I updated my CentOS 7 system. Why is Meltdown/Spectre only partially mitigated?

Like many of us, I spent yesterday updating a whole lot of systems to mitigate the Meltdown and Spectre attacks. As I understand it, it is necessary to install two packages and reboot:

kernel-3.10.0-693.11.6.el7.x86_64
microcode_ctl-2.1-22.2.el7.x86_64

I have two CentOS 7 systems on which I've installed these packages and rebooted.

According to Red Hat, I can check the status of mitigation by checking these sysctls and ensuring that they are all 1. However, on these systems, they are not all 1:

# cat /sys/kernel/debug/x86/pti_enabled
1
# cat /sys/kernel/debug/x86/ibpb_enabled
0
# cat /sys/kernel/debug/x86/ibrs_enabled
0

And I can't set them to 1, either:

# echo 1 > /sys/kernel/debug/x86/ibpb_enabled
-bash: echo: write error: No such device
# echo 1 > /sys/kernel/debug/x86/ibrs_enabled
-bash: echo: write error: No such device

I confirmed that Intel microcode appears to have loaded on boot:

# systemctl status microcode -l
● microcode.service - Load CPU microcode update
   Loaded: loaded (/usr/lib/systemd/system/microcode.service; enabled; vendor preset: enabled)
   Active: inactive (dead) since Fri 2018-01-05 16:42:25 UTC; 9min ago
  Process: 30383 ExecStart=/usr/bin/bash -c grep -l GenuineIntel /proc/cpuinfo | xargs grep -l -E "model[[:space:]]*: 79$" > /dev/null || echo 1 > /sys/devices/system/cpu/microcode/reload (code=exited, status=0/SUCCESS)
 Main PID: 30383 (code=exited, status=0/SUCCESS)

Jan 05 16:42:25 makrura systemd[1]: Starting Load CPU microcode update...
Jan 05 16:42:25 makrura systemd[1]: Started Load CPU microcode update.

Even dmesg seems to have confirmed it:

[    3.245580] microcode: CPU0 sig=0x50662, pf=0x10, revision=0xf
[    3.245627] microcode: CPU1 sig=0x50662, pf=0x10, revision=0xf
[    3.245674] microcode: CPU2 sig=0x50662, pf=0x10, revision=0xf
[    3.245722] microcode: CPU3 sig=0x50662, pf=0x10, revision=0xf
[    3.245768] microcode: CPU4 sig=0x50662, pf=0x10, revision=0xf
[    3.245816] microcode: CPU5 sig=0x50662, pf=0x10, revision=0xf
[    3.245869] microcode: CPU6 sig=0x50662, pf=0x10, revision=0xf
[    3.245880] microcode: CPU7 sig=0x50662, pf=0x10, revision=0xf
[    3.245924] microcode: CPU8 sig=0x50662, pf=0x10, revision=0xf
[    3.245972] microcode: CPU9 sig=0x50662, pf=0x10, revision=0xf
[    3.245989] microcode: CPU10 sig=0x50662, pf=0x10, revision=0xf
[    3.246036] microcode: CPU11 sig=0x50662, pf=0x10, revision=0xf
[    3.246083] microcode: CPU12 sig=0x50662, pf=0x10, revision=0xf
[    3.246131] microcode: CPU13 sig=0x50662, pf=0x10, revision=0xf
[    3.246179] microcode: CPU14 sig=0x50662, pf=0x10, revision=0xf
[    3.246194] microcode: CPU15 sig=0x50662, pf=0x10, revision=0xf
[    3.246273] microcode: Microcode Update Driver: v2.01 <tigran@aivazian.fsnet.co.uk>, Peter Oruba

I have an Intel CPU formerly code named Broadwell:

processor       : 15
vendor_id       : GenuineIntel
cpu family      : 6
model           : 86
model name      : Intel(R) Xeon(R) CPU D-1540 @ 2.00GHz
stepping        : 2
microcode       : 0xf
cpu MHz         : 2499.921
cache size      : 12288 KB
physical id     : 0
siblings        : 16
core id         : 7
cpu cores       : 8
apicid          : 15
initial apicid  : 15
fpu             : yes
fpu_exception   : yes
cpuid level     : 20
wp              : yes
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 invpcid_single intel_pt tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts
bogomips        : 3999.90
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

The cpuid utility reports:

# cpuid -1
Disclaimer: cpuid may not support decoding of all cpuid registers.
CPU:
   vendor_id = "GenuineIntel"
   version information (1/eax):
      processor type  = primary processor (0)
      family          = Intel Pentium Pro/II/III/Celeron/Core/Core 2/Atom, AMD Athlon/Duron, Cyrix M2, VIA C3 (6)
      model           = 0x6 (6)
      stepping id     = 0x2 (2)
      extended family = 0x0 (0)
      extended model  = 0x5 (5)
      (simple synth)  = Intel Xeon D-1500 (Broadwell-DE V1), 14nm
   miscellaneous (1/ebx):
      process local APIC physical ID = 0x9 (9)
      cpu count                      = 0x10 (16)
      CLFLUSH line size              = 0x8 (8)
      brand index                    = 0x0 (0)
   brand id = 0x00 (0): unknown
   feature information (1/edx):
      x87 FPU on chip                        = true
      virtual-8086 mode enhancement          = true
      debugging extensions                   = true
      page size extensions                   = true
      time stamp counter                     = true
      RDMSR and WRMSR support                = true
      physical address extensions            = true
      machine check exception                = true
      CMPXCHG8B inst.                        = true
      APIC on chip                           = true
      SYSENTER and SYSEXIT                   = true
      memory type range registers            = true
      PTE global bit                         = true
      machine check architecture             = true
      conditional move/compare instruction   = true
      page attribute table                   = true
      page size extension                    = true
      processor serial number                = false
      CLFLUSH instruction                    = true
      debug store                            = true
      thermal monitor and clock ctrl         = true
      MMX Technology                         = true
      FXSAVE/FXRSTOR                         = true
      SSE extensions                         = true
      SSE2 extensions                        = true
      self snoop                             = true
      hyper-threading / multi-core supported = true
      therm. monitor                         = true
      IA64                                   = false
      pending break event                    = true
   feature information (1/ecx):
      PNI/SSE3: Prescott New Instructions     = true
      PCLMULDQ instruction                    = true
      64-bit debug store                      = true
      MONITOR/MWAIT                           = true
      CPL-qualified debug store               = true
      VMX: virtual machine extensions         = true
      SMX: safer mode extensions              = true
      Enhanced Intel SpeedStep Technology     = true
      thermal monitor 2                       = true
      SSSE3 extensions                        = true
      context ID: adaptive or shared L1 data  = false
      FMA instruction                         = true
      CMPXCHG16B instruction                  = true
      xTPR disable                            = true
      perfmon and debug                       = true
      process context identifiers             = true
      direct cache access                     = true
      SSE4.1 extensions                       = true
      SSE4.2 extensions                       = true
      extended xAPIC support                  = true
      MOVBE instruction                       = true
      POPCNT instruction                      = true
      time stamp counter deadline             = true
      AES instruction                         = true
      XSAVE/XSTOR states                      = true
      OS-enabled XSAVE/XSTOR                  = true
      AVX: advanced vector extensions         = true
      F16C half-precision convert instruction = true
      RDRAND instruction                      = true
      hypervisor guest status                 = false
   cache and TLB information (2):
      0x63: data TLB: 1G pages, 4-way, 4 entries
      0x03: data TLB: 4K pages, 4-way, 64 entries
      0x76: instruction TLB: 2M/4M pages, fully, 8 entries
      0xff: cache data is in CPUID 4
      0xb5: instruction TLB: 4K, 8-way, 64 entries
      0xf0: 64 byte prefetching
      0xc3: L2 TLB: 4K/2M pages, 6-way, 1536 entries
   processor serial number: 0005-0662-0000-0000-0000-0000
   deterministic cache parameters (4):
      --- cache 0 ---
      cache type                           = data cache (1)
      cache level                          = 0x1 (1)
      self-initializing cache level        = true
      fully associative cache              = false
      extra threads sharing this cache     = 0x1 (1)
      extra processor cores on this die    = 0x7 (7)
      system coherency line size           = 0x3f (63)
      physical line partitions             = 0x0 (0)
      ways of associativity                = 0x7 (7)
      ways of associativity                = 0x0 (0)
      WBINVD/INVD behavior on lower caches = false
      inclusive to lower caches            = false
      complex cache indexing               = false
      number of sets - 1 (s)               = 63
      --- cache 1 ---
      cache type                           = instruction cache (2)
      cache level                          = 0x1 (1)
      self-initializing cache level        = true
      fully associative cache              = false
      extra threads sharing this cache     = 0x1 (1)
      extra processor cores on this die    = 0x7 (7)
      system coherency line size           = 0x3f (63)
      physical line partitions             = 0x0 (0)
      ways of associativity                = 0x7 (7)
      ways of associativity                = 0x0 (0)
      WBINVD/INVD behavior on lower caches = false
      inclusive to lower caches            = false
      complex cache indexing               = false
      number of sets - 1 (s)               = 63
      --- cache 2 ---
      cache type                           = unified cache (3)
      cache level                          = 0x2 (2)
      self-initializing cache level        = true
      fully associative cache              = false
      extra threads sharing this cache     = 0x1 (1)
      extra processor cores on this die    = 0x7 (7)
      system coherency line size           = 0x3f (63)
      physical line partitions             = 0x0 (0)
      ways of associativity                = 0x7 (7)
      ways of associativity                = 0x0 (0)
      WBINVD/INVD behavior on lower caches = false
      inclusive to lower caches            = false
      complex cache indexing               = false
      number of sets - 1 (s)               = 511
      --- cache 3 ---
      cache type                           = unified cache (3)
      cache level                          = 0x3 (3)
      self-initializing cache level        = true
      fully associative cache              = false
      extra threads sharing this cache     = 0xf (15)
      extra processor cores on this die    = 0x7 (7)
      system coherency line size           = 0x3f (63)
      physical line partitions             = 0x0 (0)
      ways of associativity                = 0xb (11)
      ways of associativity                = 0x6 (6)
      WBINVD/INVD behavior on lower caches = false
      inclusive to lower caches            = true
      complex cache indexing               = true
      number of sets - 1 (s)               = 16383
   MONITOR/MWAIT (5):
      smallest monitor-line size (bytes)       = 0x40 (64)
      largest monitor-line size (bytes)        = 0x40 (64)
      enum of Monitor-MWAIT exts supported     = true
      supports intrs as break-event for MWAIT  = true
      number of C0 sub C-states using MWAIT    = 0x0 (0)
      number of C1 sub C-states using MWAIT    = 0x2 (2)
      number of C2 sub C-states using MWAIT    = 0x1 (1)
      number of C3 sub C-states using MWAIT    = 0x2 (2)
      number of C4 sub C-states using MWAIT    = 0x0 (0)
      number of C5 sub C-states using MWAIT    = 0x0 (0)
      number of C6 sub C-states using MWAIT    = 0x0 (0)
      number of C7 sub C-states using MWAIT    = 0x0 (0)
   Thermal and Power Management Features (6):
      digital thermometer                     = true
      Intel Turbo Boost Technology            = true
      ARAT always running APIC timer          = true
      PLN power limit notification            = true
      ECMD extended clock modulation duty     = true
      PTM package thermal management          = true
      HWP base registers                      = false
      HWP notification                        = false
      HWP activity window                     = false
      HWP energy performance preference       = false
      HWP package level request               = false
      HDC base registers                      = false
      digital thermometer thresholds          = 0x2 (2)
      ACNT/MCNT supported performance measure = true
      ACNT2 available                         = false
      performance-energy bias capability      = true
   extended feature flags (7):
      FSGSBASE instructions                    = true
      IA32_TSC_ADJUST MSR supported            = true
      SGX: Software Guard Extensions supported = false
      BMI instruction                          = true
      HLE hardware lock elision                = true
      AVX2: advanced vector extensions 2       = true
      FDP_EXCPTN_ONLY                          = false
      SMEP supervisor mode exec protection     = true
      BMI2 instructions                        = true
      enhanced REP MOVSB/STOSB                 = true
      INVPCID instruction                      = true
      RTM: restricted transactional memory     = true
      QM: quality of service monitoring        = true
      deprecated FPU CS/DS                     = true
      intel memory protection extensions       = false
      PQE: platform quality of service enforce = true
      AVX512F: AVX-512 foundation instructions = false
      AVX512DQ: double & quadword instructions = false
      RDSEED instruction                       = true
      ADX instructions                         = true
      SMAP: supervisor mode access prevention  = true
      AVX512IFMA: fused multiply add           = false
      CLFLUSHOPT instruction                   = false
      CLWB instruction                         = false
      Intel processor trace                    = true
      AVX512PF: prefetch instructions          = false
      AVX512ER: exponent & reciprocal instrs   = false
      AVX512CD: conflict detection instrs      = false
      SHA instructions                         = false
      AVX512BW: byte & word instructions       = false
      AVX512VL: vector length                  = false
      PREFETCHWT1                              = false
      AVX512VBMI: vector byte manipulation     = false
      UMIP: user-mode instruction prevention   = false
      PKU protection keys for user-mode        = false
      OSPKE CR4.PKE and RDPKRU/WRPKRU          = false
      BNDLDX/BNDSTX MAWAU value in 64-bit mode = 0x0 (0)
      RDPID: read processor D supported        = false
      SGX_LC: SGX launch config supported      = false
      AVX512_4VNNIW: neural network instrs     = false
      AVX512_4FMAPS: multiply acc single prec  = false
   Direct Cache Access Parameters (9):
      PLATFORM_DCA_CAP MSR bits = 1
   Architecture Performance Monitoring Features (0xa/eax):
      version ID                               = 0x3 (3)
      number of counters per logical processor = 0x4 (4)
      bit width of counter                     = 0x30 (48)
      length of EBX bit vector                 = 0x7 (7)
   Architecture Performance Monitoring Features (0xa/ebx):
      core cycle event not available           = false
      instruction retired event not available  = false
      reference cycles event not available     = false
      last-level cache ref event not available = false
      last-level cache miss event not avail    = false
      branch inst retired event not available  = false
      branch mispred retired event not avail   = false
   Architecture Performance Monitoring Features (0xa/edx):
      number of fixed counters    = 0x3 (3)
      bit width of fixed counters = 0x30 (48)
   x2APIC features / processor topology (0xb):
      --- level 0 (thread) ---
      bits to shift APIC ID to get next = 0x1 (1)
      logical processors at this level  = 0x2 (2)
      level number                      = 0x0 (0)
      level type                        = thread (1)
      extended APIC ID                  = 9
      --- level 1 (core) ---
      bits to shift APIC ID to get next = 0x4 (4)
      logical processors at this level  = 0x10 (16)
      level number                      = 0x1 (1)
      level type                        = core (2)
      extended APIC ID                  = 9
   XSAVE features (0xd/0):
      XCR0 lower 32 bits valid bit field mask = 0x00000007
      XCR0 upper 32 bits valid bit field mask = 0x00000000
         XCR0 supported: x87 state            = true
         XCR0 supported: SSE state            = true
         XCR0 supported: AVX state            = true
         XCR0 supported: MPX BNDREGS          = false
         XCR0 supported: MPX BNDCSR           = false
         XCR0 supported: AVX-512 opmask       = false
         XCR0 supported: AVX-512 ZMM_Hi256    = false
         XCR0 supported: AVX-512 Hi16_ZMM     = false
         IA32_XSS supported: PT state         = false
         XCR0 supported: PKRU state           = false
      bytes required by fields in XCR0        = 0x00000340 (832)
      bytes required by XSAVE/XRSTOR area     = 0x00000340 (832)
   XSAVE features (0xd/1):
      XSAVEOPT instruction                        = true
      XSAVEC instruction                          = false
      XGETBV instruction                          = false
      XSAVES/XRSTORS instructions                 = false
      SAVE area size in bytes                     = 0x00000000 (0)
      IA32_XSS lower 32 bits valid bit field mask = 0x00000000
      IA32_XSS upper 32 bits valid bit field mask = 0x00000000
   AVX/YMM features (0xd/2):
      AVX/YMM save state byte size             = 0x00000100 (256)
      AVX/YMM save state byte offset           = 0x00000240 (576)
      supported in IA32_XSS or XCR0            = XCR0 (user state)
      64-byte alignment in compacted XSAVE     = false
   Quality of Service Monitoring Resource Type (0xf/0):
      Maximum range of RMID = 63
      supports L3 cache QoS monitoring = false
   L3 Cache Quality of Service Monitoring (0xf/1):
      Conversion factor from IA32_QM_CTR to bytes = 32768
      Maximum range of RMID                       = 63
      supports L3 occupancy monitoring       = true
      supports L3 total bandwidth monitoring = true
      supports L3 local bandwidth monitoring = true
   Resource Director Technology allocation (0x10/0):
      L3 cache allocation technology supported = true
      L2 cache allocation technology supported = false
   L3 Cache Allocation Technology (0x10/1):
      length of capacity bit mask - 1 = 0xb (11)
      Bit-granular map of isolation/contention    = 0x00000c00
      infrequent updates of COS              = true
      code and data prioritization supported = false
      highest COS number supported = 0xb (11)
   0x00000011 0x00: eax=0x00000000 ebx=0x00000000 ecx=0x00000000 edx=0x00000000
   SGX capability (0x12/0):
      SGX1 supported                         = false
      SGX2 supported                         = false
      MISCSELECT.EXINFO supported: #PF & #GP = false
      MaxEnclaveSize_Not64 (log2)            = 0x0 (0)
      MaxEnclaveSize_64 (log2)               = 0x0 (0)
   0x00000013 0x00: eax=0x00000000 ebx=0x00000000 ecx=0x00000000 edx=0x00000000
   Intel Processor Trace (0x14):
      IA32_RTIT_CR3_MATCH is accessible      = true
      configurable PSB & cycle-accurate      = false
      IP & TraceStop filtering; PT preserve  = false
      MTC timing packet; suppress COFI-based = false
      PTWRITE support                        = false
      power event trace support              = false
      IA32_RTIT_CTL can enable tracing  = true
      ToPA can hold many output entries = false
      single-range output scheme        = false
      output to trace transport         = false
      IP payloads have LIP values & CS  = false
   extended feature flags (0x80000001/edx):
      SYSCALL and SYSRET instructions        = true
      execution disable                      = true
      1-GB large page support                = true
      RDTSCP                                 = true
      64-bit extensions technology available = true
   Intel feature flags (0x80000001/ecx):
      LAHF/SAHF supported in 64-bit mode     = true
      LZCNT advanced bit manipulation        = true
      3DNow! PREFETCH/PREFETCHW instructions = true
   brand = "Intel(R) Xeon(R) CPU D-1540 @ 2.00GHz"
   L1 TLB/cache information: 2M/4M pages & L1 TLB (0x80000005/eax):
      instruction # entries     = 0x0 (0)
      instruction associativity = 0x0 (0)
      data # entries            = 0x0 (0)
      data associativity        = 0x0 (0)
   L1 TLB/cache information: 4K pages & L1 TLB (0x80000005/ebx):
      instruction # entries     = 0x0 (0)
      instruction associativity = 0x0 (0)
      data # entries            = 0x0 (0)
      data associativity        = 0x0 (0)
   L1 data cache information (0x80000005/ecx):
      line size (bytes) = 0x0 (0)
      lines per tag     = 0x0 (0)
      associativity     = 0x0 (0)
      size (KB)         = 0x0 (0)
   L1 instruction cache information (0x80000005/edx):
      line size (bytes) = 0x0 (0)
      lines per tag     = 0x0 (0)
      associativity     = 0x0 (0)
      size (KB)         = 0x0 (0)
   L2 TLB/cache information: 2M/4M pages & L2 TLB (0x80000006/eax):
      instruction # entries     = 0x0 (0)
      instruction associativity = L2 off (0)
      data # entries            = 0x0 (0)
      data associativity        = L2 off (0)
   L2 TLB/cache information: 4K pages & L2 TLB (0x80000006/ebx):
      instruction # entries     = 0x0 (0)
      instruction associativity = L2 off (0)
      data # entries            = 0x0 (0)
      data associativity        = L2 off (0)
   L2 unified cache information (0x80000006/ecx):
      line size (bytes) = 0x40 (64)
      lines per tag     = 0x0 (0)
      associativity     = 8-way (6)
      size (KB)         = 0x100 (256)
   L3 cache information (0x80000006/edx):
      line size (bytes)     = 0x0 (0)
      lines per tag         = 0x0 (0)
      associativity         = L2 off (0)
      size (in 512KB units) = 0x0 (0)
   Advanced Power Management Features (0x80000007/edx):
      temperature sensing diode      = false
      frequency ID (FID) control     = false
      voltage ID (VID) control       = false
      thermal trip (TTP)             = false
      thermal monitor (TM)           = false
      software thermal control (STC) = false
      100 MHz multiplier control     = false
      hardware P-State control       = false
      TscInvariant                   = true
   Physical Address and Linear Address Size (0x80000008/eax):
      maximum physical address bits         = 0x2e (46)
      maximum linear (virtual) address bits = 0x30 (48)
      maximum guest physical address bits   = 0x0 (0)
   Logical CPU cores (0x80000008/ecx):
      number of CPU cores - 1 = 0x0 (0)
      ApicIdCoreIdSize        = 0x0 (0)
   (multi-processing synth): multi-core (c=8), hyper-threaded (t=2)
   (multi-processing method): Intel leaf 0xb
   (APIC widths synth): CORE_width=4 SMT_width=1
   (APIC synth): PKG_ID=0 CORE_ID=4 SMT_ID=1
   (synth) = Intel Xeon D-1500 (Broadwell-DE V1), 14nm

The system is fully up to date:

# yum upgrade
Loaded plugins: fastestmirror, langpacks
Loading mirror speeds from cached hostfile
 * base: centos.mirror.colo-serv.net
 * epel: mirror.steadfast.net
 * extras: centos.mirror.colo-serv.net
 * updates: centos.mirror.colo-serv.net
No packages marked for update

I feel like I've missed something important, but at this point I really don't know what it could be. What's going on here? How do I get the system fully mitigated?

I am also seeing the same behavior on Fedora 27 workstations, a desktop with a Core i7-3770 CPU and a laptop with a Core i7-7500U.

As noted in https://access.redhat.com/articles/3311301

CVE-2017-5715 (variant #2/Spectre) is an indirect branching poisoning attack that can lead to data leakage. This attack allows for a virtualized guest to read memory from the host system. This issue is corrected with microcode, along with kernel and virtualization updates to both guest and host virtualization software. This vulnerability requires both updated microcode and kernel patches. Variant #2 behavior is controlled by the ibrs and ibpb tunables (noibrs/ibrs_enabled and noibpb/ibpb_enabled), which work in conjunction with the microcode

...

As noted, installing the microcode update for your hardware, if provided by the hardware vendor, is necessary to protect against variant 2. Please contact your hardware vendor for microcode updates.

It seems that you also need a BIOS update to enable the mitigations for CVE-2017-5715.

I read this elsewhere too earlier but can't find the reference right now.