I have all my annotations loaded up, now my annotation track just has the spinning wheel in it. i can do other things, like add users, switch organims, etc, but my annotation won't load. Though right now it says Loading... and I can't do anything.

I thought that maybe it might be a memory problem, but here are my settings.

tomcat     1378      1  1 Jun16 ?        00:49:21 /usr/lib/jvm/jre/bin/java -Xms1g -Xmx2g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -classpath /usr/share/tomcat/bin/bootstrap.jar:/usr/share/tomcat/bin/tomcat-juli.jar:/usr/share/java/commons-daemon.jar -Dcatalina.base=/usr/share/tomcat -Dcatalina.home=/usr/share/tomcat -Djava.endorsed.dirs= -Djava.io.tmpdir=/var/cache/tomcat/temp -Djava.util.logging.config.file=/usr/share/tomcat/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager org.apache.catalina.startup.Bootstrap start


Any ideas?

Thank you again!!
Sofia






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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