Re: [AMBER] Error installing amber macOS M1

From: Rodrigo da Silva Bitzer <>
Date: Thu, 30 Sep 2021 17:16:56 +0000

Dear David,

Thank you for your reply.

patch is installed on /opt/homebrew/bin. I am using homebrew.
About my hardware, it has chip apple M1 and 16 GB RAM.

Rodrigo S. Bitzer
Professor Adjunto A (Assistant Professor)
Molecular Modeling, Computational Catalysis and Supramolecular Chemistry
Departamento de Físico-Química, Instituto de Química
Universidade Federal do Rio de Janeiro, Brazil;
From: David A Case <>
Sent: Tuesday, September 28, 2021 10:40 PM
To: <>
Subject: Re: [AMBER] Error installing amber macOS M1
On Tue, Sep 28, 2021, Rodrigo da Silva Bitzer wrote:
>I have tried your proposed procedure and it did not work, giving a strange
>error message:
>% pwd
>% patch -p0 < update.1
>patch: **** out of memory
Aha!  My guess is this: the update_amber script internally calls patch.
It did not know what to do with the out-of-memory error, and ended up
saying it thought it had a previously-installed patch file.  But the upshot
is that it did not apply the patch, and hence the sebomd_module.F90 file
was never updated.  This later leads to a compilation error.
It's not clear whether any of the updates were ever really applied, since
it seems one cannot trust the messages that update_amber is giving you.
For everyone: have people successfully installed AmberTools21 on a M1 OSX
machine?  (I don't have one myself, but I thought others had been
successful.)  Have there been any update- or patch-related issues?
For Rodrigo: what is the output of typing "which patch"?  Is it possible
that you are not accessing /usr/bin/patch?  Also, what is your hardware?
Are you using homebrew or macports or similar packages?  Is there anything
that might be unusal about your installation that you can think of?
Thanks for your patience, and for running the tests.   I'm cc-ing to Jason,
in case he has any thoughts here -- Jason: the original behavior is
described below.
>On Tue, Sep 28, 2021, Rodrigo da Silva Bitzer wrote:
>>After paying careful attention to the update process, I have observed
>>that update.1 has constantly failed. Please take a look the message
>>$ ./update_amber --update
>>Preparing to apply updates... please wait.
>>Downloading updates for AmberTools 21
>>Downloading AmberTools 21/update.1 (4.51 KB)
>>Applying AmberTools 21/update.1
>>/Users/rodrigobitzer/Documents/RESEARCH/MD/amber/amber20_src/updateutils/ PatchingWarning: Previously applied patch detected. Skipping.
>>  PatchingWarning)
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Received on Thu Sep 30 2021 - 10:30:02 PDT
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