https://github.com/haozeke/quip-nix

https://github.com/haozeke/quip-nix

Last synced: 22 days ago
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• Host: GitHub
• URL: https://github.com/haozeke/quip-nix
• Owner: HaoZeke
• License: wtfpl
• Created: 2020-08-15T22:43:03.000Z (about 4 years ago)
• Default Branch: master
• Last Pushed: 2024-07-18T18:00:30.000Z (4 months ago)
• Last Synced: 2024-07-19T00:40:56.073Z (4 months ago)
• Language: Jupyter Notebook
• Homepage:
• Size: 335 KB
• Stars: 0
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: readme.org
  • License: LICENSE

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README

        
* About

Some derivations to use QUIP on my cluster. Note that because of the psuedo-proprietary nature of GAP and some other aspects of this workflow, the sources cannot be provided here.

** Sources

- GAP (Gaussian Approximation Potentials) from [[http://www.libatoms.org/gap/gap_download.html][here]] or now; [[https://github.com/libAtoms/GAP][from Git]]

    - My own setup used a branch which included support for the TurboSOAP descriptor

- TurboSOAP sources

  - Some explanation of this might be [[https://turbogap.fi/wiki/index.php/Quick_start][found here]]

- [[https://github.com/libAtoms/QUIP][QUIP]] itself

- Fortran XML parser ([[https://github.com/libAtoms/fox][FoX]])

  - This comes with QUIP, as a submodule

I can and will however, provide the directory listing:

#+BEGIN_SRC bash :results raw

tree QUIP -d -L 2

#+END_SRC

#+begin_src bash

QUIP

├── arch

├── bin

│   └── __pycache__

├── build

│   └── linux_x86_64_gfortran

├── doc

│   ├── _static

│   ├── _templates

│   └── Tutorials

├── quippy

│   ├── __pycache__

│   └── quippy

├── share

│   ├── Parameters

│   └── Structures

├── src

│   ├── f90wrap

│   ├── FilePot_drivers

│   ├── fox

│   ├── GAP

│   ├── libAtoms

│   ├── Potentials

│   ├── Programs

│   ├── Structure_processors

│   ├── turbogap

│   └── Utils

├── tests

│   ├── do_not_run

│   └── rules

└── travis

30 directories

#+end_src bash

- Note the additions to the ~src~ folder

- Also, the TurboSOAP sources are ABSOLUTE PATHS for some reason

** Nix Shell

With the derivation in place, we can build and enter the environment.

#+BEGIN_SRC bash

nix-shell -v --run "zsh"

#+END_SRC

Use the following command to find out what to put in  ~MATH_LINKOPTS=~.

#+BEGIN_SRC bash

pkg-config --libs blas

pkg-config --libs lapack

#+END_SRC

With the current ~openblas~ setup, these will both be the same.

** Patches

We need to apply the ~patches~ in ~files~:

#+begin_src bash

patch -ruN -d QUIP/quippy < files/quippyF90wrap.patch

#+end_src

** QUIP-GAP

Now we can finally set this up.

#+BEGIN_SRC bash

nix-shell --run "zsh"

mkdir -p out/{bin,structs}

cd QUIP

mkdir -p build/$QUIP_ARCH

cp ../files/$QUIP_ARCH-Makefile.inc build/$QUIP_ARCH/Makefile.inc

make

make install

make install-quippy

make libquip

#+END_SRC

** Nix Shell

To get the integrated build just run:

#+BEGIN_SRC bash

nix-shell --run "zsh"

#+END_SRC

For permission errors use another terminal to run:

#+BEGIN_SRC bash

watch sudo chmod 777 /nix/store/2cg51vw7iws7ayawzwwr7rfv2ix5yws3-python3-3.8.5-env/lib/python3.8/site-packages -R

#+END_SRC

*The shell is required for* ~quippy~.

** Nix Build

After setting up the shell environment, we can build and install the binary.

#+BEGIN_SRC bash

nix-build -v

# Test it

nix-env -i ./result

#+END_SRC

** Conda Build

*** Obtain Sources

We will start by getting QUIP and TurboGAP.

#+begin_src bash

git clone --recursive https://github.com/libAtoms/QUIP.git QUIP

cd QUIP/src

git clone --recursive https://github.com/mcaroba/turbogap.git

mkdir ThirdParty

# In QUIP/src

cp -r ../../scme ThirdParty/

#+end_src

Now we have both of these ready to be made.

*** Environment Initialization

For this we use either ~conda~ or ~micromamba~.

#+begin_src bash

# from the root directory

conda env create -f environment.yml

conda activate quip-conda

# or

micromamba create -f environment.yml

micromamba activate quip-conda

#+end_src

Also we need to initialize some variables.

#+begin_src bash

source ./setEnvVars.sh

#+end_src

These essentially determine the different exported paths.

*** Building

We will assume any further explanation that:

- Compilers are present

- OpenBlas is present

On an HPC, this can be something like:

#+begin_src bash

ml avail openblas

ml avail gcc

ml load GCC/11.2.0

ml load OpenBLAS/0.3.18-GCC-11.2.0

#+end_src

Finally we need to build all the things.

#+begin_src bash

cd QUIP

mkdir -p build/$QUIP_ARCH

mkdir -p "$QUIP_STRUCTS_DIR"

cp ../files/$QUIP_ARCH-Makefile.inc build/$QUIP_ARCH/Makefile.inc

make

make libquip

make install

make install-quippy

#+end_src

* License

[[http://www.wtfpl.net/about/][WTFPL]]