[Rd] R on Solaris 10 x64

Fri Apr 13 21:43:21 CEST 2007

Prof Brian Ripley wrote:
> What did the maintainer of this unmentioned contributed package (hdf5) say 
> when you ask him?
>
> [Hint: you *have* read the posting guide at
>
> http://www.r-project.org/posting-guide.html
>
> and done as it asks?]
>
> There is no evidence here that this is anything to do with R itself.
>
>   
Er, Brian, I think you are misfiring this time. As I understand it, they 
(David/Greg) are well aware that they are debugging an issue in a 
contributed package which occurs with an uncommon compiler on a maybe 
not so uncommon platform. They are just looking for hints on how to 
proceed to pinpoint the issue.

--------------

2 things caught my eye (except that their "R code" is clearly C): The 
dbx output doesn't show off[curr_seq], which could actually be the 
culprit, and the _memcpy call on the stack looks odd:

_memcpy(0x0, 0xfdebc707, 0x9f5c4f0)

(What happened to the length and how did NULL get in there.) If memcpy() 
is a  macro, I think I'd take a closer look at the include files and see 
if something is getting expanded  in an unintended way.

> On Fri, 13 Apr 2007, Tai-Wei (David) Lin wrote:
>
>   
>> 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.
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>     
>
>