ODK timing out during data pull

Hello Team,
My team conducting a survey can push data to ODK but during pulling of data
we get the error below;
"
Error: retrieving next chunk of instances from server...

NOT ALL SUBMISSIONS RETRIEVED: Error fetching list of submissions: Fetch of
submission download chunk failed. Detailed error: Unexpected
java.net.SocketTimeoutException: Read timed out

FAILED.

Activity done:
"

Has anyone experienced this too? What more steps can i take to isolate the
issue? How can i solve this?

We've already tried to;

  • increase tomcat Connection timeout
  • increase Java Heap Settings
  • increased MySQL interaction and wait timeouts
  • Verified network connection to the server

We are currently running ODK Aggregate 1.4.7 on Centos 6.7 , 5GB RAM, MySQL
5.1.73

The command-line pull does the same. pulls for a bit then throws an error.
attached is the stack trace.

cli stack trace.txt (54.2 KB)

··· On Monday, 11 April 2016 13:55:01 UTC+3, Luwum Patrick wrote: > > Hello Team, > My team conducting a survey can push data to ODK but during pulling of > data we get the error below; > " > Error: retrieving next chunk of instances from server... > > NOT ALL SUBMISSIONS RETRIEVED: Error fetching list of submissions: Fetch of > submission download chunk failed. Detailed error: Unexpected > java.net.SocketTimeoutException: Read timed out > > FAILED. > > Activity done: > " > > Has anyone experienced this too? What more steps can i take to isolate the > issue? How can i solve this? > > > We've already tried to; > - increase tomcat Connection timeout > - increase Java Heap Settings > - increased MySQL interaction and wait timeouts > - Verified network connection to the server > > We are currently running ODK Aggregate 1.4.7 on Centos 6.7 , 5GB RAM, > MySQL 5.1.73 >

Luwum,

It sounds like the issue is probably your network connection. I don't
know how technical you are, but you could always run Briefcase locally
on the server via the command line interface to do the pull and rsync
or Dropbox the data to where you need it to go.

Yaw

··· -- Need ODK consultants? Nafundi provides form design, server setup, in-field training, and software development for ODK. Go to https://nafundi.com to get started.

On Mon, Apr 11, 2016 at 12:55 PM, Luwum Patrick luwyxx@gmail.com wrote:

Hello Team,
My team conducting a survey can push data to ODK but during pulling of data
we get the error below;
"
Error: retrieving next chunk of instances from server...

NOT ALL SUBMISSIONS RETRIEVED: Error fetching list of submissions: Fetch of
submission download chunk failed. Detailed error: Unexpected
java.net.SocketTimeoutException: Read timed out

FAILED.

Activity done:
"

Has anyone experienced this too? What more steps can i take to isolate the
issue? How can i solve this?

We've already tried to;

  • increase tomcat Connection timeout
  • increase Java Heap Settings
  • increased MySQL interaction and wait timeouts
  • Verified network connection to the server

We are currently running ODK Aggregate 1.4.7 on Centos 6.7 , 5GB RAM, MySQL
5.1.73

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I am fairly technical however i don't know the commands to pull data from
the command line. Please share them with me.

··· On Monday, 11 April 2016 14:02:58 UTC+3, Yaw Anokwa wrote: > > Luwum, > > It sounds like the issue is probably your network connection. I don't > know how technical you are, but you could always run Briefcase locally > on the server via the command line interface to do the pull and rsync > or Dropbox the data to where you need it to go. > > Yaw > -- > Need ODK consultants? Nafundi provides form design, server setup, > in-field training, and software development for ODK. Go to > https://nafundi.com to get started. > > On Mon, Apr 11, 2016 at 12:55 PM, Luwum Patrick <luw...@gmail.com > wrote: > > Hello Team, > > My team conducting a survey can push data to ODK but during pulling of > data > > we get the error below; > > " > > Error: retrieving next chunk of instances from server... > > > > NOT ALL SUBMISSIONS RETRIEVED: Error fetching list of submissions: Fetch > of > > submission download chunk failed. Detailed error: Unexpected > > java.net.SocketTimeoutException: Read timed out > > > > FAILED. > > > > Activity done: > > " > > > > Has anyone experienced this too? What more steps can i take to isolate > the > > issue? How can i solve this? > > > > > > We've already tried to; > > - increase tomcat Connection timeout > > - increase Java Heap Settings > > - increased MySQL interaction and wait timeouts > > - Verified network connection to the server > > > > We are currently running ODK Aggregate 1.4.7 on Centos 6.7 , 5GB RAM, > MySQL > > 5.1.73 > > > > -- > > -- > > Post: opend...@googlegroups.com > > Unsubscribe: opendatakit...@googlegroups.com > > Options: http://groups.google.com/group/opendatakit?hl=en > > > > --- > > You received this message because you are subscribed to the Google > Groups > > "ODK Community" group. > > To unsubscribe from this group and stop receiving emails from it, send > an > > email to opendatakit...@googlegroups.com . > > For more options, visit https://groups.google.com/d/optout. >

Luwum,

The CLI interface examples are at https://opendatakit.org/use/briefcase/

Can you confirm that you are running Briefcase on the server that
houses the data? That is, you've SSHed into the Centos box, and you
are running the Briefcase jar locally on that machine.

Yaw

··· -- Need ODK consultants? Nafundi provides form design, server setup, in-field training, and software development for ODK. Go to https://nafundi.com to get started.

On Mon, Apr 11, 2016 at 3:51 PM, Luwum Patrick luwyxx@gmail.com wrote:

The command-line pull does the same. pulls for a bit then throws an error.
attached is the stack trace.

On Monday, 11 April 2016 13:55:01 UTC+3, Luwum Patrick wrote:

Hello Team,
My team conducting a survey can push data to ODK but during pulling of
data we get the error below;
"
Error: retrieving next chunk of instances from server...

NOT ALL SUBMISSIONS RETRIEVED: Error fetching list of submissions: Fetch
of
submission download chunk failed. Detailed error: Unexpected
java.net.SocketTimeoutException: Read timed out

FAILED.

Activity done:
"

Has anyone experienced this too? What more steps can i take to isolate the
issue? How can i solve this?

We've already tried to;

  • increase tomcat Connection timeout
  • increase Java Heap Settings
  • increased MySQL interaction and wait timeouts
  • Verified network connection to the server

We are currently running ODK Aggregate 1.4.7 on Centos 6.7 , 5GB RAM,
MySQL 5.1.73

--

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Yes i can confirm this. also the https://domain.ug aggregate url used
resolves to localhost (127.0.0.1)

··· On Monday, 11 April 2016 17:06:53 UTC+3, Yaw Anokwa wrote: > > Luwum, > > The CLI interface examples are at https://opendatakit.org/use/briefcase/ > > Can you confirm that you are running Briefcase on the server that > houses the data? That is, you've SSHed into the Centos box, and you > are running the Briefcase jar locally on that machine. > > Yaw > -- > Need ODK consultants? Nafundi provides form design, server setup, > in-field training, and software development for ODK. Go to > https://nafundi.com to get started. > > On Mon, Apr 11, 2016 at 3:51 PM, Luwum Patrick <luw...@gmail.com > wrote: > > The command-line pull does the same. pulls for a bit then throws an > error. > > attached is the stack trace. > > > > On Monday, 11 April 2016 13:55:01 UTC+3, Luwum Patrick wrote: > >> > >> Hello Team, > >> My team conducting a survey can push data to ODK but during pulling of > >> data we get the error below; > >> " > >> Error: retrieving next chunk of instances from server... > >> > >> NOT ALL SUBMISSIONS RETRIEVED: Error fetching list of submissions: > Fetch > >> of > >> submission download chunk failed. Detailed error: Unexpected > >> java.net.SocketTimeoutException: Read timed out > >> > >> FAILED. > >> > >> Activity done: > >> " > >> > >> Has anyone experienced this too? What more steps can i take to isolate > the > >> issue? How can i solve this? > >> > >> > >> We've already tried to; > >> - increase tomcat Connection timeout > >> - increase Java Heap Settings > >> - increased MySQL interaction and wait timeouts > >> - Verified network connection to the server > >> > >> We are currently running ODK Aggregate 1.4.7 on Centos 6.7 , 5GB RAM, > >> MySQL 5.1.73 > > > > -- > > -- > > Post: opend...@googlegroups.com > > Unsubscribe: opendatakit...@googlegroups.com > > Options: http://groups.google.com/group/opendatakit?hl=en > > > > --- > > You received this message because you are subscribed to the Google > Groups > > "ODK Community" group. > > To unsubscribe from this group and stop receiving emails from it, send > an > > email to opendatakit...@googlegroups.com . > > For more options, visit https://groups.google.com/d/optout. >

Curious. Next step then is to check the Tomcat and MySQL logs to see
if there is a failure at the same time as you see in Briefcase.

Yaw

··· -- Need ODK consultants? Nafundi provides form design, server setup, in-field training, and software development for ODK. Go to https://nafundi.com to get started.

On Mon, Apr 11, 2016 at 4:40 PM, Luwum Patrick luwyxx@gmail.com wrote:

Yes i can confirm this. also the https://domain.ug aggregate url used
resolves to localhost (127.0.0.1)

On Monday, 11 April 2016 17:06:53 UTC+3, Yaw Anokwa wrote:

Luwum,

The CLI interface examples are at https://opendatakit.org/use/briefcase/

Can you confirm that you are running Briefcase on the server that
houses the data? That is, you've SSHed into the Centos box, and you
are running the Briefcase jar locally on that machine.

Yaw

Need ODK consultants? Nafundi provides form design, server setup,
in-field training, and software development for ODK. Go to
https://nafundi.com to get started.

On Mon, Apr 11, 2016 at 3:51 PM, Luwum Patrick luw...@gmail.com wrote:

The command-line pull does the same. pulls for a bit then throws an
error.
attached is the stack trace.

On Monday, 11 April 2016 13:55:01 UTC+3, Luwum Patrick wrote:

Hello Team,
My team conducting a survey can push data to ODK but during pulling of
data we get the error below;
"
Error: retrieving next chunk of instances from server...

NOT ALL SUBMISSIONS RETRIEVED: Error fetching list of submissions:
Fetch
of
submission download chunk failed. Detailed error: Unexpected
java.net.SocketTimeoutException: Read timed out

FAILED.

Activity done:
"

Has anyone experienced this too? What more steps can i take to isolate
the
issue? How can i solve this?

We've already tried to;

  • increase tomcat Connection timeout
  • increase Java Heap Settings
  • increased MySQL interaction and wait timeouts
  • Verified network connection to the server

We are currently running ODK Aggregate 1.4.7 on Centos 6.7 , 5GB RAM,
MySQL 5.1.73

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MySQL log shows okay but tomcat log has errors. see dump attached.

tomcat tail.txt (38.2 KB)

··· On Monday, 11 April 2016 17:49:11 UTC+3, Yaw Anokwa wrote: > > Curious. Next step then is to check the Tomcat and MySQL logs to see > if there is a failure at the same time as you see in Briefcase. > > Yaw > -- > Need ODK consultants? Nafundi provides form design, server setup, > in-field training, and software development for ODK. Go to > https://nafundi.com to get started. > > On Mon, Apr 11, 2016 at 4:40 PM, Luwum Patrick <luw...@gmail.com > wrote: > > Yes i can confirm this. also the https://domain.ug aggregate url used > > resolves to localhost (127.0.0.1) > > > > On Monday, 11 April 2016 17:06:53 UTC+3, Yaw Anokwa wrote: > >> > >> Luwum, > >> > >> The CLI interface examples are at > https://opendatakit.org/use/briefcase/ > >> > >> Can you confirm that you are running Briefcase on the server that > >> houses the data? That is, you've SSHed into the Centos box, and you > >> are running the Briefcase jar locally on that machine. > >> > >> Yaw > >> -- > >> Need ODK consultants? Nafundi provides form design, server setup, > >> in-field training, and software development for ODK. Go to > >> https://nafundi.com to get started. > >> > >> On Mon, Apr 11, 2016 at 3:51 PM, Luwum Patrick wrote: > >> > The command-line pull does the same. pulls for a bit then throws an > >> > error. > >> > attached is the stack trace. > >> > > >> > On Monday, 11 April 2016 13:55:01 UTC+3, Luwum Patrick wrote: > >> >> > >> >> Hello Team, > >> >> My team conducting a survey can push data to ODK but during pulling > of > >> >> data we get the error below; > >> >> " > >> >> Error: retrieving next chunk of instances from server... > >> >> > >> >> NOT ALL SUBMISSIONS RETRIEVED: Error fetching list of submissions: > >> >> Fetch > >> >> of > >> >> submission download chunk failed. Detailed error: Unexpected > >> >> java.net.SocketTimeoutException: Read timed out > >> >> > >> >> FAILED. > >> >> > >> >> Activity done: > >> >> " > >> >> > >> >> Has anyone experienced this too? What more steps can i take to > isolate > >> >> the > >> >> issue? How can i solve this? > >> >> > >> >> > >> >> We've already tried to; > >> >> - increase tomcat Connection timeout > >> >> - increase Java Heap Settings > >> >> - increased MySQL interaction and wait timeouts > >> >> - Verified network connection to the server > >> >> > >> >> We are currently running ODK Aggregate 1.4.7 on Centos 6.7 , 5GB > RAM, > >> >> MySQL 5.1.73 > >> > > >> > -- > >> > -- > >> > Post: opend...@googlegroups.com > >> > Unsubscribe: opendatakit...@googlegroups.com > >> > Options: http://groups.google.com/group/opendatakit?hl=en > >> > > >> > --- > >> > You received this message because you are subscribed to the Google > >> > Groups > >> > "ODK Community" group. > >> > To unsubscribe from this group and stop receiving emails from it, > send > >> > an > >> > email to opendatakit...@googlegroups.com. > >> > For more options, visit https://groups.google.com/d/optout. > > > > -- > > -- > > Post: opend...@googlegroups.com > > Unsubscribe: opendatakit...@googlegroups.com > > Options: http://groups.google.com/group/opendatakit?hl=en > > > > --- > > You received this message because you are subscribed to the Google > Groups > > "ODK Community" group. > > To unsubscribe from this group and stop receiving emails from it, send > an > > email to opendatakit...@googlegroups.com . > > For more options, visit https://groups.google.com/d/optout. >

Just had an idea. Does this happen with just one form or all forms?
What if you use a single question form?

Yaw

··· -- Need ODK consultants? Nafundi provides form design, server setup, in-field training, and software development for ODK. Go to https://nafundi.com to get started.

On Mon, Apr 11, 2016 at 5:15 PM, Luwum Patrick luwyxx@gmail.com wrote:

MySQL log shows okay but tomcat log has errors. see dump attached.

On Monday, 11 April 2016 17:49:11 UTC+3, Yaw Anokwa wrote:

Curious. Next step then is to check the Tomcat and MySQL logs to see
if there is a failure at the same time as you see in Briefcase.

Yaw

Need ODK consultants? Nafundi provides form design, server setup,
in-field training, and software development for ODK. Go to
https://nafundi.com to get started.

On Mon, Apr 11, 2016 at 4:40 PM, Luwum Patrick luw...@gmail.com wrote:

Yes i can confirm this. also the https://domain.ug aggregate url used
resolves to localhost (127.0.0.1)

On Monday, 11 April 2016 17:06:53 UTC+3, Yaw Anokwa wrote:

Luwum,

The CLI interface examples are at
https://opendatakit.org/use/briefcase/

Can you confirm that you are running Briefcase on the server that
houses the data? That is, you've SSHed into the Centos box, and you
are running the Briefcase jar locally on that machine.

Yaw

Need ODK consultants? Nafundi provides form design, server setup,
in-field training, and software development for ODK. Go to
https://nafundi.com to get started.

On Mon, Apr 11, 2016 at 3:51 PM, Luwum Patrick luw...@gmail.com wrote:

The command-line pull does the same. pulls for a bit then throws an
error.
attached is the stack trace.

On Monday, 11 April 2016 13:55:01 UTC+3, Luwum Patrick wrote:

Hello Team,
My team conducting a survey can push data to ODK but during pulling
of
data we get the error below;
"
Error: retrieving next chunk of instances from server...

NOT ALL SUBMISSIONS RETRIEVED: Error fetching list of submissions:
Fetch
of
submission download chunk failed. Detailed error: Unexpected
java.net.SocketTimeoutException: Read timed out

FAILED.

Activity done:
"

Has anyone experienced this too? What more steps can i take to
isolate
the
issue? How can i solve this?

We've already tried to;

  • increase tomcat Connection timeout
  • increase Java Heap Settings
  • increased MySQL interaction and wait timeouts
  • Verified network connection to the server

We are currently running ODK Aggregate 1.4.7 on Centos 6.7 , 5GB
RAM,
MySQL 5.1.73

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It happens for 3 out of 5 forms configured on ODK. Am thinking these other
forms have alot of data associated with them or something. What do you
think?

··· On Tuesday, 3 May 2016 11:21:13 UTC+3, Yaw Anokwa wrote: > > Just had an idea. Does this happen with just one form or all forms? > What if you use a single question form? > > Yaw > -- > Need ODK consultants? Nafundi provides form design, server setup, > in-field training, and software development for ODK. Go to > https://nafundi.com to get started. > > On Mon, Apr 11, 2016 at 5:15 PM, Luwum Patrick <luw...@gmail.com > wrote: > > MySQL log shows okay but tomcat log has errors. see dump attached. > > > > On Monday, 11 April 2016 17:49:11 UTC+3, Yaw Anokwa wrote: > >> > >> Curious. Next step then is to check the Tomcat and MySQL logs to see > >> if there is a failure at the same time as you see in Briefcase. > >> > >> Yaw > >> -- > >> Need ODK consultants? Nafundi provides form design, server setup, > >> in-field training, and software development for ODK. Go to > >> https://nafundi.com to get started. > >> > >> On Mon, Apr 11, 2016 at 4:40 PM, Luwum Patrick wrote: > >> > Yes i can confirm this. also the https://domain.ug aggregate url > used > >> > resolves to localhost (127.0.0.1) > >> > > >> > On Monday, 11 April 2016 17:06:53 UTC+3, Yaw Anokwa wrote: > >> >> > >> >> Luwum, > >> >> > >> >> The CLI interface examples are at > >> >> https://opendatakit.org/use/briefcase/ > >> >> > >> >> Can you confirm that you are running Briefcase on the server that > >> >> houses the data? That is, you've SSHed into the Centos box, and you > >> >> are running the Briefcase jar locally on that machine. > >> >> > >> >> Yaw > >> >> -- > >> >> Need ODK consultants? Nafundi provides form design, server setup, > >> >> in-field training, and software development for ODK. Go to > >> >> https://nafundi.com to get started. > >> >> > >> >> On Mon, Apr 11, 2016 at 3:51 PM, Luwum Patrick wrote: > >> >> > The command-line pull does the same. pulls for a bit then throws > an > >> >> > error. > >> >> > attached is the stack trace. > >> >> > > >> >> > On Monday, 11 April 2016 13:55:01 UTC+3, Luwum Patrick wrote: > >> >> >> > >> >> >> Hello Team, > >> >> >> My team conducting a survey can push data to ODK but during > pulling > >> >> >> of > >> >> >> data we get the error below; > >> >> >> " > >> >> >> Error: retrieving next chunk of instances from server... > >> >> >> > >> >> >> NOT ALL SUBMISSIONS RETRIEVED: Error fetching list of > submissions: > >> >> >> Fetch > >> >> >> of > >> >> >> submission download chunk failed. Detailed error: Unexpected > >> >> >> java.net.SocketTimeoutException: Read timed out > >> >> >> > >> >> >> FAILED. > >> >> >> > >> >> >> Activity done: > >> >> >> " > >> >> >> > >> >> >> Has anyone experienced this too? What more steps can i take to > >> >> >> isolate > >> >> >> the > >> >> >> issue? How can i solve this? > >> >> >> > >> >> >> > >> >> >> We've already tried to; > >> >> >> - increase tomcat Connection timeout > >> >> >> - increase Java Heap Settings > >> >> >> - increased MySQL interaction and wait timeouts > >> >> >> - Verified network connection to the server > >> >> >> > >> >> >> We are currently running ODK Aggregate 1.4.7 on Centos 6.7 , 5GB > >> >> >> RAM, > >> >> >> MySQL 5.1.73 > >> >> > > >> >> > -- > >> >> > -- > >> >> > Post: opend...@googlegroups.com > >> >> > Unsubscribe: opendatakit...@googlegroups.com > >> >> > Options: http://groups.google.com/group/opendatakit?hl=en > >> >> > > >> >> > --- > >> >> > You received this message because you are subscribed to the Google > >> >> > Groups > >> >> > "ODK Community" group. > >> >> > To unsubscribe from this group and stop receiving emails from it, > >> >> > send > >> >> > an > >> >> > email to opendatakit...@googlegroups.com. > >> >> > For more options, visit https://groups.google.com/d/optout. > >> > > >> > -- > >> > -- > >> > Post: opend...@googlegroups.com > >> > Unsubscribe: opendatakit...@googlegroups.com > >> > Options: http://groups.google.com/group/opendatakit?hl=en > >> > > >> > --- > >> > You received this message because you are subscribed to the Google > >> > Groups > >> > "ODK Community" group. > >> > To unsubscribe from this group and stop receiving emails from it, > send > >> > an > >> > email to opendatakit...@googlegroups.com. > >> > For more options, visit https://groups.google.com/d/optout. > > > > -- > > -- > > Post: opend...@googlegroups.com > > Unsubscribe: opendatakit...@googlegroups.com > > Options: http://groups.google.com/group/opendatakit?hl=en > > > > --- > > You received this message because you are subscribed to the Google > Groups > > "ODK Community" group. > > To unsubscribe from this group and stop receiving emails from it, send > an > > email to opendatakit...@googlegroups.com . > > For more options, visit https://groups.google.com/d/optout. >

Compare the size of forms (number of nodes) and submissions for the 3
that fail and the 2 that don't. Is there a pattern there?

Wherever there is strange behavior on Aggregate, it's almost always
related to running out of RAM. Turn on garbage collection logging on
Tomcat and see if it correlates to the timeouts.

Yaw

··· -- Need ODK consultants? Nafundi provides form design, server setup, in-field training, and software development for ODK. Go to https://nafundi.com to get started.

On Wed, May 4, 2016 at 2:49 PM, Luwum Patrick luwyxx@gmail.com wrote:

It happens for 3 out of 5 forms configured on ODK. Am thinking these other
forms have alot of data associated with them or something. What do you
think?

On Tuesday, 3 May 2016 11:21:13 UTC+3, Yaw Anokwa wrote:

Just had an idea. Does this happen with just one form or all forms?
What if you use a single question form?

Yaw

Need ODK consultants? Nafundi provides form design, server setup,
in-field training, and software development for ODK. Go to
https://nafundi.com to get started.

On Mon, Apr 11, 2016 at 5:15 PM, Luwum Patrick luw...@gmail.com wrote:

MySQL log shows okay but tomcat log has errors. see dump attached.

On Monday, 11 April 2016 17:49:11 UTC+3, Yaw Anokwa wrote:

Curious. Next step then is to check the Tomcat and MySQL logs to see
if there is a failure at the same time as you see in Briefcase.

Yaw

Need ODK consultants? Nafundi provides form design, server setup,
in-field training, and software development for ODK. Go to
https://nafundi.com to get started.

On Mon, Apr 11, 2016 at 4:40 PM, Luwum Patrick luw...@gmail.com wrote:

Yes i can confirm this. also the https://domain.ug aggregate url used
resolves to localhost (127.0.0.1)

On Monday, 11 April 2016 17:06:53 UTC+3, Yaw Anokwa wrote:

Luwum,

The CLI interface examples are at
https://opendatakit.org/use/briefcase/

Can you confirm that you are running Briefcase on the server that
houses the data? That is, you've SSHed into the Centos box, and you
are running the Briefcase jar locally on that machine.

Yaw

Need ODK consultants? Nafundi provides form design, server setup,
in-field training, and software development for ODK. Go to
https://nafundi.com to get started.

On Mon, Apr 11, 2016 at 3:51 PM, Luwum Patrick luw...@gmail.com wrote:

The command-line pull does the same. pulls for a bit then throws
an
error.
attached is the stack trace.

On Monday, 11 April 2016 13:55:01 UTC+3, Luwum Patrick wrote:

Hello Team,
My team conducting a survey can push data to ODK but during
pulling
of
data we get the error below;
"
Error: retrieving next chunk of instances from server...

NOT ALL SUBMISSIONS RETRIEVED: Error fetching list of
submissions:
Fetch
of
submission download chunk failed. Detailed error: Unexpected
java.net.SocketTimeoutException: Read timed out

FAILED.

Activity done:
"

Has anyone experienced this too? What more steps can i take to
isolate
the
issue? How can i solve this?

We've already tried to;

  • increase tomcat Connection timeout
  • increase Java Heap Settings
  • increased MySQL interaction and wait timeouts
  • Verified network connection to the server

We are currently running ODK Aggregate 1.4.7 on Centos 6.7 , 5GB
RAM,
MySQL 5.1.73

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Yes there is a pattern, i couldnt access the exact number of nodes but a
listing of the mysql table files shows considerably larger tables for the
forms that time out , they are upward of 8GB+.

Also top command shows RAM and CPU is being considerably maxed out by MySQL
and Java. am guessing this a result query interaction between MySQL and
TOMCAT. Is there a way to optimize this for the resources available on my
server? or maybe away to split the DB or something into smaller manageable
size? or anything that helps!!!!

··· On Wednesday, 4 May 2016 16:03:42 UTC+3, Yaw Anokwa wrote: > > Compare the size of forms (number of nodes) and submissions for the 3 > that fail and the 2 that don't. Is there a pattern there? > > Wherever there is strange behavior on Aggregate, it's almost always > related to running out of RAM. Turn on garbage collection logging on > Tomcat and see if it correlates to the timeouts. > > Yaw > -- > Need ODK consultants? Nafundi provides form design, server setup, > in-field training, and software development for ODK. Go to > https://nafundi.com to get started. > > On Wed, May 4, 2016 at 2:49 PM, Luwum Patrick <luw...@gmail.com > wrote: > > It happens for 3 out of 5 forms configured on ODK. Am thinking these > other > > forms have alot of data associated with them or something. What do you > > think? > > > > On Tuesday, 3 May 2016 11:21:13 UTC+3, Yaw Anokwa wrote: > >> > >> Just had an idea. Does this happen with just one form or all forms? > >> What if you use a single question form? > >> > >> Yaw > >> -- > >> Need ODK consultants? Nafundi provides form design, server setup, > >> in-field training, and software development for ODK. Go to > >> https://nafundi.com to get started. > >> > >> On Mon, Apr 11, 2016 at 5:15 PM, Luwum Patrick wrote: > >> > MySQL log shows okay but tomcat log has errors. see dump attached. > >> > > >> > On Monday, 11 April 2016 17:49:11 UTC+3, Yaw Anokwa wrote: > >> >> > >> >> Curious. Next step then is to check the Tomcat and MySQL logs to see > >> >> if there is a failure at the same time as you see in Briefcase. > >> >> > >> >> Yaw > >> >> -- > >> >> Need ODK consultants? Nafundi provides form design, server setup, > >> >> in-field training, and software development for ODK. Go to > >> >> https://nafundi.com to get started. > >> >> > >> >> On Mon, Apr 11, 2016 at 4:40 PM, Luwum Patrick wrote: > >> >> > Yes i can confirm this. also the https://domain.ug aggregate url > used > >> >> > resolves to localhost (127.0.0.1) > >> >> > > >> >> > On Monday, 11 April 2016 17:06:53 UTC+3, Yaw Anokwa wrote: > >> >> >> > >> >> >> Luwum, > >> >> >> > >> >> >> The CLI interface examples are at > >> >> >> https://opendatakit.org/use/briefcase/ > >> >> >> > >> >> >> Can you confirm that you are running Briefcase on the server that > >> >> >> houses the data? That is, you've SSHed into the Centos box, and > you > >> >> >> are running the Briefcase jar locally on that machine. > >> >> >> > >> >> >> Yaw > >> >> >> -- > >> >> >> Need ODK consultants? Nafundi provides form design, server setup, > >> >> >> in-field training, and software development for ODK. Go to > >> >> >> https://nafundi.com to get started. > >> >> >> > >> >> >> On Mon, Apr 11, 2016 at 3:51 PM, Luwum Patrick wrote: > >> >> >> > The command-line pull does the same. pulls for a bit then > throws > >> >> >> > an > >> >> >> > error. > >> >> >> > attached is the stack trace. > >> >> >> > > >> >> >> > On Monday, 11 April 2016 13:55:01 UTC+3, Luwum Patrick wrote: > >> >> >> >> > >> >> >> >> Hello Team, > >> >> >> >> My team conducting a survey can push data to ODK but during > >> >> >> >> pulling > >> >> >> >> of > >> >> >> >> data we get the error below; > >> >> >> >> " > >> >> >> >> Error: retrieving next chunk of instances from server... > >> >> >> >> > >> >> >> >> NOT ALL SUBMISSIONS RETRIEVED: Error fetching list of > >> >> >> >> submissions: > >> >> >> >> Fetch > >> >> >> >> of > >> >> >> >> submission download chunk failed. Detailed error: Unexpected > >> >> >> >> java.net.SocketTimeoutException: Read timed out > >> >> >> >> > >> >> >> >> FAILED. > >> >> >> >> > >> >> >> >> Activity done: > >> >> >> >> " > >> >> >> >> > >> >> >> >> Has anyone experienced this too? What more steps can i take to > >> >> >> >> isolate > >> >> >> >> the > >> >> >> >> issue? How can i solve this? > >> >> >> >> > >> >> >> >> > >> >> >> >> We've already tried to; > >> >> >> >> - increase tomcat Connection timeout > >> >> >> >> - increase Java Heap Settings > >> >> >> >> - increased MySQL interaction and wait timeouts > >> >> >> >> - Verified network connection to the server > >> >> >> >> > >> >> >> >> We are currently running ODK Aggregate 1.4.7 on Centos 6.7 , > 5GB > >> >> >> >> RAM, > >> >> >> >> MySQL 5.1.73 > >> >> >> > > >> >> >> > -- > >> >> >> > -- > >> >> >> > Post: opend...@googlegroups.com > >> >> >> > Unsubscribe: opendatakit...@googlegroups.com > >> >> >> > Options: http://groups.google.com/group/opendatakit?hl=en > >> >> >> > > >> >> >> > --- > >> >> >> > You received this message because you are subscribed to the > Google > >> >> >> > Groups > >> >> >> > "ODK Community" group. > >> >> >> > To unsubscribe from this group and stop receiving emails from > it, > >> >> >> > send > >> >> >> > an > >> >> >> > email to opendatakit...@googlegroups.com. > >> >> >> > For more options, visit https://groups.google.com/d/optout. > >> >> > > >> >> > -- > >> >> > -- > >> >> > Post: opend...@googlegroups.com > >> >> > Unsubscribe: opendatakit...@googlegroups.com > >> >> > Options: http://groups.google.com/group/opendatakit?hl=en > >> >> > > >> >> > --- > >> >> > You received this message because you are subscribed to the Google > >> >> > Groups > >> >> > "ODK Community" group. > >> >> > To unsubscribe from this group and stop receiving emails from it, > >> >> > send > >> >> > an > >> >> > email to opendatakit...@googlegroups.com. > >> >> > For more options, visit https://groups.google.com/d/optout. > >> > > >> > -- > >> > -- > >> > Post: opend...@googlegroups.com > >> > Unsubscribe: opendatakit...@googlegroups.com > >> > Options: http://groups.google.com/group/opendatakit?hl=en > >> > > >> > --- > >> > You received this message because you are subscribed to the Google > >> > Groups > >> > "ODK Community" group. > >> > To unsubscribe from this group and stop receiving emails from it, > send > >> > an > >> > email to opendatakit...@googlegroups.com. > >> > For more options, visit https://groups.google.com/d/optout. > > > > -- > > -- > > Post: opend...@googlegroups.com > > Unsubscribe: opendatakit...@googlegroups.com > > Options: http://groups.google.com/group/opendatakit?hl=en > > > > --- > > You received this message because you are subscribed to the Google > Groups > > "ODK Community" group. > > To unsubscribe from this group and stop receiving emails from it, send > an > > email to opendatakit...@googlegroups.com . > > For more options, visit https://groups.google.com/d/optout. >

The easiest solution is to add a lot more RAM, say 16 GB.

You could also try moving the MySQL DB to another machine on the same
network and allocate all RAM to Tomcat, but that still might not work.

This is why we try to deploy on the cloud. Makes scaling up and down a
lot easier...

Yaw

··· On Wed, May 4, 2016 at 3:32 PM, Luwum Patrick wrote: > Yes there is a pattern, i couldnt access the exact number of nodes but a > listing of the mysql table files shows considerably larger tables for the > forms that time out , they are upward of 8GB+. > > Also top command shows RAM and CPU is being considerably maxed out by MySQL > and Java. am guessing this a result query interaction between MySQL and > TOMCAT. Is there a way to optimize this for the resources available on my > server? or maybe away to split the DB or something into smaller manageable > size? or anything that helps!!!! > > On Wednesday, 4 May 2016 16:03:42 UTC+3, Yaw Anokwa wrote: >> >> Compare the size of forms (number of nodes) and submissions for the 3 >> that fail and the 2 that don't. Is there a pattern there? >> >> Wherever there is strange behavior on Aggregate, it's almost always >> related to running out of RAM. Turn on garbage collection logging on >> Tomcat and see if it correlates to the timeouts. >> >> Yaw >> -- >> Need ODK consultants? Nafundi provides form design, server setup, >> in-field training, and software development for ODK. Go to >> https://nafundi.com to get started. >> >> On Wed, May 4, 2016 at 2:49 PM, Luwum Patrick wrote: >> > It happens for 3 out of 5 forms configured on ODK. Am thinking these >> > other >> > forms have alot of data associated with them or something. What do you >> > think? >> > >> > On Tuesday, 3 May 2016 11:21:13 UTC+3, Yaw Anokwa wrote: >> >> >> >> Just had an idea. Does this happen with just one form or all forms? >> >> What if you use a single question form? >> >> >> >> Yaw >> >> -- >> >> Need ODK consultants? Nafundi provides form design, server setup, >> >> in-field training, and software development for ODK. Go to >> >> https://nafundi.com to get started. >> >> >> >> On Mon, Apr 11, 2016 at 5:15 PM, Luwum Patrick wrote: >> >> > MySQL log shows okay but tomcat log has errors. see dump attached. >> >> > >> >> > On Monday, 11 April 2016 17:49:11 UTC+3, Yaw Anokwa wrote: >> >> >> >> >> >> Curious. Next step then is to check the Tomcat and MySQL logs to see >> >> >> if there is a failure at the same time as you see in Briefcase. >> >> >> >> >> >> Yaw >> >> >> -- >> >> >> Need ODK consultants? Nafundi provides form design, server setup, >> >> >> in-field training, and software development for ODK. Go to >> >> >> https://nafundi.com to get started. >> >> >> >> >> >> On Mon, Apr 11, 2016 at 4:40 PM, Luwum Patrick wrote: >> >> >> > Yes i can confirm this. also the https://domain.ug aggregate url >> >> >> > used >> >> >> > resolves to localhost (127.0.0.1) >> >> >> > >> >> >> > On Monday, 11 April 2016 17:06:53 UTC+3, Yaw Anokwa wrote: >> >> >> >> >> >> >> >> Luwum, >> >> >> >> >> >> >> >> The CLI interface examples are at >> >> >> >> https://opendatakit.org/use/briefcase/ >> >> >> >> >> >> >> >> Can you confirm that you are running Briefcase on the server that >> >> >> >> houses the data? That is, you've SSHed into the Centos box, and >> >> >> >> you >> >> >> >> are running the Briefcase jar locally on that machine. >> >> >> >> >> >> >> >> Yaw >> >> >> >> -- >> >> >> >> Need ODK consultants? Nafundi provides form design, server setup, >> >> >> >> in-field training, and software development for ODK. Go to >> >> >> >> https://nafundi.com to get started. >> >> >> >> >> >> >> >> On Mon, Apr 11, 2016 at 3:51 PM, Luwum Patrick wrote: >> >> >> >> > The command-line pull does the same. pulls for a bit then >> >> >> >> > throws >> >> >> >> > an >> >> >> >> > error. >> >> >> >> > attached is the stack trace. >> >> >> >> > >> >> >> >> > On Monday, 11 April 2016 13:55:01 UTC+3, Luwum Patrick wrote: >> >> >> >> >> >> >> >> >> >> Hello Team, >> >> >> >> >> My team conducting a survey can push data to ODK but during >> >> >> >> >> pulling >> >> >> >> >> of >> >> >> >> >> data we get the error below; >> >> >> >> >> " >> >> >> >> >> Error: retrieving next chunk of instances from server... >> >> >> >> >> >> >> >> >> >> NOT ALL SUBMISSIONS RETRIEVED: Error fetching list of >> >> >> >> >> submissions: >> >> >> >> >> Fetch >> >> >> >> >> of >> >> >> >> >> submission download chunk failed. Detailed error: Unexpected >> >> >> >> >> java.net.SocketTimeoutException: Read timed out >> >> >> >> >> >> >> >> >> >> FAILED. >> >> >> >> >> >> >> >> >> >> Activity done: >> >> >> >> >> " >> >> >> >> >> >> >> >> >> >> Has anyone experienced this too? What more steps can i take to >> >> >> >> >> isolate >> >> >> >> >> the >> >> >> >> >> issue? How can i solve this? >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> We've already tried to; >> >> >> >> >> - increase tomcat Connection timeout >> >> >> >> >> - increase Java Heap Settings >> >> >> >> >> - increased MySQL interaction and wait timeouts >> >> >> >> >> - Verified network connection to the server >> >> >> >> >> >> >> >> >> >> We are currently running ODK Aggregate 1.4.7 on Centos 6.7 , >> >> >> >> >> 5GB >> >> >> >> >> RAM, >> >> >> >> >> MySQL 5.1.73 >> >> >> >> > >> >> >> >> > -- >> >> >> >> > -- >> >> >> >> > Post: opend...@googlegroups.com >> >> >> >> > Unsubscribe: opendatakit...@googlegroups.com >> >> >> >> > Options: http://groups.google.com/group/opendatakit?hl=en >> >> >> >> > >> >> >> >> > --- >> >> >> >> > You received this message because you are subscribed to the >> >> >> >> > Google >> >> >> >> > Groups >> >> >> >> > "ODK Community" group. >> >> >> >> > To unsubscribe from this group and stop receiving emails from >> >> >> >> > it, >> >> >> >> > send >> >> >> >> > an >> >> >> >> > email to opendatakit...@googlegroups.com. >> >> >> >> > For more options, visit https://groups.google.com/d/optout. >> >> >> > >> >> >> > -- >> >> >> > -- >> >> >> > Post: opend...@googlegroups.com >> >> >> > Unsubscribe: opendatakit...@googlegroups.com >> >> >> > Options: http://groups.google.com/group/opendatakit?hl=en >> >> >> > >> >> >> > --- >> >> >> > You received this message because you are subscribed to the Google >> >> >> > Groups >> >> >> > "ODK Community" group. >> >> >> > To unsubscribe from this group and stop receiving emails from it, >> >> >> > send >> >> >> > an >> >> >> > email to opendatakit...@googlegroups.com. >> >> >> > For more options, visit https://groups.google.com/d/optout. >> >> > >> >> > -- >> >> > -- >> >> > Post: opend...@googlegroups.com >> >> > Unsubscribe: opendatakit...@googlegroups.com >> >> > Options: http://groups.google.com/group/opendatakit?hl=en >> >> > >> >> > --- >> >> > You received this message because you are subscribed to the Google >> >> > Groups >> >> > "ODK Community" group. >> >> > To unsubscribe from this group and stop receiving emails from it, >> >> > send >> >> > an >> >> > email to opendatakit...@googlegroups.com. >> >> > For more options, visit https://groups.google.com/d/optout. >> > >> > -- >> > -- >> > Post: opend...@googlegroups.com >> > Unsubscribe: opendatakit...@googlegroups.com >> > Options: http://groups.google.com/group/opendatakit?hl=en >> > >> > --- >> > You received this message because you are subscribed to the Google >> > Groups >> > "ODK Community" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> > an >> > email to opendatakit...@googlegroups.com. >> > For more options, visit https://groups.google.com/d/optout. > > -- > -- > Post: opendatakit@googlegroups.com > Unsubscribe: opendatakit+unsubscribe@googlegroups.com > Options: http://groups.google.com/group/opendatakit?hl=en > > --- > You received this message because you are subscribed to the Google Groups > "ODK Community" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to opendatakit+unsubscribe@googlegroups.com. > For more options, visit https://groups.google.com/d/optout.

The classic architecture is to have the database on a separate server from
the Tomcat webserver(s).

This allows you to add Tomcat webservers to scale the access-rate on the
server (generally not an issue with typical ODK Aggregate usage patterns
unless you are talking about country-wide surveys).

And it also allows the database server to have much more main memory so it
can hold many of its database indices and tables in RAM for faster access;
that becomes important as individual tables get into the 8GB range and the
indices into those tables get in to the 100MB range.

If you are using an older ODK Aggregate version (1.4.4 or earlier), or have
upgraded from an older version
, the tables created with that older version
can have poor performance due to the way MySQL manages primary key indices.
You may get better performance if you drop the primary key index and
re-create it as a non-unique hash-style index.

New database tables created by 1.4.5 or after have this performance
improvement.

With MySQL (or any database system), there are many ways a skilled database
administrator can optimize the performance of the system. If you continue
to have performance issues after increasing RAM and perhaps splitting the
servers, you should hire a MySQL database admin consultant to tune your
database.

··· On Wed, May 4, 2016 at 7:27 AM, Yaw Anokwa wrote:

The easiest solution is to add a lot more RAM, say 16 GB.

You could also try moving the MySQL DB to another machine on the same
network and allocate all RAM to Tomcat, but that still might not work.

This is why we try to deploy on the cloud. Makes scaling up and down a
lot easier...

Yaw

On Wed, May 4, 2016 at 3:32 PM, Luwum Patrick luwyxx@gmail.com wrote:

Yes there is a pattern, i couldnt access the exact number of nodes but a
listing of the mysql table files shows considerably larger tables for the
forms that time out , they are upward of 8GB+.

Also top command shows RAM and CPU is being considerably maxed out by
MySQL
and Java. am guessing this a result query interaction between MySQL and
TOMCAT. Is there a way to optimize this for the resources available on my
server? or maybe away to split the DB or something into smaller
manageable
size? or anything that helps!!!!

On Wednesday, 4 May 2016 16:03:42 UTC+3, Yaw Anokwa wrote:

Compare the size of forms (number of nodes) and submissions for the 3
that fail and the 2 that don't. Is there a pattern there?

Wherever there is strange behavior on Aggregate, it's almost always
related to running out of RAM. Turn on garbage collection logging on
Tomcat and see if it correlates to the timeouts.

Yaw

Need ODK consultants? Nafundi provides form design, server setup,
in-field training, and software development for ODK. Go to
https://nafundi.com to get started.

On Wed, May 4, 2016 at 2:49 PM, Luwum Patrick luw...@gmail.com wrote:

It happens for 3 out of 5 forms configured on ODK. Am thinking these
other
forms have alot of data associated with them or something. What do you
think?

On Tuesday, 3 May 2016 11:21:13 UTC+3, Yaw Anokwa wrote:

Just had an idea. Does this happen with just one form or all forms?
What if you use a single question form?

Yaw

Need ODK consultants? Nafundi provides form design, server setup,
in-field training, and software development for ODK. Go to
https://nafundi.com to get started.

On Mon, Apr 11, 2016 at 5:15 PM, Luwum Patrick luw...@gmail.com wrote:

MySQL log shows okay but tomcat log has errors. see dump attached.

On Monday, 11 April 2016 17:49:11 UTC+3, Yaw Anokwa wrote:

Curious. Next step then is to check the Tomcat and MySQL logs to
see

if there is a failure at the same time as you see in Briefcase.

Yaw

Need ODK consultants? Nafundi provides form design, server setup,
in-field training, and software development for ODK. Go to
https://nafundi.com to get started.

On Mon, Apr 11, 2016 at 4:40 PM, Luwum Patrick luw...@gmail.com wrote:

Yes i can confirm this. also the https://domain.ug aggregate
url

used
resolves to localhost (127.0.0.1)

On Monday, 11 April 2016 17:06:53 UTC+3, Yaw Anokwa wrote:

Luwum,

The CLI interface examples are at
https://opendatakit.org/use/briefcase/

Can you confirm that you are running Briefcase on the server
that

houses the data? That is, you've SSHed into the Centos box, and
you
are running the Briefcase jar locally on that machine.

Yaw

Need ODK consultants? Nafundi provides form design, server
setup,

in-field training, and software development for ODK. Go to
https://nafundi.com to get started.

On Mon, Apr 11, 2016 at 3:51 PM, Luwum Patrick < luw...@gmail.com> wrote:

The command-line pull does the same. pulls for a bit then
throws
an
error.
attached is the stack trace.

On Monday, 11 April 2016 13:55:01 UTC+3, Luwum Patrick wrote:

Hello Team,
My team conducting a survey can push data to ODK but during
pulling
of
data we get the error below;
"
Error: retrieving next chunk of instances from server...

NOT ALL SUBMISSIONS RETRIEVED: Error fetching list of
submissions:
Fetch
of
submission download chunk failed. Detailed error:
Unexpected

java.net.SocketTimeoutException: Read timed out

FAILED.

Activity done:
"

Has anyone experienced this too? What more steps can i take
to

isolate
the
issue? How can i solve this?

We've already tried to;

  • increase tomcat Connection timeout
  • increase Java Heap Settings
  • increased MySQL interaction and wait timeouts
  • Verified network connection to the server

We are currently running ODK Aggregate 1.4.7 on Centos 6.7 ,
5GB
RAM,
MySQL 5.1.73

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Mitch Sundt
Software Engineer
University of Washington
mitchellsundt@gmail.com

A post was split to a new topic: Partial pull or download of data from ODK aggregate server