Сделал Ваш пример "Студенческий отдел кадров в виде Enterprise приложения". У меня вместо класса ManagementSystemBean создается класс ManagementSystem. При запуске сервер ругается на EntityManager em. В простейшем приложении я его закомментировал, оно открылось, но к базе, разумеется, я не смог обратиться. У меня NetBeans 7.0, J2EE6 ( и в J2EE5 я тоже делал - эффект тот же.) Там в примере нигде опечаток нет?  Если нет, то может быть Вы подскажете в чем дело? С уважением ....

Покажите хотя бы стэктрэйсы. Как именно ругается?

Стэктрейс StudentsApp (run):
pre-run-deploy:
Запуск GlassFish Server 3.1
GlassFish Server 3.1 выполняется.
Начальное развертывание StudentsApp на /home/vasiliy/NetBeansProjects/StudentsApp/dist/gfdeploy/StudentsApp
Завершено начальное распространение StudentsApp
Initializing...
deploy?DEFAULT=/home/vasiliy/NetBeansProjects/StudentsApp/dist/gfdeploy/StudentsApp&name=StudentsApp&force=true отказ на GlassFish Server 3.1 
 Error occurred during deployment: Exception while preparing the app : Could not resolve a persistence unit corresponding to the persistence-context-ref-name [students.logic.ManagementSystem/em] in the scope of the module called [StudentsApp#StudentsApp-ejb.jar]. Please verify your application.. Please see server.log for more details.
Exception while invoking class org.glassfish.persistence.jpa.JPADeployer prepare method : java.lang.RuntimeException: Could not resolve a persistence unit corresponding to the persistence-context-ref-name [students.logic.ManagementSystem/em] in the scope of the module called [StudentsApp#StudentsApp-ejb.jar]. Please verify your application.
Could not resolve a persistence unit corresponding to the persistence-context-ref-name [students.logic.ManagementSystem/em] in the scope of the module called [StudentsApp#StudentsApp-ejb.jar]. Please verify your application.
/home/vasiliy/NetBeansProjects/StudentsApp/nbproject/build-impl.xml:288: 
Модуль не развернут.
    at org.netbeans.modules.j2ee.deployment.devmodules.api.Deployment.deploy(Deployment.java:210)
    at org.netbeans.modules.j2ee.ant.Deploy.execute(Deploy.java:106)
    at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
    at sun.reflect.GeneratedMethodAccessor51.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
    at org.apache.tools.ant.Task.perform(Task.java:348)
    at org.apache.tools.ant.Target.execute(Target.java:390)
    at org.apache.tools.ant.Target.performTasks(Target.java:411)
    at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
    at org.apache.tools.ant.Project.executeTarget(Project.java:1368)
    at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
    at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
    at org.apache.tools.ant.module.bridge.impl.BridgeImpl.run(BridgeImpl.java:284)
    at org.apache.tools.ant.module.run.TargetExecutor.run(TargetExecutor.java:539)
    at org.netbeans.core.execution.RunClassThread.run(RunClassThread.java:153)
ПОСТРОЕНИЕ ЗАВЕРШЕНО СО СБОЕМ (общее время: 41 секунд)

Стэктрейс GlassFishServer-3.1:
Launching GlassFish on Felix platform
INFO: Registered org.glassfish.ha.store.adapter.cache.ShoalBackingStoreProxy for persistence-type = replicated in BackingStoreFactoryRegistry
INFO: Grizzly Framework 1.9.31 started in: 140ms - bound to [0.0.0.0:8181]
INFO: Grizzly Framework 1.9.31 started in: 128ms - bound to [0.0.0.0:4848]
INFO: Grizzly Framework 1.9.31 started in: 101ms - bound to [0.0.0.0:7676]
INFO: Grizzly Framework 1.9.31 started in: 171ms - bound to [0.0.0.0:8080]
INFO: Grizzly Framework 1.9.31 started in: 116ms - bound to [0.0.0.0:3700]
INFO: The Admin Console is already installed, but not yet loaded.
INFO: SEC1002: Security Manager is OFF.
INFO: SEC1010: Entering Security Startup Service
INFO: SEC1143: Loading policy provider com.sun.enterprise.security.provider.PolicyWrapper.
INFO: SEC1115: Realm [admin-realm] of classtype [com.sun.enterprise.security.auth.realm.file.FileRealm] successfully created.
INFO: SEC1115: Realm [file] of classtype [com.sun.enterprise.security.auth.realm.file.FileRealm] successfully created.
INFO: SEC1115: Realm [certificate] of classtype [com.sun.enterprise.security.auth.realm.certificate.CertificateRealm] successfully created.
INFO: SEC1011: Security Service(s) Started Successfully
INFO: WEB0169: Created HTTP listener [http-listener-1] on host/port [0.0.0.0:8080]
INFO: WEB0169: Created HTTP listener [http-listener-2] on host/port [0.0.0.0:8181]
INFO: WEB0169: Created HTTP listener [admin-listener] on host/port [0.0.0.0:4848]
INFO: WEB0171: Created virtual server [server]
INFO: WEB0171: Created virtual server [__asadmin]
INFO: WEB0172: Virtual server [server] loaded default web module []
INFO: Initializing Mojarra 2.1.0 (FCS 2.1.0-b11) for context '/login'
INFO: WEB0671: Loading application [login] at [/login]
INFO: CORE10010: Loading application login done in 5 942 ms
INFO: Initializing Mojarra 2.1.0 (FCS 2.1.0-b11) for context '/jsfDemo'
INFO: WEB0671: Loading application [jsfDemo] at [/jsfDemo]
INFO: CORE10010: Loading application jsfDemo done in 510 ms
INFO: Hibernate Validator 4.1.0.Final
INFO: Instantiated an instance of org.hibernate.validator.engine.resolver.JPATraversableResolver.
INFO: Initializing Mojarra 2.1.0 (FCS 2.1.0-b11) for context '/scrumtoys'
INFO: Monitoring jndi:/server/scrumtoys/WEB-INF/faces-config.xml for modifications
INFO: WEB0671: Loading application [ScrumToys] at [/scrumtoys]
INFO: CORE10010: Loading application ScrumToys done in 3 293 ms
INFO: WEB0671: Loading application [IFPWAFCAD] at [/IFPWAFCAD]
INFO: CORE10010: Loading application IFPWAFCAD done in 396 ms
INFO: GlassFish Server Open Source Edition 3.1 (43) startup time : Felix (11 839ms), startup services(11 478ms), total(23 317ms)
INFO: User [] from host localhost.localdomain does not have administration access
INFO: JMXStartupService: Started JMXConnector, JMXService URL = service:jmx:rmi://vasiliy-desktop:8686/jndi/rmi://vasiliy-desktop:8686/jmxrmi
INFO: Instantiated an instance of org.hibernate.validator.engine.resolver.JPATraversableResolver.
INFO: WEB0169: Created HTTP listener [http-listener-1] on host/port [0.0.0.0:8080]
INFO: Grizzly Framework 1.9.31 started in: 4ms - bound to [0.0.0.0:8080]
INFO: WEB0169: Created HTTP listener [http-listener-2] on host/port [0.0.0.0:8181]
INFO: Grizzly Framework 1.9.31 started in: 3ms - bound to [0.0.0.0:8181]
SEVERE: Exception while invoking class org.glassfish.persistence.jpa.JPADeployer prepare method
SEVERE: Exception while invoking class org.glassfish.javaee.full.deployment.EarDeployer prepare method
SEVERE: Exception while preparing the app
SEVERE: Could not resolve a persistence unit corresponding to the persistence-context-ref-name [students.logic.ManagementSystem/em] in the scope of the module called [StudentsApp#StudentsApp-ejb.jar]. Please verify your application.
org.glassfish.deployment.common.DeploymentException: Could not resolve a persistence unit corresponding to the persistence-context-ref-name [students.logic.ManagementSystem/em] in the scope of the module called [StudentsApp#StudentsApp-ejb.jar]. Please verify your application.
    at org.glassfish.javaee.full.deployment.EarDeployer.prepare(EarDeployer.java:166)
    at com.sun.enterprise.v3.server.ApplicationLifecycle.prepareModule(ApplicationLifecycle.java:870)
    at com.sun.enterprise.v3.server.ApplicationLifecycle.deploy(ApplicationLifecycle.java:410)
    at com.sun.enterprise.v3.server.ApplicationLifecycle.deploy(ApplicationLifecycle.java:240)
    at org.glassfish.deployment.admin.DeployCommand.execute(DeployCommand.java:370)
    at com.sun.enterprise.v3.admin.CommandRunnerImpl$1.execute(CommandRunnerImpl.java:355)
    at com.sun.enterprise.v3.admin.CommandRunnerImpl.doCommand(CommandRunnerImpl.java:370)
    at com.sun.enterprise.v3.admin.CommandRunnerImpl.doCommand(CommandRunnerImpl.java:1067)
    at com.sun.enterprise.v3.admin.CommandRunnerImpl.access$1200(CommandRunnerImpl.java:96)
    at com.sun.enterprise.v3.admin.CommandRunnerImpl$ExecutionContext.execute(CommandRunnerImpl.java:1247)
    at com.sun.enterprise.v3.admin.CommandRunnerImpl$ExecutionContext.execute(CommandRunnerImpl.java:1235)
    at com.sun.enterprise.v3.admin.AdminAdapter.doCommand(AdminAdapter.java:465)
    at com.sun.enterprise.v3.admin.AdminAdapter.service(AdminAdapter.java:222)
    at com.sun.grizzly.tcp.http11.GrizzlyAdapter.service(GrizzlyAdapter.java:168)
    at com.sun.enterprise.v3.server.HK2Dispatcher.dispath(HK2Dispatcher.java:117)
    at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:234)
    at com.sun.grizzly.http.ProcessorTask.invokeAdapter(ProcessorTask.java:822)
    at com.sun.grizzly.http.ProcessorTask.doProcess(ProcessorTask.java:719)
    at com.sun.grizzly.http.ProcessorTask.process(ProcessorTask.java:1013)
    at com.sun.grizzly.http.DefaultProtocolFilter.execute(DefaultProtocolFilter.java:225)
    at com.sun.grizzly.DefaultProtocolChain.executeProtocolFilter(DefaultProtocolChain.java:137)
    at com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:104)
    at com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:90)
    at com.sun.grizzly.http.HttpProtocolChain.execute(HttpProtocolChain.java:79)
    at com.sun.grizzly.ProtocolChainContextTask.doCall(ProtocolChainContextTask.java:54)
    at com.sun.grizzly.SelectionKeyContextTask.call(SelectionKeyContextTask.java:59)
    at com.sun.grizzly.ContextTask.run(ContextTask.java:71)
    at com.sun.grizzly.util.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:532)
    at com.sun.grizzly.util.AbstractThreadPool$Worker.run(AbstractThreadPool.java:513)
    at java.lang.Thread.run(Thread.java:662)
Caused by: java.lang.RuntimeException: Could not resolve a persistence unit corresponding to the persistence-context-ref-name [students.logic.ManagementSystem/em] in the scope of the module called [StudentsApp#StudentsApp-ejb.jar]. Please verify your application.
    at com.sun.enterprise.deployment.BundleDescriptor.findReferencedPUViaEMRef(BundleDescriptor.java:693)
    at com.sun.enterprise.deployment.BundleDescriptor.findReferencedPUsViaPCRefs(BundleDescriptor.java:681)
    at com.sun.enterprise.deployment.EjbBundleDescriptor.findReferencedPUs(EjbBundleDescriptor.java:901)
    at org.glassfish.persistence.jpa.JPADeployer.createEMFs(JPADeployer.java:184)
    at org.glassfish.persistence.jpa.JPADeployer.prepare(JPADeployer.java:166)
    at com.sun.enterprise.v3.server.ApplicationLifecycle.prepareModule(ApplicationLifecycle.java:870)
    at org.glassfish.javaee.full.deployment.EarDeployer.prepareBundle(EarDeployer.java:290)
    at org.glassfish.javaee.full.deployment.EarDeployer.access$200(EarDeployer.java:86)
    at org.glassfish.javaee.full.deployment.EarDeployer$1.doBundle(EarDeployer.java:141)
    at org.glassfish.javaee.full.deployment.EarDeployer$1.doBundle(EarDeployer.java:138)
    at org.glassfish.javaee.full.deployment.EarDeployer.doOnBundles(EarDeployer.java:215)
    at org.glassfish.javaee.full.deployment.EarDeployer.doOnAllTypedBundles(EarDeployer.java:224)
    at org.glassfish.javaee.full.deployment.EarDeployer.doOnAllBundles(EarDeployer.java:250)
    at org.glassfish.javaee.full.deployment.EarDeployer.prepare(EarDeployer.java:138)
    ... 29 more

SEVERE: Exception while preparing the app : Could not resolve a persistence unit corresponding to the persistence-context-ref-name [students.logic.ManagementSystem/em] in the scope of the module called [StudentsApp#StudentsApp-ejb.jar]. Please verify your application.
java.lang.RuntimeException: Could not resolve a persistence unit corresponding to the persistence-context-ref-name [students.logic.ManagementSystem/em] in the scope of the module called [StudentsApp#StudentsApp-ejb.jar]. Please verify your application.
    at com.sun.enterprise.deployment.BundleDescriptor.findReferencedPUViaEMRef(BundleDescriptor.java:693)
    at com.sun.enterprise.deployment.BundleDescriptor.findReferencedPUsViaPCRefs(BundleDescriptor.java:681)
    at com.sun.enterprise.deployment.EjbBundleDescriptor.findReferencedPUs(EjbBundleDescriptor.java:901)
    at org.glassfish.persistence.jpa.JPADeployer.createEMFs(JPADeployer.java:184)
    at org.glassfish.persistence.jpa.JPADeployer.prepare(JPADeployer.java:166)
    at com.sun.enterprise.v3.server.ApplicationLifecycle.prepareModule(ApplicationLifecycle.java:870)
    at org.glassfish.javaee.full.deployment.EarDeployer.prepareBundle(EarDeployer.java:290)
    at org.glassfish.javaee.full.deployment.EarDeployer.access$200(EarDeployer.java:86)
    at org.glassfish.javaee.full.deployment.EarDeployer$1.doBundle(EarDeployer.java:141)
    at org.glassfish.javaee.full.deployment.EarDeployer$1.doBundle(EarDeployer.java:138)
    at org.glassfish.javaee.full.deployment.EarDeployer.doOnBundles(EarDeployer.java:215)
    at org.glassfish.javaee.full.deployment.EarDeployer.doOnAllTypedBundles(EarDeployer.java:224)
    at org.glassfish.javaee.full.deployment.EarDeployer.doOnAllBundles(EarDeployer.java:250)
    at org.glassfish.javaee.full.deployment.EarDeployer.prepare(EarDeployer.java:138)
    at com.sun.enterprise.v3.server.ApplicationLifecycle.prepareModule(ApplicationLifecycle.java:870)
    at com.sun.enterprise.v3.server.ApplicationLifecycle.deploy(ApplicationLifecycle.java:410)
    at com.sun.enterprise.v3.server.ApplicationLifecycle.deploy(ApplicationLifecycle.java:240)
    at org.glassfish.deployment.admin.DeployCommand.execute(DeployCommand.java:370)
    at com.sun.enterprise.v3.admin.CommandRunnerImpl$1.execute(CommandRunnerImpl.java:355)
    at com.sun.enterprise.v3.admin.CommandRunnerImpl.doCommand(CommandRunnerImpl.java:370)
    at com.sun.enterprise.v3.admin.CommandRunnerImpl.doCommand(CommandRunnerImpl.java:1067)
    at com.sun.enterprise.v3.admin.CommandRunnerImpl.access$1200(CommandRunnerImpl.java:96)
    at com.sun.enterprise.v3.admin.CommandRunnerImpl$ExecutionContext.execute(CommandRunnerImpl.java:1247)
    at com.sun.enterprise.v3.admin.CommandRunnerImpl$ExecutionContext.execute(CommandRunnerImpl.java:1235)
    at com.sun.enterprise.v3.admin.AdminAdapter.doCommand(AdminAdapter.java:465)
    at com.sun.enterprise.v3.admin.AdminAdapter.service(AdminAdapter.java:222)
    at com.sun.grizzly.tcp.http11.GrizzlyAdapter.service(GrizzlyAdapter.java:168)
    at com.sun.enterprise.v3.server.HK2Dispatcher.dispath(HK2Dispatcher.java:117)
    at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:234)
    at com.sun.grizzly.http.ProcessorTask.invokeAdapter(ProcessorTask.java:822)
    at com.sun.grizzly.http.ProcessorTask.doProcess(ProcessorTask.java:719)
    at com.sun.grizzly.http.ProcessorTask.process(ProcessorTask.java:1013)
    at com.sun.grizzly.http.DefaultProtocolFilter.execute(DefaultProtocolFilter.java:225)
    at com.sun.grizzly.DefaultProtocolChain.executeProtocolFilter(DefaultProtocolChain.java:137)
    at com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:104)
    at com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:90)
    at com.sun.grizzly.http.HttpProtocolChain.execute(HttpProtocolChain.java:79)
    at com.sun.grizzly.ProtocolChainContextTask.doCall(ProtocolChainContextTask.java:54)
    at com.sun.grizzly.SelectionKeyContextTask.call(SelectionKeyContextTask.java:59)
    at com.sun.grizzly.ContextTask.run(ContextTask.java:71)
    at com.sun.grizzly.util.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:532)
    at com.sun.grizzly.util.AbstractThreadPool$Worker.run(AbstractThreadPool.java:513)
    at java.lang.Thread.run(Thread.java:662)

В общем, SEVERE exception говорят что-то невнятное про ManagementSystem/em