mm: numa: group related processes based on VMA flags instead of page table flags

These are three follow-on patches based on the xfsrepair workload Dave
Chinner reported was problematic in 4.0-rc1 due to changes in page table
management -- https://lkml.org/lkml/2015/3/1/226.

Much of the problem was reduced by commit 53da3bc2 ("mm: fix up numa
read-only thread grouping logic") and commit ba68bc01 ("mm: thp:
Return the correct value for change_huge_pmd").  It was known that the
performance in 3.19 was still better even if is far less safe.  This
series aims to restore the performance without compromising on safety.

For the test of this mail, I'm comparing 3.19 against 4.0-rc4 and the
three patches applied on top

  autonumabench
                                                3.19.0             4.0.0-rc4             4.0.0-rc4             4.0.0-rc4             4.0.0-rc4
                                               vanilla               vanilla          vmwrite-v5r8         preserve-v5r8         slowscan-v5r8
  Time System-NUMA01                  124.00 (  0.00%)      161.86 (-30.53%)      107.13 ( 13.60%)      103.13 ( 16.83%)      145.01 (-16.94%)
  Time System-NUMA01_THEADLOCAL       115.54 (  0.00%)      107.64 (  6.84%)      131.87 (-14.13%)       83.30 ( 27.90%)       92.35 ( 20.07%)
  Time System-NUMA02                    9.35 (  0.00%)       10.44 (-11.66%)        8.95 (  4.28%)       10.72 (-14.65%)        8.16 ( 12.73%)
  Time System-NUMA02_SMT                3.87 (  0.00%)        4.63 (-19.64%)        4.57 (-18.09%)        3.99 ( -3.10%)        3.36 ( 13.18%)
  Time Elapsed-NUMA01                 570.06 (  0.00%)      567.82 (  0.39%)      515.78 (  9.52%)      517.26 (  9.26%)      543.80 (  4.61%)
  Time Elapsed-NUMA01_THEADLOCAL      393.69 (  0.00%)      384.83 (  2.25%)      384.10 (  2.44%)      384.31 (  2.38%)      380.73 (  3.29%)
  Time Elapsed-NUMA02                  49.09 (  0.00%)       49.33 ( -0.49%)       48.86 (  0.47%)       48.78 (  0.63%)       50.94 ( -3.77%)
  Time Elapsed-NUMA02_SMT              47.51 (  0.00%)       47.15 (  0.76%)       47.98 ( -0.99%)       48.12 ( -1.28%)       49.56 ( -4.31%)

                3.19.0   4.0.0-rc4   4.0.0-rc4   4.0.0-rc4   4.0.0-rc4
               vanilla     vanillavmwrite-v5r8preserve-v5r8slowscan-v5r8
  User        46334.60    46391.94    44383.95    43971.89    44372.12
  System        252.84      284.66      252.61      201.24      249.00
  Elapsed      1062.14     1050.96      998.68     1000.94     1026.78

Overall the system CPU usage is comparable and the test is naturally a
bit variable.  The slowing of the scanner hurts numa01 but on this
machine it is an adverse workload and patches that dramatically help it
often hurt absolutely everything else.

Due to patch 2, the fault activity is interesting

                                  3.19.0   4.0.0-rc4   4.0.0-rc4   4.0.0-rc4   4.0.0-rc4
                                 vanilla     vanillavmwrite-v5r8preserve-v5r8slowscan-v5r8
  Minor Faults                   2097811     2656646     2597249     1981230     1636841
  Major Faults                       362         450         365         364         365

Note the impact preserving the write bit across protection updates and
fault reduces faults.

  NUMA alloc hit                 1229008     1217015     1191660     1178322     1199681
  NUMA alloc miss                      0           0           0           0           0
  NUMA interleave hit                  0           0           0           0           0
  NUMA alloc local               1228514     1216317     1190871     1177448     1199021
  NUMA base PTE updates        245706197   240041607   238195516   244704842   115012800
  NUMA huge PMD updates           479530      468448      464868      477573      224487
  NUMA page range updates      491225557   479886983   476207932   489222218   229950144
  NUMA hint faults                659753      656503      641678      656926      294842
  NUMA hint local faults          381604      373963      360478      337585      186249
  NUMA hint local percent             57          56          56          51          63
  NUMA pages migrated            5412140     6374899     6266530     5277468     5755096
  AutoNUMA cost                    5121%       5083%       4994%       5097%       2388%

Here the impact of slowing the PTE scanner on migratrion failures is
obvious as "NUMA base PTE updates" and "NUMA huge PMD updates" are
massively reduced even though the headline performance is very similar.

As xfsrepair was the reported workload here is the impact of the series
on it.

  xfsrepair
                                         3.19.0             4.0.0-rc4             4.0.0-rc4             4.0.0-rc4             4.0.0-rc4
                                        vanilla               vanilla          vmwrite-v5r8         preserve-v5r8         slowscan-v5r8
  Min      real-fsmark        1183.29 (  0.00%)     1165.73 (  1.48%)     1152.78 (  2.58%)     1153.64 (  2.51%)     1177.62 (  0.48%)
  Min      syst-fsmark        4107.85 (  0.00%)     4027.75 (  1.95%)     3986.74 (  2.95%)     3979.16 (  3.13%)     4048.76 (  1.44%)
  Min      real-xfsrepair      441.51 (  0.00%)      463.96 ( -5.08%)      449.50 ( -1.81%)      440.08 (  0.32%)      439.87 (  0.37%)
  Min      syst-xfsrepair      195.76 (  0.00%)      278.47 (-42.25%)      262.34 (-34.01%)      203.70 ( -4.06%)      143.64 ( 26.62%)
  Amean    real-fsmark        1188.30 (  0.00%)     1177.34 (  0.92%)     1157.97 (  2.55%)     1158.21 (  2.53%)     1182.22 (  0.51%)
  Amean    syst-fsmark        4111.37 (  0.00%)     4055.70 (  1.35%)     3987.19 (  3.02%)     3998.72 (  2.74%)     4061.69 (  1.21%)
  Amean    real-xfsrepair      450.88 (  0.00%)      468.32 ( -3.87%)      454.14 ( -0.72%)      442.36 (  1.89%)      440.59 (  2.28%)
  Amean    syst-xfsrepair      199.66 (  0.00%)      290.60 (-45.55%)      277.20 (-38.84%)      204.68 ( -2.51%)      150.55 ( 24.60%)
  Stddev   real-fsmark           4.12 (  0.00%)       10.82 (-162.29%)       4.14 ( -0.28%)        5.98 (-45.05%)        4.60 (-11.53%)
  Stddev   syst-fsmark           2.63 (  0.00%)       20.32 (-671.82%)       0.37 ( 85.89%)       16.47 (-525.59%)      15.05 (-471.79%)
  Stddev   real-xfsrepair        6.87 (  0.00%)        4.55 ( 33.75%)        3.46 ( 49.58%)        1.78 ( 74.12%)        0.52 ( 92.50%)
  Stddev   syst-xfsrepair        3.02 (  0.00%)       10.30 (-241.37%)      13.17 (-336.37%)       0.71 ( 76.63%)        5.00 (-65.61%)
  CoeffVar real-fsmark           0.35 (  0.00%)        0.92 (-164.73%)       0.36 ( -2.91%)        0.52 (-48.82%)        0.39 (-12.10%)
  CoeffVar syst-fsmark           0.06 (  0.00%)        0.50 (-682.41%)       0.01 ( 85.45%)        0.41 (-543.22%)       0.37 (-478.78%)
  CoeffVar real-xfsrepair        1.52 (  0.00%)        0.97 ( 36.21%)        0.76 ( 49.94%)        0.40 ( 73.62%)        0.12 ( 92.33%)
  CoeffVar syst-xfsrepair        1.51 (  0.00%)        3.54 (-134.54%)       4.75 (-214.31%)       0.34 ( 77.20%)        3.32 (-119.63%)
  Max      real-fsmark        1193.39 (  0.00%)     1191.77 (  0.14%)     1162.90 (  2.55%)     1166.66 (  2.24%)     1188.50 (  0.41%)
  Max      syst-fsmark        4114.18 (  0.00%)     4075.45 (  0.94%)     3987.65 (  3.08%)     4019.45 (  2.30%)     4082.80 (  0.76%)
  Max      real-xfsrepair      457.80 (  0.00%)      474.60 ( -3.67%)      457.82 ( -0.00%)      444.42 (  2.92%)      441.03 (  3.66%)
  Max      syst-xfsrepair      203.11 (  0.00%)      303.65 (-49.50%)      294.35 (-44.92%)      205.33 ( -1.09%)      155.28 ( 23.55%)

The really relevant lines as syst-xfsrepair which is the system CPU
usage when running xfsrepair.  Note that on my machine the overhead was
45% higher on 4.0-rc4 which may be part of what Dave is seeing.  Once we
preserve the write bit across faults, it's only 2.51% higher on average.
With the full series applied, system CPU usage is 24.6% lower on
average.

Again, the impact of preserving the write bit on minor faults is obvious
and the impact of slowing scanning after migration failures is obvious
on the PTE updates.  Note also that the number of pages migrated is much
reduced even though the headline performance is comparable.

                                  3.19.0   4.0.0-rc4   4.0.0-rc4   4.0.0-rc4   4.0.0-rc4
                                 vanilla     vanillavmwrite-v5r8preserve-v5r8slowscan-v5r8
  Minor Faults                 153466827   254507978   249163829   153501373   105737890
  Major Faults                       610         702         690         649         724
  NUMA base PTE updates        217735049   210756527   217729596   216937111   144344993
  NUMA huge PMD updates           129294       85044      106921      127246       79887
  NUMA pages migrated           21938995    29705270    28594162    22687324    16258075

                        3.19.0   4.0.0-rc4   4.0.0-rc4   4.0.0-rc4   4.0.0-rc4
                       vanilla     vanillavmwrite-v5r8preserve-v5r8slowscan-v5r8
  Mean sdb-avgqusz       13.47        2.54        2.55        2.47        2.49
  Mean sdb-avgrqsz      202.32      140.22      139.50      139.02      138.12
  Mean sdb-await         25.92        5.09        5.33        5.02        5.22
  Mean sdb-r_await        4.71        0.19        0.83        0.51        0.11
  Mean sdb-w_await      104.13        5.21        5.38        5.05        5.32
  Mean sdb-svctm          0.59        0.13        0.14        0.13        0.14
  Mean sdb-rrqm           0.16        0.00        0.00        0.00        0.00
  Mean sdb-wrqm           3.59     1799.43     1826.84     1812.21     1785.67
  Max  sdb-avgqusz      111.06       12.13       14.05       11.66       15.60
  Max  sdb-avgrqsz      255.60      190.34      190.01      187.33      191.78
  Max  sdb-await        168.24       39.28       49.22       44.64       65.62
  Max  sdb-r_await      660.00       52.00      280.00       76.00       12.00
  Max  sdb-w_await     7804.00       39.28       49.22       44.64       65.62
  Max  sdb-svctm          4.00        2.82        2.86        1.98        2.84
  Max  sdb-rrqm           8.30        0.00        0.00        0.00        0.00
  Max  sdb-wrqm          34.20     5372.80     5278.60     5386.60     5546.15

FWIW, I also checked SPECjbb in different configurations but it's
similar observations -- minor faults lower, PTE update activity lower
and performance is roughly comparable against 3.19.

This patch (of 3):

Threads that share writable data within pages are grouped together as
related tasks.  This decision is based on whether the PTE is marked
dirty which is subject to timing races between the PTE scanner update
and when the application writes the page.  If the page is file-backed,
then background flushes and sync also affect placement.  This is
unpredictable behaviour which is impossible to reason about so this
patch makes grouping decisions based on the VMA flags.
Signed-off-by: Mel Gorman <mgorman@suse.de>
Reported-by: Dave Chinner <david@fromorbit.com>
Tested-by: Dave Chinner <david@fromorbit.com>
Cc: Ingo Molnar <mingo@kernel.org>
Cc: Aneesh Kumar <aneesh.kumar@linux.vnet.ibm.com>
Signed-off-by: Andrew Morton <akpm@linux-foundation.org>
Signed-off-by: Linus Torvalds <torvalds@linux-foundation.org>

mm/huge_memory.c

@@ -1291,17 +1291,8 @@ int do_huge_pmd_numa_page(struct mm_struct *mm, struct vm_area_struct *vma,
 		flags |= TNF_FAULT_LOCAL;
 	}
 
-	/*
-	 * Avoid grouping on DSO/COW pages in specific and RO pages
-	 * in general, RO pages shouldn't hurt as much anyway since
-	 * they can be in shared cache state.
-	 *
-	 * FIXME! This checks "pmd_dirty()" as an approximation of
-	 * "is this a read-only page", since checking "pmd_write()"
-	 * is even more broken. We haven't actually turned this into
-	 * a writable page, so pmd_write() will always be false.
-	 */
-	if (!pmd_dirty(pmd))
+	/* See similar comment in do_numa_page for explanation */
+	if (!(vma->vm_flags & VM_WRITE))
 		flags |= TNF_NO_GROUP;
 
 	/*

mm/memory.c

@@ -3069,16 +3069,19 @@ static int do_numa_page(struct mm_struct *mm, struct vm_area_struct *vma,
 	}
 
 	/*
-	 * Avoid grouping on DSO/COW pages in specific and RO pages
-	 * in general, RO pages shouldn't hurt as much anyway since
-	 * they can be in shared cache state.
-	 *
-	 * FIXME! This checks "pmd_dirty()" as an approximation of
-	 * "is this a read-only page", since checking "pmd_write()"
-	 * is even more broken. We haven't actually turned this into
-	 * a writable page, so pmd_write() will always be false.
-	 */
-	if (!pte_dirty(pte))
+	 * Avoid grouping on RO pages in general. RO pages shouldn't hurt as
+	 * much anyway since they can be in shared cache state. This misses
+	 * the case where a mapping is writable but the process never writes
+	 * to it but pte_write gets cleared during protection updates and
+	 * pte_dirty has unpredictable behaviour between PTE scan updates,
+	 * background writeback, dirty balancing and application behaviour.
+	 *
+	 * TODO: Note that the ideal here would be to avoid a situation where a
+	 * NUMA fault is taken immediately followed by a write fault in
+	 * some cases which would have lower overhead overall but would be
+	 * invasive as the fault paths would need to be unified.
+	 */
+	if (!(vma->vm_flags & VM_WRITE))
 		flags |= TNF_NO_GROUP;
 
 	/*