Installing AWS Palace on Ubuntu and Mac

In terminal, run:

sudo apt update
sudo apt install file bzip2 ca-certificates g++ gcc gfortran git gzip lsb-release patch python3 tar unzip xz-utils zstd
sudo apt install libxft-dev libglu1-mesa libxi-dev libxmu-dev libglu1-mesa-dev build-essential

Make a new directory where we clone all repositories:

cd ~
mkdir repo
cd repo

Now clone the spack source and enter its environment here:

git clone --depth=2 https://github.com/spack/spack.git
. spack/share/spack/setup-env.sh

Update spack compilers:

spack compiler find

Ensure that it says gcc is at least above version 11.

Clone palace and install using spack:

git clone https://github.com/awslabs/palace.git

From here, we go through the Palace installation process for Ubuntu and Mac separately, before covering the installation of Paraview and Pyvista.

Ubuntu

Now the idea is that we create a local virtual environment in spack called spack-env, add local palace install as a repo in it and concretize+install. Note that you can skip the creation and activation of the environment, but you may run into issues due to dependecies if you have used spack previously. This is done via:

source ./spack/share/spack/setup-env.sh
spack repo add ./palace/spack_repo/local
spack env create spack-env
spack env activate spack-env
spack add local.palace@develop

Now concretize+install via:

spack concretize -f
spack install --only-concrete
find -name palace*

The second command will find the path of the Palace binary. Basically it’s somewhere like (remember to add the ~/ for the full absolute path):

./spack/opt/spack/linux-ubuntu24.04-zen2/gcc-13.3.0/palace-develop-36rxmgzatchgymg5tcbfz3qrmkf4jnmj/bin/palace

Executing the above block should show the command-line switches required for Palace.

Mac

Note that the exact process for Mac installation changes depending on your chip and operating system. The method documented here has been tested on a M5 MacBook with Tahoe 26.1 installed.

To install Palace, ope the terminal from the directory containing /spack, run:

source ./spack/share/spack/setup-env.sh
spack install veclibfort
spack install palace +mumps +slepc ^blas=veclibfort ^lapack=veclibfort

The first line activates spack in your shell. The second line installs a wrapper for the builtin MacOS Accelerator (which can replace BLAS and LAPACK). The third line initiates a full Palace installation that is suitable for arm64 MacBooks.

After the installation is complete (roughly 30 mins) the Palace binary can be found in spack/opt/spack/darwin-m1/palace-0.14.0-aijcrhkhxpjki7lbvx336dbzvwh52enp/bin/palace.

OLD NOTES LEFT IN CASE OF ISSUES - TO BE REMOVED IN FUTURE

This method has been tested to work on Kubuntu. Ensure GIT has been installed via:

`bash sudo apt-get install git `

Now install the Spack Package Manager by running in console (in some directory of preference - e.g. somewhere in the home directory):

cd ~/
git clone -c feature.manyFiles=true --depth=2 https://github.com/spack/spack.git
cd ~/spack
. share/spack/setup-env.sh

On MacOS, you will have to install and setup Sundials before installing Palace. This is done by running:

spack install sundials
export SUNDIALS_DIR=$(spack location -i sundials)

Now run (@develop tag is required to get the latest version, i.e, 0.13 or newer):

spack install palace@develop
find -name palace*

The second command will find the path of the Palace binary. Basically it’s somewhere like (remember to add the ~/ for the full absolute path):

./spack/opt/spack/linux-ubuntu24.04-zen2/gcc-13.3.0/palace-develop-36rxmgzatchgymg5tcbfz3qrmkf4jnmj/bin/palace

Executing the above block should show the command-line switches required for Palace.

Optionally, install Paraview:

sudo apt install paraview

If this fails (e.g. some dependency clash), use its flatpak:

sudo apt install flatpak
flatpak remote-add --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo
sudo flatpak install flathub org.paraview.ParaView

Finally, in the Python virtual environment, if it has not been already installed, run:

pip install pyvista

This is required to open the simulation field data via the API functions.

Troubleshooting

Errors can appear after updating the Linux system. Simply reinstall palace as above (starting from the setup-env.sh command). However, first run:

sudo rm -r .spack/

Alternatively, edit the compilers.yaml file to the latest GCC version.

If OpenMPI processes fail to spawn (i.e. Palace does not start and/or throws the error local rank failed   --> Returned value Not found (-13) instead of ORTE_SUCCESS), try running the following command in terminal <https://askubuntu.com/questions/730/how-do-i-set-environment-variables>`__:

export PMIX_MCA_gds=hash

In the case of a Jupyter Notebook (i.e. running the commands in SQDMetal), add this to the initialisation cell:

import os
os.environ["PMIX_MCA_gds"]="hash"

If it throws an error for libCEED (see here for details) or an error like SUNDIALS: Core: *** NOT FOUND ***, first open the file:

nano ~/spack/var/spack/repos/builtin/packages/palace/package.py

Edit the line which says depends_on(“libxsmm@main”) to depends_on(“libxsmm@=main”) (note the = sign). Then add depends_on(“sundials”) after the line depends_on(“eigen”). Now proceed with the installation by running the palace installation command once more.

Upgrading

Delete all traces of spack via:

sudo rm -r .spack/
sudo rm -r spack/

Then start from the beginning to reinstall to the latest version of spack and subsequently the latest version of palace.

Installing Palace v0.13 As of 18 Feb, 2024, Palace v0.13 is not available by default to install in spack. To install Palace v0.13.0, you need to edit the spack palace installation information contained in package.py:

spack edit palace

Add the following line (where the Palace versions are listed) to add v0.13.0 to available installs:

version("0.13.0", tag="v0.13.0", commit="a61c8cbe0cacf496cde3c62e93085fae0d6299ac")

Save the package.py file for the Palace install, and then run

spack install palace@0.13