[Gluster-users] Hundreds of duplicate files
Olav Peeters
opeeters at gmail.com
Fri Feb 20 21:47:07 UTC 2015
Thanks Joe,
for the answers!
I was not clear enough about the set up apparently.
The Gluster cluster consist of 3 nodes with each 14 bricks. The bricks
are formatted as xfs, mounted locally as xfs. There is one volume, type:
Distributed-Replicate (replica 2). The configuration is so that bricks
are mirrored on two different nodes.
The NFS mount which was alive but not used during reboot when the
problem started are from clients (2 XenServer machines configured as a
pool - a shared storage set-up). The comparisons I give below are
between (other) clients mounting via either glusterfs or NFS. Similar
problem with the exception that the first listing (via ls) after a fresh
mount via NFS actually does find the files with data. A second listing
only finds the 0 bit file with the same name.
So all the 0bit files in mode 0644 can be safely removed?
Why do I see three files with the same name (and modification timestamp
etc.) via either a glusterfs or NFS mount from a client? Deleting one of
the three will probably not solve the issue either.. this seems to me an
indexing issue in the gluster cluster.
How do I get Gluster to replicate the files correctly, only 2 versions
of the same file, not three, and on two bricks on different machines?
Cheers,
Olav
On 20/02/15 21:51, Joe Julian wrote:
>
> On 02/20/2015 12:21 PM, Olav Peeters wrote:
>> Let's take one file (3009f448-cf6e-413f-baec-c3b9f0cf9d72.vhd) as an
>> example...
>> On the 3 nodes where all bricks are formatted as XFS and mounted in
>> /export and 272b2366-dfbf-ad47-2a0f-5d5cc40863e3 is the mounting
>> point of a NFS shared storage connection from XenServer machines:
> Did I just read this correctly? Your bricks are NFS mounts? ie,
> GlusterFS Client <-> GlusterFS Server <-> NFS <-> XFS
>>
>> [root at gluster01 ~]# find
>> /export/*/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/ -name '300*' -exec ls
>> -la {} \;
>> -rw-r--r--. 2 root root 44332659200 Feb 17 23:55
>> /export/brick13gfs01/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/3009f448-cf6e-413f-baec-c3b9f0cf9d72.vhd
> Supposedly, this is the actual file.
>> -rw-r--r--. 2 root root 0 Feb 18 00:51
>> /export/brick14gfs01/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/3009f448-cf6e-413f-baec-c3b9f0cf9d72.vhd
> This is not a linkfile. Note it's mode 0644. How it got there with
> those permissions would be a matter of history and would require
> information that's probably lost.
>>
>> root at gluster02 ~]# find
>> /export/*/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/ -name '300*' -exec ls
>> -la {} \;
>> -rw-r--r--. 2 root root 44332659200 Feb 17 23:55
>> /export/brick13gfs02/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/3009f448-cf6e-413f-baec-c3b9f0cf9d72.vhd
>>
>> [root at gluster03 ~]# find
>> /export/*/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/ -name '300*' -exec ls
>> -la {} \;
>> -rw-r--r--. 2 root root 44332659200 Feb 17 23:55
>> /export/brick13gfs03/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/3009f448-cf6e-413f-baec-c3b9f0cf9d72.vhd
>> -rw-r--r--. 2 root root 0 Feb 18 00:51
>> /export/brick14gfs03/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/3009f448-cf6e-413f-baec-c3b9f0cf9d72.vhd
> Same analysis as above.
>>
>> 3 files with information, 2 x a 0-bit file with the same name
>>
>> Checking the 0-bit files:
>> [root at gluster01 ~]# getfattr -m . -d -e hex
>> /export/brick14gfs01/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/3009f448-cf6e-413f-baec-c3b9f0cf9d72.vhd
>> getfattr: Removing leading '/' from absolute path names
>> # file:
>> export/brick14gfs01/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/3009f448-cf6e-413f-baec-c3b9f0cf9d72.vhd
>> security.selinux=0x73797374656d5f753a6f626a6563745f723a66696c655f743a733000
>> trusted.afr.dirty=0x000000000000000000000000
>> trusted.afr.sr_vol01-client-34=0x000000000000000000000000
>> trusted.afr.sr_vol01-client-35=0x000000000000000000000000
>> trusted.gfid=0xaefd184508414a8f8408f1ab8aa7a417
>>
>> [root at gluster03 ~]# getfattr -m . -d -e hex
>> /export/brick14gfs03/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/3009f448-cf6e-413f-baec-c3b9f0cf9d72.vhd
>> getfattr: Removing leading '/' from absolute path names
>> # file:
>> export/brick14gfs03/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/3009f448-cf6e-413f-baec-c3b9f0cf9d72.vhd
>> security.selinux=0x73797374656d5f753a6f626a6563745f723a66696c655f743a733000
>> trusted.afr.dirty=0x000000000000000000000000
>> trusted.afr.sr_vol01-client-34=0x000000000000000000000000
>> trusted.afr.sr_vol01-client-35=0x000000000000000000000000
>> trusted.gfid=0xaefd184508414a8f8408f1ab8aa7a417
>>
>> This is not a glusterfs link file since there is no
>> "trusted.glusterfs.dht.linkto", am I correct?
> You are correct.
>>
>> And checking the "good" files:
>>
>> # file:
>> export/brick13gfs01/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/3009f448-cf6e-413f-baec-c3b9f0cf9d72.vhd
>> security.selinux=0x756e636f6e66696e65645f753a6f626a6563745f723a66696c655f743a733000
>> trusted.afr.dirty=0x000000000000000000000000
>> trusted.afr.sr_vol01-client-32=0x000000000000000000000000
>> trusted.afr.sr_vol01-client-33=0x000000000000000000000000
>> trusted.afr.sr_vol01-client-34=0x000000000000000000000000
>> trusted.afr.sr_vol01-client-35=0x000000010000000100000000
>> trusted.gfid=0xaefd184508414a8f8408f1ab8aa7a417
>>
>> [root at gluster02 ~]# getfattr -m . -d -e hex
>> /export/brick13gfs02/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/3009f448-cf6e-413f-baec-c3b9f0cf9d72.vhd
>> getfattr: Removing leading '/' from absolute path names
>> # file:
>> export/brick13gfs02/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/3009f448-cf6e-413f-baec-c3b9f0cf9d72.vhd
>> security.selinux=0x73797374656d5f753a6f626a6563745f723a66696c655f743a733000
>> trusted.afr.dirty=0x000000000000000000000000
>> trusted.afr.sr_vol01-client-32=0x000000000000000000000000
>> trusted.afr.sr_vol01-client-33=0x000000000000000000000000
>> trusted.gfid=0xaefd184508414a8f8408f1ab8aa7a417
>>
>> [root at gluster03 ~]# getfattr -m . -d -e hex
>> /export/brick13gfs03/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/3009f448-cf6e-413f-baec-c3b9f0cf9d72.vhd
>> getfattr: Removing leading '/' from absolute path names
>> # file:
>> export/brick13gfs03/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/3009f448-cf6e-413f-baec-c3b9f0cf9d72.vhd
>> security.selinux=0x73797374656d5f753a6f626a6563745f723a66696c655f743a733000
>> trusted.afr.dirty=0x000000000000000000000000
>> trusted.afr.sr_vol01-client-40=0x000000000000000000000000
>> trusted.afr.sr_vol01-client-41=0x000000000000000000000000
>> trusted.gfid=0xaefd184508414a8f8408f1ab8aa7a417
>>
>>
>>
>> Seen from a client via a glusterfs mount:
>> [root at client ~]# ls -al
>> /mnt/glusterfs/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/300*
>> -rw-r--r--. 1 root root 0 Feb 18 00:51
>> /mnt/glusterfs/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/3009f448-cf6e-413f-baec-c3b9f0cf9d72.vhd
>> -rw-r--r--. 1 root root 0 Feb 18 00:51
>> /mnt/glusterfs/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/3009f448-cf6e-413f-baec-c3b9f0cf9d72.vhd
>> -rw-r--r--. 1 root root 0 Feb 18 00:51
>> /mnt/glusterfs/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/3009f448-cf6e-413f-baec-c3b9f0cf9d72.vhd
>>
>>
>>
>> Via NFS (just after performing a umount and mount the volume again):
>> [root at client ~]# ls -al
>> /mnt/nfs/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/300*
>> -rw-r--r--. 1 root root 44332659200 Feb 17 23:55
>> /mnt/test/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/3009f448-cf6e-413f-baec-c3b9f0cf9d72.vhd
>> -rw-r--r--. 1 root root 44332659200 Feb 17 23:55
>> /mnt/test/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/3009f448-cf6e-413f-baec-c3b9f0cf9d72.vhd
>> -rw-r--r--. 1 root root 44332659200 Feb 17 23:55
>> /mnt/test/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/3009f448-cf6e-413f-baec-c3b9f0cf9d72.vhd
>>
>> Doing the same list a couple of seconds later:
>> [root at client ~]# ls -al
>> /mnt/nfs/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/300*
>> -rw-r--r--. 1 root root 0 Feb 18 00:51
>> /mnt/test/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/3009f448-cf6e-413f-baec-c3b9f0cf9d72.vhd
>> -rw-r--r--. 1 root root 0 Feb 18 00:51
>> /mnt/test/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/3009f448-cf6e-413f-baec-c3b9f0cf9d72.vhd
>> -rw-r--r--. 1 root root 0 Feb 18 00:51
>> /mnt/test/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/3009f448-cf6e-413f-baec-c3b9f0cf9d72.vhd
>> And again, and again, and again:
>> [root at client ~]# ls -al
>> /mnt/nfs/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/300*
>> -rw-r--r--. 1 root root 0 Feb 18 00:51
>> /mnt/test/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/3009f448-cf6e-413f-baec-c3b9f0cf9d72.vhd
>> -rw-r--r--. 1 root root 0 Feb 18 00:51
>> /mnt/test/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/3009f448-cf6e-413f-baec-c3b9f0cf9d72.vhd
>> -rw-r--r--. 1 root root 0 Feb 18 00:51
>> /mnt/test/272b2366-dfbf-ad47-2a0f-5d5cc40863e3/3009f448-cf6e-413f-baec-c3b9f0cf9d72.vhd
>>
>> This really seems odd. Why do we get to see "real data file" once only?
>>
>> It seems more and more that this crazy file duplication (and writing
>> of sticky bit files) was actually triggered when rebooting one of the
>> three nodes while there still is an active (even when there is no
>> data exchange at all) NFS connection, since all 0-bit files (of the
>> non Sticky bit type) were either created at 00:51 or 00:41, the exact
>> moment one of the three nodes in the cluster were rebooted. This
>> would mean that replication currently with GlusterFS creates hardly
>> any redundancy. Quiet the opposite, if one of the machines goes down,
>> all of your data seriously gets disorganised. I am buzzy configuring
>> a test installation to see how this can be best reproduced for a bug
>> report..
>>
>> Does anyone have a suggestion how to best get rid of the duplicates,
>> or rather get this mess organised the way it should be?
>> This is a cluster with millions of files. A rebalance does not fix
>> the issue, neither does a rebalance fix-layout help. Since this is a
>> replicated volume all files should be their 2x, not 3x. Can I safely
>> just remove all the 0 bit files outside of the .glusterfs directory
>> including the sticky bit files?
>>
>> The empty 0 bit files outside of .glusterfs on every brick I can
>> probably safely removed like this:
>> find /export/* -path */.glusterfs -prune -o -type f -size 0 -perm
>> 1000 -exec rm {} \;
>> not?
>>
>> Thanks!
>>
>> Cheers,
>> Olav
>> On 18/02/15 22:10, Olav Peeters wrote:
>>> Thanks Tom and Joe,
>>> for the fast response!
>>>
>>> Before I started my upgrade I stopped all clients using the volume
>>> and stopped all VM's with VHD on the volume, but I guess, and this
>>> may be the missing thing to reproduce this in a lab, I did not
>>> detach a NFS shared storage mount from a XenServer pool to this
>>> volume, since this is an extremely risky business. I also did not
>>> stop the volume. This I guess was a bit stupid, but since I did
>>> upgrades in the past this way without any issues I skipped this step
>>> (a really bad habit). I'll make amends and file a proper bug report
>>> :-). I agree with you Joe, this should never happen, even when
>>> someone ignores the advice of stopping the volume. If it would also
>>> be nessessary to detach shared storage NFS connections to a volume,
>>> than franky, glusterfs is unusable in a private cloud. No one can
>>> afford downtime of the whole infrastructure just for a glusterfs
>>> upgrade. Ideally a replicated gluster volume should even be able to
>>> remain online and used during (at least a minor version) upgrade.
>>>
>>> I don't know whether a heal was maybe buzzy when I started the
>>> upgrade. I forgot to check. I did check the CPU activity on the
>>> gluster nodes which were very low (in the 0.0X range via top), so I
>>> doubt it. I will add this to the bug report as a suggestion should
>>> they not be able to reproduce with an open NFS connection.
>>>
>>> By the way, is it sufficient to do:
>>> service glusterd stop
>>> service glusterfsd stop
>>> and do a:
>>> ps aux | gluster*
>>> to see if everything has stopped and kill any leftovers should this
>>> be necessary?
>>>
>>> For the fix, do you agree that if I run e.g.:
>>> find /export/* -type f -size 0 -perm 1000 -exec /bin/rm {} \;
>>> on every node if /export is the location of all my bricks, also in a
>>> replicated set-up, this will be save?
>>> No necessary 0bit files will be deleted in e.g. the .glusterfs of
>>> every brick?
>>>
>>> Thanks for your support!
>>>
>>> Cheers,
>>> Olav
>>>
>>>
>>>
>>>
>>>
>>> On 18/02/15 20:51, Joe Julian wrote:
>>>>
>>>> On 02/18/2015 11:43 AM, tbenzvi at 3vgeomatics.com wrote:
>>>>> Hi Olav,
>>>>>
>>>>> I have a hunch that our problem was caused by improper unmounting
>>>>> of the gluster volume, and have since found that the proper order
>>>>> should be: kill all jobs using volume -> unmount volume on clients
>>>>> -> gluster volume stop -> stop gluster service (if necessary)
>>>>> In my case, I wrote a Python script to find duplicate files on the
>>>>> mounted volume, then delete the corresponding link files on the
>>>>> bricks (making sure to also delete files in the .glusterfs directory)
>>>>> However, your find command was also suggested to me and I think
>>>>> it's a simpler solution. I believe removing all link files (even
>>>>> ones that are not causing duplicates) is fine since the next file
>>>>> access gluster will do a lookup on all bricks and recreate any
>>>>> link files if necessary. Hopefully a gluster expert can chime in
>>>>> on this point as I'm not completely sure.
>>>>
>>>> You are correct.
>>>>
>>>>> Keep in mind your setup is somewhat different than mine as I have
>>>>> only 5 bricks with no replication.
>>>>> Regards,
>>>>> Tom
>>>>>
>>>>> --------- Original Message ---------
>>>>> Subject: Re: [Gluster-users] Hundreds of duplicate files
>>>>> From: "Olav Peeters" <opeeters at gmail.com>
>>>>> Date: 2/18/15 10:52 am
>>>>> To: gluster-users at gluster.org, tbenzvi at 3vgeomatics.com
>>>>>
>>>>> Hi all,
>>>>> I'm have this problem after upgrading from 3.5.3 to 3.6.2.
>>>>> At the moment I am still waiting for a heal to finish (on a
>>>>> 31TB volume with 42 bricks, replicated over three nodes).
>>>>>
>>>>> Tom,
>>>>> how did you remove the duplicates?
>>>>> with 42 bricks I will not be able to do this manually..
>>>>> Did a:
>>>>> find $brick_root -type f -size 0 -perm 1000 -exec /bin/rm {} \;
>>>>> work for you?
>>>>>
>>>>> Should this type of thing ideally not be checked and mended by
>>>>> a heal?
>>>>>
>>>>> Does anyone have an idea yet how this happens in the first
>>>>> place? Can it be connected to upgrading?
>>>>>
>>>>> Cheers,
>>>>> Olav
>>>>>
>>>>>
>>>>>
>>>>> On 01/01/15 03:07, tbenzvi at 3vgeomatics.com wrote:
>>>>>
>>>>> No, the files can be read on a newly mounted client! I
>>>>> went ahead and deleted all of the link files associated
>>>>> with these duplicates, and then remounted the volume. The
>>>>> problem is fixed!
>>>>> Thanks again for the help, Joe and Vijay.
>>>>> Tom
>>>>>
>>>>> --------- Original Message ---------
>>>>> Subject: Re: [Gluster-users] Hundreds of duplicate files
>>>>> From: "Vijay Bellur" <vbellur at redhat.com>
>>>>> Date: 12/28/14 3:23 am
>>>>> To: tbenzvi at 3vgeomatics.com, gluster-users at gluster.org
>>>>>
>>>>> On 12/28/2014 01:20 PM, tbenzvi at 3vgeomatics.com wrote:
>>>>> > Hi Vijay,
>>>>> > Yes the files are still readable from the .glusterfs
>>>>> path.
>>>>> > There is no explicit error. However, trying to read
>>>>> a text file in
>>>>> > python simply gives me null characters:
>>>>> >
>>>>> > >>> open('ott_mf_itab').readlines()
>>>>> >
>>>>> ['\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00']
>>>>> >
>>>>> > And reading binary files does the same
>>>>> >
>>>>>
>>>>> Is this behavior seen with a freshly mounted client too?
>>>>>
>>>>> -Vijay
>>>>>
>>>>> > --------- Original Message ---------
>>>>> > Subject: Re: [Gluster-users] Hundreds of duplicate files
>>>>> > From: "Vijay Bellur" <vbellur at redhat.com>
>>>>> > Date: 12/27/14 9:57 pm
>>>>> > To: tbenzvi at 3vgeomatics.com, gluster-users at gluster.org
>>>>> >
>>>>> > On 12/28/2014 10:13 AM, tbenzvi at 3vgeomatics.com wrote:
>>>>> > > Thanks Joe, I've read your blog post as well as
>>>>> your post
>>>>> > regarding the
>>>>> > > .glusterfs directory.
>>>>> > > I found some unneeded duplicate files which were
>>>>> not being read
>>>>> > > properly. I then deleted the link file from the
>>>>> brick. This always
>>>>> > > removes the duplicate file from the listing, but
>>>>> the file does not
>>>>> > > always become readable. If I also delete the
>>>>> associated file in the
>>>>> > > .glusterfs directory on that brick, then some more
>>>>> files become
>>>>> > > readable. However this solution still doesn't work
>>>>> for all files.
>>>>> > > I know the file on the brick is not corrupt as it
>>>>> can be read
>>>>> > directly
>>>>> > > from the brick directory.
>>>>> >
>>>>> > For files that are not readable from the client, can
>>>>> you check if the
>>>>> > file is readable from the .glusterfs/ path?
>>>>> >
>>>>> > What is the specific error that is seen while trying
>>>>> to read one such
>>>>> > file from the client?
>>>>> >
>>>>> > Thanks,
>>>>> > Vijay
>>>>> >
>>>>> >
>>>>> >
>>>>> > _______________________________________________
>>>>> > Gluster-users mailing list
>>>>> > Gluster-users at gluster.org
>>>>> > http://www.gluster.org/mailman/listinfo/gluster-users
>>>>> >
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Gluster-users mailing list
>>>>> Gluster-users at gluster.org
>>>>> http://www.gluster.org/mailman/listinfo/gluster-users
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Gluster-users mailing list
>>>>> Gluster-users at gluster.org
>>>>> http://www.gluster.org/mailman/listinfo/gluster-users
>>>>
>>>>
>>>>
>>>> _______________________________________________
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>>
>
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