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Since yesterday, I added a brand new SSD in my PC, and I am experiencing a very fast boot from grub menu. The problem is before arriving to this menu, I must wait for a long time (~30s in most cases). I installed grub on the SSD. After the BIOS, I sometimes see "Grub loading" immediately, sometimes just a blinking cursor, but the time to reach the menu seems to be the same. I tried adding debug=disk (and even debug=all to my grub.cfg), but logs appear only after the unexplained period of time waiting ends.

I have 3 disks: - sda, marked as bootable with a windows boot loader on it - sdb, which is the SSD - sdc, which holds the swap partition and a data partition. It had my previous installation of Fedora 18 until yesterday

parted description:

Model: ATA ST3250410AS (scsi)
Disk /dev/sda: 250GB
Sector size (logical/physical): 512B/512B
Partition Table: msdos
Disk Flags: 

Number  Start   End    Size   Type     File system  Flags
 1      32.3kB  250GB  250GB  primary  ntfs         boot

Model: ATA M4-CT128M4SSD2 (scsi)
Disk /dev/sdb: 128GB
Sector size (logical/physical): 512B/512B
Partition Table: msdos
Disk Flags: 

Number  Start   End     Size    Type     File system  Flags
 1      1049kB  1075MB  1074MB  primary  ext4         boot
 2      1075MB  11.8GB  10.7GB  primary  ext4
 3      11.8GB  33.7GB  21.9GB  primary  ext4

Model: ATA ST3160827AS (scsi)
Disk /dev/sdc: 160GB
Sector size (logical/physical): 512B/512B
Partition Table: msdos
Disk Flags: 

Number  Start   End     Size    Type     File system     Flags
 1      1049kB  2149MB  2147MB  primary  linux-swap(v1)
 2      52.4GB  160GB   107GB   primary  fat32           lba

When going under Windows (on sda1), I also have unexplained hanging times when shutting down, but this has occurred first one year ago.

EDIT Unplugging the 250GB drive makes the latency go away. The HDD LED does not blink during the waiting time.

What is going on?

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I edited my question. I replugged the sda drive on another SATA port, with the same results. I checked BIOS settings, did not see anything dubious... I don't have Intel Management Engine (I have an ASUS P5Q) motherboard. – greg0ire Mar 10 '13 at 2:46
I didn't try swapping the drives, not sure what you meant by that... swapping the SATA cables plug locations? Or modifying my grub configuration? – greg0ire Mar 10 '13 at 13:13
Ok, I'll try that (I think I might already have tried it by repluggining the drive in a different location). And yes unplugging the 250GB drive fixes the problem. It has a boot flag, is this really needed? – greg0ire Mar 10 '13 at 13:29
Tried booting with only SSD + HD160GB: same result. Tried swapping SDD and HD250GB, grub tells me "no such partition". I then think the old HD160GB still has a grub that points to nothing. I look in the BIOS, and it was not booting on the SSD anymore. Changed that back and... problem solved! Can you explain this mystery in an answer? I'll accept it and upvote you. – greg0ire Mar 10 '13 at 14:46
let us continue this discussion in chat – don_crissti Mar 10 '13 at 15:39
up vote 2 down vote accepted

Try to plug the SSD in the first SATA port and select it as the first boot device in BIOS. Otherwise it's usually a matter of fiddling with the drives and making sure GRUB configuration matches the actual drives numbering, i.e. hd0 designates HD0 in BIOS etc.

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