PHOTOX · danielhollas · Oct 4, 2021 · Sep 28, 2021
diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml
@@ -179,7 +179,7 @@ jobs:
       fail-fast: false
       matrix:
          gcc_v: [7, 9, 10]
-         mpich_v: ["3.3.2", "3.4.1"]
+         mpich_v: ["3.3.2", "3.4.2"]
     env:
       # To speed-up MPICH build
       CFLAGS: -O0

diff --git a/dev_scripts/install_mpich.sh b/dev_scripts/install_mpich.sh
@@ -8,7 +8,7 @@
 set -euo pipefail
 
 # Path as an optional first parameter
-MPICH_DIR="${1-/home/$USER/mpich}"
+MPICH_DIR="${1-$HOME/mpich}"
 # We take current stable version as default
 # (as of 06 Nov 2020).
 MPICH_VERSION="${2-"3.3.2"}"

diff --git a/dev_scripts/install_openmpi.sh b/dev_scripts/install_openmpi.sh
@@ -8,7 +8,7 @@
 set -euo pipefail
 
 # Path as an optional first parameter
-OPENMPI_DIR="${1-/home/$USER/openmpi}"
+OPENMPI_DIR="${1-$HOME/openmpi}"
 # We take current stable version as default
 # (as of 06 Nov 2020)
 OPENMPI_VERSION=${2-"4.0"}

diff --git a/dev_scripts/install_pfunit.sh b/dev_scripts/install_pfunit.sh
@@ -3,11 +3,16 @@
 # Exit script immediately upon error
 set -euo pipefail
 
-REPO_DIR="/home/$USER/pfunit"
+REPO_DIR="$HOME/pfunit"
 if [[ "$#" -eq 1 && ! -z $1 ]];then
    REPO_DIR=$1
 fi
 
+if [[ -e $REPO_DIR ]];then
+  echo "ERROR: $REPO_DIR already exists."
+  exit 1
+fi
+
 git clone --recursive https://github.com/Goddard-Fortran-Ecosystem/pFUnit $REPO_DIR && cd $REPO_DIR
 
 mkdir -p build && cd build

diff --git a/dev_scripts/install_plumed.sh b/dev_scripts/install_plumed.sh
@@ -8,7 +8,7 @@
 set -euo pipefail
 
 # Path as an optional first parameter
-PLUMED_DIR="${1-/home/$USER/plumed}"
+PLUMED_DIR="${1-$HOME/plumed}"
 # We take the current stable version as default
 # (as of 17 Dec 2020)
 PLUMED_VERSION="${2-"2.6.2"}"

diff --git a/src/modules.F90 b/src/modules.F90
@@ -443,6 +443,7 @@ end subroutine mass_init
 end module mod_system
 
 ! module for permanent file handling
+! TODO: Move this to a separate file.
 module mod_files
    implicit none
    public
@@ -612,7 +613,7 @@ subroutine files_init(isbc, phase, ndist, nang, ndih)
          write (UCHARGES, *) '# Time_step Bead_index ', (names(i), i=1, natom)
 
          open (UDIP, file=chfiles(UDIP), access=chaccess, action='write')
-         write (UDIP, *) '# Time  |D| Dx Dy Dz'
+         write (UDIP, *) '# Time Bead_index |D| Dx Dy Dz'
       end if
 
       if (isbc == 1) then

diff --git a/tests/MINI/input.in b/tests/MINI/input.in
@@ -1,5 +1,4 @@
-This is a sample input file for ABIN 
-NOTE: order of input sections matters!!
+Very naive steepest descent minimization.
 
 &general
 nstep=100,
@@ -8,6 +7,7 @@ irest=0,		! should we restart from restart.xyz? (ignoring mini.dat), NOT working
 pot='mmwater'		!not done yet,options should be g09,orca,tera,turbo,molpro,nab,harm,morse,guillot,2dho
 ipimd=3,		!classical simulation 0, quantum simulation 1
 nwalk=1,		!number of random walkers 
+! TODO: Reduce the number of steps to reduce numerical differences between compilers.
 nstep=200,		!equilibration period,!not properly implemented yet
 istage=0,		!staging transformation (1), without staging (0)
 
@@ -27,4 +27,3 @@ natom=3,		!number of atoms
 inose=0,		! Thermostating: Nose-Hoover 1, microcanonical 0,GLE 2, LE 3
 temp=298.15,		! initial temperature for Maxwell-Boltzmann sampling [au]
 /
-
diff --git a/tests/TERAPI-FAILS/test.sh b/tests/TERAPI-FAILS/test.sh
@@ -34,8 +34,6 @@ check_for_openmpi
 # Compile default TC server
 $MPICXX $TCSRC -Wall -o $TCEXE
 
-#trap cleanup INT ABRT TERM EXIT
-
 echo "########### SUBTEST 1 ###################"
 ./test1.sh
 echo "########### SUBTEST 2 ###################"

diff --git a/tests/TERAPI-FAILS/test1.sh b/tests/TERAPI-FAILS/test1.sh
@@ -8,6 +8,16 @@ set -euo pipefail
 
 source ../test_tc_server_utils.sh
 
+# Rewrite cleanup function from utils sourced above.
+function cleanup {
+  kill -9 $tcpid $abinpid > /dev/null 2>&1 || true
+  grep 'what()' $TCOUT > TC_ERROR$IDX
+  if [[ -f ERROR ]];then
+    mv ERROR ABIN_ERROR$IDX
+  fi
+  exit 0
+}
+
 IDX=1
 ABININ=input.in$IDX
 ABINOUT=${ABINOUT}$IDX
@@ -20,28 +30,17 @@ $MPICXX $TCSRC -Wall -o $TCEXE
 
 launch_hydra_nameserver $MPICH_HYDRA
 
-hostname=$HOSTNAME
-MPIRUN="$MPIRUN -nameserver $hostname -n 1"
+MPIRUN="$MPIRUN -nameserver $HOSTNAME -n 1"
 
 TC_PORT="test1.$$"
 ABIN_CMD="$ABINEXE -i $ABININ -x $ABINGEOM -M $TC_PORT"
 TC_CMD="./$TCEXE $TC_PORT.1"
 
+trap cleanup INT ABRT TERM EXIT
 $MPIRUN $TC_CMD > $TCOUT 2>&1 || true &
 tcpid=$!
 
 $MPIRUN $ABIN_CMD > $ABINOUT 2>&1 || true &
 abinpid=$!
 
-function cleanup {
-  kill -9 $tcpid $abinpid > /dev/null 2>&1 || true
-  grep 'what()' $TCOUT > TC_ERROR$IDX
-  if [[ -f ERROR ]];then
-    mv ERROR ABIN_ERROR$IDX
-  fi
-  exit 0
-}
-
-trap cleanup INT ABRT TERM EXIT
-
 check_running_processes $abinpid $tcpid
diff --git a/tests/TERAPI-FAILS/test2.sh b/tests/TERAPI-FAILS/test2.sh
@@ -8,34 +8,34 @@ set -euo pipefail
 
 source ../test_tc_server_utils.sh
 
+function cleanup {
+  kill -9 $tcpid $abinpid > /dev/null 2>&1 || true
+  grep 'what()' $TCOUT > TC_ERROR$IDX
+  if [[ -f ERROR ]];then
+    mv ERROR ABIN_ERROR$IDX
+  fi
+  exit 0
+}
+
 IDX=2
 ABININ=input.in$IDX
 ABINOUT=${ABINOUT}$IDX
 TCOUT=${TCOUT}$IDX
 
 launch_hydra_nameserver $MPICH_HYDRA
-hostname=$HOSTNAME
-MPIRUN="$MPIRUN -nameserver $hostname -n 1"
+
+MPIRUN="$MPIRUN -nameserver $HOSTNAME -n 1"
 
 TC_PORT="test$IDX.$$"
 ABIN_CMD="$ABINEXE -i $ABININ -x $ABINGEOM -M $TC_PORT"
 TC_CMD="./$TCEXE $TC_PORT.1"
 
+trap cleanup INT ABRT TERM EXIT
+
 $MPIRUN $TC_CMD > $TCOUT 2>&1 || true &
 tcpid=$!
 
 $MPIRUN $ABIN_CMD > $ABINOUT 2>&1 || true &
 abinpid=$!
 
-function cleanup {
-  kill -9 $tcpid $abinpid > /dev/null 2>&1 || true
-  grep 'what()' $TCOUT > TC_ERROR$IDX
-  if [[ -f ERROR ]];then
-    mv ERROR ABIN_ERROR$IDX
-  fi
-  exit 0
-}
-
-trap cleanup INT ABRT TERM EXIT
-
 check_running_processes $abinpid $tcpid
diff --git a/tests/TERAPI-FAILS/test3.sh b/tests/TERAPI-FAILS/test3.sh
@@ -5,6 +5,15 @@
 set -euo pipefail
 source ../test_tc_server_utils.sh
 
+function cleanup {
+  kill -9 ${job_pids[@]} > /dev/null 2>&1 || true
+  grep 'what()' $TCOUT.* > TC_ERROR$IDX
+  if [[ -f ERROR ]];then
+    mv ERROR ABIN_ERROR$IDX
+  fi
+  exit 0
+}
+
 IDX=3
 ABININ=input.in$IDX
 ABINOUT=${ABINOUT}$IDX
@@ -15,11 +24,15 @@ MPIRUN="$MPIRUN -n 1"
 ABIN_CMD="$ABINEXE -i $ABININ -x $ABINGEOM"
 
 declare -A job_pids
+
+trap cleanup INT ABRT TERM EXIT
+
 for ((itera=1;itera<=N_TERA_SERVERS;itera++)) {
    $MPIRUN ./$TCEXE > $TCOUT.$itera 2>&1 &
    job_pids[$itera]=$!
 }
 sleep 1
+
 # Grep port names from TC outputs, pass to ABIN via a file.
 for ((itera=1;itera<=N_TERA_SERVERS;itera++)) {
   grep 'port name' $TCOUT.$itera | awk -F"port name: " '{print $2;exit}' > $TC_PORT_FILE.$itera
@@ -28,15 +41,4 @@ for ((itera=1;itera<=N_TERA_SERVERS;itera++)) {
 $MPIRUN $ABIN_CMD > $ABINOUT 2>&1 &
 job_pids[$(expr $N_TERA_SERVERS + 1)]=$!
 
-function cleanup {
-  kill -9 ${job_pids[@]} > /dev/null 2>&1 || true
-  grep 'what()' $TCOUT.* > TC_ERROR$IDX
-  if [[ -f ERROR ]];then
-    mv ERROR ABIN_ERROR$IDX
-  fi
-  exit 0
-}
-
-trap cleanup INT ABRT TERM EXIT
-
 check_running_processes ${job_pids[@]}
diff --git a/tests/TERAPI-FAILS/test4.sh b/tests/TERAPI-FAILS/test4.sh
@@ -8,6 +8,15 @@ set -euo pipefail
 
 source ../test_tc_server_utils.sh
 
+function cleanup {
+  kill -9 $tcpid $abinpid > /dev/null 2>&1 || true
+  grep 'what()' $TCOUT > TC_ERROR$IDX
+  if [[ -f ERROR ]];then
+    mv ERROR ABIN_ERROR$IDX
+  fi
+  exit 0
+}
+
 IDX=4
 ABININ=input.in$IDX
 ABINOUT=${ABINOUT}$IDX
@@ -20,28 +29,18 @@ $MPICXX $TCSRC -Wall -o $TCEXE
 
 launch_hydra_nameserver $MPICH_HYDRA
 
-hostname=$HOSTNAME
-MPIRUN="$MPIRUN -nameserver $hostname -n 1"
+MPIRUN="$MPIRUN -nameserver $HOSTNAME -n 1"
 
 TC_PORT="test$IDX.$$"
 ABIN_CMD="$ABINEXE -i $ABININ -x $ABINGEOM -M $TC_PORT"
 TC_CMD="./$TCEXE $TC_PORT.1"
 
+trap cleanup INT ABRT TERM EXIT
+
 $MPIRUN $TC_CMD > $TCOUT 2>&1 || true &
 tcpid=$!
 
 $MPIRUN $ABIN_CMD > $ABINOUT 2>&1 || true &
 abinpid=$!
 
-function cleanup {
-  kill -9 $tcpid $abinpid > /dev/null 2>&1 || true
-  grep 'what()' $TCOUT > TC_ERROR$IDX
-  if [[ -f ERROR ]];then
-    mv ERROR ABIN_ERROR$IDX
-  fi
-  exit 0
-}
-
-trap cleanup INT ABRT TERM EXIT
-
 check_running_processes $abinpid $tcpid
diff --git a/tests/TERAPI-FAILS/test5.sh b/tests/TERAPI-FAILS/test5.sh
@@ -7,29 +7,26 @@ set -euo pipefail
 
 source ../test_tc_server_utils.sh
 
+function cleanup {
+  kill -9 $abinpid > /dev/null 2>&1 || true
+  if [[ -f ERROR ]];then
+    mv ERROR ABIN_ERROR$IDX
+  fi
+  exit 0
+}
+
 IDX=5
 ABININ=input.in$IDX
 ABINOUT=${ABINOUT}$IDX
 
 launch_hydra_nameserver $MPICH_HYDRA
 
-hostname=$HOSTNAME
-#MPIRUN="$MPIRUN -nameserver $hostname -n 1"
-
 TC_PORT="test$IDX.$$"
 ABIN_CMD="$ABINEXE -i $ABININ -x $ABINGEOM -M $TC_PORT"
 
+trap cleanup INT ABRT TERM EXIT
+
 $MPIRUN $ABIN_CMD > $ABINOUT 2>&1 || true &
 abinpid=$!
 
-function cleanup {
-  kill -9 $abinpid > /dev/null 2>&1 || true
-  if [[ -f ERROR ]];then
-    mv ERROR ABIN_ERROR$IDX
-  fi
-  exit 0
-}
-
-trap cleanup INT ABRT TERM EXIT
-
 check_running_processes $abinpid
diff --git a/tests/TERAPI-FAILS/test6.sh b/tests/TERAPI-FAILS/test6.sh
@@ -7,6 +7,14 @@ set -euo pipefail
 
 source ../test_tc_server_utils.sh
 
+function cleanup {
+  kill -9 $abinpid > /dev/null 2>&1 || true
+  if [[ -f ERROR ]];then
+    mv ERROR ABIN_ERROR$IDX
+  fi
+  exit 0
+}
+
 IDX=6
 ABININ=input.in$IDX
 ABINOUT=${ABINOUT}$IDX
@@ -17,17 +25,9 @@ MPIRUN="$MPIRUN -n 1"
 
 ABIN_CMD="$ABINEXE -i $ABININ -x $ABINGEOM"
 
+trap cleanup INT ABRT TERM EXIT
+
 $MPIRUN $ABIN_CMD > $ABINOUT 2>&1 || true &
 abinpid=$!
 
-function cleanup {
-  kill -9 $abinpid > /dev/null 2>&1 || true
-  if [[ -f ERROR ]];then
-    mv ERROR ABIN_ERROR$IDX
-  fi
-  exit 0
-}
-
-trap cleanup INT ABRT TERM EXIT
-
 check_running_processes $abinpid