@floion,
Before any custom variable using balenaCloud Dashboard is created in the device.
root@ee9dba3:~# cat /mnt/boot/config.txt
....
....
## pwr_led_gpio
## Set which GPIO to use for the PWR LED
##
## In case you want to connect it to an external device
##
## Not available on Model A/B boards.
##
## Default 35.
##
#dtparam=pwr_led_gpio=35
# Enable UART
enable_uart=1
dtparam=i2c_arm=on
dtparam=spi=on
disable_splash=1
dtparam=audio=on
After the RESIN_HOST_CONFIG_dtoverlay
is created using the Dashboard
root@ee9dba3:~# cat /mnt/boot/config.txt
disable_splash=1
dtoverlay=sdio
dtoverlay=poll_once=off
dtoverlay=sdio_overclock=25
dtoverlay=gpios_34_39
dtparam=i2c_arm=on
dtparam=spi=on
dtparam=audio=on
enable_uart=1
gpu_mem=16
root@ee9dba3:~# dmesg
[ 0.000000] Booting Linux on physical CPU 0x0
[ 0.000000] Linux version 4.19.71 (oe-user@oe-host) (gcc version 8.3.0 (GCC)) #1 SMP Tue Sep 17 04:58:50 UTC 2019
[ 0.000000] CPU: ARMv7 Processor [410fd034] revision 4 (ARMv7), cr=10c5383d
[ 0.000000] CPU: div instructions available: patching division code
[ 0.000000] CPU: PIPT / VIPT nonaliasing data cache, VIPT aliasing instruction cache
[ 0.000000] OF: fdt: Machine model: Raspberry Pi Compute Module 3 Plus Rev 1.0
[ 0.000000] Memory policy: Data cache writealloc
[ 0.000000] cma: Reserved 8 MiB at 0x3dc00000
[ 0.000000] On node 0 totalpages: 255488
[ 0.000000] Normal zone: 2246 pages used for memmap
[ 0.000000] Normal zone: 0 pages reserved
[ 0.000000] Normal zone: 255488 pages, LIFO batch:63
[ 0.000000] random: get_random_bytes called from start_kernel+0xb0/0x4b4 with crng_init=0
[ 0.000000] percpu: Embedded 17 pages/cpu s39564 r8192 d21876 u69632
[ 0.000000] pcpu-alloc: s39564 r8192 d21876 u69632 alloc=17*4096
[ 0.000000] pcpu-alloc: [0] 0 [0] 1 [0] 2 [0] 3
[ 0.000000] Built 1 zonelists, mobility grouping on. Total pages: 253242
[ 0.000000] Kernel command line: coherent_pool=1M bcm2708_fb.fbwidth=656 bcm2708_fb.fbheight=416 bcm2708_fb.fbdepth=16 bcm2708_fb.fbswap=1 smsc95xx.macaddr=B8:27:EB:67:C1:46 vc_mem.mem_base=0x3f000000 vc_mem.mem_size=0x3f600000 dwc_otg.lpm_enable=0 console=tty1 console=ttyAMA0,115200 rootfstype=ext4 rootwait root=PARTUUID=b8a83ef0-02 rootwait
[ 0.000000] Dentry cache hash table entries: 131072 (order: 7, 524288 bytes)
[ 0.000000] Inode-cache hash table entries: 65536 (order: 6, 262144 bytes)
[ 0.000000] Memory: 983644K/1021952K available (8192K kernel code, 655K rwdata, 2328K rodata, 7168K init, 828K bss, 30116K reserved, 8192K cma-reserved)
[ 0.000000] Virtual kernel memory layout:
vector : 0xffff0000 - 0xffff1000 ( 4 kB)
fixmap : 0xffc00000 - 0xfff00000 (3072 kB)
vmalloc : 0xbe800000 - 0xff800000 (1040 MB)
lowmem : 0x80000000 - 0xbe600000 ( 998 MB)
modules : 0x7f000000 - 0x80000000 ( 16 MB)
.text : 0x(ptrval) - 0x(ptrval) (9184 kB)
.init : 0x(ptrval) - 0x(ptrval) (7168 kB)
.data : 0x(ptrval) - 0x(ptrval) ( 656 kB)
.bss : 0x(ptrval) - 0x(ptrval) ( 829 kB)
[ 0.000000] SLUB: HWalign=64, Order=0-3, MinObjects=0, CPUs=4, Nodes=1
[ 0.000000] ftrace: allocating 28729 entries in 85 pages
[ 0.000000] rcu: Hierarchical RCU implementation.
[ 0.000000] NR_IRQS: 16, nr_irqs: 16, preallocated irqs: 16
[ 0.000000] arch_timer: cp15 timer(s) running at 19.20MHz (phys).
[ 0.000000] clocksource: arch_sys_counter: mask: 0xffffffffffffff max_cycles: 0x46d987e47, max_idle_ns: 440795202767 ns
[ 0.000007] sched_clock: 56 bits at 19MHz, resolution 52ns, wraps every 4398046511078ns
[ 0.000022] Switching to timer-based delay loop, resolution 52ns
[ 0.000269] Console: colour dummy device 80x30
[ 0.000898] console [tty1] enabled
[ 0.000954] Calibrating delay loop (skipped), value calculated using timer frequency.. 38.40 BogoMIPS (lpj=192000)
[ 0.001000] pid_max: default: 32768 minimum: 301
[ 0.001364] Mount-cache hash table entries: 2048 (order: 1, 8192 bytes)
[ 0.001399] Mountpoint-cache hash table entries: 2048 (order: 1, 8192 bytes)
[ 0.002336] CPU: Testing write buffer coherency: ok
[ 0.002811] CPU0: thread -1, cpu 0, socket 0, mpidr 80000000
[ 0.003481] Setting up static identity map for 0x100000 - 0x10003c
[ 0.003647] rcu: Hierarchical SRCU implementation.
[ 0.004457] smp: Bringing up secondary CPUs ...
[ 0.005306] CPU1: thread -1, cpu 1, socket 0, mpidr 80000001
[ 0.006226] CPU2: thread -1, cpu 2, socket 0, mpidr 80000002
[ 0.007082] CPU3: thread -1, cpu 3, socket 0, mpidr 80000003
[ 0.007204] smp: Brought up 1 node, 4 CPUs
[ 0.007285] SMP: Total of 4 processors activated (153.60 BogoMIPS).
[ 0.007309] CPU: All CPU(s) started in HYP mode.
[ 0.007330] CPU: Virtualization extensions available.
[ 0.008345] devtmpfs: initialized
[ 0.020936] VFP support v0.3: implementor 41 architecture 3 part 40 variant 3 rev 4
[ 0.021204] clocksource: jiffies: mask: 0xffffffff max_cycles: 0xffffffff, max_idle_ns: 19112604462750000 ns
[ 0.021253] futex hash table entries: 1024 (order: 4, 65536 bytes)
[ 0.021873] pinctrl core: initialized pinctrl subsystem
[ 0.022746] NET: Registered protocol family 16
[ 0.025694] DMA: preallocated 1024 KiB pool for atomic coherent allocations
[ 0.031316] hw-breakpoint: found 5 (+1 reserved) breakpoint and 4 watchpoint registers.
[ 0.031351] hw-breakpoint: maximum watchpoint size is 8 bytes.
[ 0.031569] Serial: AMBA PL011 UART driver
[ 0.033862] bcm2835-mbox 3f00b880.mailbox: mailbox enabled
[ 0.068944] bcm2835-dma 3f007000.dma: DMA legacy API manager at (ptrval), dmachans=0x1
[ 0.070659] SCSI subsystem initialized
[ 0.070901] usbcore: registered new interface driver usbfs
[ 0.070976] usbcore: registered new interface driver hub
[ 0.071091] usbcore: registered new device driver usb
[ 0.090112] raspberrypi-firmware soc:firmware: Attached to firmware from 2019-08-28 15:08, variant start_cd
[ 0.100364] raspberrypi-firmware soc:firmware: Firmware hash is 31098ceed842ca10c8ffd02ffe3640bf6c0190b4
[ 0.111721] clocksource: Switched to clocksource arch_sys_counter
[ 0.203418] VFS: Disk quotas dquot_6.6.0
[ 0.203539] VFS: Dquot-cache hash table entries: 1024 (order 0, 4096 bytes)
[ 0.203750] FS-Cache: Loaded
[ 0.203979] CacheFiles: Loaded
[ 0.214002] NET: Registered protocol family 2
[ 0.214784] tcp_listen_portaddr_hash hash table entries: 512 (order: 0, 6144 bytes)
[ 0.214850] TCP established hash table entries: 8192 (order: 3, 32768 bytes)
[ 0.214980] TCP bind hash table entries: 8192 (order: 4, 65536 bytes)
[ 0.215184] TCP: Hash tables configured (established 8192 bind 8192)
[ 0.215339] UDP hash table entries: 512 (order: 2, 16384 bytes)
[ 0.215404] UDP-Lite hash table entries: 512 (order: 2, 16384 bytes)
[ 0.215736] NET: Registered protocol family 1
[ 0.216336] RPC: Registered named UNIX socket transport module.
[ 0.216363] RPC: Registered udp transport module.
[ 0.216385] RPC: Registered tcp transport module.
[ 0.216406] RPC: Registered tcp NFSv4.1 backchannel transport module.
[ 0.277353] hw perfevents: enabled with armv7_cortex_a7 PMU driver, 7 counters available
[ 0.280411] Initialise system trusted keyrings
[ 0.280654] workingset: timestamp_bits=14 max_order=18 bucket_order=4
[ 0.290153] squashfs: version 4.0 (2009/01/31) Phillip Lougher
[ 0.290207] FS-Cache: Netfs 'nfs' registered for caching
[ 0.290784] NFS: Registering the id_resolver key type
[ 0.290835] Key type id_resolver registered
[ 0.290856] Key type id_legacy registered
[ 0.290887] nfs4filelayout_init: NFSv4 File Layout Driver Registering...
[ 0.292790] aufs 4.19.17+-20190211
[ 0.294276] Key type asymmetric registered
[ 0.294303] Asymmetric key parser 'x509' registered
[ 0.294375] Block layer SCSI generic (bsg) driver version 0.4 loaded (major 250)
[ 0.294543] io scheduler noop registered
[ 0.294567] io scheduler deadline registered
[ 0.294760] io scheduler cfq registered (default)
[ 0.294786] io scheduler mq-deadline registered
[ 0.294808] io scheduler kyber registered
[ 0.298040] bcm2708_fb soc:fb: FB found 1 display(s)
[ 0.306957] Console: switching to colour frame buffer device 82x26
[ 0.314941] bcm2708_fb soc:fb: Registered framebuffer for display 0, size 656x416
[ 0.322634] bcm2835-rng 3f104000.rng: hwrng registered
[ 0.325877] vc-mem: phys_addr:0x00000000 mem_base=0x3f000000 mem_size:0x3f600000(1014 MiB)
[ 0.332227] vc-sm: Videocore shared memory driver
[ 0.335462] gpiomem-bcm2835 3f200000.gpiomem: Initialised: Registers at 0x3f200000
[ 0.351971] brd: module loaded
[ 0.364867] loop: module loaded
[ 0.368331] Loading iSCSI transport class v2.0-870.
[ 0.371995] libphy: Fixed MDIO Bus: probed
[ 0.374952] tun: Universal TUN/TAP device driver, 1.6
[ 0.378046] dwc_otg: version 3.00a 10-AUG-2012 (platform bus)
[ 0.381169] dwc_otg 3f980000.usb: base=(ptrval)
[ 0.584331] Core Release: 2.80a
[ 0.587209] Setting default values for core params
[ 0.590085] Finished setting default values for core params
[ 0.793232] Using Buffer DMA mode
[ 0.796031] Periodic Transfer Interrupt Enhancement - disabled
[ 0.798952] Multiprocessor Interrupt Enhancement - disabled
[ 0.801942] OTG VER PARAM: 0, OTG VER FLAG: 0
[ 0.804947] Dedicated Tx FIFOs mode
[ 0.808390] WARN::dwc_otg_hcd_init:1045: FIQ DMA bounce buffers: virt = bdd04000 dma = 0xfdd04000 len=9024
[ 0.814616] FIQ FSM acceleration enabled for :
Non-periodic Split Transactions
Periodic Split Transactions
High-Speed Isochronous Endpoints
Interrupt/Control Split Transaction hack enabled
[ 0.829203] dwc_otg: Microframe scheduler enabled
[ 0.829262] WARN::hcd_init_fiq:457: FIQ on core 1
[ 0.832081] WARN::hcd_init_fiq:458: FIQ ASM at 80682390 length 36
[ 0.834845] WARN::hcd_init_fiq:497: MPHI regs_base at be810000
[ 0.837517] dwc_otg 3f980000.usb: DWC OTG Controller
[ 0.840238] dwc_otg 3f980000.usb: new USB bus registered, assigned bus number 1
[ 0.843083] dwc_otg 3f980000.usb: irq 56, io mem 0x00000000
[ 0.845892] Init: Port Power? op_state=1
[ 0.848628] Init: Power Port (0)
[ 0.851549] usb usb1: New USB device found, idVendor=1d6b, idProduct=0002, bcdDevice= 4.19
[ 0.857108] usb usb1: New USB device strings: Mfr=3, Product=2, SerialNumber=1
[ 0.860069] usb usb1: Product: DWC OTG Controller
[ 0.863024] usb usb1: Manufacturer: Linux 4.19.71 dwc_otg_hcd
[ 0.865969] usb usb1: SerialNumber: 3f980000.usb
[ 0.869433] hub 1-0:1.0: USB hub found
[ 0.872343] hub 1-0:1.0: 1 port detected
[ 0.875681] dwc_otg: FIQ enabled
[ 0.875687] dwc_otg: NAK holdoff enabled
[ 0.875693] dwc_otg: FIQ split-transaction FSM enabled
[ 0.875705] Module dwc_common_port init
[ 0.875970] usbcore: registered new interface driver usb-storage
[ 0.879002] mousedev: PS/2 mouse device common for all mice
[ 0.882737] bcm2835-wdt bcm2835-wdt: Broadcom BCM2835 watchdog timer
[ 0.885834] bcm2835-cpufreq: min=600000 max=1200000
[ 0.889210] sdhci: Secure Digital Host Controller Interface driver
[ 0.892062] sdhci: Copyright(c) Pierre Ossman
[ 0.894022] mmc-bcm2835 3f300000.mmc: could not get clk, deferring probe
[ 0.895708] sdhost-bcm2835 3f202000.mmc: could not get clk, deferring probe
[ 0.897289] sdhci-pltfm: SDHCI platform and OF driver helper
[ 0.899068] ledtrig-cpu: registered to indicate activity on CPUs
[ 0.900635] hidraw: raw HID events driver (C) Jiri Kosina
[ 0.902286] usbcore: registered new interface driver usbhid
[ 0.903843] usbhid: USB HID core driver
[ 0.905809] vchiq: vchiq_init_state: slot_zero = (ptrval), is_master = 0
[ 0.908372] [vc_sm_connected_init]: start
[ 0.911231] vc_vchi_sm_init: failed to open VCHI service (-1)
[ 0.911235] [vc_sm_connected_init]: failed to initialize shared memory service
[ 0.914497] [vc_sm_connected_init]: end - returning -1
[ 0.917527] Initializing XFRM netlink socket
[ 0.919490] NET: Registered protocol family 10
[ 0.921659] Segment Routing with IPv6
[ 0.923227] NET: Registered protocol family 17
[ 0.924738] bridge: filtering via arp/ip/ip6tables is no longer available by default. Update your scripts to load br_netfilter if you need this.
[ 0.927902] Key type dns_resolver registered
[ 0.929745] Registering SWP/SWPB emulation handler
[ 0.931718] registered taskstats version 1
[ 0.933290] Loading compiled-in X.509 certificates
[ 0.938832] uart-pl011 3f201000.serial: cts_event_workaround enabled
[ 0.940482] 3f201000.serial: ttyAMA0 at MMIO 0x3f201000 (irq = 81, base_baud = 0) is a PL011 rev2
[ 1.967856] console [ttyAMA0] enabled
[ 1.974170] mmc-bcm2835 3f300000.mmc: mmc_debug:0 mmc_debug2:0
[ 1.981575] mmc-bcm2835 3f300000.mmc: DMA channel allocated
[ 2.014552] sdhost: log_buf @ (ptrval) (fdd07000)
[ 2.069407] mmc0: sdhost-bcm2835 loaded - DMA enabled (>1)
[ 2.077506] of_cfs_init
[ 2.083119] of_cfs_init: OK
[ 2.089269] uart-pl011 3f201000.serial: no DMA platform data
[ 2.096921] Indeed it is in host mode hprt0 = 00021501
[ 2.170694] Freeing unused kernel memory: 7168K
[ 2.178824] Run /init as init process
[ 2.189658] random: fast init done
[ 2.213320] mmc0: new high speed MMC card at address 0001
[ 2.221108] mmcblk0: mmc0:0001 BJTD4R 29.1 GiB
[ 2.227745] mmcblk0boot0: mmc0:0001 BJTD4R partition 1 4.00 MiB
[ 2.235785] mmcblk0boot1: mmc0:0001 BJTD4R partition 2 4.00 MiB
[ 2.243597] mmcblk0rpmb: mmc0:0001 BJTD4R partition 3 4.00 MiB, chardev (246:0)
[ 2.257178] mmcblk0: p1 p2 p3 p4 < p5 p6 >
[ 2.311786] usb 1-1: new high-speed USB device number 2 using dwc_otg
[ 2.320386] Indeed it is in host mode hprt0 = 00001101
[ 2.564247] usb 1-1: New USB device found, idVendor=05e3, idProduct=0610, bcdDevice= 6.54
[ 2.575688] usb 1-1: New USB device strings: Mfr=1, Product=2, SerialNumber=0
[ 2.584605] usb 1-1: Product: USB2.1 Hub
[ 2.589992] usb 1-1: Manufacturer: GenesysLogic
[ 2.596568] hub 1-1:1.0: USB hub found
[ 2.602155] hub 1-1:1.0: 4 ports detected
[ 2.941786] usb 1-1.1: new high-speed USB device number 3 using dwc_otg
[ 3.049576] CP437: Invalid argument
[ 3.114801] usb 1-1.1: New USB device found, idVendor=0b95, idProduct=7720, bcdDevice= 0.01
[ 3.129143] usb 1-1.1: New USB device strings: Mfr=1, Product=2, SerialNumber=3
[ 3.139691] usb 1-1.1: Product: AX88772A
[ 3.144576] fsck.fat 4.1 (2017-01-24)
/dev/disk/by-label/resin-boot: 153 files, 16363/80628 clusters
[ 3.146771] usb 1-1.1: Manufacturer: ASIX Elec. Corp.
[ 3.171860] usb 1-1.1: SerialNumber: 00081A
[ 3.181968] resin-rootA: clean, 5927/39936 files, 223157/319488 blocks
[ 3.203785] resin-rootB: clean, 11/39936 files, 15349/319488 blocks
[ 3.258999] resin-state: clean, 59/5136 files, 1895/20480 blocks
[ 3.581101] mmcblk0: p1 p2 p3 p4 < p5 p6 >
[ 4.686605] EXT4-fs (mmcblk0p2): mounted filesystem with ordered data mode. Opts: (null)
[ 4.718184] EXT4-fs (mmcblk0p5): mounted filesystem with ordered data mode. Opts: (null)
[ 5.122386] EXT4-fs (mmcblk0p2): re-mounted. Opts: (null)
[ 5.137198] aufs au_opts_verify:1609:init[1]: dirperm1 breaks the protection by the permission bits on the lower branch
[ 5.503605] systemd[1]: System time before build time, advancing clock.
[ 5.529495] systemd[1]: systemd 241-9-gc1f8ff8+ running in system mode. (-PAM -AUDIT -SELINUX +IMA -APPARMOR +SMACK +SYSVINIT +UTMP -LIBCRYPTSETUP -GCRYPT -GNUTLS +ACL +XZ -LZ4 -SECCOMP +BLKID -ELFUTILS +KMOD -IDN2 -IDN -PCRE2 default-hierarchy=hybrid)
[ 5.559577] systemd[1]: Detected architecture arm.
[ 5.601977] systemd[1]: No hostname configured.
[ 5.608283] systemd[1]: Set hostname to <localhost>.
[ 5.624523] systemd[1]: Failed to bump fs.file-max, ignoring: Invalid argument
[ 5.634470] systemd[1]: Hardware watchdog 'Broadcom BCM2835 Watchdog timer', version 0
[ 5.645926] systemd[1]: Set hardware watchdog to 10s.
[ 5.718586] systemd[1]: File /lib/systemd/system/systemd-journald.service:12 configures an IP firewall (IPAddressDeny=any), but the local system does not support BPF/cgroup based firewalling.
[ 5.741357] systemd[1]: Proceeding WITHOUT firewalling in effect! (This warning is only shown for the first loaded unit using IP firewalling.)
[ 5.926544] systemd[1]: /lib/systemd/system/chronyd.service:9: PIDFile= references path below legacy directory /var/run/, updating /var/run/chrony/chronyd.pid \xe2\x86\x92 /run/chrony/chronyd.pid; please update the unit file accordingly.
[ 6.072124] random: systemd: uninitialized urandom read (16 bytes read)
[ 6.080775] random: systemd: uninitialized urandom read (16 bytes read)
[ 6.102155] random: systemd: uninitialized urandom read (16 bytes read)
[ 8.138096] EXT4-fs (mmcblk0p6): mounted filesystem with ordered data mode. Opts: (null)
[ 10.253257] vc_sm_cma: module is from the staging directory, the quality is unknown, you have been warned.
[ 10.272641] bcm2835_vc_sm_cma_probe: Videocore shared memory driver
[ 10.282770] [vc_sm_connected_init]: start
[ 10.289125] vc_sm_cma_vchi_init: failed to open VCHI service (-1)
[ 10.289133] [vc_sm_connected_init]: failed to initialize shared memory service
[ 10.328157] media: Linux media interface: v0.10
[ 10.367952] videodev: Linux video capture interface: v2.00
[ 10.389596] snd_bcm2835: module is from the staging directory, the quality is unknown, you have been warned.
[ 10.422389] bcm2835_audio soc:audio: card created with 8 channels
[ 10.429453] bcm2835_mmal_vchiq: module is from the staging directory, the quality is unknown, you have been warned.
[ 10.434365] bcm2835_mmal_vchiq: module is from the staging directory, the quality is unknown, you have been warned.
[ 10.482440] bcm2835_v4l2: module is from the staging directory, the quality is unknown, you have been warned.
[ 10.501876] bcm2835_mmal_vchiq: Failed to open VCHI service connection (status=-1)
[ 10.516642] bcm2835_codec: module is from the staging directory, the quality is unknown, you have been warned.
[ 10.533719] bcm2835_mmal_vchiq: Failed to open VCHI service connection (status=-1)
[ 10.860410] asix 1-1.1:1.0 eth0: register 'asix' at usb-3f980000.usb-1.1, ASIX AX88772 USB 2.0 Ethernet, 00:0e:c6:53:36:d7
[ 10.876458] usbcore: registered new interface driver asix
[ 14.515615] i2c /dev entries driver
[ 14.758165] cfg80211: Loading compiled-in X.509 certificates for regulatory database
[ 14.792994] cfg80211: Loaded X.509 cert 'sforshee: 00b28ddf47aef9cea7'
[ 14.802092] platform regulatory.0: Direct firmware load for regulatory.db failed with error -2
[ 14.814921] cfg80211: failed to load regulatory.db
[ 15.256206] IPv6: ADDRCONF(NETDEV_UP): eth0: link is not ready
[ 15.265163] IPv6: ADDRCONF(NETDEV_UP): eth0: link is not ready
[ 15.397667] IPv6: ADDRCONF(NETDEV_CHANGE): eth0: link becomes ready
[ 15.408914] asix 1-1.1:1.0 eth0: link up, 100Mbps, full-duplex, lpa 0x45E1
[ 82.439568] random: crng init done
[ 82.442991] random: 7 urandom warning(s) missed due to ratelimiting
[ 83.049709] Bridge firewalling registered
[ 83.600967] IPv6: ADDRCONF(NETDEV_UP): supervisor0: link is not ready
[ 83.794696] IPv6: ADDRCONF(NETDEV_UP): balena0: link is not ready
[ 84.001808] IPv6: ADDRCONF(NETDEV_UP): br-f3f7664da110: link is not ready
Look like the overlay was applied. However the dmesg command does not show a new sdio interface being detected 
Using Raspian I see someting like mmc1: new high speed MMC card at address
which indicates the CM3 OS detected a new sdio high speed interface.
I will re-check the wiring to discard hardware problems.
Any hints?
Thank you.