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Preclear very slow in step 2 of 10

Featured Replies

Hello, I'm building my first Unraid box and need some help with it :)

 

The box in made from old parts (I know its junk  ;D ):

Unraid v4.5.6 in USB Flash Disk 4GB Apacer AH325

PCI 4xSATA controller: Delock 70154 - NonRaid BIOS, Chip SiL3114 (on PCI 4)

Motherboard: QDI Superb 4FX, SIS648FX, Soc 748

RAM: TwinMOS M2G5J16A-TT 512MB 184p PC2700, and SAMSUNG 256MB 3-3-5-2 333 DDR

MemTest ran for 2 cycles with no errors

NVidia GF4 Ti AGP card

Zalman PSU ZM460B-APS 460W

Ethernet PCI card 10/100 ALN-330 Chip Realtek 8139C (on PCI 5)

 

CPU:

root@Christine:/var/log# cat /proc/cpuinfo
processor       : 0
vendor_id       : GenuineIntel
cpu family      : 15
model           : 2
model name      : Intel(R) Pentium(R) 4 CPU 2.40GHz
stepping        : 4
cpu MHz         : 2405.437
cache size      : 512 KB
fdiv_bug        : no
hlt_bug         : no
f00f_bug        : no
coma_bug        : no
fpu             : yes
fpu_exception   : yes
cpuid level     : 2
wp              : yes
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmxfxsr sse sse2 ss ht tm up pebs bts
bogomips        : 4810.87
clflush size    : 64
cache_alignment : 128
address sizes   : 36 bits physical, 32 bits virtual

 

The HDD's installed are:

1) WD IDE 1 80GB model:WD800JB-00JJC0 - (Will become Unraid Disk 4)

2) SG SATA CON3 250GB model:ST3250310NS - (Will become Unraid Disk 2)

3) SG SATA CON2 250GB model:ST3250410AS - (Will become Unraid Disk 1)

4) WD SATA CON1 1TB WD Green WD10EAVS - (Will become Unraid Parity)

Ripped off a WD My Book studio, got two more waiting after I test the box and copy their files in it.

This is a WD10EAVS Drive, does this drive need a pin7-8 jumper setting? (Like EARS Drives) ???

 

5) SG SATA CON 4 80GB model:ST380815AS - (Will become Unraid Disk 3)

All the disks have data on them, I have not erased the existing partitions or run format on them.

Except the WD green that has a Truecrypt container, all drives have NTFS partitions.

 

The array is stopped no disks assigned yet

 

I'm preclearing one of the 250GB disks (only one preclear running) and its in step 2/10 "Copying zeros to remainder of disk to clear it".

It started at 38MB/s speed and near the end 96%-97% it dropped to 3.8MB/s, its been 20 hrs since it started, now its in 99% 247,953,944,576  bytes out of  250,059,350,016 - 3.4MB/s

I believe this is extremely slow

is this normal or could this mean trouble?  ???

 

The disk is /dev/sdb

From the system log:

Nov  2 15:22:13 Christine kernel: ata2: SATA link up 1.5 Gbps (SStatus 113 SControl 310)                       
Nov  2 15:22:13 Christine kernel: ata2.00: ATA-7: ST3250410AS, 4.AAA, max UDMA/133                             
Nov  2 15:22:13 Christine kernel: ata2.00: 488397168 sectors, multi 16: LBA48 NCQ (depth 0/32)                 
Nov  2 15:22:13 Christine kernel: ata2.00: configured for UDMA/100                                             
Nov  2 15:22:13 Christine kernel: scsi 2:0:0:0: Direct-Access     ATA      ST3250410AS      4.AA PQ: 0 ANSI: 5 
Nov  2 15:22:13 Christine kernel: sd 2:0:0:0: [sdb] 488397168 512-byte logical blocks: (250 GB/232 GiB)        
Nov  2 15:22:13 Christine kernel: sd 2:0:0:0: [sdb] Write Protect is off                                       
Nov  2 15:22:13 Christine kernel: sd 2:0:0:0: [sdb] Mode Sense: 00 3a 00 00                                    
Nov  2 15:22:13 Christine kernel: sd 2:0:0:0: [sdb] Write cache: enabled, read cache: enabled, doesn't support DPO or FUA                                                                                                     
Nov  2 15:22:13 Christine kernel:  sdb: sdb1 sdb2                                                              
Nov  2 15:22:13 Christine kernel: sd 2:0:0:0: [sdb] Attached SCSI disk

 

and SMART:

Nov  2 16:09:37 Christine preclear_disk-start[1577]: smartctl version 5.38 [i486-slackware-linux-gnu] Copyright (C) 2002-8 Bruce Allen                                                                                        
Nov  2 16:09:37 Christine preclear_disk-start[1577]: Home page is http://smartmontools.sourceforge.net/        
Nov  2 16:09:37 Christine preclear_disk-start[1577]:                                                           
Nov  2 16:09:37 Christine preclear_disk-start[1577]: === START OF INFORMATION SECTION ===                      
Nov  2 16:09:37 Christine preclear_disk-start[1577]: Model Family:     Seagate Barracuda 7200.10 family        
Nov  2 16:09:37 Christine preclear_disk-start[1577]: Device Model:     ST3250410AS                             
Nov  2 16:09:37 Christine preclear_disk-start[1577]: Serial Number:    6RYEEGS1                                
Nov  2 16:09:37 Christine preclear_disk-start[1577]: Firmware Version: 4.AAA                                   
Nov  2 16:09:37 Christine preclear_disk-start[1577]: User Capacity:    250,059,350,016 bytes                   
Nov  2 16:09:37 Christine preclear_disk-start[1577]: Device is:        In smartctl database [for details use: -P show]                                                                                                        
Nov  2 16:09:37 Christine preclear_disk-start[1577]: ATA Version is:   7                                       
Nov  2 16:09:37 Christine preclear_disk-start[1577]: ATA Standard is:  Exact ATA specification draft version not indicated                                                                                                    
Nov  2 16:09:37 Christine preclear_disk-start[1577]: Local Time is:    Tue Nov  2 16:09:37 2010 EET            
Nov  2 16:09:37 Christine preclear_disk-start[1577]: SMART support is: Available - device has SMART capability.
Nov  2 16:09:37 Christine preclear_disk-start[1577]: SMART support is: Enabled                                 

bla
bla
ulala
                                                                         
Nov  2 16:09:37 Christine preclear_disk-start[1577]:                                                           
Nov  2 16:09:37 Christine preclear_disk-start[1577]: SMART Error Log Version: 1                                
Nov  2 16:09:37 Christine preclear_disk-start[1577]: No Errors Logged                                          
Nov  2 16:09:37 Christine preclear_disk-start[1577]:                                                           
Nov  2 16:09:37 Christine preclear_disk-start[1577]: SMART Self-test log structure revision number 1           
Nov  2 16:09:37 Christine preclear_disk-start[1577]:                                                           
Nov  2 16:09:37 Christine preclear_disk-start[1577]: SMART Selective self-test log data structure revision number 1                                                                                                           
Nov  2 16:09:37 Christine preclear_disk-start[1577]:  SPAN  MIN_LBA  MAX_LBA  CURRENT_TEST_STATUS              
Nov  2 16:09:37 Christine preclear_disk-start[1577]:     1        0        0  Not_testing                      
Nov  2 16:09:37 Christine preclear_disk-start[1577]:     2        0        0  Not_testing                      
Nov  2 16:09:37 Christine preclear_disk-start[1577]:     3        0        0  Not_testing                      
Nov  2 16:09:37 Christine preclear_disk-start[1577]:     4        0        0  Not_testing                      
Nov  2 16:09:37 Christine preclear_disk-start[1577]:     5        0        0  Not_testing                      
Nov  2 16:09:37 Christine preclear_disk-start[1577]: Selective self-test flags (0x0):                          
Nov  2 16:09:37 Christine preclear_disk-start[1577]:   After scanning selected spans, do NOT read-scan remainder of disk.                                                                                                     
Nov  2 16:09:37 Christine preclear_disk-start[1577]: If Selective self-test is pending on power-up, resume after 0 minute delay.                                                                                              
Nov  2 16:09:37 Christine preclear_disk-start[1577]:

                             

 

Its still running, used telnet to get the log (syslog1.txt file attached to the post)

 

Also searched the log (but I'm no good at reading it properly):

 

Nov  2 15:22:13 Christine kernel: Phoenix BIOS detected: BIOS may corrupt low RAM, working around it.

This makes me think that "BIOS Casheable" is enabled, should I disable it?

 

Nov  2 15:22:13 Christine kernel: ACPI: I/O resource it87 [0x295-0x296] conflicts with ACPI region IP__ [0x295-0x296]                                                                                                         
Nov  2 15:22:13 Christine kernel: ACPI: If an ACPI driver is available for this device, you should use it instead of the native driver

 

Nov  2 15:22:13 Christine kernel: read_file: error 2 opening /boot/config/super.dat                            
Nov  2 15:22:13 Christine kernel: md: could not read superblock from /boot/config/super.dat

 

And the most interesting  :(these lines repeat several times:

Nov  3 12:11:26 Christine kernel: ata2.00: exception Emask 0x0 SAct 0x0 SErr 0x0 action 0x6 frozen
Nov  3 12:11:26 Christine kernel: ata2.00: failed command: IDENTIFY DEVICE
Nov  3 12:11:26 Christine kernel: ata2.00: cmd ec/00:00:00:00:00/00:00:00:00:00/00 tag 0 pio 512 in
Nov  3 12:11:26 Christine kernel:          res 40/00:01:01:4f:c2/00:00:00:00:00/10 Emask 0x4 (timeout)
Nov  3 12:11:26 Christine kernel: ata2.00: status: { DRDY }
Nov  3 12:11:26 Christine kernel: ata2: hard resetting link
Nov  3 12:11:31 Christine kernel: ata2: link is slow to respond, please be patient (ready=-19)

 

UPDATE: the preclear finished after 21:30hrs

===========================================================================
=                unRAID server Pre-Clear disk /dev/sdb
=                       cycle 1 of 1
= Disk Pre-Clear-Read completed                                 DONE
= Step 1 of 10 - Copying zeros to first 2048k bytes             DONE
= Step 2 of 10 - Copying zeros to remainder of disk to clear it DONE
= Step 3 of 10 - Disk is now cleared from MBR onward.           DONE
= Step 4 of 10 - Clearing MBR bytes for partition 2,3 & 4       DONE
= Step 5 of 10 - Clearing MBR code area                         DONE
= Step 6 of 10 - Setting MBR signature bytes                    DONE
= Step 7 of 10 - Setting partition 1 to precleared state        DONE
= Step 8 of 10 - Notifying kernel we changed the partitioning   DONE
= Step 9 of 10 - Creating the /dev/disk/by* entries             DONE
= Step 10 of 10 - Testing if the clear has been successful.     DONE
=
Elapsed Time:  21:30:27
============================================================================
==
== SORRY: Disk /dev/sdb MBR could NOT be precleared
==
== out4= 00000
== out5= 00000
============================================================================
0+0 records in
0+0 records out
0 bytes (0 B) copied, 5.3594e-05 s, 0.0 kB/s
0000000

 

Between the reports it produced several errors like:

Elapsed Time:  21:29:50                                                    
dd: writing `/dev/sdb': Input/output error                                 
1+0 records in                                                             
0+0 records out                                                            
0 bytes (0 B) copied, 0.00211996 s, 0.0 kB/s                               
dd: writing `/dev/sdb': Input/output error                                 
1+0 records in                                                             
0+0 records out                                                            
0 bytes (0 B) copied, 0.00310989 s, 0.0 kB/s          

 

You can find everything in preclear.txt - file attached

 

Thank you for your help!

Christopher

PS. Sorry for my poor English, I'm from Greece.

syslog1.txt

preclear.txt

You have 5 older disks connected to a power supply with multiple 12 volt rails.  You may be near or at its limits.  The 12V1 rail is rated at 16 Amps... part of that capacity  will be probably used by the 24 pin motherboard connector and possibly one of the CPU power connectors.

 

The 12V2 rail is probably only used for the PCIe connectors and CPU power

 

The manufacturer does not give any details in their manual.

 

Your older drives probably draw near 3 amps per drive when spinning up and 2 amps per drive once spinning.  

 

The disk drive you were clearing stopped responding  (You saw the time-out in the syslog).  It might be because it failed.  It might be because a cable to it got loose. It might be because the power supply was not adequate to power all you have connected to it, and that specific drive was the most sensitive to the noise and poor voltage regulation of the overloaded supply.

 

Finally, the disk was not successfully pre-cleared as shown in the final output:

============================================================================

==

== SORRY: Disk /dev/sdb MBR could NOT be precleared

 

Edit: according to one review site:

This power supply features two +12 V virtual rails distributed like this:

 

    * +12V1 (solid yellow wire): All cables but the ATX12V.

    * +12V2 (yellow with black stripe wire): ATX12V connector.

 

Basically, you are only using one of the 12 volt rails. 

Joe L.

  • Author

Thank you very much for the fast reply  :)

 

The cables are new, but I will replace them anyway

I will also remove the two 80GB drives and try again, I believe the PSU can handle 3 HDD's

 

do you think I should put a jumper in the WD10EAVS 7-8 pins?

 

Again, thank you for taking the time to read and reply

do you think I should put a jumper in the WD10EAVS 7-8 pins?

 

No, that drive should not need a jumper.

  • Author

Thank you for your reply

 

Got some results this time :)

 

The 7-8 pins must be for the Advanced Format feature, it seems that this model does not use that architecture

 

From the WD Green family probably only WD20EARS, WD15EARS, WD10EARS, WD8000AARS and WD6400AARS use Advanced Format

http://wdc.custhelp.com/cgi-bin/wdc.cfg/php/enduser/std_adp.php?p_faqid=5324&p_created=1263858658&p_sid=S8AsQ7ek&p_accessibility=0&p_redirect=&p_srch=1&p_lva=&p_sp=cF9zcmNoPTEmcF9zb3J0X2J5PSZwX2dyaWRzb3J0PSZwX3Jvd19jbnQ9NTMsNTMmcF9wcm9kcz0yMjcsMjk0JnBfY2F0cz0mcF9wdj0yLjI5NCZwX2N2PSZwX3BhZ2U9MSZwX3NlYXJjaF90ZXh0PWFkdmFuY2VkIGZvcm1hdA!!&p_li=&p_topview=1

 

also found some explanation for the other errors

Nov  2 15:22:13 Christine kernel: md: could not read superblock from /boot/config/super.dat

It does not appear as if you've assigned any of your disks to the array...  That was the reason for the message

http://lime-technology.com/forum/index.php?topic=4223.0;wap2

 

Nov  2 15:22:13 Christine kernel: Phoenix BIOS detected: BIOS may corrupt low RAM, working around it.

It just seems that the low 64K memory is reserved.

root@Christine:/proc# cat meminfo                                                                              
MemTotal:         774480 kB                                                                                    
MemFree:          614636 kB                                                                                    
Buffers:              24 kB                                                                                    
Cached:           147208 kB                                                                                    
SwapCached:            0 kB                                                                                    
Active:            11092 kB                                                                                    
Inactive:           4056 kB                                                                                    
Active(anon):        104 kB                                                                                    
Inactive(anon):     4048 kB                                                                                    
Active(file):      10988 kB                                                                                    
Inactive(file):        8 kB                                                                                    
Unevictable:      136172 kB
Mlocked:               0 kB
HighTotal:             0 kB
HighFree:              0 kB
LowTotal:         774480 kB
LowFree:          614636 kB
SwapTotal:             0 kB
SwapFree:              0 kB
Dirty:                 0 kB
Writeback:             0 kB
AnonPages:          4088 kB
Mapped:             5564 kB
Shmem:                64 kB
Slab:               4468 kB
SReclaimable:       2148 kB
SUnreclaim:         2320 kB
KernelStack:         448 kB
PageTables:          432 kB
NFS_Unstable:          0 kB
Bounce:                0 kB
WritebackTmp:          0 kB
CommitLimit:      387240 kB
Committed_AS:      26440 kB
VmallocTotal:     247864 kB
VmallocUsed:         204 kB
VmallocChunk:     247340 kB
DirectMap4k:        4032 kB
DirectMap2M:      782336 kB

 

As for the disk problem I had, it must have been disk failure, I tried again using only 3 HDD's with new cables (removed the 80GB HDD's) and got the same error for the same disk by just running fdisk -l  :D

I removed that disk and precleared the next one, got some new errors in the final SMART report, I'm not sure if they are serious errors  :-\, but preclear completed this time.

 

===========================================================================
=                unRAID server Pre-Clear disk /dev/sdb                     
=                       cycle 1 of 1                                       
= Disk Pre-Clear-Read completed                                 DONE       
= Step 1 of 10 - Copying zeros to first 2048k bytes             DONE       
= Step 2 of 10 - Copying zeros to remainder of disk to clear it DONE       
= Step 3 of 10 - Disk is now cleared from MBR onward.           DONE       
= Step 4 of 10 - Clearing MBR bytes for partition 2,3 & 4       DONE       
= Step 5 of 10 - Clearing MBR code area                         DONE       
= Step 6 of 10 - Setting MBR signature bytes                    DONE       
= Step 7 of 10 - Setting partition 1 to precleared state        DONE       
= Step 8 of 10 - Notifying kernel we changed the partitioning   DONE       
= Step 9 of 10 - Creating the /dev/disk/by* entries             DONE
= Step 10 of 10 - Testing if the clear has been successful.     DONE
= Disk Post-Clear-Read completed                                DONE
Disk Temperature: 32C, Elapsed Time:  5:18:16
============================================================================
==
== Disk /dev/sdb has been successfully precleared
==
============================================================================
S.M.A.R.T. error count differences detected after pre-clear
note, some 'raw' values may change, but not be an indication of a problem
54c54
<   1 Raw_Read_Error_Rate     0x000f   073   063   044    Pre-fail  Always       -       22787603
---
>   1 Raw_Read_Error_Rate     0x000f   077   063   044    Pre-fail  Always       -       56241726
58c58
<   7 Seek_Error_Rate         0x000f   074   060   030    Pre-fail  Always       -       4321088183
---
>   7 Seek_Error_Rate         0x000f   074   060   030    Pre-fail  Always       -       4321102718
65,66c65,66
< 190 Airflow_Temperature_Cel 0x0022   071   060   045    Old_age   Always       -       29 (Lifetime Min/Max 28/29)
< 195 Hardware_ECC_Recovered  0x001a   043   034   000    Old_age   Always
---
> 190 Airflow_Temperature_Cel 0x0022   068   060   045    Old_age   Always       -       32 (Lifetime Min/Max 28/32)
> 195 Hardware_ECC_Recovered  0x001a   066   034   000    Old_age   Always
============================================================================

 

 

 

 

 

Those are not errors... Just difference in the smart reports from before and after.

 

In fact the "normalized" value for raw read errors increased (improved) to 77 from its starting value of 73.  The raw read error rate improved during the pre-clear process.

 

Joe L.

  • Author

Thank you all for the warm welcome and all the help :)

Everything seems to work now.

Precleared the WD Green drive with no errors.

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Chrome (Android)
  1. Tap the lock icon next to the address bar.
  2. Tap Permissions → Notifications.
  3. Adjust your preference.
Chrome (Desktop)
  1. Click the padlock icon in the address bar.
  2. Select Site settings.
  3. Find Notifications and adjust your preference.