[Rd] R problems with lapack with gfortran

Tomas Kalibera tom@@@k@||ber@ @end|ng |rom gm@||@com
Fri May 3 11:55:38 CEST 2019

Dear Thomas,

thank you for your input. I've debugged one of the packages and I 
confirm that the breakage is related to passing of strings from C to 
Fortran. Indeed, BLAS and LAPACK define a large number of subroutines 
that take one or more explicit single-character strings as arguments. 
Other than that, BLAS has only one function (xerbla), which takes a 
string of unspecified length, LAPACK only has four (ilaenv, 
ilaenv2stage, lsamen, xerbla). The C interfaces to BLAS/LAPACK from 
Netlib depend on the historic behavior that explicit single-character 
strings are interoperable, concretely CBLAS and LAPACKE provide C 
interfaces/code that calls into Fortran BLAS/LAPACK without passing the 
1s as lengths of the character strings (functions taking a string of 
unspecified length are trivial and re-implemented in C). This has been 
working fine for very many years as the Fortran code never needed to 
access the length it knew was 1. R has been using the same practice, 
which long predates ISO_C_BINDING/BIND(C), and I've seen online 
discussions where people assumed interoperability of length 1 strings, 
once mentioning also a citation from Fortran 2003 Handbook that says "A 
Fortran character string with a length other than 1 is not 
interoperable" (which invites interpretation that length 1 strings were 
). I am not an expert to say whether the current Fortran standard 
requires that interoperability and I assume that it does not given this 
gfortran change.

This gfortran change breaks this interoperability: if a C function calls 
a Fortran function, passing it a single-character string for a parameter 
taking explicit single-character Fortran string, it may crash. I've 
debugged one case with R package BDgraph, this example 
"library(BDgraph); data.sim <- bdgraph.sim( n = 70, p = 5, size = 7, vis 
= TRUE )" crashes due to corruption of C stack by Fortran function 
DPOSV, when compiled with the new gfortran and with -O2. To see the 
problem, one can just look at the disassembly of DPOSV (LAPACK), neither 
the package nor R is not necessary:


In one case, DPOSV calls DPOTRS before returning. The new gfortran with 
-O2 performs tail-call optimization, jumping to DPOTRS. In the annotated 
disassembly snippet, at 11747f1, DPOSV tries to ensure that there is 
constant 1 as string length of UPLO when tail-calling into DPOTRS, so it 
writes it to stack where there already should have been 1 as length of 
UPLO passed to DPOSV. But this argument has not been passed to DPOSV, so 
this causes stack corruption.

  1174ce:       0f 85 62 ff ff ff       jne    117436 <dposv_+0xb6> <== jump if ERROR


   1174d4:       48 8b 04 24             mov    (%rsp),%rax <======= rax holds LDB

   1174d8:       4c 89 7c 24 68          mov    %r15,0x68(%rsp) <=== save INFO to output param

   1174dd:       49 89 d8                mov    %rbx,%r8 <========== pass LDA as LDA

   1174e0:       4c 89 e1                mov    %r12,%rcx <========= pass A as A

   1174e3:       4c 8b 4c 24 08          mov    0x8(%rsp),%r9 <===== pass B as B

   1174e8:       4c 89 ea                mov    %r13,%rdx <========= pass NRHS as NRHS

   1174eb:       48 89 ee                mov    %rbp,%rsi <========= pass N as N

   1174ee:       4c 89 f7                mov    %r14,%rdi <========= pass UPLO as UPLO

   1174f1:       48 c7 44 24 70 01 00    movq   $0x1,0x70(%rsp) <=== pass 1 hidden arg on stack CORRUPTS C STACK

   1174f8:       00 00

   1174fa:       48 89 44 24 60          mov    %rax,0x60(%rsp) <=== pass LDB as LDB (stack)


   1174ff:       48 83 c4 28             add    $0x28,%rsp <== remove 5 vars from stack (sframe)

   117503:       5b                      pop    %rbx

   117504:       5d                      pop    %rbp

   117505:       41 5c                   pop    %r12

   117507:       41 5d                   pop    %r13

   117509:       41 5e                   pop    %r14

   11750b:       41 5f                   pop    %r15 <=== restore register to level before call


   11750d:       e9 de 56 ef ff          jmpq   cbf0 <dpotrs_ using plt> <=== tail call to dpotrs

Note that DPOSV never uses the length of the string (UPLO) from the 
hidden argument, the compiler clearly knows that its length is 1. In 
calls where the length is passed in registers, this does not cause 
trouble (like LSAME) and indeed is needed as the registers have 
different values

       IF( .NOT.LSAME( UPLO, 'U' ) .AND. .NOT.LSAME( UPLO, 'L' ) ) THEN

   117448:       b9 01 00 00 00          mov    $0x1,%ecx

   11744d:       ba 01 00 00 00          mov    $0x1,%edx

   117452:       48 8d 35 bb 12 09 00    lea    0x912bb(%rip),%rsi        # 1a8714 <ipivot.4261+0xd14>

   117459:       4c 89 f7                mov    %r14,%rdi

   11745c:       e8 1f 3d ef ff          callq  b180 <lsame_ using plt>

but it seems to me that the compiler could just refrain from setting the 
length to be 1 on the stack at 1174f1, since it knows it should have 
already been there. It would be a nice property if Fortran code that 
never accesses the hidden arguments with the lengths of the strings, 
because it knows what those lengths are, would also never write to those 
hidden arguments on the stack when it knows what they are (should be).

Before the gfortran change, DPOSV would call to DPOTRS normally (no 
tail-call optimization), so this problem would not occur (I tested with 
268974). By disabling tail call optimization via 
-fno-optimize-sibling-calls, the problem goes away also for other 
packages my colleagues have identified as crashing with the new 
gfortran. Did you know of any other optimization that could break this 
interoperability of 1-length strings? It would be really nice to users 
if this interoperability could be preserved, and if not by default than 
at least with some option.

Traditionally, BLAS/LAPACK implementations are interchangeable at 
dynamic linking time, using the Fortran interface that is however also 
used from C, without passing lengths for fixed 1-character strings. R 
supports this too, at least on some Linux distributions including 
Debian/Ubuntu it is packaged so that it runs with the BLAS/LAPACK 
implementation installed on the system. Even though this is probably not 
correct wrt to the todays Fortran standard (I don't know for sure), this 
is the common practice, and fixing this would not be easy - one would 
have to create a new interface to be used from C, separate from the 
Fortran one, and all software would have to start using that interface 
from C. In the current situation when the Fortran interface is used, 
confusion will arise with this gfortran change as different BLAS/LAPACK 
implementations are built by different Fortran compilers and use a 
different mix of Fortran/C for different computational subroutines. Note 
CBLAS could not be readily used as it itself breaks with the current 
gfortran change as well.

The same interoperability considerations apply to R packages, which 
include native code that calls from C or from Fortran into the (same) 
Fortran interface of BLAS/LAPACK. There would have to be a commonly 
accepted C interface instead by the BLAS/LAPACK implementations, and all 
of these packages would have to be modified to use that interface. If we 
created such a C interface just inside R and asked all package 
maintainers to update their packages, we would still have the problem 
with substitution of external BLAS(/LAPACK) implementations at dynamic 
linking time.

Indeed, it would be very hard to identify these problems by testing, 
because at least now the crashes are quite rate (for the tail-call 
optimization, a number of conditions have to be met to cause memory 
corruption, first the tail optimization has to happen, then the number 
of arguments has to be so large (on x86) that the lengths are passed on 
stack and not in registers, we have to be lucky for the memory 
corruption to map to a crash, etc).

So, any help we could get from you would be highly appreciated, be it 
just a compile option to keep the old behavior or an assurance that we 
are fine if we just disable the tail-call optimization. Appreciated by 
us but I believe also many others who use or develop BLAS/LAPACK, but 
may not have yet run into the problem, as they may not have been 
regularly testing bleeding-edge versions of compilers or may not have 
such a large code base to test as we have on CRAN.


On 4/24/19 11:32 PM, Thomas König wrote:
> Hi,
> I have tried to pinpoint potential problems which could lead to the
> LAPACK issues that are currently seen in R.  I built the current R
> trunk using
> AR=gcc-ar RANLIB=gcc-ranlib ./configure --prefix=$HOME --enable-lto 
> --enable-BLAS-shlib=no --without-recommended-packages
> and used this to find problem areas.
> There are quite a few warnings that were flagged, due to mismatches
> in function types.
> The prototypes that R has in its header files, for example BLAS.h,
> are often not compatible with gfortran function declarations.  To take
> one small example, in src/main/print.c, we have
> void NORET F77_NAME(xerbla)(const char *srname, int *info)
> so xerbla_ is defined with two arguments.
> However, gfortran passes string lengths as hidden arguments.
> You can see this by compiling the small example
> $ cat xer.f
>       END
> $ gfortran -c -fdump-tree-original xer.f
> $ cat xer.f.004t.original
> foo ()
> {
>   integer(kind=4) info;
>   xerbla (&"FOO"[1]{lb: 1 sz: 1}, &info, 3);
> }
> so here we have three arguments. This mismatch is flagged
> by -Wlto-type-mismatch, which, for example, yields
> print.c:1120:12: note: type 'void' should match type 'long int'
> ../../src/extra/blas/blas.f:357:20: warning: type of 'xerbla' does not 
> match original declaration [-Wlto-type-mismatch]
>   357 |          CALL XERBLA( 'DGBMV ', INFO )
> So, why can gcc's r268992 / r269349 matter? Before these patches,
> gfortran used the variadic calling convention for calling procedures
> outside the current file, and the non-variadic calling convention for
> calling procedures found in the current file.
> Because the procedures were all compiled as non-variadic, the caller and
> the calle's signature did not match if they were not in the same
> source file, which is an ABI violation.
> This violation manifested itself in https://gcc.gnu.org/PR87689 ,
> where the the problem resulted in crashes on a primary gcc platform,
> How can this potentially affect R?  After the fix for PR87689,
> gfortran's calls to external procedures are no longer variadic. It is
> quite possible that, while this "works" most of the time, there
> is a problem with a particular LAPACK routine, the call sequence
> leading up to it or the procedures it calls.
> How to fix this problem?  The only clear way I see is to fix this
> on the R side, by adding the string lengths to the prototypes.
> These are size_t (64 bit on 64-bit systems, 32 bit on 32-bit
> systems).  You should then try to make --enable-lto pass
> without any warnings.
> Regarding LAPACK itself, the default build system for R builds
> it as a shared library.  Offhand, I did not see any way to
> build a *.a file instead, so I could not use LTO to check
> for mismatched prototypes between R and LAPACK.
> Of course, I cannot be sure that this is really the root cause
> of the problem you are seeing,but it does seem to fit quite well.
> I hope this analysis helps in resolving this.
> Regards
>     Thomas
> ______________________________________________
> R-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

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