OutOfMemoryError asking me to increase heap memory Follow

I am getting OutOfMemoryError asking me to increase heap memory,
each time i open the project i work on (Moodle, which is 140MB)
while it is building/refreshing indices

I have 3GB ram on a linux (debian 6.0) os
phpstorm and firefox are the only applications running (on top of KDE 4.4)

Clicking ignore or shutdown buttons (and setting higher values) does not seem to have any affect
~/PhpStorm-102.206/bin/webide.vmoptions
-Xms32m
-Xmx512m
-XX:MaxPermSize=512m
-ea
-Didea.platform.prefix=PhpStorm

Each time the OutOfMemoryError dialog opens up with "unknown" Xmx & XX:MaxPermSize values
as if they are not read from the vmoptions file.

In both cases, i continue to work without any difficulty.

What can i do?

---

phpstorm
Java HotSpot(TM) 64-Bit Server VM (build 17.1-b03, mixed mode)
[YourKit Java Profiler 8.0.29] JVMTI version 3001016d; 17.1-b03; Sun Microsystems Inc.; mixed mode, sharing; Linux; 64-bit JVM
[YourKit Java Profiler 8.0.29] Profiler agent is listening on port 10001...
[YourKit Java Profiler 8.0.29] *** HINT ***: To get profiling results, connect to the application from the profiler UI
java.lang.OutOfMemoryError: Java heap space
Dumping heap to java_pid13344.hprof ...
Heap dump file created [455448787 bytes in 41.544 secs]
ERROR: Java heap space
java.lang.OutOfMemoryError: Java heap space
        at java.util.WeakHashMap$KeySet.iterator(WeakHashMap.java:829)
        at java.util.AbstractCollection.toArray(AbstractCollection.java:162)
        at java.util.Collections$SynchronizedCollection.toArray(Collections.java:1569)
        at com.intellij.util.Timed.disposeTimed(Timed.java:91)
        at com.intellij.util.Timed$1.run(Timed.java:81)
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
        at java.util.concurrent.FutureTask$Sync.innerRunAndReset(FutureTask.java:317)
        at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:150)
        at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$101(ScheduledThreadPoolExecutor.java:98)
        at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.runPeriodic(ScheduledThreadPoolExecutor.java:180)
        at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:204)
        at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
        at java.lang.Thread.run(Thread.java:662)
Jan 23, 2011 11:58:05 AM net.sf.ehcache.distribution.MulticastKeepaliveHeartbeatSender$MulticastServerThread run
INFO: Unexpected throwable in run thread. Continuing...Java heap space
java.lang.OutOfMemoryError: Java heap space
        at java.util.HashMap.newValueIterator(HashMap.java:843)
        at java.util.HashMap$Values.iterator(HashMap.java:910)
        at net.sf.ehcache.distribution.RMICacheManagerPeerListener.getBoundCachePeers(RMICacheManagerPeerListener.java:441)
        at net.sf.ehcache.distribution.MulticastKeepaliveHeartbeatSender$MulticastServerThread.createCachePeersPayload(MulticastKeepaliveHeartbeatSender.java:174)
        at net.sf.ehcache.distribution.MulticastKeepaliveHeartbeatSender$MulticastServerThread.run(MulticastKeepaliveHeartbeatSender.java:131)
[ 207723]  ERROR - api.project.CacheUpdateSession - Error while indexing /var/www/moodle-latest-stable/sources/moodle/nadavkav_Pegasus2/mod/quiz/tcpdf/fonts/uni2cid_ac15.php
To reindex this file IDEA has to be restarted
java.lang.OutOfMemoryError: Java heap space
        at java.lang.String.substring(String.java:1939)
        at java.lang.String.subSequence(String.java:1972)
        at com.intellij.psi.impl.source.CharTableImpl.intern(CharTableImpl.java:60)
        at com.intellij.lang.impl.PsiBuilderImpl.createLeaf(PsiBuilderImpl.java:1462)
        at com.intellij.lang.impl.PsiBuilderImpl.insertLeaves(PsiBuilderImpl.java:1134)
        at com.intellij.lang.impl.PsiBuilderImpl.bind(PsiBuilderImpl.java:1093)
        at com.intellij.lang.impl.PsiBuilderImpl.buildTree(PsiBuilderImpl.java:905)
        at com.intellij.lang.impl.PsiBuilderImpl.getTreeBuilt(PsiBuilderImpl.java:881)
        at com.jetbrains.php.lang.parser.PhpPsiBuilder.getTreeBuilt(PhpPsiBuilder.java:92)
        at com.jetbrains.php.lang.parser.PhpPsiParser.parse(PhpPsiParser.java:25)
        at com.intellij.psi.tree.IFileElementType.parseContents(IFileElementType.java:41)
        at com.intellij.psi.impl.source.tree.LazyParseableElement.ensureParsed(LazyParseableElement.java:173)
        at com.intellij.psi.impl.source.tree.LazyParseableElement.getFirstChildNode(LazyParseableElement.java:214)
        at com.intellij.psi.impl.source.tree.LazyParseableElement.getFirstChildNode(LazyParseableElement.java:31)
        at com.intellij.psi.impl.source.tree.SharedImplUtil.getFirstChild(SharedImplUtil.java:47)
        at com.intellij.psi.impl.source.PsiFileImpl.getFirstChild(PsiFileImpl.java:709)
        at com.intellij.psi.stubs.DefaultStubBuilder.buildStubTreeFor(DefaultStubBuilder.java:59)
        at com.intellij.psi.stubs.DefaultStubBuilder.buildStubTree(DefaultStubBuilder.java:34)
        at com.intellij.psi.stubs.StubUpdatingIndex.buildStubTree(StubUpdatingIndex.java:159)
        at com.intellij.psi.stubs.StubUpdatingIndex$3$1.run(StubUpdatingIndex.java:112)
        at com.intellij.openapi.application.impl.ApplicationImpl.runReadAction(ApplicationImpl.java:757)
        at com.intellij.psi.stubs.StubUpdatingIndex$3.map(StubUpdatingIndex.java:110)
        at com.intellij.psi.stubs.StubUpdatingIndex$3.map(StubUpdatingIndex.java:105)
        at com.intellij.util.indexing.MapReduceIndex.update(MapReduceIndex.java:200)
        at com.intellij.util.indexing.FileBasedIndex$21.run(FileBasedIndex.java:1377)
        at com.intellij.openapi.progress.impl.ProgressManagerImpl.executeNonCancelableSection(ProgressManagerImpl.java:142)
        at com.intellij.util.indexing.FileBasedIndex.updateSingleIndex(FileBasedIndex.java:1374)
        at com.intellij.util.indexing.FileBasedIndex.indexFileContent(FileBasedIndex.java:1340)
        at com.intellij.util.indexing.UnindexedFilesUpdater.processFile(UnindexedFilesUpdater.java:60)
        at com.intellij.openapi.project.CacheUpdateSession.processFile(CacheUpdateSession.java:102)
        at com.intellij.openapi.project.CacheUpdateRunner$MyRunnable$1.run(CacheUpdateRunner.java:223)
        at com.intellij.openapi.application.impl.ApplicationImpl.runReadAction(ApplicationImpl.java:770)
[ 207726]  ERROR - api.project.CacheUpdateSession - JetBrains PhpStorm (PhpStorm) PS-102.206  Build #PS-102.206
[ 207726]  ERROR - api.project.CacheUpdateSession - JDK: 1.6.0_22
[ 207726]  ERROR - api.project.CacheUpdateSession - VM: Java HotSpot(TM) 64-Bit Server VM
[ 207726]  ERROR - api.project.CacheUpdateSession - Vendor: Sun Microsystems Inc.
[ 207726]  ERROR - api.project.CacheUpdateSession - OS: Linux
[ 207726]  ERROR - api.project.CacheUpdateSession - Last Action:  
java.lang.OutOfMemoryError: Java heap space
        at java.lang.String.substring(String.java:1939)
        at java.lang.String.subSequence(String.java:1972)
        at com.intellij.psi.impl.source.CharTableImpl.intern(CharTableImpl.java:60)
        at com.intellij.lang.impl.PsiBuilderImpl.createLeaf(PsiBuilderImpl.java:1462)
        at com.intellij.lang.impl.PsiBuilderImpl.insertLeaves(PsiBuilderImpl.java:1134)
        at com.intellij.lang.impl.PsiBuilderImpl.bind(PsiBuilderImpl.java:1093)
        at com.intellij.lang.impl.PsiBuilderImpl.buildTree(PsiBuilderImpl.java:905)
        at com.intellij.lang.impl.PsiBuilderImpl.getTreeBuilt(PsiBuilderImpl.java:881)
        at com.jetbrains.php.lang.parser.PhpPsiBuilder.getTreeBuilt(PhpPsiBuilder.java:92)
        at com.jetbrains.php.lang.parser.PhpPsiParser.parse(PhpPsiParser.java:25)
        at com.intellij.psi.tree.IFileElementType.parseContents(IFileElementType.java:41)
        at com.intellij.psi.impl.source.tree.LazyParseableElement.ensureParsed(LazyParseableElement.java:173)
        at com.intellij.psi.impl.source.tree.LazyParseableElement.getFirstChildNode(LazyParseableElement.java:214)
        at com.intellij.psi.impl.source.tree.LazyParseableElement.getFirstChildNode(LazyParseableElement.java:31)
        at com.intellij.psi.impl.source.tree.SharedImplUtil.getFirstChild(SharedImplUtil.java:47)
        at com.intellij.psi.impl.source.PsiFileImpl.getFirstChild(PsiFileImpl.java:709)
        at com.intellij.psi.stubs.DefaultStubBuilder.buildStubTreeFor(DefaultStubBuilder.java:59)
        at com.intellij.psi.stubs.DefaultStubBuilder.buildStubTree(DefaultStubBuilder.java:34)
        at com.intellij.psi.stubs.StubUpdatingIndex.buildStubTree(StubUpdatingIndex.java:159)
        at com.intellij.psi.stubs.StubUpdatingIndex$3$1.run(StubUpdatingIndex.java:112)
        at com.intellij.openapi.application.impl.ApplicationImpl.runReadAction(ApplicationImpl.java:757)
        at com.intellij.psi.stubs.StubUpdatingIndex$3.map(StubUpdatingIndex.java:110)
        at com.intellij.psi.stubs.StubUpdatingIndex$3.map(StubUpdatingIndex.java:105)
        at com.intellij.util.indexing.MapReduceIndex.update(MapReduceIndex.java:200)
        at com.intellij.util.indexing.FileBasedIndex$21.run(FileBasedIndex.java:1377)
        at com.intellij.openapi.progress.impl.ProgressManagerImpl.executeNonCancelableSection(ProgressManagerImpl.java:142)
        at com.intellij.util.indexing.FileBasedIndex.updateSingleIndex(FileBasedIndex.java:1374)
        at com.intellij.util.indexing.FileBasedIndex.indexFileContent(FileBasedIndex.java:1340)
        at com.intellij.util.indexing.UnindexedFilesUpdater.processFile(UnindexedFilesUpdater.java:60)
        at com.intellij.openapi.project.CacheUpdateSession.processFile(CacheUpdateSession.java:102)
        at com.intellij.openapi.project.CacheUpdateRunner$MyRunnable$1.run(CacheUpdateRunner.java:223)
        at com.intellij.openapi.application.impl.ApplicationImpl.runReadAction(ApplicationImpl.java:770)