Hello, I have issue using apache-tomcat-6.0.29 on Ubuntu and Gentoo Linux. After deploying my .war file to server Tomcat doesn't stop it's process when run bin/shutdown.sh script. This issue is also reproducible with tomcat-7.0.8.
Steps to reproduce: 1. Download apache-tomcat-6.0.29.tar.gz from http://tomcat.apache.org ; 2. Extract archive; 3. Copy .war files to webapps/ folder; 4. Start tomcat running script bin/startup.sh; 5. Wait for server to start all services and shutdown tomcat using script bin/shutdown.sh; 6. Use "ps -ef | grep tomcat" command to find tomcat process. Additional comments: after restarting tomcat there will be one more process. Every tomcat restart creates new process. Here is pmap output for zombie process: pmap 5324 5324: /etc/java-config-2/current-system-vm/bin/java -Djava.util.logging.config.file=/home/user/apache-tomcat-6.0.29/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Djava.endorsed.dirs=/home/user/apache-tomcat-6.0.29/endorsed -classpath /home/user/apache-tomcat-6.0.29/bin/bootstrap.jar -Dcatalina.base=/home/user/apache-tomcat-6.0.29 -Dcatalina.home=/home/user/apache-tomcat-6.0.29 -Djava.io.tmpdir=/home/user/apache-tomcat-6.0.29/temp org.apache.catalina.startu 08048000 40K r-x-- /opt/sun-jdk-1.6.0.23/bin/java 08052000 4K rwx-- /opt/sun-jdk-1.6.0.23/bin/java 08053000 17748K rwx-- [ anon ] 7dbbc000 12K ----- [ anon ] 7dbbf000 312K rwx-- [ anon ] 7dc0d000 12K ----- [ anon ] 7dc10000 312K rwx-- [ anon ] 7dc5e000 12K ----- [ anon ] 7dc61000 312K rwx-- [ anon ] 7dcaf000 12K ----- [ anon ] 7dcb2000 312K rwx-- [ anon ] 7de0d000 12K ----- [ anon ] 7de10000 312K rwx-- [ anon ] 7de5e000 12K ----- [ anon ] 7de61000 312K rwx-- [ anon ] 7deaf000 12K ----- [ anon ] 7deb2000 312K rwx-- [ anon ] 7dfaf000 12K ----- [ anon ] 7dfb2000 312K rwx-- [ anon ] 7e100000 1000K rwx-- [ anon ] 7e1fa000 24K ----- [ anon ] 7e200000 732K rwx-- [ anon ] 7e2b7000 292K ----- [ anon ] 7e300000 1016K rwx-- [ anon ] 7e3fe000 8K ----- [ anon ] 7e400000 1020K rwx-- [ anon ] 7e4ff000 4K ----- [ anon ] 7e500000 1024K rwx-- [ anon ] 7e60d000 12K ----- [ anon ] 7e610000 312K rwx-- [ anon ] 7e65e000 12K ----- [ anon ] 7e661000 312K rwx-- [ anon ] 7e6af000 12K ----- [ anon ] 7e6b2000 312K rwx-- [ anon ] 7e700000 796K rwx-- [ anon ] 7e7c7000 228K ----- [ anon ] 7e800000 996K rwx-- [ anon ] 7e8f9000 28K ----- [ anon ] 7e900000 2048K rwx-- [ anon ] 7eb00000 952K rwx-- [ anon ] 7ebee000 72K ----- [ anon ] 7ec00000 904K rwx-- [ anon ] 7ece2000 120K ----- [ anon ] 7ed00000 1008K rwx-- [ anon ] 7edfc000 16K ----- [ anon ] 7ee00000 1020K rwx-- [ anon ] 7eeff000 4K ----- [ anon ] 7ef00000 1004K rwx-- [ anon ] 7effb000 20K ----- [ anon ] 7f00a000 12K ----- [ anon ] 7f00d000 312K rwx-- [ anon ] 7f05b000 12K ----- [ anon ] 7f05e000 312K rwx-- [ anon ] 7f0ac000 12K ----- [ anon ] 7f0af000 312K rwx-- [ anon ] 7f0fd000 12K r-xs- /opt/sun-jdk-1.6.0.23/jre/lib/ext/localedata.jar 7f100000 1024K rwx-- [ anon ] 7f300000 1016K rwx-- [ anon ] 7f3fe000 8K ----- [ anon ] 7f406000 28K r-xs- /opt/sun-jdk-1.6.0.23/jre/lib/jsse.jar 7f40d000 32K r-xs- /opt/sun-jdk-1.6.0.23/jre/lib/resources.jar 7f415000 28K r-x-- /opt/sun-jdk-1.6.0.23/jre/lib/i386/libnio.so 7f41c000 4K rwx-- /opt/sun-jdk-1.6.0.23/jre/lib/i386/libnio.so 7f44e000 80K r-x-- /opt/sun-jdk-1.6.0.23/jre/lib/i386/libnet.so 7f462000 4K rwx-- /opt/sun-jdk-1.6.0.23/jre/lib/i386/libnet.so 7f463000 12K ----- [ anon ] 7f466000 312K rwx-- [ anon ] 7f4b4000 8K r-xs- /home/user/apache-tomcat-6.0.29/lib/tomcat-i18n-ja.jar 7f4b6000 12K r-xs- /home/user/apache-tomcat-6.0.29/lib/tomcat-i18n-es.jar 7f4b9000 44K r-xs- /home/user/apache-tomcat-6.0.29/lib/tomcat-coyote.jar 7f4c4000 16K r-xs- /home/user/apache-tomcat-6.0.29/lib/tomcat-dbcp.jar 7f4c8000 8K r-xs- /home/user/apache-tomcat-6.0.29/lib/catalina-ha.jar 7f4ca000 48K r-xs- /home/user/apache-tomcat-6.0.29/lib/jasper-jdt.jar 7f4d6000 12K r-xs- /home/user/apache-tomcat-6.0.29/lib/jasper-el.jar 7f4d9000 8K r-xs- /home/user/apache-tomcat-6.0.29/lib/catalina-ant.jar 7f4db000 8K r-xs- /home/user/apache-tomcat-6.0.29/lib/jsp-api.jar 7f4dd000 60K r-xs- /home/user/apache-tomcat-6.0.29/lib/catalina.jar 7f4ec000 20K r-xs- /home/user/apache-tomcat-6.0.29/lib/catalina-tribes.jar 7f4f1000 32K r-xs- /home/user/apache-tomcat-6.0.29/lib/jasper.jar 7f4f9000 24K r-x-- /opt/sun-jdk-1.6.0.23/jre/lib/i386/libmanagement.so 7f4ff000 4K rwx-- /opt/sun-jdk-1.6.0.23/jre/lib/i386/libmanagement.so 7f500000 4K ----- [ anon ] 7f501000 512K rwx-- [ anon ] 7f581000 12K ----- [ anon ] 7f584000 312K rwx-- [ anon ] 7f5d2000 12K ----- [ anon ] 7f5d5000 504K rwx-- [ anon ] 7f653000 12K ----- [ anon ] 7f656000 504K rwx-- [ anon ] 7f6d4000 12K ----- [ anon ] 7f6d7000 312K rwx-- [ anon ] 7f725000 2048K r-x-- /usr/lib/locale/locale-archive 7f925000 12K ----- [ anon ] 7f928000 312K rwx-- [ anon ] 7f976000 12K ----- [ anon ] 7f979000 312K rwx-- [ anon ] 7f9c7000 4K ----- [ anon ] 7f9c8000 720K rwx-- [ anon ] 7fa7c000 1628K r-xs- /opt/sun-jdk-1.6.0.23/jre/lib/rt.jar 7fc13000 4K ----- [ anon ] 7fc14000 512K rwx-- [ anon ] 7fc94000 4K ----- [ anon ] 7fc95000 544K rwx-- [ anon ] 7fd1d000 96K rwx-- [ anon ] 7fd35000 64K rwx-- [ anon ] 7fd45000 952K rwx-- [ anon ] 7fe33000 32K rwx-- [ anon ] 7fe3b000 96K rwx-- [ anon ] 7fe53000 64K rwx-- [ anon ] 7fe63000 948K rwx-- [ anon ] 7ff50000 108K rwx-- [ anon ] 7ff6b000 400K rwx-- [ anon ] 7ffcf000 16388K rwx-- [ anon ] 80fd0000 49152K rwx-- [ anon ] 83fd0000 32384K rwx-- [ anon ] 85f70000 486464K rwx-- [ anon ] a3a80000 52864K rwx-- [ anon ] a6e20000 206528K rwx-- [ anon ] b37d2000 4K r-xs- /home/user/apache-tomcat-6.0.29/lib/el-api.jar b37d3000 4K r-xs- /home/user/apache-tomcat-6.0.29/lib/annotations-api.jar b37d4000 8K r-xs- /home/user/apache-tomcat-6.0.29/lib/tomcat-i18n-fr.jar b37d6000 36K rwx-- [ anon ] b37df000 732K rwx-- [ anon ] b3896000 2304K rwx-- [ anon ] b3ad6000 46848K rwx-- [ anon ] b6896000 40K r-x-- /lib/libnss_files-2.11.2.so b68a0000 4K r-x-- /lib/libnss_files-2.11.2.so b68a1000 4K rwx-- /lib/libnss_files-2.11.2.so b68a2000 36K r-x-- /lib/libnss_nis-2.11.2.so b68ab000 4K r-x-- /lib/libnss_nis-2.11.2.so b68ac000 4K rwx-- /lib/libnss_nis-2.11.2.so b68ad000 76K r-x-- /lib/libnsl-2.11.2.so b68c0000 4K r-x-- /lib/libnsl-2.11.2.so b68c1000 4K rwx-- /lib/libnsl-2.11.2.so b68c2000 8K rwx-- [ anon ] b68c5000 8K r-xs- /home/user/apache-tomcat-6.0.29/lib/servlet-api.jar b68c7000 4K r-xs- /home/user/apache-tomcat-6.0.29/bin/tomcat-juli.jar b68c8000 4K r-xs- /home/user/apache-tomcat-6.0.29/bin/commons-daemon.jar b68c9000 60K r-x-- /opt/sun-jdk-1.6.0.23/jre/lib/i386/libzip.so b68d8000 8K rwx-- /opt/sun-jdk-1.6.0.23/jre/lib/i386/libzip.so b68da000 32K rwxs- /home/user/apache-tomcat-6.0.29/temp/hsperfdata_user/5324 b68e2000 140K r-x-- /opt/sun-jdk-1.6.0.23/jre/lib/i386/libjava.so b6905000 8K rwx-- /opt/sun-jdk-1.6.0.23/jre/lib/i386/libjava.so b6907000 28K r-x-- /lib/librt-2.11.2.so b690e000 4K r-x-- /lib/librt-2.11.2.so b690f000 4K rwx-- /lib/librt-2.11.2.so b6910000 12K ----- [ anon ] b6913000 312K rwx-- [ anon ] b6961000 144K r-x-- /lib/libm-2.11.2.so b6985000 4K r-x-- /lib/libm-2.11.2.so b6986000 4K rwx-- /lib/libm-2.11.2.so b6987000 7572K r-x-- /opt/sun-jdk-1.6.0.23/jre/lib/i386/server/libjvm.so b70ec000 332K rwx-- /opt/sun-jdk-1.6.0.23/jre/lib/i386/server/libjvm.so b713f000 4220K rwx-- [ anon ] b755e000 1276K r-x-- /lib/libc-2.11.2.so b769d000 8K r-x-- /lib/libc-2.11.2.so b769f000 4K rwx-- /lib/libc-2.11.2.so b76a0000 16K rwx-- [ anon ] b76a4000 8K r-x-- /lib/libdl-2.11.2.so b76a6000 4K r-x-- /lib/libdl-2.11.2.so b76a7000 4K rwx-- /lib/libdl-2.11.2.so b76a8000 28K r-x-- /opt/sun-jdk-1.6.0.23/jre/lib/i386/jli/libjli.so b76af000 8K rwx-- /opt/sun-jdk-1.6.0.23/jre/lib/i386/jli/libjli.so b76b1000 84K r-x-- /lib/libpthread-2.11.2.so b76c6000 4K r-x-- /lib/libpthread-2.11.2.so b76c7000 4K rwx-- /lib/libpthread-2.11.2.so b76c8000 8K rwx-- [ anon ] b76ca000 4K r-xs- /home/user/apache-tomcat-6.0.29/bin/bootstrap.jar b76cb000 24K r-x-- /lib/libnss_compat-2.11.2.so b76d1000 4K r-x-- /lib/libnss_compat-2.11.2.so b76d2000 4K rwx-- /lib/libnss_compat-2.11.2.so b76d3000 24K r-x-- /opt/sun-jdk-1.6.0.23/jre/lib/i386/native_threads/libhpi.so b76d9000 4K rwx-- /opt/sun-jdk-1.6.0.23/jre/lib/i386/native_threads/libhpi.so b76da000 4K rwx-- [ anon ] b76db000 4K r-x-- [ anon ] b76dc000 44K r-x-- /opt/sun-jdk-1.6.0.23/jre/lib/i386/libverify.so b76e7000 4K rwx-- /opt/sun-jdk-1.6.0.23/jre/lib/i386/libverify.so b76e8000 4K rwx-- [ anon ] b76e9000 112K r-x-- /lib/ld-2.11.2.so b7705000 4K r-x-- /lib/ld-2.11.2.so b7706000 4K rwx-- /lib/ld-2.11.2.so bfeae000 140K rwx-- [ stack ] ffffe000 4K r-x-- [ anon ] total 959240K