I think i know the problem... i am using iRedMail-0.7.1 version and  dovecot is the old version..
i guess i need to upgrade to new one.. below is the output

mailserver.ird.gov.np-root@mailserver:/var/www/roundcubemail/plugins/calendar/config # dovecot -n
# 1.2.16: /etc/dovecot.conf
# OS: Linux 2.6.18-194.el5PAE i686 CentOS release 5.5 (Final)
log_path: /var/log/dovecot.log
protocols: pop3 pop3s imap imaps managesieve
listen(default): *
listen(imap): *
listen(pop3): *
listen(managesieve): 127.0.0.1:2000
ssl_ca_file: /etc/pki/tls/certs/iRedMail_CA.pem
ssl_cert_file: /etc/pki/tls/certs/iRedMail_CA.pem
ssl_key_file: /etc/pki/tls/private/iRedMail.key
login_dir: /var/run/dovecot/login
login_executable(default): /usr/libexec/dovecot/imap-login
login_executable(imap): /usr/libexec/dovecot/imap-login
login_executable(pop3): /usr/libexec/dovecot/pop3-login
login_executable(managesieve): /usr/libexec/dovecot/managesieve-login
last_valid_uid: 500
mail_uid: 500
mail_gid: 500
mail_location: maildir:/%Lh/Maildir/:INDEX=/%Lh/Maildir/
mail_executable(default): /usr/libexec/dovecot/imap
mail_executable(imap): /usr/libexec/dovecot/imap
mail_executable(pop3): /usr/libexec/dovecot/pop3
mail_executable(managesieve): /usr/libexec/dovecot/managesieve
mail_process_size: 1024
mail_plugins(default): quota imap_quota autocreate
mail_plugins(imap): quota imap_quota autocreate
mail_plugins(pop3): quota
mail_plugins(managesieve):
mail_plugin_dir(default): /usr/lib/dovecot/imap
mail_plugin_dir(imap): /usr/lib/dovecot/imap
mail_plugin_dir(pop3): /usr/lib/dovecot/pop3
mail_plugin_dir(managesieve): /usr/lib/dovecot/managesieve
imap_client_workarounds(default): tb-extra-mailbox-sep
imap_client_workarounds(imap): tb-extra-mailbox-sep
imap_client_workarounds(pop3):
imap_client_workarounds(managesieve):
pop3_client_workarounds(default):
pop3_client_workarounds(imap):
pop3_client_workarounds(pop3): outlook-no-nuls oe-ns-eoh
pop3_client_workarounds(managesieve):
namespace:
  type: private
  separator: /
  inbox: yes
  list: yes
  subscriptions: yes
namespace:
  type: shared
  separator: /
  prefix: Shared/%%u/
  location: maildir:/%%Lh/Maildir/:INDEX=/%%Lh/Maildir/Shared/%%u
  list: children
  subscriptions: yes
lda:
  postmaster_address: root
  auth_socket_path: /var/run/dovecot/auth-master
  mail_plugins: quota sieve autocreate
  sieve_global_path: /home/vmail/sieve/dovecot.sieve
  log_path: /var/log/sieve.log
auth default:
  mechanisms: plain login
  default_realm: ird.gov.np
  user: vmail
  passdb:
    driver: ldap
    args: /etc/dovecot-ldap.conf
  userdb:
    driver: ldap
    args: /etc/dovecot-ldap.conf
  socket:
    type: listen
    client:
      path: /var/spool/postfix/dovecot-auth
      mode: 438
      user: postfix
      group: postfix
    master:
      path: /var/run/dovecot/auth-master
      mode: 438
      user: vmail
      group: vmail
plugin:
  quota_warning: storage=85%% /usr/local/bin/dovecot-quota-warning.sh 85 %u
  quota_warning2: storage=90%% /usr/local/bin/dovecot-quota-warning.sh 90 %u
  quota_warning3: storage=95%% /usr/local/bin/dovecot-quota-warning.sh 95 %u
  quota: dict:user::proxy::quotadict
  quota_rule: *:storage=0
  expire: Trash 7 Trash/* 7 Junk 30
  expire_dict: proxy::expire
  auth_socket_path: /var/run/dovecot/auth-master
  sieve: /home/vmail/sieve/%Ld/%Ln/dovecot.sieve
  autocreate: INBOX
  autocreate2: Sent
  autocreate3: Trash
  autocreate4: Drafts
  autocreate5: Junk
  autosubscribe: INBOX
  autosubscribe2: Sent
  autosubscribe3: Trash
  autosubscribe4: Drafts
  autosubscribe5: Junk
  acl: vfile
  acl_shared_dict: proxy::acl
  sieve: /home/vmail/sieve/%Ld/%Ln/dovecot.sieve
  sieve_dir: /home/vmail/sieve/%Ld/%Ln/
dict:
  expire: db:/var/lib/dovecot/expire/expire.db
  quotadict: mysql:/etc/dovecot-used-quota.conf
  acl: mysql:/etc/dovecot-share-folder.conf

Hi ZhangHuangbin,

I checked the settings against the link you gave me and all setting looks fine. I could see the table used_quota being populated.

+-------------------+-----------+----------+
| username          | bytes     | messages |
+-------------------+-----------+----------+
| bikesh@ird.gov.np | 156207468 |      824 | 
+-------------------+-----------+----------+
1 row in set (0.01 sec)

Anything else I need to check.

Thanks,
Bikrish