Fix self-contained QE/BerkeleyGW task installers

Replace obsolete task-local wrappers and failed build residue with deterministic installers backed by the pinned QE 6.7.0 / BerkeleyGW 4.0 runtime package.

tasks/physical_sciences/mose2_bse_absorption_soc/base/software/bin/absorption.cplx.x

@@ -1,6 +0,0 @@
-#!/usr/bin/env bash
-set -euo pipefail
-export OMPI_MCA_btl="^openib"
-export OPAL_PREFIX="/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw"
-export LD_LIBRARY_PATH="/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw/lib:${LD_LIBRARY_PATH:-}"
-exec "/opt/qe-bgw-6.7.0-4.0/src/BerkeleyGW-4.0/BSE/absorption.cplx.x" "$@"

tasks/physical_sciences/mose2_bse_absorption_soc/base/software/bin/activate-qe-bgw.sh

@@ -1,12 +0,0 @@
-#!/usr/bin/env bash
-set -euo pipefail
-export OMPI_MCA_btl="^openib"
-export OPAL_PREFIX="/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw"
-export LD_LIBRARY_PATH="/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw/lib:${LD_LIBRARY_PATH:-}"
-export PATH="/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw/bin:/opt/qe-bgw-6.7.0-4.0/src/BerkeleyGW-4.0/Epsilon:/opt/qe-bgw-6.7.0-4.0/src/BerkeleyGW-4.0/Sigma:/opt/qe-bgw-6.7.0-4.0/src/BerkeleyGW-4.0/BSE:/opt/qe-bgw-6.7.0-4.0/src/BerkeleyGW-4.0/Common:/opt/qe-bgw-6.7.0-4.0/src/BerkeleyGW-4.0/bin:$PATH"
-
-if [ "$#" -gt 0 ]; then
-  exec "$@"
-fi
-
-exec "${SHELL:-/bin/bash}" -l

tasks/physical_sciences/mose2_bse_absorption_soc/base/software/bin/epsilon.cplx.x

@@ -1,6 +0,0 @@
-#!/usr/bin/env bash
-set -euo pipefail
-export OMPI_MCA_btl="^openib"
-export OPAL_PREFIX="/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw"
-export LD_LIBRARY_PATH="/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw/lib:${LD_LIBRARY_PATH:-}"
-exec "/opt/qe-bgw-6.7.0-4.0/src/BerkeleyGW-4.0/Epsilon/epsilon.cplx.x" "$@"

tasks/physical_sciences/mose2_bse_absorption_soc/base/software/bin/gfortran

@@ -1,6 +0,0 @@
-#!/usr/bin/env bash
-set -euo pipefail
-export OMPI_MCA_btl="^openib"
-export OPAL_PREFIX="/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw"
-export LD_LIBRARY_PATH="/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw/lib:${LD_LIBRARY_PATH:-}"
-exec "/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw/bin/gfortran" "$@"

tasks/physical_sciences/mose2_bse_absorption_soc/base/software/bin/git

@@ -1,6 +0,0 @@
-#!/usr/bin/env bash
-set -euo pipefail
-export OMPI_MCA_btl="^openib"
-export OPAL_PREFIX="/media/user/data/agenthle/materials_science/mose2_bse_absorption_soc/base/software/runtime/envs/qe-bgw"
-export LD_LIBRARY_PATH="/media/user/data/agenthle/materials_science/mose2_bse_absorption_soc/base/software/runtime/envs/qe-bgw/lib:${LD_LIBRARY_PATH:-}"
-exec "/media/user/data/agenthle/materials_science/mose2_bse_absorption_soc/base/software/runtime/envs/qe-bgw/bin/git" "$@"

tasks/physical_sciences/mose2_bse_absorption_soc/base/software/bin/inteqp.cplx.x

@@ -1,6 +0,0 @@
-#!/usr/bin/env bash
-set -euo pipefail
-export OMPI_MCA_btl="^openib"
-export OPAL_PREFIX="/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw"
-export LD_LIBRARY_PATH="/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw/lib:${LD_LIBRARY_PATH:-}"
-exec "/opt/qe-bgw-6.7.0-4.0/src/BerkeleyGW-4.0/BSE/inteqp.cplx.x" "$@"

tasks/physical_sciences/mose2_bse_absorption_soc/base/software/bin/kernel.cplx.x

@@ -1,6 +0,0 @@
-#!/usr/bin/env bash
-set -euo pipefail
-export OMPI_MCA_btl="^openib"
-export OPAL_PREFIX="/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw"
-export LD_LIBRARY_PATH="/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw/lib:${LD_LIBRARY_PATH:-}"
-exec "/opt/qe-bgw-6.7.0-4.0/src/BerkeleyGW-4.0/BSE/kernel.cplx.x" "$@"

tasks/physical_sciences/mose2_bse_absorption_soc/base/software/bin/mpicc

@@ -1,6 +0,0 @@
-#!/usr/bin/env bash
-set -euo pipefail
-export OMPI_MCA_btl="^openib"
-export OPAL_PREFIX="/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw"
-export LD_LIBRARY_PATH="/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw/lib:${LD_LIBRARY_PATH:-}"
-exec "/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw/bin/mpicc" "$@"

tasks/physical_sciences/mose2_bse_absorption_soc/base/software/bin/mpicxx

@@ -1,6 +0,0 @@
-#!/usr/bin/env bash
-set -euo pipefail
-export OMPI_MCA_btl="^openib"
-export OPAL_PREFIX="/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw"
-export LD_LIBRARY_PATH="/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw/lib:${LD_LIBRARY_PATH:-}"
-exec "/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw/bin/mpicxx" "$@"

tasks/physical_sciences/mose2_bse_absorption_soc/base/software/bin/mpifort

@@ -1,6 +0,0 @@
-#!/usr/bin/env bash
-set -euo pipefail
-export OMPI_MCA_btl="^openib"
-export OPAL_PREFIX="/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw"
-export LD_LIBRARY_PATH="/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw/lib:${LD_LIBRARY_PATH:-}"
-exec "/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw/bin/mpifort" "$@"

tasks/physical_sciences/mose2_bse_absorption_soc/base/software/bin/mpirun

@@ -1,6 +0,0 @@
-#!/usr/bin/env bash
-set -euo pipefail
-export OMPI_MCA_btl="^openib"
-export OPAL_PREFIX="/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw"
-export LD_LIBRARY_PATH="/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw/lib:${LD_LIBRARY_PATH:-}"
-exec "/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw/bin/mpirun" "$@"

tasks/physical_sciences/mose2_bse_absorption_soc/base/software/bin/pw.x

@@ -1,6 +0,0 @@
-#!/usr/bin/env bash
-set -euo pipefail
-export OMPI_MCA_btl="^openib"
-export OPAL_PREFIX="/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw"
-export LD_LIBRARY_PATH="/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw/lib:${LD_LIBRARY_PATH:-}"
-exec "/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw/bin/pw.x" "$@"

tasks/physical_sciences/mose2_bse_absorption_soc/base/software/bin/python

@@ -1,6 +0,0 @@
-#!/usr/bin/env bash
-set -euo pipefail
-export OMPI_MCA_btl="^openib"
-export OPAL_PREFIX="/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw"
-export LD_LIBRARY_PATH="/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw/lib:${LD_LIBRARY_PATH:-}"
-exec "/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw/bin/python" "$@"

tasks/physical_sciences/mose2_bse_absorption_soc/base/software/bin/sigma.cplx.x

@@ -1,6 +0,0 @@
-#!/usr/bin/env bash
-set -euo pipefail
-export OMPI_MCA_btl="^openib"
-export OPAL_PREFIX="/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw"
-export LD_LIBRARY_PATH="/opt/qe-bgw-6.7.0-4.0/envs/qe-bgw/lib:${LD_LIBRARY_PATH:-}"
-exec "/opt/qe-bgw-6.7.0-4.0/src/BerkeleyGW-4.0/Sigma/sigma.cplx.x" "$@"

tasks/physical_sciences/mose2_bse_absorption_soc/base/software/bootstrap_remote_software.sh

@@ -1,145 +1,7 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-TASK_ROOT="/media/user/data/agenthle/materials_science/mose2_bse_absorption_soc/base"
-SOFTWARE_ROOT="$TASK_ROOT/software"
-INSTALL_ROOT="$SOFTWARE_ROOT/runtime"
-MAMBA_ROOT="$INSTALL_ROOT/micromamba"
-ENV_PREFIX="$INSTALL_ROOT/envs/qe-bgw"
-SRC_ROOT="$INSTALL_ROOT/src"
-LOG_DIR="$SOFTWARE_ROOT/logs"
-BIN_DIR="$SOFTWARE_ROOT/bin"
-MICROMAMBA_VERSION="2.5.0"
-
-SEED_RUNTIME_ROOT="/media/user/data/agenthle/materials_science/computational_materials_science/base/software/runtime"
-
-clone_runtime_from_seed() {
-  if [ -d "$INSTALL_ROOT" ] && find "$INSTALL_ROOT" -mindepth 1 -maxdepth 1 | read -r _; then
-    return
-  fi
-  if [ ! -d "$SEED_RUNTIME_ROOT" ]; then
-    log "missing verified seed runtime at $SEED_RUNTIME_ROOT"
-    return 1
-  fi
-
-  log "cloning verified runtime from $SEED_RUNTIME_ROOT into $INSTALL_ROOT"
-  mkdir -p "$(dirname "$INSTALL_ROOT")"
-  rm -rf "$INSTALL_ROOT"
-  cp -al "$SEED_RUNTIME_ROOT" "$INSTALL_ROOT"
-}
-
-
-mkdir -p "$SOFTWARE_ROOT" "$LOG_DIR" "$BIN_DIR"
-
-log() {
-  printf '[bootstrap] %s\n' "$*"
-}
-
-install_micromamba() {
-  if [ -x "$MAMBA_ROOT/bin/micromamba" ]; then
-    log "micromamba already present at $MAMBA_ROOT/bin/micromamba"
-    return
-  fi
-
-  log "installing micromamba under $MAMBA_ROOT"
-  rm -rf "$MAMBA_ROOT.tmp"
-  mkdir -p "$MAMBA_ROOT.tmp"
-  curl -L "https://micro.mamba.pm/api/micromamba/linux-64/${MICROMAMBA_VERSION}" | tar -xj -C "$MAMBA_ROOT.tmp"
-  rm -rf "$MAMBA_ROOT"
-  mv "$MAMBA_ROOT.tmp" "$MAMBA_ROOT"
-}
-
-create_env() {
-  export MAMBA_ROOT_PREFIX="$MAMBA_ROOT/root"
-
-  if [ ! -x "$MAMBA_ROOT/bin/micromamba" ]; then
-    log "micromamba binary missing"
-    return 1
-  fi
-
-  if [ -x "$ENV_PREFIX/bin/pw.x" ] && [ -x "$ENV_PREFIX/bin/mpirun" ] && [ -x "$ENV_PREFIX/bin/gfortran" ]; then
-    log "QE toolchain env already exists at $ENV_PREFIX"
-    return
-  fi
-
-  log "creating QE/MPI/compiler environment at $ENV_PREFIX"
-  "$MAMBA_ROOT/bin/micromamba" create -y -p "$ENV_PREFIX" -c conda-forge \
-    python=3.11.15 \
-    qe=6.7.0 \
-    fortran-compiler=1.11.0 \
-    c-compiler=1.11.0 \
-    cxx-compiler=1.11.0 \
-    openmpi=4.1.6 \
-    cmake=4.3.1 \
-    make=4.4.1 \
-    pkg-config=0.29.2 \
-    git=2.53.0 \
-    fftw=3.3.10 \
-    scalapack=2.2.0
-}
-
-write_wrappers() {
-  cat > "$BIN_DIR/activate-qe-bgw.sh" <<EOF
-#!/usr/bin/env bash
-set -euo pipefail
-export OMPI_MCA_btl="^openib"
-export OPAL_PREFIX="$ENV_PREFIX"
-export LD_LIBRARY_PATH="$ENV_PREFIX/lib:\${LD_LIBRARY_PATH:-}"
-export MAMBA_ROOT_PREFIX="$MAMBA_ROOT/root"
-eval "\$("$MAMBA_ROOT/bin/micromamba" shell hook -s bash)"
-micromamba activate "$ENV_PREFIX"
-exec "\$@"
-EOF
-  chmod +x "$BIN_DIR/activate-qe-bgw.sh"
-
-  for exe in pw.x mpirun mpicc mpicxx mpifort gfortran git python; do
-    cat > "$BIN_DIR/$exe" <<EOF
-#!/usr/bin/env bash
-set -euo pipefail
-export OMPI_MCA_btl="^openib"
-export OPAL_PREFIX="$ENV_PREFIX"
-export LD_LIBRARY_PATH="$ENV_PREFIX/lib:\${LD_LIBRARY_PATH:-}"
-exec "$ENV_PREFIX/bin/$exe" "\$@"
-EOF
-    chmod +x "$BIN_DIR/$exe"
-  done
-}
-
-write_bgw_wrappers() {
-  local srcdir="$SRC_ROOT/BerkeleyGW-4.0"
-  for exe in epsilon.cplx.x sigma.cplx.x kernel.cplx.x absorption.cplx.x inteqp.cplx.x epsilon.real.x sigma.real.x kernel.real.x absorption.real.x; do
-    if [ -x "$srcdir/bin/$exe" ]; then
-      cat > "$BIN_DIR/$exe" <<EOF
-#!/usr/bin/env bash
-set -euo pipefail
-export OMPI_MCA_btl="^openib"
-export OPAL_PREFIX="$ENV_PREFIX"
-export LD_LIBRARY_PATH="$ENV_PREFIX/lib:\${LD_LIBRARY_PATH:-}"
-exec "$srcdir/bin/$exe" "\$@"
-EOF
-      chmod +x "$BIN_DIR/$exe"
-    fi
-  done
-  return 0
-}
-
-main() {
-  log "task root = $TASK_ROOT"
-  clone_runtime_from_seed
-  install_micromamba
-  create_env
-  write_wrappers
-  write_bgw_wrappers
-
-  for exe in epsilon.cplx.x sigma.cplx.x kernel.cplx.x absorption.cplx.x; do
-    if [ ! -x "$BIN_DIR/$exe" ]; then
-      log "missing required BerkeleyGW wrapper after bootstrap: $BIN_DIR/$exe"
-      return 1
-    fi
-  done
-
-  log "installed wrappers:"
-  find "$BIN_DIR" -maxdepth 1 -type f | sort
-}
-
-main "$@"
+# Compatibility entry point retained for existing operator commands. Runtime
+# provisioning is owned by requiredSystemPackages: qe-bgw-6.7.0-4.0.
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+exec "$SCRIPT_DIR/install_software.sh" "$@"

tasks/physical_sciences/mose2_bse_absorption_soc/base/software/install_software.sh

@@ -0,0 +1,78 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+TASK_ROOT="${TASK_ROOT:-/media/user/data/agenthle/physical_sciences/mose2_bse_absorption_soc/base}"
+INSTALL_ROOT="${QE_BGW_ROOT:-/opt/qe-bgw-6.7.0-4.0}"
+BIN_DIR="$TASK_ROOT/software/bin"
+ENV_PREFIX="$INSTALL_ROOT/envs/qe-bgw"
+BGW_ROOT="$INSTALL_ROOT/src/BerkeleyGW-4.0"
+
+declare -A TARGETS=(
+  [pw.x]="$ENV_PREFIX/bin/pw.x"
+  [pw2bgw.x]="$ENV_PREFIX/bin/pw2bgw.x"
+  [bands.x]="$ENV_PREFIX/bin/bands.x"
+  [mpirun]="$ENV_PREFIX/bin/mpirun"
+  [python]="$ENV_PREFIX/bin/python"
+  [epsilon.cplx.x]="$BGW_ROOT/Epsilon/epsilon.cplx.x"
+  [sigma.cplx.x]="$BGW_ROOT/Sigma/sigma.cplx.x"
+  [kernel.cplx.x]="$BGW_ROOT/BSE/kernel.cplx.x"
+  [absorption.cplx.x]="$BGW_ROOT/BSE/absorption.cplx.x"
+  [inteqp.cplx.x]="$BGW_ROOT/BSE/inteqp.cplx.x"
+)
+
+log() { printf '[qe-bgw-task-runtime] %s\n' "$*"; }
+
+write_wrapper() {
+  local name="$1" target="${TARGETS[$1]}"
+  cat >"$BIN_DIR/$name" <<EOF
+#!/usr/bin/env bash
+set -euo pipefail
+export OMPI_MCA_btl="^openib"
+export OPAL_PREFIX="$ENV_PREFIX"
+export LD_LIBRARY_PATH="$ENV_PREFIX/lib:\${LD_LIBRARY_PATH:-}"
+exec "$target" "\$@"
+EOF
+  chmod 0755 "$BIN_DIR/$name"
+}
+
+verify_elf_closure() {
+  local path="$1" missing
+  missing="$(LD_LIBRARY_PATH="$ENV_PREFIX/lib:${LD_LIBRARY_PATH:-}" ldd "$path" | awk '/not found/{print}')"
+  if [ -n "$missing" ]; then
+    printf '%s\n' "$missing" >&2
+    log "unresolved shared libraries for $path"
+    return 1
+  fi
+}
+
+main() {
+  mkdir -p "$BIN_DIR"
+
+  local name target
+  for name in "${!TARGETS[@]}"; do
+    target="${TARGETS[$name]}"
+    test -x "$target" || { log "missing required executable: $target"; exit 1; }
+    verify_elf_closure "$target"
+    write_wrapper "$name"
+  done
+
+  "$BIN_DIR/pw.x" -h >"$BIN_DIR/.pw-version.txt" 2>&1 || true
+  grep -q 'PWSCF v.6.7MaX' "$BIN_DIR/.pw-version.txt"
+  "$BIN_DIR/mpirun" --help >"$BIN_DIR/.mpi-version.txt" 2>&1 || true
+  grep -q 'mpirun (Open MPI) 4.1.6' "$BIN_DIR/.mpi-version.txt"
+  "$BIN_DIR/python" --version >"$BIN_DIR/.python-version.txt" 2>&1
+  grep -q 'Python 3.11.15' "$BIN_DIR/.python-version.txt"
+  rm -f "$BIN_DIR/.pw-version.txt" "$BIN_DIR/.mpi-version.txt" "$BIN_DIR/.python-version.txt"
+
+  for name in epsilon.cplx.x sigma.cplx.x kernel.cplx.x absorption.cplx.x inteqp.cplx.x; do
+    grep -a -q 'BerkeleyGW' "${TARGETS[$name]}" || {
+      log "BerkeleyGW marker missing from ${TARGETS[$name]}"
+      exit 1
+    }
+  done
+
+  log "verified QE 6.7MaX, Open MPI 4.1.6, Python 3.11.15, and BerkeleyGW 4.0"
+  log "wrote task-local wrappers under $BIN_DIR"
+}
+
+main "$@"

tasks/physical_sciences/mose2_bse_absorption_soc/base/software/logs/berkeleygw-build.log

@@ -1,28 +0,0 @@
-+ export PATH=/media/user/data/agenthle/materials_science/mose2_bse_absorption_soc/base/software/runtime/envs/qe-bgw/bin:/home/user/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/snap/bin
-+ PATH=/media/user/data/agenthle/materials_science/mose2_bse_absorption_soc/base/software/runtime/envs/qe-bgw/bin:/home/user/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/snap/bin
-+ export CC=/media/user/data/agenthle/materials_science/mose2_bse_absorption_soc/base/software/runtime/envs/qe-bgw/bin/mpicc
-+ CC=/media/user/data/agenthle/materials_science/mose2_bse_absorption_soc/base/software/runtime/envs/qe-bgw/bin/mpicc
-+ export CXX=/media/user/data/agenthle/materials_science/mose2_bse_absorption_soc/base/software/runtime/envs/qe-bgw/bin/mpicxx
-+ CXX=/media/user/data/agenthle/materials_science/mose2_bse_absorption_soc/base/software/runtime/envs/qe-bgw/bin/mpicxx
-+ export FC=/media/user/data/agenthle/materials_science/mose2_bse_absorption_soc/base/software/runtime/envs/qe-bgw/bin/mpifort
-+ FC=/media/user/data/agenthle/materials_science/mose2_bse_absorption_soc/base/software/runtime/envs/qe-bgw/bin/mpifort
-+ export F77=/media/user/data/agenthle/materials_science/mose2_bse_absorption_soc/base/software/runtime/envs/qe-bgw/bin/mpifort
-+ F77=/media/user/data/agenthle/materials_science/mose2_bse_absorption_soc/base/software/runtime/envs/qe-bgw/bin/mpifort
-+ export F90=/media/user/data/agenthle/materials_science/mose2_bse_absorption_soc/base/software/runtime/envs/qe-bgw/bin/mpifort
-+ F90=/media/user/data/agenthle/materials_science/mose2_bse_absorption_soc/base/software/runtime/envs/qe-bgw/bin/mpifort
-+ export 'BLAS_LIBS=-L/media/user/data/agenthle/materials_science/mose2_bse_absorption_soc/base/software/runtime/envs/qe-bgw/lib -lopenblas'
-+ BLAS_LIBS='-L/media/user/data/agenthle/materials_science/mose2_bse_absorption_soc/base/software/runtime/envs/qe-bgw/lib -lopenblas'
-+ export 'LAPACK_LIBS=-L/media/user/data/agenthle/materials_science/mose2_bse_absorption_soc/base/software/runtime/envs/qe-bgw/lib -lopenblas'
-+ LAPACK_LIBS='-L/media/user/data/agenthle/materials_science/mose2_bse_absorption_soc/base/software/runtime/envs/qe-bgw/lib -lopenblas'
-+ export 'SCALAPACK_LIBS=-L/media/user/data/agenthle/materials_science/mose2_bse_absorption_soc/base/software/runtime/envs/qe-bgw/lib -lscalapack'
-+ SCALAPACK_LIBS='-L/media/user/data/agenthle/materials_science/mose2_bse_absorption_soc/base/software/runtime/envs/qe-bgw/lib -lscalapack'
-+ export FFTW_INC=/media/user/data/agenthle/materials_science/mose2_bse_absorption_soc/base/software/runtime/envs/qe-bgw/include
-+ FFTW_INC=/media/user/data/agenthle/materials_science/mose2_bse_absorption_soc/base/software/runtime/envs/qe-bgw/include
-+ export 'FFTW_LIBS=-L/media/user/data/agenthle/materials_science/mose2_bse_absorption_soc/base/software/runtime/envs/qe-bgw/lib -lfftw3 -lfftw3f'
-+ FFTW_LIBS='-L/media/user/data/agenthle/materials_science/mose2_bse_absorption_soc/base/software/runtime/envs/qe-bgw/lib -lfftw3 -lfftw3f'
-+ cd /media/user/data/agenthle/materials_science/mose2_bse_absorption_soc/base/software/runtime/src/BerkeleyGW-4.0
-+ cat
-+ cp flavor_cplx.mk flavor.mk
-+ make epsilon sigma bse -j2
-arch.mk:26: *** missing separator.  Stop.
-+ true

tasks/physical_sciences/silicon_bse_absorption/base/software/bootstrap_remote_software.sh

@@ -1,210 +1,7 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-TASK_ROOT="/media/user/data/agenthle/materials_science/silicon_bse_absorption/base"
-SOFTWARE_ROOT="$TASK_ROOT/software"
-INSTALL_ROOT="$SOFTWARE_ROOT/runtime"
-MAMBA_ROOT="$INSTALL_ROOT/micromamba"
-ENV_PREFIX="$INSTALL_ROOT/envs/qe-bgw"
-SRC_ROOT="$INSTALL_ROOT/src"
-LOG_DIR="$SOFTWARE_ROOT/logs"
-BIN_DIR="$SOFTWARE_ROOT/bin"
-
-SEED_RUNTIME_ROOT="/media/user/data/agenthle/materials_science/computational_materials_science/base/software/runtime"
-
-clone_runtime_from_seed() {
-  if [ -d "$INSTALL_ROOT" ] && find "$INSTALL_ROOT" -mindepth 1 -maxdepth 1 | read -r _; then
-    return
-  fi
-  if [ ! -d "$SEED_RUNTIME_ROOT" ]; then
-    return
-  fi
-
-  log "cloning verified runtime from $SEED_RUNTIME_ROOT into $INSTALL_ROOT"
-  mkdir -p "$(dirname "$INSTALL_ROOT")"
-  rm -rf "$INSTALL_ROOT"
-  cp -al "$SEED_RUNTIME_ROOT" "$INSTALL_ROOT"
-}
-
-
-mkdir -p "$SOFTWARE_ROOT" "$LOG_DIR" "$BIN_DIR"
-
-log() {
-  printf '[bootstrap] %s\n' "$*"
-}
-
-install_micromamba() {
-  if [ -x "$MAMBA_ROOT/bin/micromamba" ]; then
-    log "micromamba already present at $MAMBA_ROOT/bin/micromamba"
-    return
-  fi
-
-  log "installing micromamba under $MAMBA_ROOT"
-  rm -rf "$MAMBA_ROOT.tmp"
-  mkdir -p "$MAMBA_ROOT.tmp"
-  curl -L https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xj -C "$MAMBA_ROOT.tmp"
-  rm -rf "$MAMBA_ROOT"
-  mv "$MAMBA_ROOT.tmp" "$MAMBA_ROOT"
-}
-
-create_env() {
-  export MAMBA_ROOT_PREFIX="$MAMBA_ROOT/root"
-
-  if [ ! -x "$MAMBA_ROOT/bin/micromamba" ]; then
-    log "micromamba binary missing"
-    return 1
-  fi
-
-  if [ -x "$ENV_PREFIX/bin/pw.x" ] && [ -x "$ENV_PREFIX/bin/mpirun" ] && [ -x "$ENV_PREFIX/bin/gfortran" ]; then
-    log "QE toolchain env already exists at $ENV_PREFIX"
-    return
-  fi
-
-  log "creating QE/MPI/compiler environment at $ENV_PREFIX"
-  "$MAMBA_ROOT/bin/micromamba" create -y -p "$ENV_PREFIX" -c conda-forge \
-    python=3.11 \
-    qe=6.7.0 \
-    fortran-compiler \
-    c-compiler \
-    cxx-compiler \
-    openmpi \
-    cmake \
-    make \
-    pkg-config \
-    git
-}
-
-write_wrappers() {
-  cat > "$BIN_DIR/activate-qe-bgw.sh" <<EOF
-#!/usr/bin/env bash
-set -euo pipefail
-export OMPI_MCA_btl="^openib"
-export MAMBA_ROOT_PREFIX="$MAMBA_ROOT/root"
-eval "\$("$MAMBA_ROOT/bin/micromamba" shell hook -s bash)"
-micromamba activate "$ENV_PREFIX"
-exec "\$@"
-EOF
-  chmod +x "$BIN_DIR/activate-qe-bgw.sh"
-
-  for exe in pw.x mpirun mpicc mpicxx mpifort gfortran git python; do
-    cat > "$BIN_DIR/$exe" <<EOF
-#!/usr/bin/env bash
-set -euo pipefail
-export OMPI_MCA_btl="^openib"
-exec "$ENV_PREFIX/bin/$exe" "\$@"
-EOF
-    chmod +x "$BIN_DIR/$exe"
-  done
-}
-
-download_berkeleygw() {
-  local tarball="$SRC_ROOT/BerkeleyGW-4.0.tar.gz"
-  local srcdir="$SRC_ROOT/BerkeleyGW-4.0"
-
-  if [ ! -f "$tarball" ]; then
-    log "downloading BerkeleyGW 4.0 source tarball"
-    curl -L https://app.box.com/shared/static/22edl07muvhfnd900tnctsjjftbtcqc4.gz -o "$tarball"
-  fi
-
-  if [ ! -d "$srcdir" ]; then
-    log "extracting BerkeleyGW source"
-    tar -xzf "$tarball" -C "$SRC_ROOT"
-  fi
-}
-
-attempt_bgw_build() {
-  local srcdir="$SRC_ROOT/BerkeleyGW-4.0"
-  local builddir="$srcdir"
-  local logfile="$LOG_DIR/berkeleygw-build.log"
-
-  if [ ! -d "$srcdir" ]; then
-    log "BerkeleyGW source tree missing"
-    return 1
-  fi
-
-  log "attempting BerkeleyGW build; logging to $logfile"
-  (
-    set -x
-    export PATH="$ENV_PREFIX/bin:$PATH"
-    export CC="$ENV_PREFIX/bin/mpicc"
-    export CXX="$ENV_PREFIX/bin/mpicxx"
-    export FC="$ENV_PREFIX/bin/mpifort"
-    export F77="$ENV_PREFIX/bin/mpifort"
-    export F90="$ENV_PREFIX/bin/mpifort"
-    export BLAS_LIBS="-L$ENV_PREFIX/lib -lopenblas"
-    export LAPACK_LIBS="-L$ENV_PREFIX/lib -lopenblas"
-    export SCALAPACK_LIBS="-L$ENV_PREFIX/lib -lscalapack"
-    export FFTW_INC="$ENV_PREFIX/include"
-    export FFTW_LIBS="-L$ENV_PREFIX/lib -lfftw3 -lfftw3f"
-    cd "$builddir"
-
-    cat > arch.mk <<EOF
-COMPFLAG  = -DGNU
-PARAFLAG  = -DMPI
-MATHFLAG  = -DUSESCALAPACK -DUSEFFTW3
-
-FCPP    = cpp -C -nostdinc
-F90free = $ENV_PREFIX/bin/mpifort -ffree-form -ffree-line-length-none -fallow-argument-mismatch
-LINK    = $ENV_PREFIX/bin/mpifort
-FOPTS   = -O2
-FNOOPTS = \$(FOPTS)
-MOD_OPT = -J
-INCFLAG = -I
-
-C_PARAFLAG = -DPARA
-CC_COMP = $ENV_PREFIX/bin/mpicxx -std=c++11
-C_COMP  = $ENV_PREFIX/bin/mpicc -std=c99
-C_LINK  = $ENV_PREFIX/bin/mpicxx
-C_OPTS  = -O2
-C_DEBUGFLAG =
-
-REMOVE = /bin/rm -f
-
-FFTWLIB      = -L$ENV_PREFIX/lib -lfftw3
-FFTWINCLUDE  = $ENV_PREFIX/include
-LAPACKLIB    = -L$ENV_PREFIX/lib -llapack -lblas
-SCALAPACKLIB = -L$ENV_PREFIX/lib -lscalapack
-EOF
-
-    cp flavor_cplx.mk flavor.mk
-    make epsilon sigma bse -j2 || true
-  ) >"$logfile" 2>&1
-
-  if find "$srcdir/bin" -maxdepth 1 -type f \( -name 'epsilon*' -o -name 'sigma*' -o -name 'kernel*' -o -name 'absorption*' \) | grep -q .; then
-    log "BerkeleyGW build produced binaries under $srcdir/bin"
-  else
-    log "BerkeleyGW build did not produce the expected binaries"
-    return 1
-  fi
-}
-
-write_bgw_wrappers() {
-  local srcdir="$SRC_ROOT/BerkeleyGW-4.0"
-  for exe in epsilon.cplx.x sigma.cplx.x kernel.cplx.x absorption.cplx.x inteqp.cplx.x epsilon.real.x sigma.real.x kernel.real.x absorption.real.x; do
-    if [ -x "$srcdir/bin/$exe" ]; then
-      cat > "$BIN_DIR/$exe" <<EOF
-#!/usr/bin/env bash
-set -euo pipefail
-export OMPI_MCA_btl="^openib"
-exec "$srcdir/bin/$exe" "\$@"
-EOF
-      chmod +x "$BIN_DIR/$exe"
-    fi
-  done
-}
-
-main() {
-  log "task root = $TASK_ROOT"
-  clone_runtime_from_seed
-  install_micromamba
-  create_env
-  write_wrappers
-  download_berkeleygw
-  attempt_bgw_build || true
-  write_bgw_wrappers
-
-  log "installed wrappers:"
-  find "$BIN_DIR" -maxdepth 1 -type f | sort
-}
-
-main "$@"
+# Compatibility entry point retained for existing operator commands. Runtime
+# provisioning is owned by requiredSystemPackages: qe-bgw-6.7.0-4.0.
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+exec "$SCRIPT_DIR/install_software.sh" "$@"

tasks/physical_sciences/silicon_bse_absorption/base/software/install_software.sh

@@ -0,0 +1,78 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+TASK_ROOT="${TASK_ROOT:-/media/user/data/agenthle/physical_sciences/silicon_bse_absorption/base}"
+INSTALL_ROOT="${QE_BGW_ROOT:-/opt/qe-bgw-6.7.0-4.0}"
+BIN_DIR="$TASK_ROOT/software/bin"
+ENV_PREFIX="$INSTALL_ROOT/envs/qe-bgw"
+BGW_ROOT="$INSTALL_ROOT/src/BerkeleyGW-4.0"
+
+declare -A TARGETS=(
+  [pw.x]="$ENV_PREFIX/bin/pw.x"
+  [pw2bgw.x]="$ENV_PREFIX/bin/pw2bgw.x"
+  [bands.x]="$ENV_PREFIX/bin/bands.x"
+  [mpirun]="$ENV_PREFIX/bin/mpirun"
+  [python]="$ENV_PREFIX/bin/python"
+  [epsilon.cplx.x]="$BGW_ROOT/Epsilon/epsilon.cplx.x"
+  [sigma.cplx.x]="$BGW_ROOT/Sigma/sigma.cplx.x"
+  [kernel.cplx.x]="$BGW_ROOT/BSE/kernel.cplx.x"
+  [absorption.cplx.x]="$BGW_ROOT/BSE/absorption.cplx.x"
+  [inteqp.cplx.x]="$BGW_ROOT/BSE/inteqp.cplx.x"
+)
+
+log() { printf '[qe-bgw-task-runtime] %s\n' "$*"; }
+
+write_wrapper() {
+  local name="$1" target="${TARGETS[$1]}"
+  cat >"$BIN_DIR/$name" <<EOF
+#!/usr/bin/env bash
+set -euo pipefail
+export OMPI_MCA_btl="^openib"
+export OPAL_PREFIX="$ENV_PREFIX"
+export LD_LIBRARY_PATH="$ENV_PREFIX/lib:\${LD_LIBRARY_PATH:-}"
+exec "$target" "\$@"
+EOF
+  chmod 0755 "$BIN_DIR/$name"
+}
+
+verify_elf_closure() {
+  local path="$1" missing
+  missing="$(LD_LIBRARY_PATH="$ENV_PREFIX/lib:${LD_LIBRARY_PATH:-}" ldd "$path" | awk '/not found/{print}')"
+  if [ -n "$missing" ]; then
+    printf '%s\n' "$missing" >&2
+    log "unresolved shared libraries for $path"
+    return 1
+  fi
+}
+
+main() {
+  mkdir -p "$BIN_DIR"
+
+  local name target
+  for name in "${!TARGETS[@]}"; do
+    target="${TARGETS[$name]}"
+    test -x "$target" || { log "missing required executable: $target"; exit 1; }
+    verify_elf_closure "$target"
+    write_wrapper "$name"
+  done
+
+  "$BIN_DIR/pw.x" -h >"$BIN_DIR/.pw-version.txt" 2>&1 || true
+  grep -q 'PWSCF v.6.7MaX' "$BIN_DIR/.pw-version.txt"
+  "$BIN_DIR/mpirun" --help >"$BIN_DIR/.mpi-version.txt" 2>&1 || true
+  grep -q 'mpirun (Open MPI) 4.1.6' "$BIN_DIR/.mpi-version.txt"
+  "$BIN_DIR/python" --version >"$BIN_DIR/.python-version.txt" 2>&1
+  grep -q 'Python 3.11.15' "$BIN_DIR/.python-version.txt"
+  rm -f "$BIN_DIR/.pw-version.txt" "$BIN_DIR/.mpi-version.txt" "$BIN_DIR/.python-version.txt"
+
+  for name in epsilon.cplx.x sigma.cplx.x kernel.cplx.x absorption.cplx.x inteqp.cplx.x; do
+    grep -a -q 'BerkeleyGW' "${TARGETS[$name]}" || {
+      log "BerkeleyGW marker missing from ${TARGETS[$name]}"
+      exit 1
+    }
+  done
+
+  log "verified QE 6.7MaX, Open MPI 4.1.6, Python 3.11.15, and BerkeleyGW 4.0"
+  log "wrote task-local wrappers under $BIN_DIR"
+}
+
+main "$@"