> Date: Sun, 25 Aug 2013 14:31:51 -0700 (PDT)
> From: Nimmy McNimmerson <nimzs...@yahoo.com>
> Subject: Re: [gmx-users] 'Command not found' after installation
> To: Discussion list for GROMACS users <gmx-users@gromacs.org>
> Message-ID:
> <1377466311.57911.yahoomail...@web122305.mail.ne1.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
>
> 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 got it working, but with gcc, only.
I would try the following:
1.) Find libiomp5.dylib
find / -iname libiomp5.dylib
2.) Update dyld search path by adding the directory from step 1
export DYLD_LIBRARY_PATH="${DYLD_LIBRARY_PATH}:/path/to/libiomp5"
to your .bashrc or GMXRC.bash
Christoph
>
>
> ________________________________
> 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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--
Christoph Junghans
Web: http://www.compphys.de
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