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
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
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University of Maryland, Baltimore
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