Re: [AMBER] Error building Amber

From: Gustaf Olsson <gustaf.olsson.lnu.se>
Date: Tue, 28 Jul 2020 09:14:47 +0000

Hello Walton


I don't know what version of Xcode you are using though the 'ld: unknown option: --no-as-needed' seems to resemble a problem that has previously occurred.


Ignoring this, from you logs I see that you are using gcc-8.2.0, if you check some previous posts I've made it seems that trying to compile amber under macOS using the gnu gcc compilers higher then version 7 will not work.


Switching is not completely straightforward using homebrew as it will always opt for the most resent version of gcc.


I have not yet double-checked though from what I remember, do a:


    $ brew install gcc.7


and then


    $ CC=/usr/bin/clang && CXX=/usr/bin/clang++ && FC=/usr/local/bin/gfortran-7


followed by a


    $ ./run_cmake MANUAL


I would do this in a clean extracted build directory as I have seem complaints from cmake regarding residual files before.


This should get you a serial version installed. Please let me know if this worked, otherwise I'll have to consult my notes later today. I have tried to get a working openMPI compilation as well though so far I have struck out completely.


Best regards

// Gustaf

________________________________
Frn: Walton Smith <smit7450.mylaurier.ca>
Skickat: den 27 juli 2020 21:50:54
Till: AMBER Mailing List
mne: Re: [AMBER] Error building Amber

Hey Dac,

Im using Catalina (10.15.5), and I do have homebrew from when I installed the open source PyMOL. In my /usr/local/lib folder I have cmake, docker, python3.7 and python 3.8 along with an unknown pkgconfig folder and several lib.dylib and .a files. I have attached the cmake.log file. Let me know if you might have any idea. Thank you so much for getting back to me so fast.


WS

> On Jul 27, 2020, at 1:48 PM, David A Case <david.case.rutgers.edu> wrote:
>
> On Mon, Jul 27, 2020, Walton Smith wrote:
>>
>>
>> Im having trouble with building AMBER. After I ./run_cmake in terminal,
>> the configuration never runs to completion. Here is the error log and
>> output log associated with my difficulties. Please let me know what I can
>> do to fix this issue, I would greatly appreciate it. Just to let you know,
>> Im not very familiar with terminal so this is all pretty new to me.
>
> It's best to post the "cmake.log" file that is created by run_cmake.
>
> Also, let us know about your operating system and configuration. It
> looks like you are using OSX, but which version? and is there anything
> odd about your setup (is homebrew or something like that installed)?
> What do you have (if anything) in your /usr/local/lib folder?
>
> ...thanks....dac
>
>
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

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Received on Tue Jul 28 2020 - 02:30:03 PDT
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