error reading collection
StefanoSpada opened this issue · comments
Hi,
I'm trying to read in R, in chunks of 50k rows at a time, a collection of about 300k rows.
dt <- dbGetQuery(mongo, arg, querystr,(i*chunk_size),chunk_size)
This is the error I get back
Error in .jcall(rmongo.object@javaMongo, "S", "dbGetQuery", collection, :
java.lang.OutOfMemoryError: Java heap space
The system has still plenty of memory available and the user I'm running the has the ulimit set to unlimited memory allocation.
Which version of Java do you have on the system?
You can increase the java heap space by setting a environment variable
see:
http://stackoverflow.com/questions/417152/how-do-i-set-javas-min-and-max-heap-size-through-environment-variables
http://stackoverflow.com/questions/12577437/how-to-set-a-java-system-property-so-that-it-is-effective-whenever-i-start-jvm-w
java version "1.7.0_55"
OpenJDK Runtime Environment (rhel-2.4.7.1.el6_5-x86_64 u55-b13)
OpenJDK 64-Bit Server VM (build 24.51-b03, mixed mode)
On Tue, Jun 3, 2014 at 9:34 AM, Tommy Chheng notifications@github.com
wrote:
Which version of Java do you have on the system?
You can increase the java heap space by setting a environment variable
see:
—
Reply to this email directly or view it on GitHub
#30 (comment).
Stefano Spada
CEO & Founder
GRANDSLA, Inc.
http://www.grandsla.com
skype: stefano.spada
g+:stefano.spada@grandsla.com
+1 650 391 4450
Did increasing the heap space by setting the ENV variable resolve the issue?
On Tue, Jun 3, 2014 at 10:54 AM, StefanoSpada notifications@github.com
wrote:
java version "1.7.0_55"
OpenJDK Runtime Environment (rhel-2.4.7.1.el6_5-x86_64 u55-b13)
OpenJDK 64-Bit Server VM (build 24.51-b03, mixed mode)
On Tue, Jun 3, 2014 at 9:34 AM, Tommy Chheng notifications@github.com
wrote:Which version of Java do you have on the system?
You can increase the java heap space by setting a environment variable
see:
—
Reply to this email directly or view it on GitHub
#30 (comment).Stefano Spada
CEO & Founder
GRANDSLA, Inc.
http://www.grandsla.com
skype: stefano.spada
g+:stefano.spada@grandsla.com
+1 650 391 4450—
Reply to this email directly or view it on GitHub
#30 (comment).
Tommy Chheng
I increased the java heap as suggested by setting
JAVA_OPTS="-Xms512m -Xmx1g"
still I get the error ...
Error in .jcall(rmongo.object@javaMongo, "S", "dbGetQuery", collection, :
java.lang.OutOfMemoryError: Java heap space
16
stop(structure(list(message = "java.lang.OutOfMemoryError: Java heap
space", call = .jcall(rmongo.object@javaMongo, "S", "dbGetQuery",
collection, query, keys, skip, limit), jobj = <S4 object of class
structure("jobjRef", package = "rJava")>), .Names = c("message", "call",
"jobj"), class = c("OutOfMemoryError", "VirtualMachineError", "Error",
"Throwable", "Object", "Exception", "error", "condition" )))
15
.jcheck(silent = FALSE)
14
.jcall(rmongo.object@javaMongo, "S", "dbGetQuery", collection, query, keys,
skip, limit)
13
dbGetQueryForKeys(rmongo.object, collection, query, "{}", skip, limit)
12
dbGetQueryForKeys(rmongo.object, collection, query, "{}", skip, limit)
11
dbGetQuery(mongo, arg, querystr, (i * chunk_size), chunk_size)
10
dbGetQuery(mongo, arg, querystr, (i * chunk_size), chunk_size) at
rserveSource.R#55
9
connect_rmongo(collection) at
rserveSource.R#97
8
eval(expr, envir, enclos)
7
eval(ei, envir)
6
withVisible(eval(ei, envir))
5
source("/home/stefano/git/server/server-mgmt/rserveSource.R") at
2mongo.R#3
4
eval(expr, envir, enclos)
3
eval(ei, envir)
2
withVisible(eval(ei, envir))
1
source("2mongo.R")
On Tue, Jun 3, 2014 at 3:25 PM, Tommy Chheng notifications@github.com
wrote:
Did increasing the heap space by setting the ENV variable resolve the
issue?On Tue, Jun 3, 2014 at 10:54 AM, StefanoSpada notifications@github.com
wrote:java version "1.7.0_55"
OpenJDK Runtime Environment (rhel-2.4.7.1.el6_5-x86_64 u55-b13)
OpenJDK 64-Bit Server VM (build 24.51-b03, mixed mode)
On Tue, Jun 3, 2014 at 9:34 AM, Tommy Chheng notifications@github.com
wrote:Which version of Java do you have on the system?
You can increase the java heap space by setting a environment variable
see:
—
Reply to this email directly or view it on GitHub
#30 (comment).Stefano Spada
CEO & Founder
GRANDSLA, Inc.
http://www.grandsla.com
skype: stefano.spada
g+:stefano.spada@grandsla.com
+1 650 391 4450—
Reply to this email directly or view it on GitHub
#30 (comment).Tommy Chheng
—
Reply to this email directly or view it on GitHub
#30 (comment).
Stefano Spada
CEO & Founder
GRANDSLA, Inc.
http://www.grandsla.com
skype: stefano.spada
g+:stefano.spada@grandsla.com
+1 650 391 4450
You need to set JAVA_TOOL_OPTIONS or _JAVA_TOOL_OPTIONS, not JAVA_OPTS