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Diffstat (limited to 'scripts/lib-pangenome-pack.sh')
| -rw-r--r-- | scripts/lib-pangenome-pack.sh | 203 |
1 files changed, 203 insertions, 0 deletions
diff --git a/scripts/lib-pangenome-pack.sh b/scripts/lib-pangenome-pack.sh new file mode 100644 index 0000000..7707928 --- /dev/null +++ b/scripts/lib-pangenome-pack.sh @@ -0,0 +1,203 @@ +# Shared helpers for the pangenome-tools image builders. +# +# Sourced from create-singularity-pangenome-tools.sh and +# create-docker-pangenome-tools.sh. Resolves versions, names the +# output, copies the pack into ~/tmp, and writes md5sum.txt and the +# Markdown inventory. +# +# Callers source this file (which assumes "$0" is the front script) +# and then call: +# +# pangenome_pack <guix-pack-format> <file-extension> <name-label> +# pangenome_write_outputs +# +# Variables PACK_TARGET, PACK_LABEL, PACK_HASH are exported back to +# the caller after pangenome_pack runs. + +set -eu + +SCRIPT_DIR=$(cd "$(dirname "$0")" && pwd) +CHANNEL_DIR=$(cd "$SCRIPT_DIR/.." && pwd) +DEST_DIR="$HOME/tmp" +mkdir -p "$DEST_DIR" + +DATE=$(date +%Y%m%d) +GB_HASH=$(git -C "$CHANNEL_DIR" rev-parse --short=8 HEAD) +# The pack is built for the host architecture (no cross-compile). +# Embed it in the filename so x86_64 / aarch64 / ... images cannot +# be confused. Optional TUNE env var passes through to +# `guix pack --tune=...` and is appended to the arch slug. +# +# Only the psABI v-levels are accepted as TUNE values: +# +# x86-64 baseline (any 64-bit Intel/AMD CPU) +# x86-64-v2 Nehalem / Bulldozer (SSE4.2 + POPCNT) +# x86-64-v3 Haswell / Zen 1 (AVX2 + BMI1/2 + FMA) +# x86-64-v4 Skylake-SP / Zen 4 (AVX-512 F/DQ/CD/BW/VL) +# +# Microarch names like `cascadelake`, `znver3`, `skylake-avx512` +# are NOT accepted: Go (which the closure pulls in via odgi etc.) +# only understands the v-levels and `guix pack --tune=cascadelake` +# fails with "compiler go@... does not support micro-architecture +# cascadelake". Pick the v-level whose feature set is implied by +# your target microarch (e.g. Cascade Lake/Zen 4 -> v4 because +# both have AVX-512). +ARCH=$(uname -m) +TUNE="${TUNE:-}" +# When TUNE is set, the v-level already implies the architecture +# (x86-64-v4 only makes sense on x86_64); use it on its own to +# avoid a redundant "x86_64-x86-64-v4" slug. +ARCH_SLUG="${TUNE:-$ARCH}" +if [ -n "$TUNE" ]; then + case "$TUNE" in + x86-64|x86-64-v2|x86-64-v3|x86-64-v4) : ;; + *) + cat >&2 <<EOF +TUNE=$TUNE is not supported. Use one of the psABI v-levels: + + x86-64 baseline (any 64-bit Intel/AMD CPU) + x86-64-v2 Nehalem / Bulldozer (SSE4.2 + POPCNT) + x86-64-v3 Haswell / Zen 1 (AVX2 + BMI1/2 + FMA) + x86-64-v4 Skylake-SP / Zen 4 (AVX-512) + +Microarch names (cascadelake, znver3, ...) are rejected because Go +in the closure only supports the v-levels. +EOF + exit 2 + ;; + esac +fi + +cpu_compat () { + case "$TUNE" in + "") printf 'Generic x86_64 -- any 64-bit Intel or AMD CPU (no AVX/AVX2/AVX-512 required).' ;; + x86-64) printf 'Any 64-bit Intel or AMD CPU (psABI baseline, since ~2003).' ;; + x86-64-v2) printf 'Intel Nehalem (1st-gen Core i7) or newer / AMD Bulldozer or newer. Requires SSE4.2 + POPCNT.' ;; + x86-64-v3) printf 'Intel Haswell (4th-gen Core) or newer / AMD Excavator / Zen 1 or newer. Requires AVX2 + BMI1/2 + FMA.' ;; + x86-64-v4) printf 'Intel Skylake-SP / Cascade Lake / Ice Lake / Sapphire Rapids (Xeon Scalable, Core-X 7900X+) / AMD Zen 4 / Zen 5. Requires AVX-512 (F/DQ/CD/BW/VL).' ;; + esac +} + +# Resolve the exact version each package contributes to the closure. +# Use `guix repl` so we read `package-version` directly -- `guix +# build -n` only prints the store path on stdout when the derivation +# is already realized, which makes it fragile after a channel update. +read IMPG_VER WFMASH_VER PGGB_VER <<EOF +$(guix repl -L "$CHANNEL_DIR" -- /dev/stdin 2>/dev/null <<'SCM' +(use-modules (guix packages) + (gn packages pangenome) + (gn packages pangenome-rust)) +(format #t "~a ~a ~a~%" + (package-version impg) + (package-version wfmash-0.14-snapshot) + (package-version pggb)) +SCM +) +EOF +[ -n "${IMPG_VER:-}" ] && [ -n "${WFMASH_VER:-}" ] && [ -n "${PGGB_VER:-}" ] \ + || { echo "could not resolve package versions" >&2; exit 1; } + +VERSION_STEM="$ARCH_SLUG-guix-bioinformatics-$GB_HASH-impg-$IMPG_VER-wfmash-$WFMASH_VER-pggb-$PGGB_VER" + +pangenome_pack () { + fmt="$1" ; ext="$2" ; label="$3" + echo "==> building $fmt pack from $CHANNEL_DIR${TUNE:+ (tune=$TUNE)}" + extra="" + [ "$fmt" = "docker" ] && extra="--entry-point=/bin/bash --image-tag=pangenome-tools:$GB_HASH" + [ -n "$TUNE" ] && extra="$extra --tune=$TUNE" + # shellcheck disable=SC2086 + STORE_PATH=$(guix pack -f "$fmt" --no-offload \ + -L "$CHANNEL_DIR" \ + -S /bin=bin -S /etc/profile=etc/profile \ + $extra \ + mempang-workshop \ + bash coreutils grep sed gzip \ + | tail -n 1) + if [ ! -e "$STORE_PATH" ]; then + echo "guix pack -f $fmt did not produce a usable store path: $STORE_PATH" >&2 + exit 1 + fi + PACK_HASH=$(basename "$STORE_PATH" | cut -c1-8) + PACK_LABEL="$label" + PACK_TARGET="$DEST_DIR/pangenome-tools-$VERSION_STEM-$label-$DATE-$PACK_HASH.$ext" + + echo "==> copying $STORE_PATH" + echo " to $PACK_TARGET" + cp -L "$STORE_PATH" "$PACK_TARGET" + chmod u+w "$PACK_TARGET" +} + +pangenome_write_outputs () { + # Append our line to md5sum.txt, deduping by filename so re-runs + # don't accumulate stale entries. + MD5SUM_FILE="$DEST_DIR/md5sum.txt" + LINE=$(cd "$DEST_DIR" && md5sum "$(basename "$PACK_TARGET")") + TMP=$(mktemp) + trap 'rm -f "$TMP"' EXIT + [ -f "$MD5SUM_FILE" ] && grep -v " $(basename "$PACK_TARGET")\$" \ + "$MD5SUM_FILE" > "$TMP" || true + printf '%s\n' "$LINE" >> "$TMP" + sort -k2 "$TMP" > "$MD5SUM_FILE" + + # Inventory is identical regardless of pack format -- name it + # by channel hash + date only. + INVENTORY="$DEST_DIR/pangenome-tools-$ARCH_SLUG-guix-bioinformatics-$GB_HASH-$DATE.md" + TOOLS_TSV=$(mktemp) + CLEAN_TSV=$(mktemp) + trap 'rm -f "$TMP" "$TOOLS_TSV" "$CLEAN_TSV"' EXIT + guix repl -L "$CHANNEL_DIR" -- /dev/stdin > "$TOOLS_TSV" <<'SCM' +(use-modules (guix packages) (guix utils) (gn packages pangenome) + (ice-9 format) (ice-9 regex)) +;; Only keep packages defined in gn/packages/pangenome.scm or +;; gn/packages/pangenome-rust.scm -- those are the real pangenome +;; tools; everything else (libc, R, python, coreutils, ...) is +;; infrastructure that ends up in the closure but isn't user-facing. +(define pangenome-file-rx + (make-regexp "gn/packages/pangenome(-rust)?\\.scm$")) +(define (pangenome-package? p) + (let ((loc (package-location p))) + (and loc (regexp-exec pangenome-file-rx (location-file loc))))) +(define seen (make-hash-table)) +(define meta-packages + '("pangenomes" "mempang-workshop-pangenomes" "mempang-workshop")) +(define (emit p) + (when (and (pangenome-package? p) + (not (member (package-name p) meta-packages)) + (not (hash-ref seen (package-name p)))) + (hash-set! seen (package-name p) #t) + (format #t "~a\t~a\t~a~%" + (package-name p) (package-version p) + (or (package-synopsis p) "")))) +(define (expand x) + (let ((p (if (pair? x) (cadr x) x))) + (emit p) + (for-each expand (package-propagated-inputs p)))) +(for-each expand (package-propagated-inputs mempang-workshop)) +SCM + grep -P '^[a-z0-9]' "$TOOLS_TSV" > "$CLEAN_TSV" + + NAME_W=4 ; VER_W=7 ; DESC_W=11 + while IFS=$(printf '\t') read -r n v d; do + [ ${#n} -gt $NAME_W ] && NAME_W=${#n} + [ ${#v} -gt $VER_W ] && VER_W=${#v} + [ ${#d} -gt $DESC_W ] && DESC_W=${#d} + done < "$CLEAN_TSV" + + dashes () { printf '%*s' "$1" '' | tr ' ' -; } + + { + echo "# pangenome-tools $DATE ($ARCH_SLUG, guix-bioinformatics @ $GB_HASH)" + echo + echo "Built from \`mempang-workshop\` in guix-bioinformatics @ $GB_HASH for $ARCH_SLUG." + echo + echo "**CPU compatibility:** $(cpu_compat)" + echo + printf "| %-${NAME_W}s | %-${VER_W}s | %-${DESC_W}s |\n" \ + "Tool" "Version" "Description" + printf "| %s | %s | %s |\n" \ + "$(dashes "$NAME_W")" "$(dashes "$VER_W")" "$(dashes "$DESC_W")" + while IFS=$(printf '\t') read -r n v d; do + printf "| %-${NAME_W}s | %-${VER_W}s | %-${DESC_W}s |\n" "$n" "$v" "$d" + done < "$CLEAN_TSV" + } > "$INVENTORY" +} |