Re: [AMBER] "Problem installing Miniconda"

From: Seibold, Steve Allan <>
Date: Thu, 18 Apr 2019 18:44:39 +0000

Hi Guys
Hard to admit, but I found the dumb mistake I was making...When I updated before installation by doing the following:

"./update_amber --upgrade",

 I was typing in "--update" INSTEAD of "upgrade"!!. Once I found this mistake and continued, it compiled fine and is running now..
I am guessing that the update includes the incorporation of installing miniconda..?


-----Original Message-----
From: David A Case <>
Sent: Thursday, April 18, 2019 12:55 PM
To: AMBER Mailing List <>
Subject: Re: [AMBER] "Problem installing Miniconda"

On Thu, Apr 18, 2019, Hai Nguyen wrote:
>You can use it with --with-python
>./configure --with-python /path/to/your/python gnu
>Otherwise, you can try to edit AmberTools/src/configure_python by
>deleting "nomkl" (which will make configure_python install very large
>block of "mkl")

I'll admit I'm lost here. Amber doesn't require either mkl or blas or
openblas. Is conda somehow trying to import openblas if -nomkl is set?
If so, we're not making any use of it.

It would be good to do a careful audit of our configure_python script:
I'm getting occasional failures there, which are generally very difficult to debug. I'd prefer to have a minimal and stable installation, even if some users have to do a "conda install xxxx"

Certainly, it would nice if configure didn't exit when conda can't find openblas, given that we are not making use of openblas anyway....


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Received on Thu Apr 18 2019 - 12:00:02 PDT
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