Add PLUMED to Github CI

.github/workflows/gfortran.yml

@@ -163,7 +163,10 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-         gcc_v: [7, 8, 9]
+         # Let's just test one version, we do not really
+         # use OpenMPI with ABIN, and we already test all GCC
+         # versions with MPICH
+         gcc_v: [7]
     env:
       ABIN_FFLAGS: -O0 -fopenmp
       # To speed-up OpenMPI build
@@ -178,7 +181,7 @@ jobs:
       run: |
         sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-${GCC_V} 100 \
         --slave /usr/bin/gfortran gfortran /usr/bin/gfortran-${GCC_V}
-    - name: OpenMPI build Cache
+    - name: OpenMPI build cache
       id: openmpi-cache
       uses: actions/cache@v2
       with:
@@ -199,26 +202,40 @@ jobs:
 
 
   plumed_build:
-    # TODO: This is just a stub for now, need to figure out how to build Plumed
-    # Once that is done, remove the following line
-    if: false
     runs-on: ubuntu-latest
     needs: basic_build
     strategy:
       fail-fast: false
       matrix:
-         gcc_v: [7, 8, 9]
+         plumed_v: [2.5.3, 2.6.2]
+
     env:
-      FFLAGS: -O2 -fopenmp
+      PLUMED_V: ${{ matrix.plumed_v}}
+      ABIN_FFLAGS: -O0 -fopenmp --coverage
+      # Speeding up the Plumed build
+      CFLAGS: -O0
+      CXXLAGS: -O0
+
     steps:
     - uses: actions/checkout@v2
-    - name: Download Plumed
-      run: mkdir ~/plumed && cd ~/plumed && wget plumed_url
-    - name: build Plumed
-      run: cd ~/plumed && ./configure && make && make install
-    # TODO: Cache plumed build
-    # TODO: Maybe try different Plumed versions?
+    - name: Plumed build cache
+      id: plumed-cache
+      uses: actions/cache@v2
+      with:
+        path: ~/plumed/${{ env.PLUMED_V }}/install
+        key: ${{runner.os}}-plumed${{env.PLUMED_V}}-${{hashFiles('scripts/install_plumed.sh')}}
+
+    - name: Build and Install PLUMED
+      if: steps.plumed-cache.outputs.cache-hit != 'true'
+      run: ./scripts/install_plumed.sh ${HOME}/plumed ${PLUMED_V}
+
     - name: build ABIN
-      run: ./configure --plumed /path/to/plumed && make
+      run: |
+        export FFLAGS=${ABIN_FFLAGS} &&\
+        ./configure --plumed "${HOME}/plumed/${PLUMED_V}/install" &&\
+        make
     - name: test ABIN
       run: make test
+
+    - name: Codecov upload
+      run:  bash <(curl -s https://codecov.io/bash)

TESTS/PLUMED/HILLS.ref

@@ -1,6 +1,7 @@
 #! FIELDS time d1 sigma_d1 height biasf
 #! SET multivariate false
-      0.012094421632525     0.2783771737280517                   0.15                      5                      1
-       0.02418884326505     0.3018492617845895                   0.15                      5                      1
-      0.036283264897575     0.3146381586239277                   0.15                      5                      1
-        0.0483776865301     0.3013179725350135                   0.15                      5                      1
+#! SET kerneltype gaussian
+      0.012094421632525     0.2783771737280517                   0.15                      5                     -1
+       0.02418884326505     0.3018492617845895                   0.15                      5                     -1
+      0.036283264897575     0.3146381586239277                   0.15                      5                     -1
+        0.0483776865301     0.3013179725350135                   0.15                      5                     -1

TESTS/test.sh

@@ -1,5 +1,7 @@
 #!/bin/bash
 
+set -uo pipefail
+
 # Parameters passed from Makefile
 ABINEXE="$PWD/$1 -x mini.dat"
 
@@ -19,6 +21,11 @@ CP2K="$6"
 ACTION="$7"
 # NOTE: For MPI tests, we rely on the fact that
 # MPI_PATH is exported in Makefile!
+if [[ $MPI = "TRUE" && -z ${MPI_PATH:-} ]];then
+  echo "ERROR: \$MPI_PATH not set"
+  echo "Make sure to set MPI_PATH in make.vars"
+  exit 1
+fi
 
 cd TESTS || exit 1
 TESTDIR=$PWD
@@ -59,7 +66,7 @@ do
    if [[ -f $file.ref ]];then
       mv $file $file.ref
    else
-      echo "Something horrible happened during makeref"
+      echo "ERROR: Something horrible happened during makeref"
       exit 1
    fi
 done
@@ -120,7 +127,7 @@ else
 
    # Only one test selected, e.g. by running
    # make test TEST=CMD
-   folders=$2
+   folders=${TESTS}
 
 fi
 

configure

@@ -135,8 +135,9 @@ CXX="c++"
 CXXFLAGS="-O2 -Wall -std=c++11"
 
 if [[ $PLUMED = "TRUE" ]];then
-   if [[ ! -f $PLUMED_PATH/lib/Plumed.inc ]];then
-      echo "File $PLUMED_PATH/lib/Plumed.inc does not exist!"
+   PLUMED_INC=${PLUMED_PATH}/lib/plumed/src/lib/Plumed.inc
+   if [[ ! -f ${PLUMED_INC} ]];then
+      echo "File $PLUMED_INC does not exist!"
       exit 1
    fi
 fi
@@ -169,7 +170,7 @@ MPI_PATH = $MPI_PATH
 
 # Compilation with Plumed library
 PLUMED = $PLUMED
-PLUMED_INC = $PLUMED_PATH/lib/Plumed.inc
+PLUMED_INC = ${PLUMED_INC:-}
 
 # FFTW library is typically shipped with your system
 # It is needed for normal mode coordinate transformation in PIMD

scripts/install_mpich.sh

@@ -5,7 +5,7 @@
 # and MPI process manager (mpirun)
 
 # Exit script immediately upon error
-set -eou pipefail
+set -euo pipefail
 
 # Path as an optional first parameter
 MPICH_DIR="${1-/home/$USER/mpich}"

scripts/install_plumed.sh

@@ -0,0 +1,64 @@
+#!/bin/bash
+
+# Install OpenMPI implementation of Message Passing Interface (MPI)
+# This script installs both the MPI compilers (mpifort,mpicc)
+# and MPI process manager (mpirun)
+
+# Exit script immediately upon error
+set -euo pipefail
+
+# Path as an optional first parameter
+PLUMED_DIR="${1-/home/$USER/plumed}"
+# We take the current stable version as default
+# (as of 17 Dec 2020)
+PLUMED_VERSION="${2-"2.6.2"}"
+# Use two processors for the build
+NPROC=2
+
+TAR_FILE="plumed-src-${PLUMED_VERSION}.tgz"
+DOWNLOAD_URL="https://github.com/plumed/plumed2/releases/download/v${PLUMED_VERSION}/${TAR_FILE}"
+INSTALL_DIR="$PLUMED_DIR/$PLUMED_VERSION/install"
+
+if [[ -d $PLUMED_DIR/$PLUMED_VERSION ]];then
+  echo "Found existing Plumed installation in $PLUMED_DIR/$PLUMED_VERSION"
+  echo "Remove this folder if you want to reinstall"
+  exit 1
+fi
+
+mkdir -p $PLUMED_DIR/$PLUMED_VERSION/src
+mkdir -p $PLUMED_DIR/$PLUMED_VERSION/pkg
+
+curl -L "$DOWNLOAD_URL" > $PLUMED_DIR/$PLUMED_VERSION/pkg/${TAR_FILE}
+cd $PLUMED_DIR/$PLUMED_VERSION/src && tar -xzf ../pkg/${TAR_FILE} 
+cd plumed-${PLUMED_VERSION}
+
+# To keep things simple, we don't compile with MPI support
+# We also disable the use of external BLAS and LAPACK
+# to prevent Gfortran version conflicts 
+# According to the manual, Plumed should ship with their default 
+# BLAS and LAPACK, that will be fine for us for now.
+
+# --enable-static-patch is needed by ABIN integration
+# It is the default, but let's be explicit
+./configure CXX=g++ CC=gcc \
+  --disable-mpi --disable-xdrfile \
+  --disable-external-lapack --disable-external-blas \
+  --enable-static-patch --enable-shared \
+  --prefix=${INSTALL_DIR} 2>&1 |\
+  tee configure.log
+
+make -j $NPROC 2>&1 | tee make.log
+
+make install 2>&1 | tee make_install.log
+
+echo "
+Succesfully installed PLUMED!
+Set the following in your ABIN make.vars
+
+PLUMED = TRUE
+PLUMED_INC = ${INSTALL_DIR}/lib/plumed/src/lib/Plumed.inc
+
+or rerun configure as
+
+./configure --plumed ${INSTALL_DIR}
+"