Gizmo2 connecting peripherals: searching issues solution

Question

The scenario

I am working on a project where I need to "evolve" several Gizmo2 board to make them specialised for some tasks. In short words the rules are the following

Desk unit : This is the most simple model; it will include a series of peripheral devices, a small case (fit back to a HDMI monitor) and an internal 60 Gb SSD disk with the entire system onboard. The provided application will be web based and the operating system will be Ununtu 14 LT, this means the entire system is 100% open source. The Gizmo2 is connected to a 1Gb switch and is part of an independent node of a local network.
Server unit: This is a single gizmo2 module that will be setup in a small expandable cluster. It should host a ssd internal disk for Linux operating system and a 500 Gb or 1 Tb external HDD for databa storage

All the machines are on the same LAN with 1Gb network

The Server unit will be clustered if needed with other self-balancing network devices

The machine external HDD machines will use the two USB3 Gizmo2 as dual raid hdd storage. USB3 has almost the same access speed than the SATA bus.

The machine will use eventually the external HDD connected to the on-board second sata port.

The machine is powered by a 4000 mA power supply giving the extra-power needed for the attached peripherals.

The second SATA connector and the SATA 5V power cables

Inside this scenario (if needed images are also available) I experience some issues that seems very probably hardware-dependent. What I need is some good check advices to verify for sure the issues causes.

Need to use components

The external parts that should be used are the following (for various kind of settings:

External 500 Gb 2.5" HDD (5V)

For now it is used a 1Tb 5" 12V + 5V HDD externally powered that will be replaced in the definitive configuration with the specific hardware. The difference in this case is meaningless Two disks will be connected to the USB3 via a SATA to USB3 converter that reaches a comparable speed. The following image shows the HDD connected in this way with an external powered dock.

mPCIe board with Parallel + serial interface

This is a micro PCIe board that has the same connector as the micro SATA. The board should be installed in the Gizmo2 bottom connector; as explained in the documentation the system will recognise automatically if the connector is used for mPCIe or mSATA with SSD drive connected.

32Gb microSD with linux boot only for emergency recovery

It has been used a class10 microSD card, 32 Gb. Both tests with Ubuntu and Debian installation has completed successfully but it is not possible to boot. Debian just stops on the black and white screen with the Booting from Hard Disk message while Ubuntu shows the grub and every try to start reboot the system.

SSD disk starting from the secondary SATA

The secondary SATA should host the operating system when the primary SSD connector (on the back side of the Gizmo2) is used as microPCI instead of microSATA The image below shows the board mounted on the mSATA to SATA adapter board.

Experienced issues

The following are the blocking issues found during some days of tests.

Installing the OS on the microSD : all the installation process works fine with Ubuntu only, then at the end of process it is required the first reboot. The system boots and the only thing shown on the screen is "Booting from HD" then the system does not goes ahead.
Installing the OS on the external HDD (both Debian and Ubutu): same as 1)
The only way until now I was able to install Linux Ubuntu 14 was on the internal SSD (120 Gb) that boot fine after installation without any issue.

Problems with the two SATA ports

The second SATA port is on the board (thanks again to for her precious previous tests and shared knowledge !!!) and it is not populated. As the documentation explain it is a second port, we should expect that it can work with the first one connected. Instead:

A. With a 120Gb SSD on the first mSATA and any kind of SSD or HDD connected to the second SATA port as explained above none of the two disks are saw at boot time (only the micro SD if present).

B. With the mPCIe adapter (Serial + Parallel) in the primary port and the HDD on the SATA port, it is saw but does not work correctly. Instead with the SSD connected to the SATA (second port) it is not saw at all at boot time.

C. As the SSD or MPICEe boards are removed from the bottom connector, the SATA disk is saw correctly. Only the HDD can be connected and the operating system installed as well.

D. Only if the 120 Gb SSD is connected to the bottom port can be formatted and the operating system installed correctly.

Problems with OS booting

The same Linux OS has been installed with success on the external HDD (via the second SATA connection and external power), the microSD and the SSD (connected on the bottom connector). The only installation version that boots correctly is when the ssd is in its place and nothing else is connected to the system. The only accepted second HDD is when it is connected to the USB3 via the SATA to USB3 dock.

After booting from the Ubuntu desktop surprisingly all the linux installations on the three different media are virtually identical, despite that does not boot or boot partially, as shown in the images below:

The only possible bootable configuration

The only possible bootable configuration is from the SSD on the bottom connector with the external HDD connected to the USB3 port.

I hope that someone has some new idea to solve the problem, suggestions etc.

Thanks in advance. Enrico

Former Member · Answer

hia Enrico!! I've got some ideas that might help overcome some if not all of these problems, I'll put them all in a post when i get more time tonight. The basics are that a bit of magic is needed to get sdcards to boot. If theyre flashed with a cd image then they act like a cd would and boot in the same way. If you want to use them as a system drive, you need to remove and rewrite a new partition table replicating the cylinder/sector layout of a bootable system disk (they werent ever meant to be used as flexibly as they are these days.. the partition structure is even different to usb drives.) once thats done, you need to make a small primary partition around 32MB usually and format it as fat 16 and set it's type to 'boot'. This can all be done in gparted. When you come to install ubuntu onto it, boot into the live environment from a usb key(try without installing option), make sure the sd card is in too. Once the ubuntu live session starts up, you can start the installation from an icon on the desktop, and have the added benefit of a working operating system to help shoehorn it on if needs be! So when the screen comes up asking where you want it installing, choose to do 'something else'. you should come to the live images version of gparted partition manager, select the sdcard from the menu at the top right and you should see the 32MB partition that you made earlier. select it and find the drop down list that says 'mount point' choose '/BOOT' . The linux sysloader that tells the computer how to read linux partitions will be installed on there along with the grub loader. You need to make some more partitions now, one needs to be the main root partition that holds the operating system, this can be almost as large as the free space or just large large enough for ubuntu and other software to install on if you plan on saving the data to a seperate partition. select your partition size, format as an ext2 or ext3 /4 primary partition and select "/" from mount point list. / is the operating systems root so thats where ubuntu will install. next is a 1.5GB primary partition formatted as a linux swap area, the mount point should automatically set to /SWAP but if it doesnt then select it. If you chose to have your data seperate then use the remaining space on the disk to make a partition of any type (recommend ext) and set it's mount point to /DATA. feel free to give them all labels etc and double check that the 32MB partition has its flag set to boot. It should be on the very right hand side of its data. you can always right click it and choose 'manage flags'. you should have: 32MB fat16 /BOOT primary boot xxGB ext2 / 1.5GB swap xxGB ext2 /DATA (optional) once happy click next to start installing! As a quick explanation, most hard drives etc.. come with a master boot record and partition table that are all set out in a standard format. The bios has access to firmware that can read that standard format, which is or was a fat16 dos format. The bios reads blocks of data from the disk, because of the formatting all of the data is arranged in blocks that are the size it's expecting. From those blocks, the bios can gather information about the partition table and most importantly read code from the disk that can understand how the other partitions work, that code block leads onto syslinux and the whole higher level boot process goes on from there. rewriting a new partition table, then making a 32MB fat16 partition replicates that mbr on an sdcard. Anything above 8GB will need the partition table arranging as an lba type, modern bioses are made to read larger blocks which allows for a greater number of file entries and a larger available storage capacity. hope it helps and im on track to solving or at least understanding better the SATA issues

Former Member · Answer

hi, i am on with this but keep getting sidetracked.. ive worked my way through the amd datasheet for the processor too. A quick bit to help along until i get back home on sunday.. The sata ports on the amd soc dont have a ssd interface only a standard sata one. gizmo2 has its own signal converter to manage this which is only capable of supporting ssd drives up to 64GB. There are only 2 ssd interfaces to the soc, each is capable of supporting 2 sata drives provided an external signal muxer is used, there arent any devices that i can find on gizmo 2 that do this directly for the sata buses so you can only use either the msata/mpcie or the sata header that you soldered on.. not both at once. there is a device on there with this potential but its been used in a reverse configuration to select between whether data from the msata port goes to the pci bus or to the sata bus. This also means that the sata port on the side doesnt work with ssd drives and unless an external ic is used, only 1 drive can go into there. I wont have chance to post more until sunday but i might make a blog video talking through some of it... as a point of interest, the soc is capable of supporting up to 8GB ddr3.