Browndye

Browndye runs on several operating systems regardless of the machine type. The main ones are: Linux, BSD, MacOS, and MS Windows. There are also Docker and Singularity container images available for running Browndye in Docker and on HPC/XSEDE computational clusters.

Browndye2 should be considered a beta release since there may still be "surprises" lurking.

Please subscribe to the Browndye mailing list to receive updates about the software and ask for help.

Source code

The preferred way to install Browndye is to download the source code and a compile it. Browndye requires Ocaml and C++ compilers. Please note that the C++17 version of C++ is now required.

You can download the latest Browndye2 release from here.
List of Fixes and Updates.

You can then proceed to compile it:

tar xvfz browndye2.tar.gz
cd browndye2
make -j 4 all

More information is available in the README file.

The development version of Browndye can be accessed on bitbucket.

Note: The following are package dependencies necessary for compilation of Browndye on different Linux distributions.

Ubuntu (20.04 and 22.04)

apt-get install make gcc g++ ocaml libexpat-dev liblapack-dev apbs

CentOS 7

The GCC/G++ compilers in CentOS 7 are too old for Browndye to compile so it is necessary to install SCL and devtoolset-9 to update the compilers. The SCL needs to be enabled before compilation.

yum install centos-release-scl epel-release
yum install devtoolset-9 ocaml expat-devel lapack-devel apbs
scl enable devtoolset-9 bash

CentOS/RockyLinux/AlmaLinux 8

dnf group install "Development Tools"
dnf install ocaml expat-devel lapack-devel

Linux

We also provide pre-compiled binary packages for Redhat/CentOS and Ubuntu distributions. This package can be installed either in user directories or in a central location (like /opt). After unpacking make sure you add installation_location/browndye2/bin to your $PATH. For example if installing in /opt add the path like this: export PATH=/opt/browndye2/bin:${PATH}.

Ubuntu 20.04

Precompiled binary for Ubuntu 20.04 (2023-12-30): browndye2-ubuntu-20.04.tar.gz
(MD5 checksum: 2a6efb815ef58cc10f925b17d6de039a)

Make sure you have the following dependencies installed:

apt-get install libexpat1 make apbs liblapack-dev

Ubuntu 22.04

Precompiled binary for Ubuntu 22.04 (2023-12-30): browndye2-ubuntu-22.04.tar.gz
(MD5 checksum: ead274864b3af0e2a978a1121694e11b)

Make sure you have the following dependencies installed:

apt-get install libexpat1 make apbs liblapack-dev

CentOS 7

Precompiled binary for CentOS 7 (2023-12-30): browndye2-centos-7.tar.gz
(MD5 checksum: e539a5aa85a29cb20cb6aa3ed7ccacb2)

Make sure you have the following dependencies installed:

yum install epel-release
yum install make lapack apbs

RockyLinux/AlmaLinux 8

Precompiled binary for RockyLinux/AlmaLinux 8 (2023-12-30): browndye2-almalinux-8.tar.gz
(MD5 checksum: 4ff8fb84dae297c136bf3162b8c0f59c)

Make sure you have the following dependencies installed:

dnf install make lapack

Windows

The simplest way to install Browndye2 on Windows 10 is to install the Windows Subsystem for Linux (WSL) and Ubuntu 20.04 image. Then download the precompiled Ubuntu 20.04 Browndye binaries available above and unpack them in your directory.

Another option is to install the Cygwin environment and compiled Browndye by yourself.

Docker container

A pre-built Docker container is available on docker.io. See README for more information on how to use it.

Singularity container

A pre-built Singularity container is available on the Singularity Hub and can be easily deployed on XSEDE HPC resources. See README for more information on how to use it.