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

[Szilárd Páll]

--
Szilárd


On Fri, Jul 27, 2012 at 4:26 AM, Szilárd Páll <szilard.pall at cbr.su.se>wrote:

> On Fri, Jul 27, 2012 at 4:06 AM, Szilárd Páll <szilard.pall at cbr.su.se>wrote:
>
>> 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).
>>
>
> Just checked and, as expected, the same compiler errors show up with gcc
> 4.4.7 as well. I'm not sure what did you change in the configuration to get
> the code built, but you must have used GMX_ACCELERATION != AVX_256.
>

And I've found an explanation for this one as well: it's another bug, the
CPU acceleration auto-detection doesn't seem work with gcc <=4.4. I'll file
a bug for this one.


>
>
>>
>>
>>> 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.
>>
>
> Unfortunately, I can confirm this crash. It seems to occur with
> OMP_NUM_THREADS=m and -nt n, where m>1 and n >1.
>
>
>>
>>
>>>
>>> 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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>>>
>>
>>
>
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