Test TeraChem MPI interface

.github/workflows/gfortran.yml

@@ -14,6 +14,9 @@ env:
   CURL_OPTS:  -S --no-silent
   CODECOV_OPTIONS: -Z -X coveragepy -X xcode
 
+  # FFLAGS for building ABIN, applicable for most jobs
+  ABIN_FFLAGS: -O0 -fopenmp -Wall --coverage -ffpe-trap=invalid,zero,overflow,denormal
+
 jobs:
 
   basic_build:
@@ -25,7 +28,6 @@ jobs:
          gcc_v: [7, 8, 9]
     env:
       FC: gfortran
-      FFLAGS: -O0 -fopenmp -Wall --coverage -ffpe-trap=invalid,zero,overflow,denormal
       GCC_V: ${{ matrix.gcc_v}}
       CODECOV_NAME: ${{format('{0} GCC-{1}', github.job, matrix.gcc_v)}}
 
@@ -56,6 +58,8 @@ jobs:
 
     - name: Build ABIN
       run: ./configure --pfunit ${HOME}/pfunit/build/installed/ && make
+      env:
+        FFLAGS: ${{ env.ABIN_FFLAGS }}
 
     - name: Run Unit tests
       run: make unittest
@@ -132,7 +136,6 @@ jobs:
       matrix:
          gcc_v: [7]
     env:
-      FFLAGS: -O0 -fopenmp -Wall --coverage -ffpe-trap=invalid,zero,overflow,denormal
       GCC_V: ${{ matrix.gcc_v}}
       CODECOV_NAME: ${{format('{0} GCC-{1}', github.job, matrix.gcc_v)}}
     steps:
@@ -156,6 +159,8 @@ jobs:
 
     - name: Build ABIN
       run: ./configure --pfunit ${HOME}/pfunit/build/installed/ --fftw && make
+      env:
+        FFLAGS: ${{ env.ABIN_FFLAGS }}
 
     - name: Run Unit tests
       run: make unittest
@@ -174,9 +179,8 @@ jobs:
       fail-fast: false
       matrix:
          gcc_v: [7, 8, 9]
-         mpich_v: ["3.1.3", "3.3.2"]
+         mpich_v: ["3.3.2", "3.4.1"]
     env:
-      ABIN_FFLAGS: -O0 -fopenmp --coverage -ffpe-trap=invalid,zero,overflow,denormal
       # To speed-up MPICH build
       CFLAGS: -O0
       GCC_V: ${{ matrix.gcc_v}}
@@ -204,10 +208,9 @@ jobs:
       run: ./dev_scripts/install_mpich.sh ${HOME}/mpich ${MPICH_V}
 
     - name: build ABIN
-      run: |
-            export FFLAGS=${ABIN_FFLAGS} &&\
-            ./configure --mpi ${HOME}/mpich/${MPICH_V}/install &&\
-            make
+      run:  ./configure --mpi ${HOME}/mpich/${MPICH_V}/install && make
+      env:
+        FFLAGS: ${{ env.ABIN_FFLAGS }} -g
     - name: test ABIN
       run: make test
       # We upload to Codecov from the OpenMPI build,
@@ -227,7 +230,6 @@ jobs:
       matrix:
          gcc_v: [7]
     env:
-      ABIN_FFLAGS: -O0 --coverage -fopenmp -ffpe-trap=invalid,zero,overflow,denormal
       # To speed-up OpenMPI build
       CFLAGS: -O0
       GCC_V: ${{ matrix.gcc_v}}
@@ -255,10 +257,9 @@ jobs:
       run: ./dev_scripts/install_openmpi.sh ${HOME}/openmpi ${OPENMPI_V} ${OPENMPI_PATCH}
 
     - name: build ABIN
-      run: |
-        export FFLAGS=${ABIN_FFLAGS} &&\
-        ./configure --mpi "${HOME}/openmpi/${OPENMPI_V}/install" &&\
-        make
+      run: ./configure --mpi "${HOME}/openmpi/${OPENMPI_V}/install" && make
+      env:
+        FFLAGS: ${{ env.ABIN_FFLAGS }}
     - name: test ABIN
       run: make test
     - name: Codecov upload
@@ -278,7 +279,6 @@ jobs:
     env:
       PLUMED_V: ${{ matrix.plumed_v}}
       GCC_V: ${{ matrix.gcc_v}}
-      ABIN_FFLAGS: -O0 -fopenmp --coverage -ffpe-trap=invalid,zero,overflow,denormal
       # Speeding up the Plumed build
       CFLAGS: -O0
       CXXLAGS: -O0
@@ -312,10 +312,11 @@ jobs:
 
     - name: build ABIN
       run: |
-        export FFLAGS=${ABIN_FFLAGS} &&\
         ./configure --plumed "${HOME}/plumed/${PLUMED_V}/install"\
                     --pfunit ~/pfunit/build/installed/ &&\
         make
+      env:
+        FFLAGS: ${{ env.ABIN_FFLAGS }}
 
     - name: Run Unit tests
       run: make unittest

codecov.yml

@@ -27,7 +27,7 @@ coverage:
     patch:
       default:
         target: auto
-        threshold: 3.0%
+        threshold: 3%
 
 parsers:
   gcov:

dev_scripts/install_mpich.sh

@@ -17,6 +17,10 @@ TAR_FILE="mpich-${MPICH_VERSION}.tar.gz"
 DOWNLOAD_URL="https://www.mpich.org/static/downloads/${MPICH_VERSION}/${TAR_FILE}"
 INSTALL_DIR="$MPICH_DIR/$MPICH_VERSION/install"
 
+# Github Actions machines have two CPUs, per:
+# https://docs.github.com/en/free-pro-team@latest/actions/reference/specifications-for-github-hosted-runners#supported-runners-and-hardware-resources
+NCPUS=2
+
 if [[ -d $MPICH_DIR/$MPICH_VERSION ]];then
   echo "Found existing MPICH installation in $MPICH_DIR/$MPICH_VERSION"
   echo "Remove this folder if you want to reinstall"
@@ -30,18 +34,23 @@ curl "$DOWNLOAD_URL" > $MPICH_DIR/$MPICH_VERSION/pkg/${TAR_FILE}
 cd $MPICH_DIR/$MPICH_VERSION/src && tar -xzf ../pkg/${TAR_FILE} && cd mpich-${MPICH_VERSION}
 
 # If you're building MPI for general use, not only for ABIN,
-# you might want to change the configure options:
-# --enable-fortran=yes Compile all versions of Fortran interfaces
-#                     This option is needed for GitHub Actions build, I don't know why
-# --with-hydra-pm=pmiserv --with-namepublisher=pmi
-#                     Needed for MPI interface with TeraChem
+# you might want change some of the configure options.
+# --enable-fortran=all Compile all versions of Fortran interfaces
+#                      In principle we don't need F77, but configure fails in that case.
+# --with-namepublisher=pmi
+#         This compiles hydra_nameserver binary, needed for MPI interface with TeraChem
+#
+# Use the two rows below for a debug build/
+# export CFLAGS='-g -O0'
+# --disable-fast --enable-g-option=all \
 ./configure FC=gfortran CC=gcc \
-  --enable-fortran=all --disable-cxx \
-  --with-hydra-pm=pmiserv --with-namepublisher=pmi \
+  --enable-fortran=all \
+  --with-pm=hydra --with-device=ch3:nemesis \
+  --with-namepublisher=pmi \
   --enable-static --disable-shared \
   --prefix=${INSTALL_DIR} 2>&1 |\
   tee configure.log
-make 2>&1 | tee make.log
+make -j $NCPUS 2>&1 | tee make.log
 make install 2>&1 | tee make_install.log
 
 echo "

src/Makefile

@@ -1,7 +1,7 @@
 F_OBJS := modules.o fortran_interfaces.o utils.o io.o random.o arrays.o qmmm.o fftw_interface.o \
           shake.o nosehoover.o gle.o transform.o potentials.o estimators.o ekin.o vinit.o plumed.o \
           remd.o force_bound.o water.o force_cp2k.o sh_integ.o surfacehop.o landau_zener.o\
-          force_mm.o force_tera.o force_terash.o force_abin.o en_restraint.o analyze_ext_template.o geom_analysis.o analysis.o \
+          force_mm.o tera_mpi_api.o force_tera.o force_terash.o force_abin.o en_restraint.o analyze_ext_template.o geom_analysis.o analysis.o \
           minimizer.o mdstep.o forces.o read_cmdline.o init.o
 
 C_OBJS := water_interface.o

src/abin.F90

@@ -43,16 +43,19 @@ program abin
    logical :: file_exists
    integer, dimension(8) :: time_start, time_end
    real(DP) :: total_cpu_time
+#ifdef USE_MPI
    integer :: ierr
-!$ integer :: nthreads, omp_get_max_threads
+#endif
 
    call date_and_time(VALUES=time_start)
 
    ! INPUT AND INITIALIZATION SECTION
    call init(dt)
 
    ! This cannot be in init because of the namelist 'system'
-   if (my_rank == 0) call clean_temp_files()
+   if (my_rank == 0) then
+      call clean_temp_files()
+   end if
 
    if (irest == 1 .and. (my_rank == 0 .or. iremd == 1)) then
       call archive_file('restart.xyz', it)
@@ -66,9 +69,7 @@ program abin
       call lz_rewind(en_array_lz)
    end if
 
-!$ nthreads = omp_get_max_threads()
    if (my_rank == 0) then
-!$    write (*, *) 'Number of OpenMP threads used = ', nthreads
       write (*, '(A)') 'Job started at: '//trim(get_formatted_date_and_time(time_start))
       write (*, *) ''
    end if
@@ -111,7 +112,7 @@ program abin
       if (ipimd == 5) call lz_rewind(en_array_lz)
 
       ! if we use reference potential with RESPA
-      if (pot_ref /= 'none') then
+      if (pot_ref /= '_none_') then
          call force_clas(fxc, fyc, fzc, x, y, z, eclas, pot_ref)
          call force_clas(fxc_diff, fyc_diff, fzc_diff, x, y, z, eclas, pot)
       end if

src/arrays.F90

@@ -105,7 +105,7 @@ subroutine allocate_arrays(natomalloc, nwalkalloc)
       fxc = 0.0D0; fyc = fxc; fzc = fxc
       fxq = fxc; fyq = fxc; fzq = fxc
       transfxc = fxc; transfyc = fxc; transfzc = fxc
-      if (pot_ref /= 'none') then
+      if (pot_ref /= '_none_') then
          allocate (fxc_diff(natomalloc, nwalkalloc))
          allocate (fyc_diff(natomalloc, nwalkalloc))
          allocate (fzc_diff(natomalloc, nwalkalloc))

src/force_abin.F90

@@ -121,12 +121,11 @@ subroutine force_abin(x, y, z, fx, fy, fz, eclas, chpot, walkmax)
       !-----MAKE THE CALL----------!
       ISTATUS = system(chsystem)
 
+      ! TODO: Verify that the below is true even for GCC >= 7
       ! Exit status 0 turns to 0
       ! For some reason, exit status 1 turns to 256
-      ! However, this one we get by default from bash, don't know why...
-      ! see this thread for explanation:
-      ! http://coding.derkeiler.com/Archive/Fortran/comp.lang.fortran/MAXUNITS07-01/msg00085.html
-      ! If the bash script wants to notify ABIN, it can use e.g. exit 2
+      ! However, this one we get by default from BASH, I don't know why.
+      ! If the BASH script wants to notify ABIN, it can use e.g. exit 2
       if (ISTATUS /= 0 .and. ISTATUS /= 256) then
          write (*, '(A)') 'ERROR during the execution of the ab initio external program.'
          write (*, '(A)') 'Please inspect the output files in&