[Fwd: Re: [Fwd: [Beowulf] serious NFS problem on Mandrake 10.0]]

H.Vidal, Jr. hvidal at tesseract-tech.com
Sat Dec 4 08:05:36 PST 2004


Keep traffic on list for benefit of others.

No, this is something I cannot share because I cannot 'direct'
you to the references. It is vendor data, based on their experimentation
and testing, in house and at customer sites.

I will try to see if I can get more info on this from engineers at
vendor, then post same.

hv

Ariel Sabiguero wrote:
> This thing is very interesting.
> Is the research available somewhere?
> I would appreciate if you help me accessing to that study.
> 
> Regards.
> 
> Ariel
> 
> H.Vidal, Jr. wrote:
> 
>> Which filesystem do you use?
>>
>> On recent research into NAS appliances, we found out
>> that things like ext2 and ext3 really don't play so nice
>> with NFS, especially under older 2.4 kernels. However,
>> in general, our vendor warned us to keep away from large,
>> multi-user shares via NFS under ext<2|3> filesystems.
>>
>> Don't know if this is helpful, perhaps just a data point.....
>>
>> hv
>>
>> David Mathog wrote:
>>
>>> I'm seeing a serious NFS problem with MDK 10.0
>>> (using a 2.6.8-1 kernel.org kernel).  All of the
>>> machines run the same OS version.
>>>
>>> In a 20 node cluster each node NFS mounts /u1 from
>>> the master.  They run a calculation and generate
>>> a file in /tmp of about 26000 lines coming to
>>> 1.3Mb (both the number of lines and total size
>>> vary a little). When it completes the process on
>>> each end node does:
>>>
>>>   mv /tmp/blah.$NODENAME .   mv -f /tmp/blah.$NODENAME /tmp/SAVEblah
>>>
>>> The home directory (".") is a couple of
>>> levels down under /u1, so this effectively performs
>>> a network copy from /tmp on the compute node to /u1
>>> on the master node.  The copies are largely asynchronous
>>> since the end nodes complete at various times.
>>>
>>> On the master node there are occasionally
>>> (defined as: 1 bad line, out of 20 files, every
>>> 3rd or 4th run) a very long bad line.
>>>
>>> Here are four lines from the original file on /tmp:
>>>
>>> '4827135'=='-22004070' (3254 9815 3391 9675) 22
>>> '4827135'=='-22004070' (75050 11805 75081 11774) 0
>>> '4827086'=='-22004070' (79588 9817 79809 9594) 28
>>> '4827086'=='-22004070' (34069 11794 34308 11555) 34
>>>
>>> Here are the four lines from the copy on /u1 .
>>>
>>> '4827135'=='-22004070' (3254 9815 3391 9675) 22
>>> '4827135'=='-22004070' (75050 11805 75081 11774) 0
>>> '4827086'=='-22004070' (79588 9817 798<NUL>(MANY times)<NULL>1
>>> '4156131'=='+22004070' (58122 9687 58250 9818) 11
>>>
>>> The final line on /u1 does appear in /tmp, but much, much
>>> farther into the file. I very carefully cut out the missing
>>> text from the original file, pasted it into a new file, and found:
>>>
>>> % wc deleted.txt
>>>   642  3849 32769 deleted.txt
>>>
>>> So it looks like a block of 32768 bytes was lost
>>> (+1 probably for an extra EOL in my deleted.txt file)
>>> during the mv operation and all bytes replaced
>>> with <NUL>.  On repeated runs on the same data (same
>>> output files each time) the problem line never occurs
>>> twice in the same place, and it hops from node to node,
>>> suggesting that it's a rare event somewhere in the
>>> data transport (mv) operation.
>>>
>>> This is very, very, VERY bad.
>>> No relevant messages show up in /var/log/messages.
>>> /u1 is /dev/sde1 and smartctl -a on that device shows
>>> no errors. On the master /u1 is in /etc/fstab as:
>>>
>>> LABEL=usrdisk           /u1             ext2    defaults,quota  1 2
>>>
>>> and is exported as:
>>>
>>> /u1              *.cluster(rw,no_root_squash)
>>>
>>> Has anybody else seen this bug?
>>>
>>> Is there a patch for it?  Possibly relevant software:
>>>
>>>
>>> coreutils-5.1.2-1mdk         #/bin/mv
>>> nfs-utils-clients-1.0.6-1mdk #nfs client
>>> kernel 2.6.8-1               #kernel.org
>>>
>>> Thanks,
>>>
>>> David Mathog
>>> mathog at caltech.edu
>>> Manager, Sequence Analysis Facility, Biology Division, Caltech
>>> _______________________________________________
>>> Beowulf mailing list, Beowulf at beowulf.org
>>> To change your subscription (digest mode or unsubscribe) visit 
>>> http://www.beowulf.org/mailman/listinfo/beowulf
>>>
>>
>>
>> ------------------------------------------------------------------------
>>
>> Subject:
>> [Beowulf] serious NFS problem on Mandrake 10.0
>> From:
>> "David Mathog" <mathog at mendel.bio.caltech.edu>
>> Date:
>> Fri, 03 Dec 2004 13:05:01 -0800
>> To:
>> beowulf at beowulf.org
>>
>> To:
>> beowulf at beowulf.org
>>
>>
>>I'm seeing a serious NFS problem with MDK 10.0
>>(using a 2.6.8-1 kernel.org kernel).  All of the
>>machines run the same OS version.
>>
>>In a 20 node cluster each node NFS mounts /u1 from
>>the master.  They run a calculation and generate
>>a file in /tmp of about 26000 lines coming to
>>1.3Mb (both the number of lines and total size
>>vary a little). When it completes the process on
>>each end node does:
>>
>>  mv /tmp/blah.$NODENAME . 
>>  mv -f /tmp/blah.$NODENAME /tmp/SAVEblah
>>
>>The home directory (".") is a couple of
>>levels down under /u1, so this effectively performs
>>a network copy from /tmp on the compute node to /u1
>>on the master node.  The copies are largely asynchronous
>>since the end nodes complete at various times.
>>
>>On the master node there are occasionally
>>(defined as: 1 bad line, out of 20 files, every
>>3rd or 4th run) a very long bad line.
>>
>>Here are four lines from the original file on /tmp:
>>
>>'4827135'=='-22004070' (3254 9815 3391 9675) 22
>>'4827135'=='-22004070' (75050 11805 75081 11774) 0
>>'4827086'=='-22004070' (79588 9817 79809 9594) 28
>>'4827086'=='-22004070' (34069 11794 34308 11555) 34
>>
>>Here are the four lines from the copy on /u1 .
>>
>>'4827135'=='-22004070' (3254 9815 3391 9675) 22
>>'4827135'=='-22004070' (75050 11805 75081 11774) 0
>>'4827086'=='-22004070' (79588 9817 798<NUL>(MANY times)<NULL>1
>>'4156131'=='+22004070' (58122 9687 58250 9818) 11
>>
>>The final line on /u1 does appear in /tmp, but much, much
>>farther into the file. I very carefully cut out the missing
>>text from the original file, pasted it into a new file, and found:
>>
>>% wc deleted.txt
>>  642  3849 32769 deleted.txt
>>
>>So it looks like a block of 32768 bytes was lost
>>(+1 probably for an extra EOL in my deleted.txt file)
>>during the mv operation and all bytes replaced
>>with <NUL>.  On repeated runs on the same data (same
>>output files each time) the problem line never occurs
>>twice in the same place, and it hops from node to node,
>>suggesting that it's a rare event somewhere in the
>>data transport (mv) operation.
>>
>>This is very, very, VERY bad. 
>>
>>No relevant messages show up in /var/log/messages.
>>/u1 is /dev/sde1 and smartctl -a on that device shows
>>no errors. On the master /u1 is in /etc/fstab as:
>>
>>LABEL=usrdisk           /u1             ext2    defaults,quota  1 2
>>
>>and is exported as:
>>
>>/u1              *.cluster(rw,no_root_squash)
>>
>>Has anybody else seen this bug?
>>
>>Is there a patch for it?  Possibly relevant software:
>>
>>
>>coreutils-5.1.2-1mdk         #/bin/mv
>>nfs-utils-clients-1.0.6-1mdk #nfs client
>>kernel 2.6.8-1               #kernel.org
>>
>>Thanks,
>>
>>David Mathog
>>mathog at caltech.edu
>>Manager, Sequence Analysis Facility, Biology Division, Caltech
>>_______________________________________________
>>Beowulf mailing list, Beowulf at beowulf.org
>>To change your subscription (digest mode or unsubscribe) visit http://www.beowulf.org/mailman/listinfo/beowulf
>>
>>  
>>
>>------------------------------------------------------------------------
>>
>>_______________________________________________
>>Beowulf mailing list, Beowulf at beowulf.org
>>To change your subscription (digest mode or unsubscribe) visit http://www.beowulf.org/mailman/listinfo/beowulf
>>  
>>
> 

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