Hi,
On Fri, Jan 27, 2023 at 04:05:25PM +0100, Freddy Bernal via AMBER wrote:
> I have tried to install Amber22 without success. We recently acquired
> the license, so it is the first time I tried the
> installation process. However, I have experience working in Ubuntu
> (using other software packages for molecular modeling). Anyhow,
> here the details:
>
> OS: Ubuntu 20.04.5 LTS
>
> Failure by miniconda environment installation (as can be seen below,
> some commands are not found in the sh script). It happened in
> two different workstations (with the same OS). Both machines work fine
> with many different applications.
>
> Could you please help me? I have followed all the instructions in
> https://ambermd.org/InstUbuntu.php before extracting from the
> tar.bz2 files and running ./run_cmake (as also indicated in the manual).
>
> As an additional option, I created a conda environment for amber and
> tried again the run_cmake disabling the -DDOWNLOAD_MINICONDA
> flag in the script, but it also led to an error.
>
>
> Output run_cmake:
>
> --
> **************************************************************************
> -- Starting configuration of Amber version 22.0.0...
> -- CMake Version: 3.25.2
> -- For how to use this build system, please read this wiki:
> -- http://ambermd.org/pmwiki/pmwiki.php/Main/CMake
> -- For a list of important CMake variables, check here:
> -- http://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Common-Options
> --
> **************************************************************************
> -- Setting C compiler to gcc
> -- Setting CXX compiler to g++
> -- Setting Fortran compiler to gfortran
> -- Amber source found, building AmberTools and Amber
> -- The C compiler identification is GNU 9.4.0
> -- The CXX compiler identification is GNU 9.4.0
> -- The Fortran compiler identification is GNU 9.4.0
> -- Detecting C compiler ABI info
> -- Detecting C compiler ABI info - done
> -- Check for working C compiler: /usr/bin/gcc - skipped
> -- Detecting C compile features
> -- Detecting C compile features - done
> -- Detecting CXX compiler ABI info
> -- Detecting CXX compiler ABI info - done
> -- Check for working CXX compiler: /usr/bin/g++ - skipped
> -- Detecting CXX compile features
> -- Detecting CXX compile features - done
> -- Detecting Fortran compiler ABI info
> -- Detecting Fortran compiler ABI info - done
> -- Check for working Fortran compiler: /usr/bin/gfortran - skipped
> -- Testing if stdlib.h can be included...
> -- Testing if stdlib.h can be included... yes
> -- Performing Test CMAKE_HAVE_LIBC_PTHREAD
> -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
> -- Looking for pthread_create in pthreads
> -- Looking for pthread_create in pthreads - not found
> -- Looking for pthread_create in pthread
> -- Looking for pthread_create in pthread - found
> -- Found Threads: TRUE
> -- Found CUDA: /usr/local/cuda (found version "11.2")
> -- Downloading Python 3 Miniconda
> -- Detected Linux OS. Downloading the Linux installer
> -- Using 64 bit miniconda
> Downloading
> http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh ->
> --2023-01-27 15:40:08--
> http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
> Resolving repo.continuum.io (repo.continuum.io)... 104.18.201.79,
> 104.18.200.79, 2606:4700::6812:c94f, ...
> Connecting to repo.continuum.io (repo.continuum.io)|104.18.201.79|:80...
> connected.
> HTTP request sent, awaiting response... 301 Moved Permanently
> Location:
> https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
> [following]
> --2023-01-27 15:40:08--
> https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
> Resolving repo.anaconda.com (repo.anaconda.com)... 104.16.130.3,
> 104.16.131.3, 2606:4700::6810:8303, ...
> Connecting to repo.anaconda.com (repo.anaconda.com)|104.16.130.3|:443...
> connected.
> HTTP request sent, awaiting response... 200 OK
> Length: 72402405 (69M) [application/x-sh]
> Saving to:
>
...
> 70700K ..... 100% 32,8M=4,3s
>
> 2023-01-27 15:40:12 (16,2 MB/s) -
> saved
> [72402405/72402405]
>
> Installing Miniconda Python.
> PREFIX=/home/tga_user/AmberInstallation/amber22_src/build/CMakeFiles/miniconda/install
> Unpacking payload ...
...
> Installing base environment...
>
>
> Downloading and Extracting Packages
>
>
> Downloading and Extracting Packages
>
> Preparing transaction: ...working... done
> Executing transaction: ...working... done
>
> Installing * environment...
>
> /home/tga_user/AmberInstallation/amber22_src/build/CMakeFiles
/miniconda/download/Miniconda3-latest-Linux-x86_64.sh:
> 438: [[: not
> found
This was fixed by ambertools update.4
Verify that you have applied that update:
cd amber22_src/
./update_amber --show-applied-patches
If it isn't applied then apply it; see the manual if necessary.
It it is applied then start debugging; maybe your system bash isn't
really bash, but that would be astronomically unlikely.
scott
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Received on Fri Jan 27 2023 - 19:00:03 PST
