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

[Jochen Hub]

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


-- 
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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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