I'm on RHEL6.1 plain my relevant package versions are as follows:
# rpm -qa ipa* 389*
ipa-server-2.1.3-9.el6.x86_64
389-ds-base-libs-1.2.9.14-1.el6_2.2.x86_64
ipa-pki-common-theme-9.0.3-7.el6.noarch
ipa-python-2.1.3-9.el6.x86_64
ipa-admintools-2.1.3-9.el6.x86_64
ipa-server-selinux-2.1.3-9.el6.x86_64
ipa-client-2.1.3-9.el6.x86_64
389-ds-base-1.2.9.14-1.el6_2.2.x86_64
ipa-pki-ca-theme-9.0.3-7.el6.noarch
# cat /etc/redhat-release 
Red Hat Enterprise Linux Server release 6.2 (Santiago)

Thanks Marc.

----- Original Message -----
From: "Rich Megginson" <rmegg...@redhat.com>
To: "Marc Grimme" <gri...@atix.de>
Cc: freeipa-users@redhat.com
Sent: Tuesday, May 22, 2012 5:29:21 PM
Subject: Re: [Freeipa-users] Howto solve database inconsistency

On 05/22/2012 06:08 AM, Marc Grimme wrote:
> Hello,
> during troubleshooting why the creation of a replica crashes I realized that 
> there are database inconsistencies in my master server.
> During ipa-replica-install the process terminated in step 21/29.
> The master log showed the following error messages:
> [18/May/2012:22:38:50 +0200] NSMMReplicationPlugin - 
> agmt="cn=meTomethusalix2.cl.atix" (methusalix2:389): Replication bind with 
> SIMPLE auth resumed
> [18/May/2012:22:38:52 +0200] NSMMReplicationPlugin - Beginning total update 
> of replica "agmt="cn=meTomethusalix2.cl.atix" (methusalix2:389)".
> [18/May/2012:22:38:53 +0200] _entry_set_tombstone_rdn - Failed to convert DN 
> idnsname=axref05-1 to RDN
> [18/May/2012:22:38:53 +0200] id2entry - str2entry returned NULL for id 299, 
> string="rdn"
> [18/May/2012:22:38:53 +0200] _entry_set_tombstone_rdn - Failed to convert DN 
> idnsName=axref05-1 to RDN
> [18/May/2012:22:38:53 +0200] id2entry - str2entry returned NULL for id 306, 
> string="rdn"
> [18/May/2012:22:38:53 +0200] _entry_set_tombstone_rdn - Failed to convert DN 
> idnsName=axref05-1 to RDN
> [18/May/2012:22:38:53 +0200] id2entry - str2entry returned NULL for id 307, 
> string="rdn"
>
> Then the ipa-repica-install process just terminates.
>
> When I then do a reindex on the database I can see the following:
> [root@axinfra01-1 scripts-CL-ATIX]# ./db2index
> [18/May/2012:22:22:50 +0200] - /etc/dirsrv/slapd-CL-ATIX/dse.ldif: 
> nsslapd-maxdescriptors: nsslapd-maxdescriptors: invalid value "8192", maximum 
> file descriptors must range from 1 to 1024 (the current process limit).  
> Server will use a setting of 1024.
> [18/May/2012:22:22:50 +0200] - Config Warning: - nsslapd-maxdescriptors: 
> invalid value "8192", maximum file descriptors must range from 1 to 1024 (the 
> current process limit).  Server will use a setting of 1024.
> [18/May/2012:22:22:50 +0200] - check_and_set_import_cache: pagesize: 4096, 
> pages: 513771, procpages: 53984
> [18/May/2012:22:22:50 +0200] - Import allocates 822032KB import cache.
> [18/May/2012:22:22:50 +0200] - Backing up file 0 
> (/var/lib/dirsrv/slapd-CL-ATIX/bak/reindex_2012_05_18_22_22_50/userRoot/cn.db4)
> [18/May/2012:22:22:50 +0200] - Backing up file 1 
> (/var/lib/dirsrv/slapd-CL-ATIX/bak/reindex_2012_05_18_22_22_50/userRoot/member.db4)
> [18/May/2012:22:22:50 +0200] - Backing up file 2 
> (/var/lib/dirsrv/slapd-CL-ATIX/bak/reindex_2012_05_18_22_22_50/userRoot/displayname.db4)
> [18/May/2012:22:22:50 +0200] - Backing up file 3 
> (/var/lib/dirsrv/slapd-CL-ATIX/bak/reindex_2012_05_18_22_22_50/userRoot/sn.db4)
> [18/May/2012:22:22:50 +0200] - Backing up file 4 
> (/var/lib/dirsrv/slapd-CL-ATIX/bak/reindex_2012_05_18_22_22_50/userRoot/id2entry.db4)
> [18/May/2012:22:22:50 +0200] - Backing up file 5 
> (/var/lib/dirsrv/slapd-CL-ATIX/bak/reindex_2012_05_18_22_22_50/userRoot/ancestorid.db4)
> [18/May/2012:22:22:50 +0200] - Backing up file 6 
> (/var/lib/dirsrv/slapd-CL-ATIX/bak/reindex_2012_05_18_22_22_50/userRoot/krbPrincipalName.db4)
> [18/May/2012:22:22:50 +0200] - Backing up file 7 
> (/var/lib/dirsrv/slapd-CL-ATIX/bak/reindex_2012_05_18_22_22_50/userRoot/uid.db4)
> [18/May/2012:22:22:50 +0200] - Backing up file 8 
> (/var/lib/dirsrv/slapd-CL-ATIX/bak/reindex_2012_05_18_22_22_50/userRoot/mail.db4)
> [18/May/2012:22:22:50 +0200] - Backing up file 9 
> (/var/lib/dirsrv/slapd-CL-ATIX/bak/reindex_2012_05_18_22_22_50/userRoot/aci.db4)
> [18/May/2012:22:22:50 +0200] - Backing up file 10 
> (/var/lib/dirsrv/slapd-CL-ATIX/bak/reindex_2012_05_18_22_22_50/userRoot/memberOf.db4)
> [18/May/2012:22:22:50 +0200] - Backing up file 11 
> (/var/lib/dirsrv/slapd-CL-ATIX/bak/reindex_2012_05_18_22_22_50/userRoot/nsuniqueid.db4)
> [18/May/2012:22:22:50 +0200] - Backing up file 12 
> (/var/lib/dirsrv/slapd-CL-ATIX/bak/reindex_2012_05_18_22_22_50/userRoot/memberUser.db4)
> [18/May/2012:22:22:50 +0200] - Backing up file 13 
> (/var/lib/dirsrv/slapd-CL-ATIX/bak/reindex_2012_05_18_22_22_50/userRoot/uidnumber.db4)
> [18/May/2012:22:22:50 +0200] - Backing up file 14 
> (/var/lib/dirsrv/slapd-CL-ATIX/bak/reindex_2012_05_18_22_22_50/userRoot/givenName.db4)
> [18/May/2012:22:22:50 +0200] - Backing up file 15 
> (/var/lib/dirsrv/slapd-CL-ATIX/bak/reindex_2012_05_18_22_22_50/userRoot/parentid.db4)
> [18/May/2012:22:22:50 +0200] - Backing up file 16 
> (/var/lib/dirsrv/slapd-CL-ATIX/bak/reindex_2012_05_18_22_22_50/userRoot/nscpEntryDN.db4)
> [18/May/2012:22:22:50 +0200] - Backing up file 17 
> (/var/lib/dirsrv/slapd-CL-ATIX/bak/reindex_2012_05_18_22_22_50/userRoot/gidnumber.db4)
> [18/May/2012:22:22:50 +0200] - Backing up file 18 
> (/var/lib/dirsrv/slapd-CL-ATIX/bak/reindex_2012_05_18_22_22_50/userRoot/entryusn.db4)
> [18/May/2012:22:22:50 +0200] - Backing up file 19 
> (/var/lib/dirsrv/slapd-CL-ATIX/bak/reindex_2012_05_18_22_22_50/userRoot/entryrdn.db4)
> [18/May/2012:22:22:50 +0200] - Backing up file 20 
> (/var/lib/dirsrv/slapd-CL-ATIX/bak/reindex_2012_05_18_22_22_50/userRoot/DBVERSION)
> [18/May/2012:22:22:50 +0200] - Backing up file 21 
> (/var/lib/dirsrv/slapd-CL-ATIX/bak/reindex_2012_05_18_22_22_50/userRoot/numsubordinates.db4)
> [18/May/2012:22:22:50 +0200] - Backing up file 22 
> (/var/lib/dirsrv/slapd-CL-ATIX/bak/reindex_2012_05_18_22_22_50/userRoot/memberHost.db4)
> [18/May/2012:22:22:50 +0200] - Backing up file 23 
> (/var/lib/dirsrv/slapd-CL-ATIX/bak/reindex_2012_05_18_22_22_50/userRoot/ou.db4)
> [18/May/2012:22:22:50 +0200] - Backing up file 24 
> (/var/lib/dirsrv/slapd-CL-ATIX/bak/reindex_2012_05_18_22_22_50/userRoot/objectclass.db4)
> [18/May/2012:22:22:50 +0200] upgrade DB - userRoot: Start upgradedb.
> [18/May/2012:22:22:50 +0200] - WARNING: Import is running with 
> nsslapd-db-private-import-mem on; No other process is allowed to access the 
> database
> [18/May/2012:22:22:50 +0200] - reindex userRoot: Index buffering enabled with 
> bucket size 100
> [18/May/2012:22:22:51 +0200] ldif2dbm - import_get_and_add_parent_rdns: 
> Failed to position at ID 297
> [18/May/2012:22:22:51 +0200] - ldbm2index: Failed to compose dn for (rdn: 
> nsuniqueid=fef36002-4da911e1-b813f830-2eedd06a,idnsname=axref05-1, ID: 299)
> [18/May/2012:22:22:51 +0200] ldif2dbm - import_get_and_add_parent_rdns: 
> Failed to position at ID 304
> [18/May/2012:22:22:51 +0200] - ldbm2index: Failed to compose dn for (rdn: 
> nsuniqueid=c1911a01-50aa11e1-b813f830-2eedd06a,idnsName=axref05-1, ID: 306)
> [18/May/2012:22:22:51 +0200] ldif2dbm - import_get_and_add_parent_rdns: 
> Failed to position at ID 304
> [18/May/2012:22:22:51 +0200] - ldbm2index: Failed to compose dn for (rdn: 
> nsuniqueid=927ba801-50ac11e1-b813f830-2eedd06a,idnsName=axref05-1, ID: 307)
> [18/May/2012:22:22:51 +0200] - reindex userRoot: WARNING: Skipping entry 
> "nsuniqueid=ffffffff-ffffffff-ffffffff-ffffffff" which has no parent, ending 
> at line 239 of file "id2entry.db4"
> ..
>
> The question is now:
> * Are those messages related to the terminating ipa-replica-install?
> * How can I resolve those inconsistencies in the db?

First - what is your platform and 389-ds-base version?  What this a 
fresh install or an upgrade from a previous version?  If an upgrade, 
what was the version you upgraded from?

>
> Thanks for your help
> Marc.
>
>
> ______________________________________________________________________________
>
> Marc Grimme
>
> E-Mail: gri...@atix.de
>
> _______________________________________________
> Freeipa-users mailing list
> Freeipa-users@redhat.com
> https://www.redhat.com/mailman/listinfo/freeipa-users

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