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

[Roland Schulz]

On Thu, Jul 26, 2012 at 8:09 AM, 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)'

What is GMX_ACCELERATION set to? Make sure it isn't set to AVX or that
if it is that your cflags contain -mavx.

> 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 ()

Did you try a version which included the bugfix for issue 900
(002c4985c1d839810816b5c1ba347634b7d7cabb)?
What exact compiler did you try? Is it LLVM-gcc or gcc with gcc
backend (not llvm)? Also so far we only saw OpenMP problems with
llvm-gcc 4.2 not 4.4. So more details would be useful to know.

> 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?
No it should work pretty well and the testsuite is run before any
commit. And the Jenkins configuration does include gcc 4.2 and 4.6 on
Mac. So it is somewhat surprising that you have 2 independent
problems.

Roland

>
> 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/
> ---------------------------------------------------
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