<br><br><div class="gmail_quote">On Sun, Apr 1, 2012 at 9:09 AM, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</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 2012-04-01 15:05, Roland Schulz wrote:<br>
><br>
><br>
> On Sun, Apr 1, 2012 at 6:20 AM, David van der Spoel<br>
</div><div><div class="h5">> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <mailto:<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>>> wrote:<br>
><br>
> On 2012-04-01 05:50, Shirts, Michael (mrs5pt) wrote:<br>
> > Hi, all-<br>
> ><br>
> > I'm very recently (with 4.6 updates in the last couple of weeks)<br>
> having<br>
> > issues with building gromacs with threads on OS X. When I try to<br>
> compile<br>
> > with shared libraries, I get:<br>
> ><br>
> > ld: warning: in /usr/local/lib/libgomp.dylib, file was built for<br>
> i386 which<br>
> > is not the architecture being linked (x86_64)<br>
> ><br>
> > When I build without shared libraries, it compiles, but crashes<br>
> when run<br>
> > with -nt more than 1.<br>
> ><br>
> > Currently using OS X 10.6.8, gcc 4.1.2 to compile.<br>
> ><br>
> > Everything works fine with 4.5.5, and with earlier versions of 4.6.<br>
> ><br>
> > Anyone else having similar problems, or know what changes could<br>
> have caused<br>
> > this?<br>
><br>
> There is a redmine for this (900).<br>
><br>
><br>
> Michael's issue is a different because it is gcc 4.1.2 and because it is<br>
> not a segfault but the linker errorr.<br>
> I'm surprised that you get a linker error. gcc 4.1 doesn't support<br>
> OpenMP and if run cmake with gcc 4.1 on Linux I get:<br>
> Could NOT find OpenMP (missing: OpenMP_C_FLAGS OpenMP_CXX_FLAGS)<br>
<br>
</div></div>He does mention a crash with -nt > 1, and it is only recently, he also<br>
links to libgomp, so it must be the same error.<br></blockquote><div><br></div><div>True. I overlooked that part. Yes that part is the same. I'm still puzzled why cmake doesn't detect that gcc 4.1 doesn't have OpenMP. </div>
<div>@Michael: Or was your compiler version a typo and you are also using gcc 4.2?</div><div><br></div><div>Roland</div><div><br></div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im"><br>
><br>
> If you rerun cmake (without a cache), do you still not get any error<br>
> during cmake?<br>
><br>
> BTW: We probably should automatic disable OpenMP if the flags can't be<br>
> found (e.g. for clang and gcc <4.2)<br>
<br>
</div>At least on Macs for now.<br>
<div class="im"><br>
><br>
> Roland<br>
><br>
><br>
> Your simplest solution is cmake -DGMX_OPENMP:BOOL=OFF<br>
><br>
> ><br>
> > Thanks!<br>
> > ~~~~~~~~~~~~<br>
> > Michael Shirts<br>
> > Assistant Professor<br>
> > Department of Chemical Engineering<br>
> > University of Virginia<br>
</div>> > <a href="mailto:michael.shirts@virginia.edu">michael.shirts@virginia.edu</a> <mailto:<a href="mailto:michael.shirts@virginia.edu">michael.shirts@virginia.edu</a>><br>
> > <a href="tel:%28434%29-243-1821" value="+14342431821">(434)-243-1821</a> <tel:%28434%29-243-1821><br>
<div class="im">> ><br>
><br>
><br>
> --<br>
> David van der Spoel, Ph.D., Professor of Biology<br>
> Dept. of Cell & Molec. Biol., Uppsala University.<br>
> Box 596, 75124 Uppsala, Sweden. Phone: <a href="tel:%2B46184714205" value="+46184714205">+46184714205</a><br>
</div>> <tel:%2B46184714205>.<br>
> <a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <mailto:<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>><br>
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><br>
><br>
<span class="HOEnZb"><font color="#888888">><br>
> --<br>
> ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov" target="_blank">cmb.ornl.gov</a> <<a href="http://cmb.ornl.gov" target="_blank">http://cmb.ornl.gov</a>><br>
</font></span><div class="im HOEnZb">> <a href="tel:865-241-1537" value="+18652411537">865-241-1537</a>, ORNL PO BOX 2008 MS6309<br>
><br>
><br>
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<br>
</div><div class="HOEnZb"><div class="h5">--<br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: <a href="tel:%2B46184714205" value="+46184714205">+46184714205</a>.<br>
<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov">cmb.ornl.gov</a><br>865-241-1537, ORNL PO BOX 2008 MS6309<br>