[gmx-developers] gmx master: compiling on mac and segfault

[Szilárd Páll]

On Thu, Jul 26, 2012 at 2:09 PM, Jochen Hub <jhub at gwdg.de> wrote:

> Hi,
>
> I am trying to compile and run the git master on my Macbook air (OS X
> Lion). Without success. If I compile with a newer gcc (4.5 or newer,
> installed from Macports), I get errors like (does this have to do with AVX?)
>
> [  1%] Building C object src/gromacs/CMakeFiles/**
> libgromacs.dir/gmxpreprocess/**add_par.c.o
> /var/folders/ys/**rh9lzqpj7854h34d2__**mznph0000gn/T//ccPxJmjg.s:66:**no
> such instruction: `vmovups 0(%r13), %ymm0'
> /var/folders/ys/**rh9lzqpj7854h34d2__**mznph0000gn/T//ccPxJmjg.s:69:**no
> such instruction: `vmovups %ymm0, 24(%rdi)'
> /var/folders/ys/**rh9lzqpj7854h34d2__**mznph0000gn/T//ccPxJmjg.s:79:**no
> such instruction: `vmovss 0(%r13), %xmm1'
> /var/folders/ys/**rh9lzqpj7854h34d2__**mznph0000gn/T//ccPxJmjg.s:83:**no
> such instruction: `vmovss %xmm1, 24(%rdi,%r9,4)'
> /var/folders/ys/**rh9lzqpj7854h34d2__**mznph0000gn/T//ccPxJmjg.s:99:**no
> such instruction: `vmovss 0(%r13), %xmm2'
> /var/folders/ys/**rh9lzqpj7854h34d2__**mznph0000gn/T//ccPxJmjg.s:102:**no
> such instruction: `vmovss %xmm2, 24(%rdi,%r9,4)'
>

I can confirm this, works on Linux, fails on Mac OS Lion with gcc 4.5 - 4.7
with GMX_ACCELERATION=AVX_256. It looks like AVX instructions are somehow
not recognized, although the aforementioned compilers are supposed to have
support for it.


> On a gcc 4.4 or earlier, compiling works fine, but mdruns stops with a
> segfault. A backtrace in gdb


That's strange as gcc 4.4 is supposed to have AVX support (
http://goo.gl/Rt3BM).


> gives the following. Seems like something goes wrong in FFTW (which was
> compiled with the same gcc and with --enable-threads --enable-sse
> --enable-sse2).
>
> Program received signal EXC_BAD_ACCESS, Could not access memory.
> Reason: KERN_INVALID_ADDRESS at address: 0x0000000000000048
> [Switching to process 44300 thread 0x1b03]
> 0x0000000100050ebd in gomp_resolve_num_threads ()
> (gdb) bt
> #0  0x0000000100050ebd in gomp_resolve_num_threads ()
> #1  0x0000000100050fc3 in GOMP_parallel_start ()
> #2  0x00000001004c0bc2 in fft5d_plan_3d ()
> #3  0x0000000100434a52 in gmx_parallel_3dfft_init ()
> #4  0x000000010046b6fc in gmx_pme_init ()
> #5  0x0000000100026ab3 in mdrunner (nthreads_requested=4, fplog=0x0,
> cr=0x102100b40, nfile=36, fnm=0x103808200, oenv=0x101000c10, bVerbose=0,
> bCompact=1, nstglobalcomm=-1, ddxyz=0x1013c0e04, dd_node_order=1, rdd=0,
> rconstr=0, dddlb_opt=0x10002e26a "auto", dlb_scale=0.800000012, ddcsx=0x0,
> ddcsy=0x0, ddcsz=0x0, nstepout=100, resetstep=-1, nmultisim=0,
> repl_ex_nst=0, repl_ex_nex=0, repl_ex_seed=-1, pforce=-1, cpt_period=15,
> max_hours=-1, deviceOptions=0x10002e276 "", Flags=7168) at
> /Users/jhub/src/gmx/gromacs/**src/programs/mdrun/runner.c:**844
> #6  0x0000000100024f2d in mdrunner_start_fn (arg=0x101005d60) at
> /Users/jhub/src/gmx/gromacs/**src/programs/mdrun/runner.c:**173
> #7  0x0000000100242bfb in tMPI_Thread_starter ()
> #8  0x00007fff9785f8bf in _pthread_start ()
> #9  0x00007fff97862b75 in thread_start ()
>

Can't confirm this one right now as there's no gcc 4.4 on the Mac OS build
server. Will check it later. However, it sounds like it's a similar issue
to the ones we've had with an ordered clause in a #pragma omp statment.


>
> Can anyone give me a hint how to fix this? Or is the master so
> experimental that it is not interned to be used at all right now?
>

Unfortunately, this affects the release-4-6 branch as well. Could you
please file a bug on Redmine on the first issue and have a look at the
related issue on the second.

Cheers,
--
Sz.


> Many thanks,
> Jochen
>
>
> --
> ------------------------------**---------------------
> Dr. Jochen Hub
> Computational Molecular Biophysics Group
> Institute for Microbiology and Genetics
> Georg-August-University of Göttingen
> Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
> Phone: +49-551-39-14189
> http://cmb.bio.uni-goettingen.**de/ <http://cmb.bio.uni-goettingen.de/>
> ------------------------------**---------------------
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