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Commit 52ccd986 authored by Adam Fekete's avatar Adam Fekete
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update quip + cleanup

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1 merge request!121Draft: Resolve "Refactoring the infrastructure"
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.gitmodules
+ 18
− 30
View file @ 52ccd986
[submodule "3rdparty/atomic-features-package"]
path = 3rdparty/atomic-features-package
url = https://gitlab.mpcdf.mpg.de/nomad-lab/atomic-features-package.git
[submodule "3rdparty/cmlkit"]
path = 3rdparty/cmlkit
url = https://gitlab.mpcdf.mpg.de/nomad-lab/cmlkit.git
[submodule "3rdparty/keras-vis"]
path = 3rdparty/keras-vis
url = https://github.com/raghakot/keras-vis.git
[submodule "3rdparty/qmmlpack"]
path = 3rdparty/qmmlpack
url = https://gitlab.com/qmml/qmmlpack.git
[submodule "3rdparty/quip"]
path = 3rdparty/quip
url = git@github.com:libAtoms/QUIP.git
[submodule "3rdparty/sissopp"]
path = 3rdparty/sissopp
url = https://gitlab.com/sissopp_developers/sissopp.git
[submodule "tutorials/analytics-compressed-sensing"]
path = tutorials/analytics-compressed-sensing
url = https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-compressed-sensing.git
......@@ -22,9 +40,6 @@
[submodule "tutorials/analytics-cmlkit"]
path = tutorials/analytics-cmlkit
url = https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-cmlkit.git
[submodule "3rdparty/qmmlpack"]
path = 3rdparty/qmmlpack
url = https://gitlab.com/qmml/qmmlpack.git
[submodule "tutorials/analytics-descriptor-role"]
path = tutorials/analytics-descriptor-role
url = https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-descriptor-role.git
......@@ -52,27 +67,12 @@
[submodule "tutorials/analytics-domain-of-applicability"]
path = tutorials/analytics-domain-of-applicability
url = https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-domain-of-applicability.git
[submodule "tutorials/analytics-query-nomad-archive"]
path = tutorials/analytics-query-nomad-archive
url = https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-query-nomad-archive.git
[submodule "tutorials/analytics-cmlkit"]
path = tutorials/analytics-cmlkit
url = https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-cmlkit.git
[submodule "3rdparty/qmmlpack"]
path = 3rdparty/qmmlpack
url = https://gitlab.com/qmml/qmmlpack.git
[submodule "tutorials/analytics-tetradymite-PRM2020"]
path = tutorials/analytics-tetradymite-PRM2020
url = https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-tetradymite-PRM2020.ipynb.git
[submodule "tutorials/analytics-clustering-tutorial"]
path = tutorials/analytics-clustering-tutorial
url = https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-clustering-tutorial.git
[submodule "3rdparty/atomic-features-package"]
path = 3rdparty/atomic-features-package
url = https://gitlab.mpcdf.mpg.de/nomad-lab/atomic-features-package.git
[submodule "3rdparty/keras-vis"]
path = 3rdparty/keras-vis
url = https://github.com/raghakot/keras-vis.git
[submodule "tutorials/analytics-arise"]
path = tutorials/analytics-arise
url = https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-arise.git
......@@ -82,9 +82,6 @@
[submodule "tutorials/analytics-atomic-features"]
path = tutorials/analytics-atomic-features
url = https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-atomic-features.git
[submodule "3rdparty/atomic-features-package"]
path = 3rdparty/atomic-features-package
url = https://gitlab.mpcdf.mpg.de/nomad-lab/atomic-features-package.git
[submodule "tutorials/analytics-sgd-alloys-oxygen-reduction-evolution"]
path = tutorials/analytics-sgd-alloys-oxygen-reduction-evolution
url = https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-sgd-alloys-oxygen-reduction-evolution.git
......@@ -106,18 +103,9 @@
[submodule "tutorials/analytics-dos-similarity-search"]
path = tutorials/analytics-dos-similarity-search
url = https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-dos-similarity-search.git
[submodule "3rdparty/cmlkit"]
path = 3rdparty/cmlkit
url = https://gitlab.mpcdf.mpg.de/nomad-lab/cmlkit.git
[submodule "tutorials/analytics-dimensionality-reduction"]
path = tutorials/analytics-dimensionality-reduction
url = https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-dimensionality-reduction.git
[submodule "tutorials/analytics-kappa-screening-sisso"]
path = tutorials/analytics-kappa-screening-sisso
url = https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-kappa-screening-sisso.git
[submodule "3rdparty/quip"]
path = 3rdparty/quip
url = git@github.com:libAtoms/QUIP.git
[submodule "3rdparty/sissopp"]
path = 3rdparty/sissopp
url = https://gitlab.com/sissopp_developers/sissopp.git
quip @ c56a5b25
Compare 7c3fe3b8 to c56a5b25
Subproject commit 7c3fe3b8fc4bd65dc4f76d7935825b3808ca7462
Subproject commit c56a5b251978b361b6e3917b90a5675e60d84a62
Dockerfile.quip
+ 19
− 86
View file @ 52ccd986
ARG BUILDER_BASE_IMAGE=jupyter/tensorflow-notebook:2022-06-27
FROM $BUILDER_BASE_IMAGE
# info: https://github.com/libAtoms/QUIP/blob/public/docker/Dockerfile
# Read more: https://github.com/libAtoms/QUIP/
# ================================================================================
# Linux applications and libraries
......@@ -9,113 +9,46 @@ FROM $BUILDER_BASE_IMAGE
USER root
# # Build tools and deps for QUIP. Followed by some useful utilities
# RUN apt-get -y update \
# && apt-get upgrade -y \
# && apt-get install -y \
# gfortran \
# cmake \
# openmpi-bin \
# libopenmpi-dev \
# liblapack-dev \
# libblas-dev \
# libnetcdf-dev \
# netcdf-bin \
# # using libzmq3-dev instead of libzmq3, this one works
# libzmq3-dev \
# # Useful tools
# pandoc \
# curl \
# vim \
# emacs-nox \
# less \
# bsdmainutils \
# man-db \
# # AtomEye
# libxpm-dev \
# libgsl0-dev \
# xterm \
# # amber
# csh \
# flex \
# # gpaw
# libxc-dev \
# && apt-get clean \
# && rm -rf /var/lib/apt/lists/*
RUN apt-get update \
&& apt-get install --yes --quite --no-install-recommends \
gcc \
&& apt-get install --yes --quiet --no-install-recommends \
gfortran \
liblapack-dev \
libblas-dev \
libnetcdf-dev \
liblapack-dev \
openmpi-bin \
libopenmpi-dev \
netcdf-bin \
libxpm-dev \
libgsl-dev \
libnetcdf-dev \
libhdf5-serial-dev \
&& rm -rf /var/lib/apt/lists/*
# NOTE: libopenblas64-openmp-dev
# # Custom compilation of OpenBLAS with OpenMP enabled (linear algebra is limited to single core in debs)
# # NUM_THREADS must be set otherwise docker build non-parallel version.
# RUN git clone -b 'v0.3.9' --single-branch --depth 1 https://github.com/xianyi/OpenBLAS.git /tmp/OpenBLAS \
# && cd /tmp/OpenBLAS/ \
# && make NO_AFFINITY=1 USE_OPENMP=1 NUM_THREADS=32 > /dev/null \
# && make NO_AFFINITY=1 USE_OPENMP=1 NUM_THREADS=32 install > /dev/null \
# && rm -rf /tmp/OpenBLAS
#
# RUN ln -s /opt/OpenBLAS/lib/libopenblas.so /usr/local/lib/libopenblas.so
# RUN ln -s /opt/OpenBLAS/lib/libopenblas.a /usr/local/lib/libopenblas.a
# ================================================================================
# QUIP + GAP + quippy
# ================================================================================
# # All the QUIPs go here; added to path in the end.
# ENV QUIP_ROOT /opt/quip
# ENV QUIP_INSTALLDIR ${QUIP_ROOT}/bin
# ENV PATH ${QUIP_INSTALLDIR}:${PATH}
#
# WORKDIR /opt/quip
#
# RUN git clone --depth 1 --recursive https://github.com/libAtoms/QUIP.git .
# All the QUIPs go here; added to path in the end.
WORKDIR /opt/quip
# QUIP for general use is the OpenMP version.
ENV QUIP_ARCH linux_x86_64_gfortran_openmp
ENV QUIP_ROOT /opt/quip
ENV QUIP_INSTALLDIR /opt/quip/bin
COPY 3rdparty/quip .
COPY 3rdparty/gap src/GAP
COPY files/Makefile.inc build/$QUIP_ARCH/
# COPY files/GIT_VERSION .
# COPY files/GAP_VERSION src/GAP/
#################################################################################
# Quip with OpenMP
#################################################################################
ENV QUIP_ARCH linux_x86_64_gfortran_openmp
ADD Makefile.inc build/${QUIP_ARCH}/Makefile.inc
COPY configs/Makefile.inc build/${QUIP_ARCH}/
COPY configs/GIT_VERSION .
COPY configs/GAP_VERSION src/GAP/
RUN make \
&& make install \
&& make quippy \
&& make install-quippy
# # Installs with no suffix, e.g. quip
# RUN make \
# && make install
#
# # Installs quippy
# RUN pip install src/f90wrap \
# && make install-quippy
#
# # Make quippy executable available from terminal
# ENV PATH /opt/quip/bin:$PATH
# ================================================================================
# Testing (it also runs durign the build process)
# ================================================================================
# RUN ulimit -n 256 \
# && make test
Dockerfile.sissopp
+ 2
− 0
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......@@ -50,3 +50,5 @@ RUN mkdir build && cd build \
# ================================================================================
RUN pytest tests/pytest
# RUN cd build \
# && cmake test
\ No newline at end of file
README.md
+ 5
− 5
View file @ 52ccd986
File changed. Contains only whitespace changes. Show whitespace changes.
configs/GAP_VERSION
+ 1
− 1
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1560529911
1656672391
configs/GIT_VERSION
+ 1
− 1
View file @ 52ccd986
https://github.com/libAtoms/QUIP.git,74a7d3a05
git@github.com:libAtoms/QUIP.git,7c3fe3b8f-dirty
configs/Makefile.inc
+ 9
− 25
View file @ 52ccd986
# Place to override setting elsewhere, in particular things set in Makefile.linux_x86_64_gfortran
# look in QUIP/arch/Makefile.linux_x86_64_gfortran for defaults set by arch
#
# F77=gfortran
# F90=gfortran
# F95=gfortran
# CC=gcc
# CPLUSPLUS=g++
# FPP=gfortran -E -x f95-cpp-input
# LINKER=gfortran
# LIBTOOL=
# OPTIM=
# COPTIM=
# DEBUG=-O0 -g -DDUMP_CORE_ON_ABORT -DDEBUG -fbounds-check
# DEBUG=
# CDEBUG=
MATH_LINKOPTS=-llapack -lblas
PYTHON=python
PIP=pip
EXTRA_LINKOPTS=
USE_MAKEDEP=0
MAKEDEP=makedep.py
HAVE_CP2K=1
HAVE_VASP=1
HAVE_CP2K=0
HAVE_VASP=0
HAVE_TB=1
HAVE_PRECON=1
HAVE_LOTF=1
HAVE_ONIOM=1
HAVE_LOCAL_E_MIX=1
HAVE_PRECON=0
HAVE_LOTF=0
HAVE_ONIOM=0
HAVE_LOCAL_E_MIX=0
HAVE_QC=1
HAVE_GAP=1
HAVE_QR=1
......@@ -37,7 +21,7 @@ HAVE_TTM_NF=0
HAVE_CH4=0
NETCDF4_LIBS=-lnetcdf
NETCDF4_FLAGS=
HAVE_NETCDF4=0
HAVE_NETCDF4=1
HAVE_MDCORE=0
HAVE_ASAP=0
HAVE_CGAL=0
......
......
configs/README.md 0 → 100644
+ 9
− 0
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# Notes
Installation of quip requires a extra steps (because all git content are excluded form the docker context).
Manually generate the files of version information before building the image:
```bash
3rdparty/quip/bin/gitversion > configs/GIT_VERSION
3rdparty/quip/src/GAP/gapversion > configs/GAP_VERSION
```
\ No newline at end of file
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