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

Jochen Hub jhub at gwdg.de
Thu Jul 26 14:09:42 CEST 2012


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 
/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 
#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,

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

More information about the gromacs.org_gmx-developers mailing list