Feature/add salmon program

docs/cx/BENCHKIT_GAP_ANALYSIS.md

@@ -283,15 +283,15 @@ Once the estimation specification is clarified, many other design decisions beco
 - 推定モデルの種別と識別方法
 - 再推定のトリガ、履歴、比較可能性と表示導線
 
-現状は `qws` が先行 app として、
+現状は `qws` と `genesis` が先行 app として、
 
 - `weakscaling`
 - `instrumented_app_sections_dummy`
 - 推定元 result の UUID / timestamp 引き回し
 - side ごとの `model` 表現
 
 まで動作確認済みである。
-したがって、入口確認段階はすでに超えており、次はこの形を複数 app に横展開できるよう引き上げる必要がある。
+したがって、入口確認段階はすでに超えており、次はこの形をさらに他 app に横展開できるよう引き上げる必要がある。
 
 #### 5.1.1 推定機構の実装 GAP 再調査 / Re-Survey of Estimation Implementation Gaps
 
@@ -333,7 +333,7 @@ Once the estimation specification is clarified, many other design decisions beco
 
 推定機構について、次の実装順を推奨する。
 
-1. `qws` 以外の app へ推定方式を横展開する
+1. `qws` / `genesis` で得た推定方式を他 app へ横展開する
 2. `not_applicable` と compare を含む推定差分 UI を portal で見やすくする
 3. 複数 detailed package 間の fallback と discovery を整理する
 4. その後に再推定比較 UI と portal 起動導線へ進む

programs/salmon/build.sh

@@ -0,0 +1,127 @@
+#!/bin/bash
+set -euo pipefail
+
+system="$1"
+
+REPO_URL="https://github.com/SALMON-TDDFT/SALMON2"
+REPO_DIR="SALMON2"
+VERSION_TAG="v.2.2.2"
+BUILD_DIR="build-benchkit"
+ARTIFACT_DIR="${PWD}/artifacts"
+
+source scripts/bk_functions.sh
+
+mkdir -p "${ARTIFACT_DIR}"
+bk_fetch_source "${REPO_URL}" "${REPO_DIR}" "${VERSION_TAG}"
+
+cd "${REPO_DIR}"
+rm -rf "${BUILD_DIR}"
+mkdir -p "${BUILD_DIR}"
+
+common_cmake_args=(
+  -DUSE_MPI=ON
+  -DUSE_SCALAPACK=OFF
+  -DUSE_EIGENEXA=OFF
+  -DUSE_LIBXC=OFF
+  -DCMAKE_BUILD_TYPE=None
+  -DCMAKE_VERBOSE_MAKEFILE=ON
+)
+
+case "${system}" in
+  Fugaku)
+    cmake_args=(
+      "${common_cmake_args[@]}"
+      -DCMAKE_Fortran_COMPILER=mpifrtpx
+      -DCMAKE_C_COMPILER=mpifccpx
+      -DCMAKE_Fortran_FLAGS="-Kfast -Kocl -Nlst=t -Koptmsg=2 -Ncheck_std=03s"
+      -DCMAKE_C_FLAGS="-Kfast -Kocl -Nlst=t -Koptmsg=2 -Xg -std=gnu99"
+      -DCMAKE_C_STANDARD_COMPUTED_DEFAULT=Fujitsu
+      "-DCMAKE_Fortran_MODDIR_FLAG=-M "
+      -DOPENMP_FLAGS="-Kopenmp -Nfjomplib"
+      -DLAPACK_VENDOR_FLAGS=-SSL2BLAMP
+      -DFortran_PP_FLAGS=-Cpp
+    )
+    ;;
+  RC_GH200)
+    module purge
+    module load system/qc-gh200 nvhpc-hpcx-cuda12/25.7
+    cmake_args=(
+      "${common_cmake_args[@]}"
+      -DCMAKE_Fortran_COMPILER=mpif90
+      -DCMAKE_C_COMPILER=mpicc
+      -DOPENMP_FLAGS=-Mnoopenmp
+      -DUSE_OPENACC=ON
+      -DUSE_CUDA=ON
+      -DUSE_MPI_DEFAULT=ON
+      -DCMAKE_SYSTEM_PROCESSOR=openacc
+      -DCMAKE_Fortran_FLAGS="-O3 -Wall -fstrict-aliasing -acc=strict -gpu=cc90,managed,ptxinfo -cudalib=cublas -cuda -Minfo=accel -DUSE_OPENACC -DUSE_CUDA"
+      -DCMAKE_C_FLAGS="-O3 -Wall -alias=ansi -acc=strict -gpu=cc90,managed,ptxinfo -cudalib=cublas -cuda -Minfo=accel -DUSE_OPENACC -DUSE_CUDA"
+      -DCMAKE_CUDA_ARCHITECTURES=90
+      -DCMAKE_CUDA_FLAGS=-arch=sm_90
+    )
+    ;;
+  RC_DGXSP)
+    source /etc/profile.d/modules.sh
+    module purge
+    module load system/ng-dgx nvhpc-hpcx-cuda13/26.3
+    cmake_args=(
+      "${common_cmake_args[@]}"
+      -DCMAKE_Fortran_COMPILER=mpif90
+      -DCMAKE_C_COMPILER=mpicc
+      -DOPENMP_FLAGS=-Mnoopenmp
+      -DUSE_OPENACC=ON
+      -DUSE_CUDA=ON
+      -DUSE_MPI_DEFAULT=ON
+      -DCMAKE_SYSTEM_PROCESSOR=openacc
+      -DCMAKE_Fortran_FLAGS="-O3 -Wall -fstrict-aliasing -acc=strict -gpu=cc90,cc100,cc120,managed,ptxinfo -cudalib=cublas -cuda -Minfo=accel -DUSE_OPENACC -DUSE_CUDA"
+      -DCMAKE_C_FLAGS="-O3 -Wall -alias=ansi -acc=strict -gpu=cc90,cc100,cc120,managed,ptxinfo -cudalib=cublas -cuda -Minfo=accel -DUSE_OPENACC -DUSE_CUDA"
+      -DCMAKE_CUDA_ARCHITECTURES="90;100;120"
+      -DCMAKE_CUDA_FLAGS=
+    )
+    ;;
+  RC_GENOA)
+    module purge
+    module load system/genoa mpi/mpich-x86_64
+    cmake_args=(
+      "${common_cmake_args[@]}"
+      -DCMAKE_Fortran_COMPILER=mpif90
+      -DCMAKE_C_COMPILER=mpicc
+      -DCMAKE_Fortran_FLAGS="-O3 -ffree-line-length-none -fallow-argument-mismatch"
+      -DCMAKE_C_FLAGS=-O3
+    )
+    ;;
+  RC_FX700)
+    module purge
+    module load system/fx700 FJSVstclanga
+    cmake_args=(
+      "${common_cmake_args[@]}"
+      -DCMAKE_Fortran_COMPILER=mpifrt
+      -DCMAKE_C_COMPILER=mpifcc
+      -DCMAKE_Fortran_FLAGS="-Kfast -Kocl -Nlst=t -Koptmsg=2 -Ncheck_std=03s"
+      -DCMAKE_C_FLAGS="-Kfast -Kocl -Nlst=t -Koptmsg=2 -Xg -std=gnu99"
+      -DCMAKE_C_STANDARD_COMPUTED_DEFAULT=Fujitsu
+      "-DCMAKE_Fortran_MODDIR_FLAG=-M "
+      -DOPENMP_FLAGS="-Kopenmp -Nfjomplib"
+      -DLAPACK_VENDOR_FLAGS=-SSL2BLAMP
+      -DFortran_PP_FLAGS=-Cpp
+    )
+    ;;
+  *)
+    echo "Unknown system: ${system}" >&2
+    exit 1
+    ;;
+esac
+
+cmake -S . -B "${BUILD_DIR}" "${cmake_args[@]}"
+cmake --build "${BUILD_DIR}" --target salmon --parallel 8
+
+salmon_bin=$(find "${BUILD_DIR}" -type f -name salmon -perm -u+x | head -n 1)
+if [[ -z "${salmon_bin}" ]]; then
+  salmon_bin=$(find "${BUILD_DIR}" -type f -name salmon | head -n 1)
+fi
+if [[ -z "${salmon_bin}" || ! -f "${salmon_bin}" ]]; then
+  echo "SALMON executable not found under ${BUILD_DIR}" >&2
+  exit 1
+fi
+
+cp "${salmon_bin}" "${ARTIFACT_DIR}/salmon"

programs/salmon/list.csv

@@ -0,0 +1,6 @@
+system,enable,nodes,numproc_node,nthreads,elapse
+Fugaku,yes,1,4,12,0:10:00
+RC_GH200,yes,1,1,1,0:10:00
+RC_DGXSP,yes,1,1,1,0:10:00
+RC_GENOA,yes,1,1,48,0:10:00
+RC_FX700,yes,1,1,48,0:30:00

programs/salmon/run.sh

@@ -0,0 +1,208 @@
+#!/bin/bash
+set -euo pipefail
+
+system="$1"
+nodes="$2"
+numproc_node="$3"
+nthreads="$4"
+n_ranks=$((nodes * numproc_node))
+
+source "${PWD}/scripts/bk_functions.sh"
+
+RESULTS_DIR="${PWD}/results"
+WORK_DIR="${PWD}/salmon_run"
+INPUT_ARCHIVE_DEFAULT="/vol0003/rccs-sdt/data/a01010/benchmark_data/SALMON.tar.gz"
+INPUT_ARCHIVE_CLOUD="/lvs0/dne1/rccs-nghpcadu/CX_input/SALMON/SALMON.tar.gz"
+GS_THEORY="${BK_SALMON_GS_THEORY:-dft}"
+RT_THEORY="${BK_SALMON_RT_THEORY:-tddft_response}"
+
+salmon_normalize_legacy_theory() {
+  local input_file="$1"
+  local theory="$2"
+
+  [[ -f "${input_file}" ]] || return 0
+  if grep -Eiq '^[[:space:]]*theory[[:space:]]*=' "${input_file}"; then
+    sed -i -E "s/^([[:space:]]*theory[[:space:]]*=[[:space:]]*)['\"][^'\"]*['\"]([[:space:]]*,?.*)$/\1'${theory}'\2/I" "${input_file}"
+    sed -i -E "s/^([[:space:]]*theory[[:space:]]*=[[:space:]]*)[^[:space:],!]+([[:space:]]*,?.*)$/\1'${theory}'\2/I" "${input_file}"
+  fi
+}
+
+mkdir -p "${RESULTS_DIR}"
+: > "${RESULTS_DIR}/result"
+
+if [[ ! -x artifacts/salmon ]]; then
+  echo "Required artifact not found or not executable: artifacts/salmon" >&2
+  exit 1
+fi
+
+case "${system}" in
+  Fugaku)
+    input_archive="${INPUT_ARCHIVE_DEFAULT}"
+    exec_gs=(-stdin Si-1-1-1.nml ./salmon)
+    exec_rt=(-stdin Si-1-1-1-tddft.nml ./salmon)
+    ;;
+  RC_GH200|RC_DGXSP|RC_GENOA)
+    input_archive="${INPUT_ARCHIVE_CLOUD}"
+    exec_gs=(./salmon)
+    exec_rt=(./salmon)
+    ;;
+  RC_FX700)
+    input_archive="${INPUT_ARCHIVE_CLOUD}"
+    exec_gs=(-stdin Si-1-1-1.nml ./salmon)
+    exec_rt=(-stdin Si-1-1-1-tddft.nml ./salmon)
+    ;;
+  *)
+    echo "Unknown system: ${system}" >&2
+    exit 1
+    ;;
+esac
+
+if [[ ! -f "${input_archive}" ]]; then
+  echo "Input archive not found: ${input_archive}" >&2
+  exit 1
+fi
+
+rm -rf "${WORK_DIR}"
+mkdir -p "${WORK_DIR}/input"
+tar -xzf "${input_archive}" -C "${WORK_DIR}/input"
+
+input_dir=$(find "${WORK_DIR}/input" -type d -path "*/Si-1-1-1/input" | head -n 1)
+if [[ -z "${input_dir}" ]]; then
+  input_dir=$(find "${WORK_DIR}/input" -type f -name "Si-1-1-1.nml" -printf '%h\n' | head -n 1)
+fi
+if [[ -z "${input_dir}" || ! -d "${input_dir}" ]]; then
+  echo "SALMON Si-1-1-1 input directory not found in ${input_archive}" >&2
+  exit 1
+fi
+
+cp artifacts/salmon "${WORK_DIR}/salmon"
+chmod +x "${WORK_DIR}/salmon"
+cp "${input_dir}"/* "${WORK_DIR}/"
+salmon_normalize_legacy_theory "${WORK_DIR}/Si-1-1-1.nml" "${GS_THEORY}"
+salmon_normalize_legacy_theory "${WORK_DIR}/Si-1-1-1-tddft.nml" "${RT_THEORY}"
+grep -Ein '^[[:space:]]*theory[[:space:]]*=' "${WORK_DIR}/Si-1-1-1.nml" "${WORK_DIR}/Si-1-1-1-tddft.nml" >&2 || true
+cd "${WORK_DIR}"
+
+case "${system}" in
+  Fugaku)
+    export OMP_NUM_THREADS="${nthreads}"
+    ;;
+  RC_GH200)
+    module purge
+    module load system/qc-gh200 nvhpc-hpcx-cuda12/25.7
+    export OMP_NUM_THREADS="${nthreads}"
+    ;;
+  RC_DGXSP)
+    source /etc/profile.d/modules.sh
+    module purge
+    module load system/ng-dgx nvhpc-hpcx-cuda13/26.3
+    export OMP_NUM_THREADS="${nthreads}"
+    ;;
+  RC_GENOA)
+    module purge
+    module load system/genoa mpi/mpich-x86_64
+    export OMP_NUM_THREADS="${nthreads}"
+    ;;
+  RC_FX700)
+    module purge
+    module load system/fx700 FJSVstclanga
+    export OMP_NUM_THREADS="${nthreads}"
+    ;;
+esac
+
+run_salmon() {
+  local logfile="$1"
+  shift
+  mpiexec -n "${n_ranks}" "$@" > "${logfile}" 2>&1
+}
+
+salmon_output_has_marker_since() {
+  local logfile="$1"
+  local marker_file="$2"
+  local success_pattern='total[[:space:]]+calculation[[:space:]]+time|total[[:space:]]+.*elapsed[[:space:]]+time|elapsed[[:space:]]+time'
+
+  if grep -Eiq "${success_pattern}" "${logfile}"; then
+    return 0
+  fi
+
+  while IFS= read -r -d '' output_file; do
+    if grep -Eiq "${success_pattern}" "${output_file}"; then
+      return 0
+    fi
+  done < <(find . -type f -newer "${marker_file}" ! -path "./input/*" -print0)
+
+  return 1
+}
+
+print_salmon_output_diagnostics() {
+  local marker_file="$1"
+  local output_file
+
+  find . -maxdepth 4 -type f -newer "${marker_file}" ! -path "./input/*" -printf '%p\n' \
+    | sort \
+    | sed -n '1,120p' >&2
+
+  while IFS= read -r -d '' output_file; do
+    echo "---- ${output_file} tail ----" >&2
+    tail -n 20 "${output_file}" >&2 || true
+  done < <(
+    find . -maxdepth 5 -type f -newer "${marker_file}" \
+      \( -name 'stdout*' -o -name 'stderr*' -o -name '*.log' \) \
+      ! -path "./input/*" -print0 \
+      | sort -z
+  )
+}
+
+touch .gs_start_marker
+gs_start=$(date +%s.%N)
+if [[ "${system}" == "RC_GH200" || "${system}" == "RC_DGXSP" || "${system}" == "RC_GENOA" ]]; then
+  run_salmon gs.log "${exec_gs[@]}" < Si-1-1-1.nml
+else
+  run_salmon gs.log "${exec_gs[@]}"
+fi
+gs_end=$(date +%s.%N)
+
+if [[ -d data_for_restart ]]; then
+  rm -rf restart
+  mv data_for_restart restart
+fi
+
+touch .rt_start_marker
+rt_start=$(date +%s.%N)
+if [[ "${system}" == "RC_GH200" || "${system}" == "RC_DGXSP" || "${system}" == "RC_GENOA" ]]; then
+  run_salmon rt.log "${exec_rt[@]}" < Si-1-1-1-tddft.nml
+else
+  run_salmon rt.log "${exec_rt[@]}"
+fi
+rt_end=$(date +%s.%N)
+
+gs_elapsed=$(awk -v start="${gs_start}" -v end="${gs_end}" 'BEGIN {printf "%.6f", end - start}')
+rt_elapsed=$(awk -v start="${rt_start}" -v end="${rt_end}" 'BEGIN {printf "%.6f", end - start}')
+total_elapsed=$(awk -v gs="${gs_elapsed}" -v rt="${rt_elapsed}" 'BEGIN {printf "%.6f", gs + rt}')
+
+cp gs.log rt.log "${RESULTS_DIR}/"
+
+if ! salmon_output_has_marker_since gs.log .gs_start_marker || ! salmon_output_has_marker_since rt.log .rt_start_marker; then
+  echo "SALMON success marker not found in both gs.log and rt.log" >&2
+  echo "---- gs.log tail ----" >&2
+  tail -n 40 gs.log >&2 || true
+  echo "---- rt.log tail ----" >&2
+  tail -n 40 rt.log >&2 || true
+  echo "---- files updated since GS start ----" >&2
+  print_salmon_output_diagnostics .gs_start_marker
+  echo "---- files updated since RT start ----" >&2
+  print_salmon_output_diagnostics .rt_start_marker
+  exit 1
+fi
+
+{
+  bk_emit_result \
+    --fom "${total_elapsed}" \
+    --fom-version "total_elapsed_time_s" \
+    --exp "Si-1-1-1" \
+    --nodes "${nodes}" \
+    --numproc-node "${numproc_node}" \
+    --nthreads "${nthreads}"
+  bk_emit_section gs "${gs_elapsed}"
+  bk_emit_section rt "${rt_elapsed}"
+} >> "${RESULTS_DIR}/result"