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CRITICAL DISK STORAGE PROBLEM WITH MD1K-2
There is a serious problem with md1k-2, one of the PowerVault MD1000's connected to s3. It will get into a state where two disks appear to have failed. A two-disk failure when using RAID-5 would mean complete data loss. Fortunately, I've found a remedy that is allowing us to copy the data to a different array.
Dell Higher Education Support 1-800-274-7799 Enter Express Service Code 43288304365 when prompted on the call.
| host | service tag | contract end | description | notes |
| c8 | CPM1NF1 | 02/15/2011 | PowerEdge 1950 | old schuster storage, moved PERC 5/E to s3 |
| s3 | GHNCVH1 | 06/22/2012 | PowerEdge 1950 | connected to md1k-2 via PERC 5/E |
| md1k-1 | FVWQLF1 | 02/07/2011 | PowerVault MD1000 | enclosure 3 |
| md1k-2 | JVWQLF1 | 02/07/2011 | PowerVault MD1000 | enclosure 2 |
| md1k-3 | 4X9NLF1 | 03/06/2011 | PowerVault MD1000 | enclosure 1 |
The following things need to be done:
- Copy the data from md1k-2 to md1k-2 (see Copying data below).
- Call Dell to resolve this problem.
- Adjust links in /afs/bx.psu.edu/depot/data/schuster_lab/sequencing/archive to reflect new data location.
It seems unlikely that so many disks would fail so close together. I'm thinking it might be a problem with the PowerVault MD1000 itself.
Description of problem we're having with md1k-2
I've narrowed down the error by looking through the adapter event logs. There will be two errors, one followed about 45 seconds after the first:
Tue Mar 23 23:09:56 2010 Error on PD 31(e2/s0) (Error f0) Tue Mar 23 23:10:43 2010 Error on PD 30(e2/s1) (Error f0)
After that, the virtual disk goes offline.
[root@s3: ~/storage]# MegaCli -LDInfo L1 -a0
Adapter 0 -- Virtual Drive Information:
Virtual Disk: 1 (Target Id: 1)
Name:md1k-2
RAID Level: Primary-5, Secondary-0, RAID Level Qualifier-3
Size:8.862 TB
State: Offline
Stripe Size: 64 KB
Number Of Drives:14
Span Depth:1
Default Cache Policy: WriteBack, ReadAheadNone, Direct, No Write Cache if Bad BBU
Current Cache Policy: WriteBack, ReadAheadNone, Direct, No Write Cache if Bad BBU
Access Policy: Read/Write
Disk Cache Policy: Disk's Default
Encryption Type: None
Number of Dedicated Hot Spares: 1
0 : EnclId - 18 SlotId - 1
If you go into the server room, you'll see flashing amber lights on the disks in md1k-2 slot 0 and 1. I can md1k-2 back using the following procedure (replace slot 0 and 1 which whichever slots are appropriate):
- Take the disks in md1k-2 slots 0 and 1 about half-way out and then push them back in.
- Wait a few seconds for the lights on md1k-2 slots 0 and 1 to return to green.
- Press the power button on s3 until it turns off.
- Press the power button on s3 again to turn it back on.
- Log into s3 as root after it has finished booting.
I then import the foreign configuration. The disk in md1k-2 slot 1 is fine, but the disk in slot 0 needs to be rebuild.
[root@s3: ~/storage]# MegaCli -CfgForeign -Scan -a0
There are 2 foreign configuration(s) on controller 0.
Exit Code: 0x00
[root@s3: ~/storage]# MegaCli -CfgForeign -Import -a0
Foreign configuration is imported on controller 0.
Exit Code: 0x00
[root@s3: ~/storage]# ./check_disk_states
PhysDrv [ 18:0 ] in md1k-2 is in Rebuild state.
command to check rebuild progress:
MegaCli -PDRbld -ShowProg -PhysDrv [ 18:0 ] -a0
command to estimate remaining rebuild time:
./time_left 18 0
[root@s3: ~/storage]# MegaCli -PDRbld -ShowProg -PhysDrv [ 18:0 ] -a0
Rebuild Progress on Device at Enclosure 18, Slot 0 Completed 56% in 139 Minutes.
Exit Code: 0x00
[root@s3: ~/storage]# ./time_left 18 0
time_left: PhysDrv [ 18:0 ] will be done rebuilding in about 1:49:12
After the disk is finished rebuilding, reboot s3 and md1k-2 will be available once again.
Log entries containing Error f0
Extracted from the PERC 5/E event log entries:
| Tue Mar 9 15:02:11 2010 | Error on PD 1d(e1/s4) (Error f0) |
| Tue Mar 9 15:02:58 2010 | Error on PD 1c(e1/s5) (Error f0) |
| Fri Mar 12 15:00:25 2010 | Error on PD 30(e2/s1) (Error f0) |
| Fri Mar 12 15:01:12 2010 | Error on PD 2f(e2/s2) (Error f0) |
| Wed Mar 17 03:55:03 2010 | Error on PD 30(e2/s1) (Error f0) |
| Wed Mar 17 03:55:50 2010 | Error on PD 2f(e2/s2) (Error f0) |
| Sat Mar 20 11:53:06 2010 | Error on PD 29(e2/s8) (Error f0) |
| Sat Mar 20 11:53:54 2010 | Error on PD 28(e2/s9) (Error f0) |
| Tue Mar 23 19:55:39 2010 | Error on PD 28(e2/s9) (Error f0) |
| Tue Mar 23 19:56:21 2010 | Error on PD 27(e2/s10) (Error f0) |
| Tue Mar 23 23:09:56 2010 | Error on PD 31(e2/s0) (Error f0) |
| Tue Mar 23 23:10:43 2010 | Error on PD 30(e2/s1) (Error f0) |
| Wed Mar 24 22:02:34 2010 | Error on PD 29(e2/s8) (Error f0) |
| Wed Mar 24 22:03:17 2010 | Error on PD 28(e2/s9) (Error f0) |
| Thu Mar 25 22:08:01 2010 | Error on PD 31(e2/s0) (Error f0) |
| Thu Mar 25 22:08:44 2010 | Error on PD 23(e2/s14) (Error f0) |
| Thu Mar 25 22:08:44 2010 | Error on PD 30(e2/s1) (Error f0) |
Copying data from md1k-2 to md1k-1
zpool md1k-2 contains zfs filesystem md1k-2/archive which is mounted on s3:/zfs/md1k-2/archive. s3:/zfs/md1k-2/archive contains archives of 454 runs from May 2009 through December 2009 and all of the Illumina runs from 2009.
We're copying the data from md1k-2 to md1k-1. There are about 7TB of data on md1k-2. Only 250GB has been copied to md1k-1 so far. Once md1k-2 is back online (should be about 1:30pm Friday March 26), I'll continue copying the data to md1k-1.
First, I make a few changes to facilitate the data copy:
[root@s3: ~/storage]# zfs unshare md1k-2/data [root@s3: ~/storage]# zfs unshare md1k-2/archive [root@s3: ~/storage]# zfs unshare md1k-1/archive [root@s3: ~/storage]# zpool set failmode=continue md1k-2 [root@s3: ~/storage]# zfs set checksum=off md1k-2/archive
Then, I use rsync within a screen to copy the data:
[root@s3: ~/storage]# screen [root@s3: ~/storage]# cd /zfs/md1k-2/archive [root@s3: ~/storage]# rsync -Pav sequencing /zfs/md1k-1/archive
After the rsync starts copying the data, I type control-a control-d to detach the screen session (that's control-a followed by a control-d).
TO reconnect to the screen session:
[root@s3: ~/storage]# screen -r
When copying is finished, undo the previous changes:
[root@s3: ~/storage]# zfs set checksum=on md1k-2/archive [root@s3: ~/storage]# zpool set failmode=wait md1k-2
After all of the data has been copied, you'll need to delete and re-create the md1k-2 zpool.
Miscellaneous
The following list is in no particular order.
- Migrate linne to bx network.
- Migrate Schuster Lab machines to bx network.
- Or at least, install AFS client.
- Automate the archiving of sequencing run directories.
- Maybe after two weeks in staging they're moved into the archive?
- Test suspending user jobs in Sun Grid Engine.
- Use Xen or something so user jobs can be stopped and not just suspended.
- User jobs could be suspended to allow signal processing jobs to run immediately.
- Combine linne and persephone clusters.
- Come up with some backup solution.
- Replace BioTeam iNquiry
- Use Galaxy instead?
- Implement a centralized database of sequencing run information.
- Basically a small LIMS.
- Maybe use Galaxy?
- After problems with md1k-2 are fixed, turn on automated scrubbing.
- Look into different storage systems.
