I don't know if this is related, but I noticed that sometimes this machine reports only one cpu in /proc/cpuinfo, and it has these dmesg entries:

Nov 30 13:57:23 joy kernel: [    6.139336] CPU 1 is now offline
Nov 30 13:57:23 joy kernel: [    6.154093] CPU 2 is now offline
Nov 30 13:57:23 joy kernel: [    6.158264] init: plymouth-stop pre-start process (1941) terminated with status 1
Nov 30 13:57:23 joy kernel: [    6.163038] CPU 3 MCA banks CMCI:2 CMCI:3 CMCI:5
Nov 30 13:57:23 joy kernel: [    6.174432] CPU 3 is now offline
Nov 30 13:57:23 joy kernel: [    6.174435] SMP alternatives: switching to UP code
Nov 30 13:57:23 joy kernel: [    6.338643] e1000e 0000:00:19.0: eth0: Unsupported Speed/Duplex configuration
Nov 30 13:57:23 joy kernel: [    6.597691] select_fallback_rq: 63 callbacks suppressed
Nov 30 13:57:23 joy kernel: [    6.597697] process 1539 (beam.smp) no longer affine to cpu1

and then later


Nov 30 15:43:33 joy kernel: [ 2033.202296] ACPI: Preparing to enter system sleep state S3
Nov 30 15:43:33 joy kernel: [ 2033.393563] PM: Saving platform NVS memory
Nov 30 15:43:33 joy kernel: [ 2033.396880] Disabling non-boot CPUs ...
Nov 30 15:43:33 joy kernel: [ 2033.501243] CPU 1 is now offline
Nov 30 15:43:33 joy kernel: [ 2033.604986] CPU 2 is now offline
Nov 30 15:43:33 joy kernel: [ 2033.606097] Broke affinity for irq 9
Nov 30 15:43:33 joy kernel: [ 2033.606108] Broke affinity for irq 23
Nov 30 15:43:33 joy kernel: [ 2033.708716] CPU 3 is now offline
Nov 30 15:43:33 joy kernel: [ 2033.709079] Extended CMOS year: 2000
Nov 30 15:43:33 joy kernel: [ 2033.709320] ACPI: Low-level resume complete
Nov 30 15:43:33 joy kernel: [ 2033.709385] PM: Restoring platform NVS memory
Nov 30 15:43:33 joy kernel: [ 2033.710095] Extended CMOS year: 2000
Nov 30 15:43:33 joy kernel: [ 2033.710163] Enabling non-boot CPUs ...
Nov 30 15:43:33 joy kernel: [ 2033.710281] Booting Node 0 Processor 1 APIC 0x1
Nov 30 15:43:33 joy kernel: [ 2033.710282] smpboot cpu 1: start_ip = 99000
Nov 30 15:43:33 joy kernel: [ 2033.821442] Switched to NOHz mode on CPU #1
Nov 30 15:43:33 joy kernel: [ 2033.833551] CPU1 is up
Nov 30 15:43:33 joy kernel: [ 2033.833728] Booting Node 0 Processor 2 APIC 0x4
Nov 30 15:43:33 joy kernel: [ 2033.833732] smpboot cpu 2: start_ip = 99000
Nov 30 15:43:33 joy kernel: [ 2033.945082] Switched to NOHz mode on CPU #2
Nov 30 15:43:33 joy kernel: [ 2033.957239] CPU2 is up
Nov 30 15:43:33 joy kernel: [ 2033.957403] Booting Node 0 Processor 3 APIC 0x5
Nov 30 15:43:33 joy kernel: [ 2033.957407] smpboot cpu 3: start_ip = 99000
Nov 30 15:43:33 joy kernel: [ 2034.068806] Switched to NOHz mode on CPU #3
Nov 30 15:43:33 joy kernel: [ 2034.080975] CPU3 is up
Nov 30 15:43:33 joy kernel: [ 2034.083353] ACPI: Waking up from system sleep state S3

and then apparently when it tries to come back up:


Nov 30 15:43:34 joy kernel: [ 2035.922303] SMP alternatives: switching to UP code
Nov 30 15:43:34 joy kernel: [ 2035.984272] e1000e 0000:00:19.0: eth0: Unsupported Speed/Duplex configuration
Nov 30 15:43:34 joy kernel: [ 2036.081101] EXT4-fs (sda5): re-mounted. Opts: errors=remount-ro,commit=600
Nov 30 15:43:34 joy kernel: [ 2036.387203] e1000e 0000:00:19.0: irq 44 for MSI/MSI-X
Nov 30 15:43:34 joy kernel: [ 2036.442887] e1000e 0000:00:19.0: irq 44 for MSI/MSI-X
Nov 30 15:43:34 joy kernel: [ 2036.444265] ADDRCONF(NETDEV_UP): eth0: link is not ready
Nov 30 16:42:44 joy kernel: [ 5577.460657] SMP alternatives: switching to SMP code
Nov 30 16:42:44 joy kernel: [ 5577.471598] Booting Node 0 Processor 1 APIC 0x1
Nov 30 16:42:44 joy kernel: [ 5577.471604] smpboot cpu 1: start_ip = 99000
Nov 30 16:42:44 joy kernel: [ 5577.586066] Switched to NOHz mode on CPU #1
Nov 30 16:42:44 joy kernel: [ 5577.639655] Booting Node 0 Processor 2 APIC 0x4
Nov 30 16:42:44 joy kernel: [ 5577.639661] smpboot cpu 2: start_ip = 99000
Nov 30 16:42:44 joy kernel: [ 5577.753619] Switched to NOHz mode on CPU #2
Nov 30 16:42:44 joy kernel: [ 5577.755520] Booting Node 0 Processor 3 APIC 0x5
Nov 30 16:42:44 joy kernel: [ 5577.755523] smpboot cpu 3: start_ip = 99000
Nov 30 16:42:44 joy kernel: [ 5577.869317] Switched to NOHz mode on CPU #3
Nov 30 16:42:45 joy kernel: [ 5578.069384] EXT4-fs (sda5): re-mounted. Opts: errors=remount-ro,commit=0

I wonder if this is connected.