[gmx-users] 'Command not found' after installation

[Nimmy McNimmerson]

That worked! Thanks a ton!


________________________________
 From: Justin Lemkul <jalemkul at vt.edu>
To: Nimmy McNimmerson <nimzster at yahoo.com>; Discussion list for GROMACS users <gmx-users at 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.abraham at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at 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 <nimzster at 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." <jbarnet4 at tulane.edu>
>> To:  <nimzster at 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.
>>
>> jbarnet4 at tulane.edu | from mobile
>>
>> <nimzster at 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." <jbarnet4 at tulane.edu>
>>> To: Nimmy McNimmerson <nimzster at yahoo.com>; Discussion list for GROMACS users <gmx-users at 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 | jbarnet4 at tulane.edu
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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