<div class="gmail_quote">On Fri, Jul 27, 2012 at 12:07 AM, Roland Schulz <span dir="ltr"><<a href="mailto:roland@utk.edu" target="_blank">roland@utk.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im">On Thu, Jul 26, 2012 at 8:09 AM, Jochen Hub <<a href="mailto:jhub@gwdg.de">jhub@gwdg.de</a>> wrote:<br>
> Hi,<br>
><br>
> I am trying to compile and run the git master on my Macbook air (OS X<br>
> Lion). Without success. If I compile with a newer gcc (4.5 or newer,<br>
> installed from Macports), I get errors like (does this have to do with AVX?)<br>
><br>
> [ 1%] Building C object<br>
> src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.c.o<br>
> /var/folders/ys/rh9lzqpj7854h34d2__mznph0000gn/T//ccPxJmjg.s:66:no such<br>
> instruction: `vmovups 0(%r13), %ymm0'<br>
> /var/folders/ys/rh9lzqpj7854h34d2__mznph0000gn/T//ccPxJmjg.s:69:no such<br>
> instruction: `vmovups %ymm0, 24(%rdi)'<br>
> /var/folders/ys/rh9lzqpj7854h34d2__mznph0000gn/T//ccPxJmjg.s:79:no such<br>
> instruction: `vmovss 0(%r13), %xmm1'<br>
> /var/folders/ys/rh9lzqpj7854h34d2__mznph0000gn/T//ccPxJmjg.s:83:no such<br>
> instruction: `vmovss %xmm1, 24(%rdi,%r9,4)'<br>
> /var/folders/ys/rh9lzqpj7854h34d2__mznph0000gn/T//ccPxJmjg.s:99:no such<br>
> instruction: `vmovss 0(%r13), %xmm2'<br>
> /var/folders/ys/rh9lzqpj7854h34d2__mznph0000gn/T//ccPxJmjg.s:102:no such<br>
> instruction: `vmovss %xmm2, 24(%rdi,%r9,4)'<br>
<br>
</div>What is GMX_ACCELERATION set to? Make sure it isn't set to AVX or that<br>
if it is that your cflags contain -mavx.<br>
<div><div class="h5"><br>
> On a gcc 4.4 or earlier, compiling works fine, but mdruns stops with a<br>
> segfault. A backtrace in gdb gives the following. Seems like something<br>
> goes wrong in FFTW (which was compiled with the same gcc and with<br>
> --enable-threads --enable-sse --enable-sse2).<br>
><br>
> Program received signal EXC_BAD_ACCESS, Could not access memory.<br>
> Reason: KERN_INVALID_ADDRESS at address: 0x0000000000000048<br>
> [Switching to process 44300 thread 0x1b03]<br>
> 0x0000000100050ebd in gomp_resolve_num_threads ()<br>
> (gdb) bt<br>
> #0 0x0000000100050ebd in gomp_resolve_num_threads ()<br>
> #1 0x0000000100050fc3 in GOMP_parallel_start ()<br>
> #2 0x00000001004c0bc2 in fft5d_plan_3d ()<br>
> #3 0x0000000100434a52 in gmx_parallel_3dfft_init ()<br>
> #4 0x000000010046b6fc in gmx_pme_init ()<br>
> #5 0x0000000100026ab3 in mdrunner (nthreads_requested=4, fplog=0x0,<br>
> cr=0x102100b40, nfile=36, fnm=0x103808200, oenv=0x101000c10, bVerbose=0,<br>
> bCompact=1, nstglobalcomm=-1, ddxyz=0x1013c0e04, dd_node_order=1, rdd=0,<br>
> rconstr=0, dddlb_opt=0x10002e26a "auto", dlb_scale=0.800000012,<br>
> ddcsx=0x0, ddcsy=0x0, ddcsz=0x0, nstepout=100, resetstep=-1,<br>
> nmultisim=0, repl_ex_nst=0, repl_ex_nex=0, repl_ex_seed=-1, pforce=-1,<br>
> cpt_period=15, max_hours=-1, deviceOptions=0x10002e276 "", Flags=7168)<br>
> at /Users/jhub/src/gmx/gromacs/src/programs/mdrun/runner.c:844<br>
> #6 0x0000000100024f2d in mdrunner_start_fn (arg=0x101005d60) at<br>
> /Users/jhub/src/gmx/gromacs/src/programs/mdrun/runner.c:173<br>
> #7 0x0000000100242bfb in tMPI_Thread_starter ()<br>
> #8 0x00007fff9785f8bf in _pthread_start ()<br>
> #9 0x00007fff97862b75 in thread_start ()<br>
<br>
</div></div>Did you try a version which included the bugfix for issue 900<br>
(002c4985c1d839810816b5c1ba347634b7d7cabb)?<br>
What exact compiler did you try? Is it LLVM-gcc or gcc with gcc<br>
backend (not llvm)? Also so far we only saw OpenMP problems with<br>
llvm-gcc 4.2 not 4.4. So more details would be useful to know.<br>
<div class="im"><br>
> Can anyone give me a hint how to fix this? Or is the master so<br>
> experimental that it is not interned to be used at all right now?<br>
</div>No it should work pretty well and the testsuite is run before any<br>
commit. And the Jenkins configuration does include gcc 4.2 and 4.6 on<br></blockquote><div><br></div><div>It does, but it uses only the auto-detected GMX_ACCELERATION which gets set to SSE4.1 (as the CPUs in the machine don't support AVX).</div>
<div><br></div><div>This does suggest to me that we might want to have more thorough (probably nightly) builds with virtually all-vs-all important settings (compilers, platforms, mandatory libraries, etc.).</div><div><br>
</div><div>--<br>Szilárd</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Mac. So it is somewhat surprising that you have 2 independent<br>
problems.<br>
<br>
Roland<br>
<div class="im HOEnZb"><br>
><br>
> Many thanks,<br>
> Jochen<br>
><br>
><br>
> --<br>
> ---------------------------------------------------<br>
> Dr. Jochen Hub<br>
> Computational Molecular Biophysics Group<br>
> Institute for Microbiology and Genetics<br>
> Georg-August-University of Göttingen<br>
> Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.<br>
> Phone: <a href="tel:%2B49-551-39-14189" value="+495513914189">+49-551-39-14189</a><br>
> <a href="http://cmb.bio.uni-goettingen.de/" target="_blank">http://cmb.bio.uni-goettingen.de/</a><br>
> ---------------------------------------------------<br>
</div><div class="im HOEnZb">> --<br>
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><br>
><br>
><br>
<br>
<br>
<br>
</div><span class="HOEnZb"><font color="#888888">--<br>
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