I C Bugs

A Brown marmorated stink bug female from a laboratory colony on a common bean leaf, photographed in the laboratory of Fondazione Edmund Mach, Italy.
A Brown marmorated stink bug female from a laboratory colony on a common bean leaf, photographed in the laboratory of Fondazione Edmund Mach, Italy.
URL: https://commons.wikimedia.org/wiki/File:Halyomorpha_halys_lab.jpg

Occasionally, I hear people complain about the strict policies of CRAN, but I for one quite apprecieate them, especially when dealing with hidden errors in compiled code.

Not twenty-four hours after I had submitted poppr version 2.6.0 to CRAN did I receive an email from none other than Brian D. Ripley. If you are unfamiliar with the name, then know that it tends to strike fear in the hearts of even the most steeled:

library("fortunes")
fortune("Ripleyed")
## 
## And the fear of getting Ripleyed on the mailing list also makes me think,
## read, and improve before submitting half baked questions to the list.
##    -- Eric Kort
##       R-help (January 2006)

This was not the first time I got an email from Ripley (and probably won’t be the last). More often than not, the emails I get from him alert me to little things that have gone wrong in memory allocation for code that I’ve written in C. The email I got from him on January 9th was informing me that there was a new note from the clang address sanitizer saying that there was a potential memory leak in bitwise_distance.c:

Please correct ASAP and before Jan 24 to safely retain the package on CRAN.

Fixing the error

I had initially attempted to try to reproduce the error using a docker container built with the address sanitizer, but quickly became frustrated with it due to errors unrelated to poppr. My next plan of action was to inspect the code using a debugger. I found Kevin Ushey’s blog post on debugging with LLDB and began to go to work.

The error occurred at the end of a “while” loop that was written four years ago. Here’s what the code looks like without the comments:

while(next_missing_index_i < nap1_length && next_missing_i < (k+1)*8 && next_missing_i >= (k*8) )
{
  mask = 1 << (next_missing_i%8); 
  if(missing_match)
  {
    tmp_sim_set |= mask; // Force the missing bit to match
  }
  else
  {
    tmp_sim_set &= ~mask; // Force the missing bit to not match
  }
  // Find the index of the next missing value in sample i.
  next_missing_index_i++; 
  next_missing_i = (int)INTEGER(R_nap1)[next_missing_index_i] - 1; // <--- BUG!
}       

I won’t go into detail what this code does, but the reason why it triggered a warning from the address sanitizer is because of a fencepost error. The loop monitors next_missing_index_i and repeats the operation until it is equal to nap1_length, which happens to be the length of the array it indexes. Because the index is incremented before the array is indexed, the last step of the loop always attempts to access a bit of memory that wasn’t allocated.

Note: to debug, be sure to change your optimization flags to -O0 for your compiler. You can do this in your ~/.R/Makevars file:

CFLAGS +=         -O0 -Wall -pipe -pedantic -std=gnu99 -fopenmp
CXXFLAGS +=       -O0 -Wall -pipe -Wno-unused -pedantic
CXX1XFLAGS +=     -O0 -pipe
PKG_CXX1XFLAGS += -O0 -pipe

Using the debugger was surprisingly easy. My process was to tweak the C code and then start R with the debugger, and install poppr:

17:47:09~/Documents/poppr (master)> R -d lldb
*** Further command line arguments ('--no-save --no-restore-data ') disregarded
*** (maybe use 'run --no-save --no-restore-data ' from *inside* lldb)

(lldb) target create "/Library/Frameworks/R.framework/Resources/bin/exec/R"
Current executable set to '/Library/Frameworks/R.framework/Resources/bin/exec/R' (x86_64).
(lldb) run --no-save --no-restore-data -q
Process 10723 launched: '/Library/Frameworks/R.framework/Resources/bin/exec/R' (x86_64)
> devtools::install()
...
> library("poppr")
...
>

After that, I could load my test data and, before I ran bitwise.dist(), I hit ctrl+c, which took me back into lldb:

> Process 10723 stopped
* thread #1: tid = 0x8251a, 0x00007fff60f01fca libsystem_kernel.dylib`__select + 10, stop reason = signal SIGSTOP
    frame #0: 0x00007fff60f01fca libsystem_kernel.dylib`__select + 10
libsystem_kernel.dylib`__select:
->  0x7fff60f01fca <+10>: jae    0x7fff60f01fd4            ; <+20>
    0x7fff60f01fcc <+12>: movq   %rax, %rdi
    0x7fff60f01fcf <+15>: jmp    0x7fff60ef90dd            ; cerror
    0x7fff60f01fd4 <+20>: retq
(lldb) 

From there, to get it to breakpoint on the specific line, I typed:

(lldb) b bitwise_distance.c:674
Breakpoint 1: where = poppr.so`.omp_outlined..4 + 1471 at bitwise_distance.c:674, address = 0x000000010f72435f
(lldb) c
Process 10723 resuming

> 

From there, when I ran bitwise.dist() it always stopped whenever it ran into that point:

Process 11033 stopped
* thread #4: tid = 0x84b9a, 0x0000000100f11394 poppr.so`.omp_outlined..4(.global_tid.=0x00007000058fcd70, .bound_tid.=0x00007000058fcd68, i=0x00007ffeefbfcafc, R_gen=0x00007ffeefbfcb70, R_chr_symbol=0x00007ffeefbfcb80, R_nap_symbol=0x00007ffeefbfcb78, nap1_length=0x00007ffeefbfcb34, R_nap1=0x00007ffeefbfcb40, chr_length=0x00007ffeefbfcb2c, R_chr1_1=0x00007ffeefbfcb60, R_chr1_2=0x00007ffeefbfcb58, missing_match=0x00007ffeefbfcb18, only_differences=0x00007ffeefbfcb14, distance_matrix=0x00007ffeefbfcae8) + 1428 at bitwise_distance.c:674, stop reason = breakpoint 1.1
    frame #0: 0x0000000100f11394 poppr.so`.omp_outlined..4(.global_tid.=0x00007000058fcd70, .bound_tid.=0x00007000058fcd68, i=0x00007ffeefbfcafc, R_gen=0x00007ffeefbfcb70, R_chr_symbol=0x00007ffeefbfcb80, R_nap_symbol=0x00007ffeefbfcb78, nap1_length=0x00007ffeefbfcb34, R_nap1=0x00007ffeefbfcb40, chr_length=0x00007ffeefbfcb2c, R_chr1_1=0x00007ffeefbfcb60, R_chr1_2=0x00007ffeefbfcb58, missing_match=0x00007ffeefbfcb18, only_differences=0x00007ffeefbfcb14, distance_matrix=0x00007ffeefbfcae8) + 1428 at bitwise_distance.c:674
   671            }
   672            // Find the index of the next missing value in sample i.
   673            next_missing_index_i++;
-> 674            next_missing_i = (int)INTEGER(R_nap1)[next_missing_index_i] - 1;
   675          }
   676          // Repeat for j
   677          while(next_missing_index_j < nap2_length && next_missing_j < (k+1)*8 && next_missing_j >= (k*8))
(lldb)

I could get a glimpse of all the variables if I typed frame variable (you can also type “fr v”):

(lldb) frame variable
(int *const __restrict) .global_tid. = 0x00007000058fcd70
(int *const __restrict) .bound_tid. = 0x00007000058fcd68
(int &) i = 0x00007ffeefbfcafc (&i = 1)
(SEXP &) R_gen = 0x00007ffeefbfcb70 (&R_gen = 0x000000010fc616a0)
(SEXP &) R_chr_symbol = 0x00007ffeefbfcb80 (&R_chr_symbol = 0x000000010bab7578)
(SEXP &) R_nap_symbol = 0x00007ffeefbfcb78 (&R_nap_symbol = 0x00000001024126d0)
(int &) nap1_length = 0x00007ffeefbfcb34 (&nap1_length = 2)
(SEXP &) R_nap1 = 0x00007ffeefbfcb40 (&R_nap1 = 0x000000010dc52e78)
(int &) chr_length = 0x00007ffeefbfcb2c (&chr_length = 4)
(SEXP &) R_chr1_1 = 0x00007ffeefbfcb60 (&R_chr1_1 = 0x000000010dc53238)
(SEXP &) R_chr1_2 = 0x00007ffeefbfcb58 (&R_chr1_2 = 0x000000010dc51cf8)
(int &) missing_match = 0x00007ffeefbfcb18 (&missing_match = 1)
(int &) only_differences = 0x00007ffeefbfcb14 (&only_differences = 0)
(int **&) distance_matrix = 0x00007ffeefbfcae8: {
  &distance_matrix = 0x0000000100a6fa50
}
(int) .omp.iv = 0
(int) .capture_expr. = 1
(int) .capture_expr. = 0
(int) j = 0
(int) .omp.lb = 0
(int) .omp.ub = 0
(int) .omp.stride = 1
(int) .omp.is_last = 1
(int) j = 0
(int) cur_distance = 0
(SEXP) R_chr2_1 = 0x000000010fa681d8
(SEXP) R_chr2_2 = 0x000000010dfe1898
(SEXP) R_nap2 = 0x000000010c7db4e0
(int) next_missing_index_j = -1
(int) next_missing_j = -1
(int) next_missing_index_i = 1
(int) next_missing_i = 4
(zygosity) set_1 = (c1 = '\0', c2 = '\x87', ch = '\x87', cd = '\0', cr = 'x')
(zygosity) set_2 = (c1 = '@', c2 = '�', ch = '�', cd = '@', cr = '\x03')
(char) tmp_sim_set = '\x94'
(int) k = 0
(char) mask = '\x10'
(int) nap2_length = 0

Notice how we have a lot of weird characters up there? That’s because this function deals with data stored in bits. You can actually tell lldb to display characters as bits:

type format add --format binary char

Now the values can actually be interpreted!

(zygosity) set_1 = (c1 = 0b00000000, c2 = 0b10000111, ch = 0b10000111, cd = 0b00000000, cr = 0b01111000)
(zygosity) set_2 = (c1 = 0b01000000, c2 = 0b11111100, ch = 0b10111100, cd = 0b01000000, cr = 0b00000011)
(char) tmp_sim_set = 0b10010100
(int) k = 0
(char) mask = 0b00010000

We can see that next_missing_i is set to 4, next_missing_index_i is currently set to 1 and the nap1_length is set to 2. If we type “n”, it will execute the current line. We can then see the new value of next_missing_i

(lldb) print next_missing_i
(int) $1 = 17

Instead of going line by line, you can type “c” to go to the next breakpoint and execute the code there. This happens to be the point of the error. You can see that if we execute line 674 and then print next_missing_i:

(lldb) print next_missing_i
(int) $2 = 536870927

The data I fed into this function only has 24 possible positions, so this huge number is the memory leak.

Solution

The solution I eventually came up with was to wrap it in another check:

  // Find the index of the next missing value in sample i.
  next_missing_index_i++; 
  if (next_missing_index_i < nap1_length){
    next_missing_i = (int)INTEGER(R_nap1)[next_missing_index_i] - 1;
  }

Is it elegant? No. Did it get the job done? Yes. I had originally moved the assignment step to the top of the loop, but had tests fail that way and I couldn’t figure out what was going on with them.

Lesson learned

This error has been in the code for four years. It wasn’t particularly malicious since it wasn’t overwriting this space of memory, but it’s the kind of error that could only be detected by these address sanitizers routinely used by the CRAN team. In fact, the Valgrind sanitizer had pointed out this very error, but, I had (wrongly) thought that this was due to the fact that it was in the middle of a parallel processing statement since the memory was only “possibly” lost. Sometimes these errors are obvious and other times it takes you over a year and a half to find these bugs and squish them).

Avatar
Zhian N. Kamvar
Research Software Engineer

I am a population geneticist, data scientist, plant pathologist, and R package developer. I currently work as the Lesson Infrastructure Technology Developer at The Carpentries.

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