R on Solaris 10 x64

Hi R Developers,

Greg is helping me with debugging R on Solaris 10 x64. Please let us
know if you have any thoughts or tips that can help us debug this.

Thanks,

David



************
Using default transfer plist
in vector_io: permuting
About to write

 *** caught segfault ***
address e8554000, cause 'memory not mapped'

Traceback:
 1: .External("do_hdf5save", call, sys.frame(sys.parent()), fileout,
 ..., PACKAGE = "hdf5")
 2: hdf5save(hdf5_Fstat, "Fstat", "geneNames", "genotype")
aborting ...
************

We've tried many things to debug it:

* dbx Runtime Checking (RTC) is not detecting any (meaningful) memory
access problems that I can see.

* The same on Solaris/SPARC.

* Neither does Valgrind on Linux.

* I've tried increasing the C stack size, assuming R could be running
out of stack size. Didn't help.

Running R under dbx (without RTC) until the crash shows this:

...
About to write
t at 1 (l at 1) signal SEGV (no mapping at the fault address) in _memcpy at
0xfe90444b
0xfe90444b: _memcpy+0x006b:     movaps   0x00000000(%esi),%xmm0
Current function is H5D_select_mgath
  379               HDmemcpy(tgath_buf,buf+off[curr_seq],curr_len);
(dbx) where
current thread: t at 1
  [1] _memcpy(0x0, 0xfdebc707, 0x9f5c4f0), at 0xfe90444b
=>[2] H5D_select_mgath(_buf = 0x9f79580, space = 0x8966770, iter =
0x8045980, nelmts = 3120U, dxpl_cache = 0xfe170078, _tgath_buf =
0x9f5c4f0), line 379 in "H5Dselect.c"
  [3] H5D_contig_write(io_info = 0x804620c, nelmts = 3120ULL, mem_type =
0x97b05c8, mem_space = 0x8966770, file_space = 0x8966770, tpath =
0x8ee7078, src_id = 201326906, dst_id = 201326904, buf = 0x9f79580),
line 1418 in "H5Dio.c"
  [4] H5D_write(dataset = 0x8f169c0, mem_type_id = 201326906, mem_space
= 0x8966770, file_space = 0x8966770, dxpl_id = 671088643, buf =
0x9f79580), line 952 in "H5Dio.c"
  [5] H5Dwrite(dset_id = 335544330, mem_type_id = 201326906,
mem_space_id = 0, file_space_id = 0, plist_id = 671088643, buf =
0x9f79580), line 586 in "H5Dio.c"
  [6] vector_io(call = 0x97234ec, writeflag = 1, dataset = 335544330,
space = 268435472, obj = 0x98386a0), line 535 in "hdf5.c"
  [7] hdf5_write_vector(call = 0x97234ec, id = 67108867, symname =
0x9cf35d0 "geneNames", val = 0x98386a0), line 693 in "hdf5.c"
  [8] hdf5_save_object(call = 0x97234ec, fid = 67108867, symname =
0x9cf35d0 "geneNames", val = 0x98386a0), line 957 in "hdf5.c"
  [9] do_hdf5save(args = 0x9723284), line 1104 in "hdf5.c"
  [10] do_External(call = 0x86d62bc, op = 0x8371cd8, args = 0x972340c,
env = 0x9723594), line 832 in "dotcode.c"
  [11] Rf_eval(e = 0x86d62bc, rho = 0x9723594), line 445 in "eval.c"
  [12] Rf_evalList(el = 0x86d6230, rho = 0x9723594, op = 0x837226c),
line 1463 in "eval.c"
  [13] Rf_eval(e = 0x86d6214, rho = 0x9723594), line 438 in "eval.c"
  [14] do_begin(call = 0x86d56bc, op = 0x836709c, args = 0x86d61dc, rho
= 0x9723594), line 1107 in "eval.c"
  [15] Rf_eval(e = 0x86d56bc, rho = 0x9723594), line 431 in "eval.c"
  [16] Rf_applyClosure(call = 0x9723738, op = 0x83c0328, arglist =
0x97236e4, rho = 0x8379b1c, suppliedenv = 0x8379b38), line 614 in "eval.c"
  [17] Rf_eval(e = 0x9723738, rho = 0x8379b1c), line 455 in "eval.c"
  [18] Rf_ReplIteration(rho = 0x8379b1c, savestack = 0, browselevel = 0,
state = 0x8047328), line 256 in "main.c"
  [19] R_ReplConsole(rho = 0x8379b1c, savestack = 0, browselevel = 0),
line 305 in "main.c"
  [20] run_Rmainloop(), line 944 in "main.c"
  [21] Rf_mainloop(), line 951 in "main.c"
  [22] main(ac = 4, av = 0x80477ac), line 33 in "Rmain.c"
(dbx) p curr_len
curr_len = 24960U
(dbx) p curr_seq
curr_seq = 0
(dbx) p of
dbx: "of" is not defined in the scope
`libhdf5.so.0.0.0`H5Dselect.c`H5D_select_mgath:347`
dbx: see `help scope' for details
(dbx) p off
off = 0x8042960
(dbx) p tgath_buf
tgath_buf = 0x9f5c4f0
"\xd87\x83^H\xa8\xf3\x82^H0^X\x82^H^X\xd4\x81^H^P\x90\x81^H\xb8m\x80^H^H'\x80^H\x88^?^?^H\x908^?^H\xb0\xf7~^H\xd8\xad~^H\xf8\xb2~^H\xb8\x8e~^H\xe8]~^H\xe8\xcb\xed^HP\xe3}^Hh\xdd\xbb^H\x98\xc4}^H\xf0\xa0}^H\xa8r}^HH}\xc3^HpO|^HH^V|^H^X\xd8|^H\xc0\xb1|^H8=}^H\x90\xcd{^H^Pm{^H\xb8#{^Hx'{^H\x90\xf8x^HpKx^H^POx^H\xa8~w^H^H>w^H\xf0\xb2w^H\xc8^Ew^HX'x^H\xf8\xdbv^H"
(dbx) p buf
buf = 0x9f79580
"\xd87\x83^H\xa8\xf3\x82^H0^X\x82^H^X\xd4\x81^H^P\x90\x81^H\xb8m\x80^H^H'\x80^H\x88^?^?^H\x908^?^H\xb0\xf7~^H\xd8\xad~^H\xf8\xb2~^H\xb8\x8e~^H\xe8]~^H\xe8\xcb\xed^HP\xe3}^Hh\xdd\xbb^H\x98\xc4}^H\xf0\xa0}^H\xa8r}^HH}\xc3^HpO|^HH^V|^H^X\xd8|^H\xc0\xb1|^H8=}^H\x90\xcd{^H^Pm{^H\xb8#{^Hx'{^H\x90\xf8x^HpKx^H^POx^H\xa8~w^H^H>w^H\xf0\xb2w^H\xc8^Ew^HX'x^H\xf8\xdbv^H"
(dbx) p nseq
nseq = 1U
(dbx) p len
len = 0x804195c
(dbx) p len[0..2]
len[0..2] =
[0] = 24960U
[1] = 140025512U
[2] = 140013048U
(dbx)


The R code in question is:

...
        /* Loop, while sequences left to process */
        for(curr_seq=0; curr_seq<nseq; curr_seq++) {
            /* Get the number of bytes in sequence */
            curr_len=len[curr_seq];

            HDmemcpy(tgath_buf,buf+off[curr_seq],curr_len);

            /* Advance offset in gather buffer */
            tgath_buf+=curr_len;
        } /* end for */
...

where

./src/hdf5-1.6.5/src/H5private.h:
#define HDmemcpy(X,Y,Z)  memcpy((char*)(X),(const char*)(Y),Z)

Maybe the "curr_len = 24960U" value is too high. I have no way of
knowing what it should be in this case.

The crash could be caused by a compiler bug, although it's not very
likely. These crashes have occurred both with and without optimization,
with and without -g.