Segfault during sorting

[KyleDKavanagh]

With v1.10.5 installed from source, newly seeing a segfault during standard grpby/assign operations on massive datatables

address 0x7fc8862fa354, cause 'memory not mapped'

Traceback:
 1: fsort(as.numeric(irows))
 2: `[.data.table`(dt, query %in% c("1", "2"), `:=`(position = as.numeric(1:.N)),     by = grpvar)
 3: dt[query %in% c("1", "2"), `:=`(position = as.numeric(1:.N)),     by = grpvar]
An irrecoverable exception occurred. R is aborting now ...```

[mattdowle]

Thanks for reporting. Any chance of a way to reproduce that dataset? It might be specific to the column type and query. I can see the query from the output, but what is query column and grpvar ? And does position exist already or is it being added?

[shrektan]

The table seems contain strings. Is it possible that it's related to the encoding issue that I've reported?

[mattdowle]

Anything is possible. @KyleDKavanagh - it's much harder (and perhaps impossible) if you make us guess.

My guess is that it's to do with the %in% optimization added recently in dev. There's a line there that converts an integer vector to numeric and passes that to fsort, for speed. From the traceback shows above, it feels like that to me. Perhaps something to do with the bit pattern of whole integers in IEEE754 that tickles out an edge condition in fsort. Or that there's an NA in that integer vector, which fsort doesn't handle. Or, fsort on very small input, like 2 items in this case.

[KyleDKavanagh]

Apologies for the delayed response - Both query and grpvar are strings. Unfortunately, I can't provide the exact dataset I've been working on as it's proprietary data for my employer.

[mattdowle]

Ok no problem. Can you provide str(DT) and perhaps edit the strings in that summary if they are proprietary. Also the output of sapply(DT, uniqueN) would be useful, again, obfuscating the column names manually as appropriate. The output with verbose=TRUE as well please. This should all help and we can go from there. Do "1" and "2" exist in the column, or are they missing? Any info like that would be useful.

[mattdowle]

My guess is that one of "1" or "2" isn't in the data. The fact that fsort doesn't handle negatives is caught, but as.numeric(NA_integer_) is not it seems.

 > fsort(c(4,5), verbose=TRUE)
nth=8, nBatch=16
Range = [4,5]
maxBit=50; MSBNbits=16; shift=35; MSBsize=65536
counts is 0MB (128 pages per nBatch=1, batchSize=1024, lastBatchSize=2)
Top 5 MSB counts: 1 1 0 0 0 
Reduced MSBsize from 65536 to 0 by excluding 0 and 1 counts
1: 0.000 ( 0.2%)
2: 0.008 (46.3%)
3: 0.000 ( 0.7%)
4: 0.003 (15.6%)
5: 0.002 (12.5%)
6: 0.002 (14.8%)
7: 0.002 ( 9.9%)
[1] 4 5

> fsort(c(4,NA), verbose=TRUE)
nth=8, nBatch=16
Range = [4,4]
maxBit=-2147483648; MSBNbits=-2147483647; shift=0; MSBsize=2
counts is 0MB (0 pages per nBatch=1, batchSize=1024, lastBatchSize=2)

 *** caught segfault ***
address (nil), cause 'unknown'

Traceback:
 1: fsort(c(4, NA), verbose = TRUE)

Hopefully @KyleDKavanagh can provide some verbose output similar to the above. But in the meantime this has to be fixed anyway. Kyle, since you can't provide the data, you could type debug(data.table:::fsort) then run the query. It will stop when it enters fsort. Then you type x and tell us what fsort is being passed. This is onerous but it would enable progress without sending us your data.

[KyleDKavanagh]

Everything below run on v1.10.4-3 after rolling back

> dt[query %in% c("1", "2"), `:=`(grpIdx=as.numeric(1:.N)),by=grpvar, verbose=T];
Using existing index 'query'
Starting bmerge ...done in 0 secs
i clause present and columns used in by detected, only these subset: grpvar
Detected that j uses these columns: <none> 
Finding groups using forderv ... 0.094 sec
Finding group sizes from the positions (can be avoided to save RAM) ... 0 sec
Getting back original order ... 0.006 sec
lapply optimization is on, j unchanged as 'list(as.numeric(1:.N))'
Old mean optimization is on, left j unchanged.
Making each group and running j (GForce FALSE) ... 
  collecting discontiguous groups took 0.130s for 289239 groups
  eval(j) took 4.950s for 289239 calls

Results from str()

Classes ‘data.table’ and 'data.frame':	13539020 obs. of  4 variables:
 $ ts_ns             : chr  "1522156437655270332" "1522156437655279062" "1522156437655286082" "1522156437655293372" ...
 $ groupvar      : chr  "" "" "" "" ...
 $ query     : chr  "1" "1" "1" "1" ...
 $ SBE.SourceSequence: chr  "0" "0" "0" "0" ...
 - attr(*, ".internal.selfref")=<externalptr> 
 - attr(*, "sorted")= chr "SBE.SourceSequence"

Results from uniqueN()

             ts_ns          groupvar                query SBE.SourceSequence 
          13539020           12173006                  4           12735508 

Values for query:

   query     num
1:     1  595317
2:     0 6193535
3:     2  758743
4:     5 5991425

fsort debug - Not sure how helpful this is because of the number of rows

Browse[2]> x
   [1]     1     2     3     4     5     6     7     8     9    10    11    12    14    16    20    21    22    24    26    27    28    30    31    32
  [25]    34    36    37    38    40    41    42    44    45    46    48    49    50    52    53    54    56    57    58    61    62    63    68    69
  [49]    70    73    75    77    78    79    80    82    84    86    88    93    94    95    97    98    99   100   103   104   105   107   109   112
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  [97]   168   170   174   175   176   178   179   180   182   184   186   187   188   265   266   267   271   272   273   294   295   296   305   306
 [121]   307   308   309   310   326   327   328   333   334   335   348   349   350   382   383   384   385   386   387   419   420   421   488   489
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 [505]  5425  5465  5466  5467  5642  5643  5644  5786  5787  5788  5797  5798  5799  5827  5828  5829  5840  5841  5842  6001  6002  6003  6019  6020
 [529]  6021  6122  6123  6124  6198  6199  6200  6219  6220  6221  6233  6234  6235  6254  6255  6256  6302  6303  6304  6314  6315  6316  6345  6346
 [553]  6347  6400  6401  6402  6428  6429  6430  6561  6562  6563  6596  6597  6598  6602  6603  6604  6666  6667  6668  6693  6694  6695  6703  6704
 [577]  6705  6739  6740  6741  6765  6766  6767  6923  6924  6925  6960  6961  6962  6978  6979  6980  7149  7150  7151  7193  7194  7195  7210  7211
 [601]  7212  7380  7381  7382  7529  7530  7531  7609  7610  7611  7664  7665  7666  7682  7683  7684  7686  7687  7688  7707  7708  7709  7797  7798
 [625]  7799  7852  7853  7854  7868  7869  7870  7887  7888  7889  7935  7936  7937  7941  7942  7943  7964  7965  7966  7979  7980  7981  8045  8046
 [649]  8047  8051  8052  8053  8085  8086  8087  8099  8100  8101  8208  8209  8210  8345  8346  8347  8360  8361  8362  8375  8376  8377  8463  8464
 [673]  8465  8498  8499  8500  8534  8535  8536  8543  8544  8545  8591  8592  8593  8657  8658  8659  8661  8662  8663  8699  8700  8701  8714  8715
 [697]  8716  8750  8751  8752  8773  8774  8775  8785  8786  8787  8946  8947  8948  9128  9129  9130  9155  9156  9157  9244  9245  9246  9252  9253
 [721]  9254  9274  9275  9276  9290  9291  9292  9293  9294  9295  9367  9368  9369  9447  9448  9449  9477  9478  9479  9484  9485  9486  9495  9496
 [745]  9497  9559  9560  9561  9695  9696  9697  9763  9764  9765  9786  9787  9788  9862  9863  9864 10013 10014 10015 10130 10131 10132 10197 10198
 [769] 10199 10235 10236 10237 10260 10261 10262 10266 10267 10268 10295 10296 10297 10313 10314 10315 10392 10393 10394 10413 10414 10415 10455 10456
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 [865] 11261 11297 11298 11299 11372 11373 11374 11404 11405 11406 11428 11429 11430 11444 11445 11446 11461 11462 11463 11504 11505 11506 11514 11515
 [889] 11516 11696 11697 11698 11816 11817 11818 11849 11850 11851 11897 11898 11899 11908 11909 11910 11962 11963 11964 11986 11987 11988 12036 12037
 [913] 12038 12058 12059 12060 12109 12110 12111 12141 12142 12143 12159 12160 12161 12166 12167 12168 12236 12237 12238 12307 12308 12309 12329 12330
 [937] 12331 12343 12344 12345 12365 12366 12367 12391 12392 12393 12421 12422 12423 12434 12435 12436 12442 12443 12444 12456 12457 12458 12472 12473
 [961] 12474 12488 12489 12490 12513 12514 12515 12562 12563 12564 12575 12576 12577 12610 12611 12612 12685 12686 12687 12696 12697 12698 12700 12701
 [985] 12702 12703 12704 12705 12709 12710 12711 12712 12713 12714 12989 13037 13041 13045 13056 13100
 [ reached getOption("max.print") -- omitted 1353060 entries ]

[mattdowle]

Thanks! That's odd as I didn't think v1.10.4-3 would call fsort in this case. I thought usage of fsort was a recent internal addition.

[mattdowle]

The query contains by=grpvar but the column name is groupvar. Is that correct? Could it possibly be picking up grpvar in calling scope? Maybe just a copy and paste type or artifact of obfuscation.

[KyleDKavanagh]

Artifact of obfuscating by hand. Confirmed that it's not picking up any wider-scoped variables.

[mattdowle]

Have been looking through, and there is a call to fsort in 1.10.4-3. But it doesn't invoke the new parallel numeric sort, which is likely where the problem lies. That call has changed in dev to do so.
Could you save that x to file? (the 1353060 vector).

save(list="x", file="/tmp/x.Rdata")

In a fresh R session, load data.table dev 1.10.5 and then do:

load("/tmp/x.Rdata")
fsort(x)

Does it crash? If anyNA(x) is TRUE then that's fine and I know why. If not, then could you send me that file? It's just a vector of row numbers; nothing proprietary. If integers, apx 5MB. If double, apx 10MB. So try email first, otherwise please place online somewhere, or attach here in GitHub might work. Thanks.

[KyleDKavanagh]

Interestingly, the segfault only seems to occur when setDTthreads=0 (Rather than the default of 16). Four tests, 2 with unlimited threads (both crashed), 2 with 16 threads (both worked). X was confirmed to be identical for all four tests

x.Rdata attached as a tgz

> anyNA(x)
[1] FALSE

xRdata.gz