Containerization of Environ build

.github/workflows/ci.yml

@@ -0,0 +1,46 @@
+name: CI
+on:
+  push:
+    branches:
+      - master
+      - develop
+  pull_request:
+
+jobs:
+  compile:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          sparse-checkout: Dockerfile
+          sparse-checkout-cone-mode: false
+      - uses: docker/setup-buildx-action@v3
+      - name: Build image
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          file: ./Dockerfile
+          tags: environ
+          outputs: type=docker,dest=/tmp/environ.tar
+      - name: Upload artifact
+        uses: actions/upload-artifact@v2
+        with:
+          name: environ
+          path: /tmp/environ.tar
+  test:
+    # if-condition source: https://github.com/orgs/community/discussions/25692#discussioncomment-3248764
+    if: github.event_name == 'pull_request' || (github.event_name == 'push' && (contains(github.ref, '/heads/master') || contains(github.ref, '/tags/v')))
+    needs: compile
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/download-artifact@v2
+        with:
+          name: environ
+          path: /tmp
+      - name: Load image
+        run: docker load --input /tmp/environ.tar
+      - name: Run tests
+        uses: addnab/docker-run-action@v3
+        with:
+          image: environ:latest
+          run: sh -c "env && cd /app/q-e/Environ/tests && make --ignore-errors run-tests | tee /app/tests.log && if grep -q **FAILED** /app/tests.log; then exit 1; fi"

Dockerfile

@@ -0,0 +1,105 @@
+# Use containerized installation
+# 0) Install Docker (https://docs.docker.com/engine/install/) or Docker Desktop (https://www.docker.com/products/docker-desktop/)
+# 1) Clone repo:     git clone https://github.com/environ-developers/Environ.git && cd Environ
+# 2) Build image:    docker build -t environ-sandbox . && docker image ls
+# 3) Run container:  docker run -i -p 8000:80 environ-sandbox && docker ps
+# 4) Access container:
+#    a) Docker Desktop
+#    b) CLI: docker exec -it <container ID> bash
+# 5) Review test and/or example logs:
+#    a) cat /app/tests.log
+#    b) cat /app/examples.log
+
+# Configure sandbox -- compiler, dependencies, openmpi, python
+
+FROM ubuntu:22.04
+RUN apt-get update
+RUN DEBIAN_FRONTEND=noninteractive apt-get install --assume-yes --no-install-recommends \
+    autoconf \
+    bc \
+    build-essential \
+    ca-certificates \
+    gfortran \
+    git-all \
+    libblas3 \
+    libc6 \
+    libelpa17 \
+    libfftw3-dev \
+    libgcc-s1 \
+    liblapack-dev \
+    libopenmpi-dev \
+    libscalapack-openmpi-dev \
+    python3 \
+    pipx \
+    wget 
+#RUN pipx install Cython numpy ase matplotlib pandas notebook --include-deps
+WORKDIR /app
+
+# Set environment variables
+# N                               number of processors
+# QE_VERSION                      Quantum ESPRESSO source version
+# QE_CONFIG                       Quantum ESPRESSO configuration options
+# ENVIRON_CONFIG                  Environ configuration options
+# DOWNLOAD_EFFICIENCY             download efficiency SSSP pseudopotential during build
+# DOWNLOAD_PRECISION              download precision SSSP pseudopotential during build
+# RUN_TESTS                       run tests during build
+# RUN_EXAMPLES                    run examples during build
+# BIN_DIR                         absolute path to binary directory (QE variable)
+# PSEUDO_DIR                      absolute path to pseudopotential directory (QE variable)
+# TMP_DIR                         absolute path of placeholder directory (QE variable)
+# OMPI_ALLOW_RUN_AS_ROOT          root-level execution permission (MPI variable)
+# OMPI_ALLOW_RUN_AS_ROOT_CONFIRM  root-level execution confirmation (MPI variable)
+ENV N=4 \
+    QE_VERSION=qe-7.2 \
+    QE_CONFIG="--enable-parallel --with-environ=/app/q-e/Environ" \
+    ENVIRON_CONFIG="--with-qe=/app/q-e" \
+    DOWNLOAD_EFFICIENCY=0 \
+    DOWNLOAD_PRECISION=0 \
+    RUN_TESTS=0 \
+    RUN_EXAMPLES=0 \
+    BIN_DIR="/app/q-e/bin" \
+    PSEUDO_DIR="/app/q-e/pseudo" \
+    TMP_DIR="/app" \
+    OMPI_ALLOW_RUN_AS_ROOT=1 \
+    OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
+
+# Compile & install QE with Environ
+
+RUN git clone https://github.com/QEF/q-e.git
+WORKDIR /app/q-e
+RUN git checkout $QE_VERSION && git clone https://github.com/environ-developers/Environ.git
+RUN grep -rl .*NETWORK_PSEUDO=http:.* | xargs sed -i "s/NETWORK_PSEUDO=http:/NETWORK_PSEUDO=https:/"
+RUN grep -rl .*NETWORK_PSEUDO=https:\/\/www.quantum-espresso.org\/wp-content\/uploads\/upf_files\/.* | xargs sed -i "s/NETWORK_PSEUDO=https:\/\/www.quantum-espresso.org\/wp-content\/uploads\/upf_files\//NETWORK_PSEUDO=https:\/\/pseudopotentials.quantum-espresso.org\/upf_files\//"
+WORKDIR /app/q-e/Environ
+RUN ./configure $ENVIRON_CONFIG && make -j $N compile
+WORKDIR /app/q-e
+RUN ./configure $QE_CONFIG && make -j $N pw
+RUN export PATH="$BIN_DIR:$PATH"
+WORKDIR /app
+
+# Download SSSP pseudopotentials
+
+ENV EFFICIENCY_TARBALL="https://archive.materialscloud.org/record/file?record_id=1732&filename=SSSP_1.3.0_PBE_efficiency.tar.gz"
+ENV PRECISION_TARBALL="https://archive.materialscloud.org/record/file?record_id=1732&filename=SSSP_1.3.0_PBE_precision.tar.gz"
+RUN if [ "$DOWNLOAD_EFFICIENCY" = "1" ]; then \
+    wget $EFFICIENCY_TARBALL --output-document=efficiency.tar.gz && \
+    tar -xvzf efficiency.tar.gz -C /app/q-e/pseudo && \
+    rm efficiency.tar.gz; fi
+RUN if [ "$DOWNLOAD_PRECISION" = "1" ]; then \
+    wget $PRECISION_TARBALL --output-document=precision.tar.gz && \
+    tar -xvzf precision.tar.gz -C /app/q-e/pseudo && \
+    rm precision.tar.gz; fi
+
+# Run Environ tests and examples
+
+WORKDIR /app/q-e/Environ/tests
+RUN if [ "$RUN_TESTS" = "1" ]; then \
+    make --ignore-errors run-tests-parallel | tee /app/tests.log; fi
+WORKDIR /app/q-e/Environ/examples/qe/pw
+RUN if [ "$RUN_EXAMPLES" = "1" ]; then \
+    ./run_all.sh | tee /app/examples.log; fi
+WORKDIR /app
+
+# Run shell
+
+CMD bash

README.md

@@ -1,13 +1,13 @@
-# Copyright (C) 2018-2022 ENVIRON (www.quantum-environ.org)
+# Copyright (C) 2018-2024 ENVIRON (www.quantum-environ.org)
 
-### This file is part of Environ version 3.0
+### This file is part of Environ version 3.1
 
-    Environ 3.0 is free software: you can redistribute it and/or modify
+    Environ 3.1 is free software: you can redistribute it and/or modify
     it under the terms of the GNU General Public License as published by
     the Free Software Foundation, either version 2 of the License, or
     (at your option) any later version.
 
-    Environ 3.0 is distributed in the hope that it will be useful,
+    Environ 3.1 is distributed in the hope that it will be useful,
     but WITHOUT ANY WARRANTY; without even the implied warranty of
     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
     GNU General Public License for more detail, either the file
@@ -20,13 +20,13 @@
 
 | Name               | Institution                                                     |
 | ------------------ | --------------------------------------------------------------- |
-| Oliviero Andreussi | Department of Physics, University of North Texas                |
+| Oliviero Andreussi | Department of Chemistry and Biochemistry, Boise State University|
 | Francesco Nattino  | THEOS and NCCR-MARVEL, Ecole Polytechnique Federale de Lausanne |
-| Iurii Timrov       | THEOS and NCCR-MARVEL, Ecole Polytechnique Federale de Lausanne |
+| Iurii Timrov       | PSI Zurich and NCCR-MARVEL                                      |
 | Ismaila Dabo       | Department of Materials Science and Engineering, Penn State     |
 | Nicola Marzari     | THEOS and NCCR-MARVEL, Ecole Polytechnique Federale de Lausanne |
 | Quinn Campbell     | Sandia National Labs                                            |
-| Edan Bainglass     | Department of Physics, University of North Texas                |
+| Edan Bainglass     | PSI Zurich and NCCR-MARVEL                                      |
 | Matthew Truscott   | Department of Physics, University of North Texas                |
 | Gabriel Medrano    | Department of Physics, University of North Texas                |
 
@@ -50,7 +50,7 @@
 
       http://www.quantum-espresso.org/
 
-# QE + Environ 3.0 Installation
+# QE + Environ 3.1 Installation
 
     The following instructions refer to Environ 3.0 installed on QE >= 7.1
     For previous versions, please refer to the instructions on the website:
@@ -111,7 +111,7 @@ If using cmake, modify the ESPRESSO_ROOT variable in the following files to refl
 
 #
 
-# Uninstall Environ 3.0
+# Uninstall Environ 3.1
 
 From Environ root:
 

src/main.f90

@@ -717,24 +717,45 @@ END FUNCTION get_vzero
     !>
     !!
     !------------------------------------------------------------------------------------
-    FUNCTION get_dvtot(this, nnr) RESULT(dvtot)
+    FUNCTION get_dvtot(this, nnr, gather) RESULT(dvtot)
         !--------------------------------------------------------------------------------
         !
         INTEGER, INTENT(IN) :: nnr
+        LOGICAL, INTENT(IN), OPTIONAL :: gather
         CLASS(environ_main), INTENT(IN) :: this
         !
         REAL(DP) :: dvtot(nnr)
         !
+        LOGICAL :: use_gather
         CHARACTER(LEN=80) :: routine = 'get_dvtot'
         !
         !--------------------------------------------------------------------------------
         !
-        IF (nnr /= this%dvtot%cell%nnr) &
-                CALL io%error(routine, "Mismatch in grid size", 1)
+        use_gather = .FALSE.
+        IF (PRESENT(gather)) use_gather = gather
+        !
+        IF (.NOT.use_gather .AND. nnr /= this%dvtot%cell%nnr) THEN
+                CALL io%error(routine, "Mismatch in local grid size", 1)
+        ELSE IF (use_gather .AND. nnr /= this%dvtot%cell%nnt) THEN
+                CALL io%error(routine, "Mismatch in global grid size", 1)
+        ENDIF
         !
         !--------------------------------------------------------------------------------
         !
-        dvtot = this%dvtot%of_r
+        IF (use_gather) THEN
+#if defined(__MPI)
+            dvtot = 0.D0
+            !
+            CALL env_gather_grid(this%setup%system_cell%dfft, this%dvtot%of_r, dvtot)
+            !
+            CALL env_mp_sum(dvtot, this%setup%system_cell%dfft%comm)
+            !
+#else
+            dvtot = this%dvtot%of_r
+#endif
+        ELSE 
+            dvtot = this%dvtot%of_r
+        END IF
         !
         !--------------------------------------------------------------------------------
     END FUNCTION get_dvtot