<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>1 apr 2012 kl. 11.19 skrev Mark Abraham:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>On 1/04/2012 6:55 PM, Dommert Florian wrote:<br><blockquote type="cite">On Sun, 2012-04-01 at 03:50 +0000, Shirts, Michael (mrs5pt) wrote:<br></blockquote><blockquote type="cite"><blockquote type="cite">Hi, all-<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I'm very recently (with 4.6 updates in the last couple of weeks) having<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">issues with building gromacs with threads on OS X. When I try to compile<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">with shared libraries, I get:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">ld: warning: in /usr/local/lib/libgomp.dylib, file was built for i386 which<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">is not the architecture being linked (x86_64)<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">When I build without shared libraries, it compiles, but crashes when run<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">with -nt more than 1.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Currently using OS X 10.6.8, gcc 4.1.2 to compile.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Everything works fine with 4.5.5, and with earlier versions of 4.6.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Anyone else having similar problems, or know what changes could have caused<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">this?<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite">I have a similar problem, but it is related to building with OpenMPI on<br></blockquote><blockquote type="cite">Ubuntu. For the releases so far, my MPI Compiler was found without any<br></blockquote><blockquote type="cite">problems. For the 4-6-release I have to explicitly declare the C and CXX<br></blockquote><blockquote type="cite">compilers as mpicc and mpic++, respectively. I am using gcc4.4.3 and<br></blockquote><blockquote type="cite">OpenMPI 1.4.3 on a 64bit Ubuntu 10.4 machine.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I would also be interest why this happens now ?<br></blockquote><br>I changed the way MPI is detected and used in commit hash 417d0affff. In the commit message there I said:<br><br>commit 417d0affff5485d10f905aa3581f14602aca873a<br>Author: Mark Abraham <<a href="mailto:mark.j.abraham@gmail.com">mark.j.abraham@gmail.com</a>><br>Date: Mon Jan 9 20:38:33 2012 +1100<br><br> Remove use of FindMPI.cmake<br><br> The functionality of FindMPI.cmake should not be needed for GROMACS,<br> since the wrapper compiler will do the complete job. This already<br> worked for Cray and BlueGene, and so far this new version is known<br> to work for OpenMPI wrapping icc and gcc.<br><br> CMake now warns the user about possible unsuitable versions of<br> OpenMPI and MVAPICH2.<br><br> The process of managing MPI is more modular than it used to be.<br><br> To use:<br><br> cmake .. -DGMX_MPI=ON -DCMAKE_C_COMPILER=`which mpicc`<br><br> or with bash<br><br> CC=mpicc cmake .. -DGMX_MPI=ON<br><br> and whatever else suits your setup.<br><br> Fixes #851 and #636.<br><br> Change-Id: Ibe41206bed8b70b83a25da1e4e29dd87b61ea17d<br><br>I have no idea whether this has any bearing on Michael's problem - what is libgomp anyway?<br></div></blockquote><div><br></div><div>That's the gnu implementation of OpenMP.</div><br><blockquote type="cite"><div><br>Mark<br>-- <br>gmx-developers mailing list<br><a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>http://lists.gromacs.org/mailman/listinfo/gmx-developers<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-developers-request@gromacs.org.<br></div></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>-----------------------------------------------</div><div>Erik Marklund, PhD</div><div>Dept. of Cell and Molecular Biology, Uppsala University.</div><div>Husargatan 3, Box 596, 75124 Uppsala, Sweden</div><div>phone: +46 18 471 6688 fax: +46 18 511 755</div><div><a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a></div><div><a href="http://www2.icm.uu.se/molbio/elflab/index.html">http://www2.icm.uu.se/molbio/elflab/index.html</a></div></div></span></div></span></span>
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