Re: [AMBER] Amber20 installation, Amber.pip file broken

From: David A Case <>
Date: Mon, 13 Sep 2021 15:32:25 -0400

On Mon, Sep 13, 2021, Oscar Conchillo-Solé wrote:

>./update_amber --update
>Preparing to apply updates... please wait.
>No new updates available for AmberTools 21
>No new updates available for Amber 20
>as you can see my versions of Amber and AmberTools are totally up to date.

As a sanity check, please try "update_amber --show-applied-patches". If you
have update.7, then that update must not be catching all of the problems.

>I have also checked my $PYTHONPATH after "sourcing"
>it is apparently well defined.
>To avoid possible conflicts I have installed python39 (I made sure
>that python39-devel was installed) and then set up alternatives for
>both python and python3
>alternatives --config python
>alternatives --config python3
>I have repeated the whole process
>cmake ../amber20_src
>make install
>and the same first error reapeared:
>-- Fixing Miniconda script shebangs
>CMake Error at /sharelab/labapps/AMBER/SRC/Amber20/amber20_src/cmake/FixCondaShebang/FixCondaShebang.cmake:26
>  file failed to open for reading (No such file or directory):
>    /sharelab/labapps/AMBER/CentOS-8/Amber20//bin/amber.pip

Just a reminder: you can totally ignore this error. It is the very last
step of the installation, and there is no need to even create an "amber.pip"
executable any way, as far as I can see.

>So I created a new Build dir
>and executed:
>cmake ../amber20_src
>make install
>this time make install completed without error
>but amber.pip was not created

This sounds good: amber.pip is not needed, and it's not supposed to report
any errors.

>I find it quite strange that make install fails the first time and not
>the second since I changed nothing just the install dir.

I have nothing to add.

>but the make test.serial fail like always
>here I'm pasting the complete "cd sanderlesapi && make test"

If you don't need the python API to sander.LES (and few people do), you
can just comment out those lines in the test (labeled "#API tests") in
the $AMBERHOME/test/Makefile. I'm not sure how to easily debug this


AMBER mailing list
Received on Mon Sep 13 2021 - 13:00:02 PDT
Custom Search