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

[David van der Spoel]

On 2012-07-26 14:09, Jochen Hub 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)'
>
> On a gcc 4.4 or earlier, compiling works fine, but mdruns stops with a
> segfault. A backtrace in gdb 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 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?
>
> Many thanks,
> Jochen
>
>
The mdrun bug has been fixed in earlier versions, there's a redmine 
issue http://redmine.gromacs.org/issues/900 about it. In fact there's 
lots of ugliness going on, and it has not really been resolved, but by 
turning off openmp you can get a working version of mdrun.


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se