Installation of DARA

Installation of DARA#

Installation from source (GitHub)#

This approach is recommended if you want to use the latest features and bug fixes. It is a good idea to install Dara in a dedicated virtual environment to avoid conflicts with other Python packages.

git clone https://github.com/idocx/dara
cd dara
pip install -e .

Special case: installation on older cluster (e.g., Lawrencium, LBNL)#

BGMN (the refinement backend) is a compiled program, and it may not be directly usable on some machines, such as computational clusters (e.g., Lawrencium at Lawrence Berkeley National Laboratory).

For example, you may see an error GLIBC versions when you run bgmn:

version `GLIBC_2.29 not found (required by …)

To fix this issue specifically, we need to install GLIBC 2.29. First, make sure to run:

module load gcc

Now follow the directions below. These are based on this post: https://stackoverflow.com/questions/50564999/lib64-libc-so-6-version-glibc-2-14-not-found-why-am-i-getting-this-error

mkdir ~/glibc229
cd ~/glibc229
wget http://ftp.gnu.org/gnu/glibc/glibc-2.29.tar.gz
tar zxvf glibc-2.29.tar.gz
cd glibc-2.29
mkdir build
cd build
../configure --prefix=$HOME/.local
make -j4
make install

Unfortunately, you can’t set LD_LIBRARY_PATH without breaking everything. Instead, we take this approach:

Installation of Patchelf#

Git clone and follow setup instructions here: NixOS/patchelf

The command below will edit every binary. First, make sure Dara is installed in a folder located as $HOME/dara/. Then run:

patchelf --set-interpreter $HOME/.local/lib/ld-linux-x86-64.so.2 --set-rpath $HOME/.local/lib/ $HOME/dara/dara/src/dara/bgmn/BGMNwin/bgmn && patchelf --set-interpreter $HOME/.local/lib/ld-linux-x86-64.so.2 --set-rpath $HOME/.local/lib/ $HOME/dara/dara/src/dara/bgmn/BGMNwin/eflech && patchelf --set-interpreter $HOME/.local/lib/ld-linux-x86-64.so.2 --set-rpath $HOME/.local/lib/ $HOME/dara/dara/src/dara/bgmn/BGMNwin/geomet && patchelf --set-interpreter $HOME/.local/lib/ld-linux-x86-64.so.2 --set-rpath $HOME/.local/lib/ $HOME/dara/dara/src/dara/bgmn/BGMNwin/gertest && patchelf --set-interpreter $HOME/.local/lib/ld-linux-x86-64.so.2 --set-rpath $HOME/.local/lib/ $HOME/dara/dara/src/dara/bgmn/BGMNwin/index && patchelf --set-interpreter $HOME/.local/lib/ld-linux-x86-64.so.2 --set-rpath $HOME/.local/lib/ $HOME/dara/dara/src/dara/bgmn/BGMNwin/lamtest && patchelf --set-interpreter $HOME/.local/lib/ld-linux-x86-64.so.2 --set-rpath $HOME/.local/lib/ $HOME/dara/dara/src/dara/bgmn/BGMNwin/makegeq && patchelf --set-interpreter $HOME/.local/lib/ld-linux-x86-64.so.2 --set-rpath $HOME/.local/lib/ $HOME/dara/dara/src/dara/bgmn/BGMNwin/output && patchelf --set-interpreter $HOME/.local/lib/ld-linux-x86-64.so.2 --set-rpath $HOME/.local/lib/ $HOME/dara/dara/src/dara/bgmn/BGMNwin/plot1 && patchelf --set-interpreter $HOME/.local/lib/ld-linux-x86-64.so.2 --set-rpath $HOME/.local/lib/ $HOME/dara/dara/src/dara/bgmn/BGMNwin/spacegrp && patchelf --set-interpreter $HOME/.local/lib/ld-linux-x86-64.so.2 --set-rpath $HOME/.local/lib/ $HOME/dara/dara/src/dara/bgmn/BGMNwin/teil && patchelf --set-interpreter $HOME/.local/lib/ld-linux-x86-64.so.2 --set-rpath $HOME/.local/lib/ $HOME/dara/dara/src/dara/bgmn/BGMNwin/verzerr

You may need to edit this command to work with your specific installation.

Note

If the earlier GLIBC installation failed, and it looks like it’s related to the version of make/gmake:

checking version of gmake... 3.82, bad

Then you must install newer version and symbolic link:

curl -O http://ftp.gnu.org/gnu/make/make-4.2.1.tar.gz
tar xvf make-4.2.1.tar.gz
cd make-4.2.1
./configure --prefix=$HOME/.local/bin && make && make install
export PATH=/$HOME/.local/bin:$PATH
ln -s $HOME/.local/bin/make $HOME/.local/bin/gmake

Now try again to install GLIBC….