That worked! Thanks a ton!
________________________________ From: Justin Lemkul <jalem...@vt.edu> To: Nimmy McNimmerson <nimzs...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Sunday, August 25, 2013 2:54 PM Subject: Re: [gmx-users] 'Command not found' after installation On 8/25/13 5:31 PM, Nimmy McNimmerson wrote: > Hmm... To be honest I'm a novice at installing complex things, I'm a computer > scientist by trade but I'm not very good at troubleshooting this kind of > thing. Has anyone actually installed GROMACS on mac and what did you do? > (Using the default gcc/g++ doesn't work for the AVX stuff) > > I used gcc/g++ (version 4.7.3 from MacPorts) and simply set -DGMX_CPU_ACCELERATION=SSE4.1. Since the install was done on my laptop, where performance does not matter (not running anything beyond simple EM locally), the acceleration didn't matter to me. -Justin > ________________________________ > From: Mark Abraham <mark.j.abra...@gmail.com> > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Sent: Sunday, August 25, 2013 12:57 AM > Subject: Re: [gmx-users] 'Command not found' after installation > > > Hi, > > I don't have any experience with icc on Mac, but I would try either > * re-reading the icc docs to see whether you should be source-ing some > configuration file to set up the dynamic loading at run time (as well > as at compile time), and/or > * making a static build (cmake -DBUILD_SHARED_LIBS=off; but some > Google hits suggests icc was broken at some point and iomp5 enforces > dynamic linking, go figure!), > * when you're really sure you've set up your build environment > correctly, complaining at Intel (again) :-) > > Mark > > On Sun, Aug 25, 2013 at 7:18 AM, Nimmy McNimmerson <nimzs...@yahoo.com> wrote: >> Hi, >> >> Apparently this is an issue with my intel compiler; the dynamic linker isn't >> finding the libiomp5.dylib library. However, I don't know how to fix this >> (the google results haven't worked.) >> >> Please help, >> >> Thanks, >> John >> >> >> ________________________________ >> From: "Barnett, James W." <jbarn...@tulane.edu> >> To: <nimzs...@yahoo.com> >> Sent: Saturday, August 24, 2013 3:07 PM >> Subject: Re: [gmx-users] 'Command not found' after installation >> >> >> Unfortunately this is now beyond what I know with a Mac. It sounds like a >> library is missing that GROMACS needs, or GROMACS can't find it, which is >> probably a simple fix. >> >> Perhaps someone more familiar with Mac will be able to weigh in. >> >> jbarn...@tulane.edu | from mobile >> >> <nimzs...@yahoo.com> wrote: >> >>> This gives the following: >>> >>> dyld: Library not loaded: libiomp5.dylib >>> Referenced from: /usr/local/gromacs/bin/g_luck >>> Reason: image not found >>> Trace/BPT trap: 5 >>> >>> If I try 'pdb2gmx', it says: >>> >>> dyld: Library not loaded: libiomp5.dylib >>> Referenced from: /usr/local/gromacs/bin/pdb2gmx >>> Reason: image not found >>> Trace/BPT trap: 5 >>> >>> Did the installation not work properly? >>> >>> >>> ________________________________ >>> From: "Barnett, James W." <jbarn...@tulane.edu> >>> To: Nimmy McNimmerson <nimzs...@yahoo.com>; Discussion list for GROMACS >>> users <gmx-users@gromacs.org> >>> Sent: Saturday, August 24, 2013 10:42 AM >>> Subject: Re: [gmx-users] 'Command not found' after installation >>> >>> >>> Try "g_luck". That's what has worked for me. >>> >>> On 08/24/2013 12:37 PM, Nimmy McNimmerson wrote: >>>> Hello all, >>>> I have been trying to get GROMACS (4.6.3) to work on my Mac (10.8.1). I >>>> downloaded the latest Intel C++ compilers and built Gromacs successfully >>>> (at least it appeared to be successful since I saw no error messages). I >>>> appended this line to my ~/.profile file: source >>>> /usr/local/gromacs/bin/GMXRC.bash, and restarted my terminal. Still, every >>>> time I type in a GROMACS command, such as "luck," it says "command not >>>> found." f I do echo $GMXDATA, it does return >>>> /usr/local/gromacs/share/gromacs, though. >>>> Thanks, >>>> John >>>> >>> >>> >>> -- >>> Wes Barnett | jbarn...@tulane.edu >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- ================================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ================================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
