Tomcat Memory leaks with spring saml

[aleale]

I noticed that after using "undeploy" with the tomcat manager,
a webapp i have integrated with spring saml module can't be cleanly destroyed.
Im using tomcat Apache Tomcat/7.0.30 and jvm 1.7.0_07-b10.
maybe it 's just something trivial, maybe with some @PreDestroy ad hoc can be fixed?

i copy here the log, any idea ? thanks

SEVERE: The web application [/XXXXXXX] appears to have started a thread named [Timer-3] but has failed to stop it. This is very likely to create a memory leak.
Feb 11, 2013 2:51:05 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/XXXXXXX] appears to have started a thread named [Timer-4] but has failed to stop it. This is very likely to create a memory leak.
Feb 11, 2013 2:51:05 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/XXXXXXX] appears to have started a thread named [Timer-5] but has failed to stop it. This is very likely to create a memory leak.
Feb 11, 2013 2:51:05 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/XXXXXXX] created a ThreadLocal with key of type [org.apache.xml.security.algorithms.SignatureAlgorithm$1] (value [org.apache.xml.security.algorithms.SignatureAlgorithm$1@b7ed90]) and a value of type [java.util.HashMap] (value [{http://www.w3.org/2000/09/xmldsig#rsa-sha1=org.apache.xml.security.algorithms.implementations.SignatureBaseRSA$SignatureRSASHA1@14d9abe}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Feb 11, 2013 2:51:05 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/XXXXXXX] created a ThreadLocal with key of type [org.apache.xml.security.algorithms.MessageDigestAlgorithm$1] (value [org.apache.xml.security.algorithms.MessageDigestAlgorithm$1@1ea5dbf]) and a value of type [java.util.HashMap] (value [{http://www.w3.org/2000/09/xmldsig#sha1=SHA-1 Message Digest from SUN,
}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Feb 11, 2013 2:51:05 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/XXXXXXX] created a ThreadLocal with key of type [org.apache.xml.security.utils.UnsyncBufferedOutputStream$1] (value [org.apache.xml.security.utils.UnsyncBufferedOutputStream$1@1b0e313]) and a value of type [byte[]] (value [[B@c2ca7]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Feb 11, 2013 2:51:05 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/XXXXXXX] created a ThreadLocal with key of type [org.apache.xml.security.algorithms.SignatureAlgorithm$3] (value [org.apache.xml.security.algorithms.SignatureAlgorithm$3@147c583]) and a value of type [java.util.HashMap] (value [{http://www.w3.org/2000/09/xmldsig#rsa-sha1=Sun RSA private CRT key, 2048 bits
modulus: 25220458843138597911636082222645174059800957638701512662873786633177145664977889972172064986486859345691610073852977080365156996616568380915745994494529219065967204508834645475880129482050807024112619269770688101633332928955828696710719079035175434992299707374136938565114383678184880653896234574453007308312485938127381162672227866211680767579104255079195096360770451186558497458040924872967071949604129137120883027621946269058128272082916327819876311961606282157130087210765164343667753562960183423936106413981140969589469744159507786182724438781175401447459676120550183022911336655012739901168557102114904963320883
public exponent: 65537
private exponent: 13196899386724322721267927547204952225960209352030013179546374796092952931765060665207388568008817424383209244589165555593974836885606290900463515101406694072496655999228931707346342986831382658313533616403653006230249876141450379118676310745888142456794388894537101701534515761722295989503083330969024819933001872553564520052642014949299800435233734768042558021776764320692577814467635819812403369590483557144383071336687635502871787005973336377100699424732138991811706325596092045761272450033801337270124221617075689447477817922371380829769945906078698857655281059029590106985047020411368792034566847958569692249665
prime p: 173818853026318258255347631959543211406042542097174207361195959762698347155450392604462146143429759160555177278716021487990330707096986466764452874687788606305668579706147141485204970472872473358323505808739336519588371462954635285489062203335842394805824860599393016287455757411051972606072767520612458352979
prime q: 145096221750582591151542469953603537677121483728280387649951483022158069659409431430014823935679085639112635979001467120725282669655560227341336292217820144987548206756941431527997734940136943034781971767937472473860209392716998171004573065557761396159693421160883995441452221874866812778813978700647098588577
prime exponent p: 4858875730415109771942518909164031971189861255810048489947830970066731342429240265062097009853415914401591235097849327341780762857648034043555207995911145257671007797452760474249591923742349683269735609527602186610401704687930357553991820750282485729958209021134443228079084297069551761818900927686070825681
prime exponent q: 90960499727217995292142184995404143391741095243547915324141426674479519843093771309369654415023196568090432110064166450325743297416706470243050514453959452779550758725741775093882645528717004205014225705871661146963497000164454733291467177295888230483864140995085508227597609529409387109839820481805484619553
crt coefficient: 103095279387637747289752690589814527091762536149098639755503972102073487811260148101767109907566425529455984422002092537272381544678305950897625210857406064185092296730838183063072386531399521370287157950867936448997321027963950435701717901616401461861958946946244201177503530074411072248445781551169929080856}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Feb 11, 2013 2:51:05 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/XXXXXXX] created a ThreadLocal with key of type [org.apache.xml.security.utils.UnsyncByteArrayOutputStream$1] (value [org.apache.xml.security.utils.UnsyncByteArrayOutputStream$1@f8506e]) and a value of type [byte[]] (value [[B@687290]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Feb 11, 2013 2:51:05 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/XXXXXXX] created a ThreadLocal with key of type [org.apache.xml.security.algorithms.SignatureAlgorithm$1] (value [org.apache.xml.security.algorithms.SignatureAlgorithm$1@b7ed90]) and a value of type [java.util.HashMap] (value [{http://www.w3.org/2000/09/xmldsig#rsa-sha1=org.apache.xml.security.algorithms.implementations.SignatureBaseRSA$SignatureRSASHA1@1397841}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Feb 11, 2013 2:51:05 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/XXXXXXX] created a ThreadLocal with key of type [org.apache.xml.security.algorithms.MessageDigestAlgorithm$1] (value [org.apache.xml.security.algorithms.MessageDigestAlgorithm$1@1ea5dbf]) and a value of type [java.util.HashMap] (value [{http://www.w3.org/2000/09/xmldsig#sha1=SHA-1 Message Digest from SUN,
}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Feb 11, 2013 2:51:05 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/XXXXXXX] created a ThreadLocal with key of type [org.apache.xml.security.utils.UnsyncBufferedOutputStream$1] (value [org.apache.xml.security.utils.UnsyncBufferedOutputStream$1@1b0e313]) and a value of type [byte[]] (value [[B@6264b]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Feb 11, 2013 2:51:05 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/XXXXXXX] created a ThreadLocal with key of type [org.apache.xml.security.algorithms.SignatureAlgorithm$3] (value [org.apache.xml.security.algorithms.SignatureAlgorithm$3@147c583]) and a value of type [java.util.HashMap] (value [{http://www.w3.org/2000/09/xmldsig#rsa-sha1=Sun RSA private CRT key, 2048 bits
modulus:
 .........................

[vsch]

Hi,

Thanks for reporting this. No idea so far, but I'll try to find a moment and will look into it.

Vladimír Schäfer

[aleale]

This seems to solve the problem.

public class ExtendedMetadataDelegate extends AbstractMetadataDelegate implements ExtendedMetadataProvider {

@PreDestroy
public void dest(){
if (getDelegate() instanceof AbstractMetadataProvider) {
AbstractMetadataProvider provider = (AbstractMetadataProvider) getDelegate();
provider.destroy();
} else {
System.out.println("Cannot stop provider");
}
}

let me know if this is correct.

[vsch]

Hi,

You're right, the cleanup of metadata was broken. The correct place to destroy it is in the MetadataManager's destroy() method though. I've just pushed an update.

It's worth noting that Tomcat seems to have issues with correctly terminated threads. Some discussion related to usage of the OpenSAML library (internal of the SAML Extension) recommend to restart server between each redeploy for this reason.

Cheers, Vladi

[aleale]

Hi,

You're right, the cleanup of metadata was broken. The correct place to destroy it is in the MetadataManager's destroy() method though. I've just pushed an update.

It's worth noting that Tomcat seems to have issues with correctly terminated threads. Some discussion related to usage of the OpenSAML library (internal of the SAML Extension) recommend to restart server between each redeploy for this reason.

Cheers, Vladi

Tried the module with the change on the metadata cleanup.
I have observed that Tomcat7 complains at first, but auto-solve the problem in 15 minutes after the "Undeploying".

Alessandro