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

[Mark Abraham]

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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