Add a Linux ARM64 builder node

3.17/bioc/kunpeng1/config.sh

@@ -0,0 +1,68 @@
+#!/usr/bin/env bash
+# ===================================
+# Settings for kunpeng1 (Linux ARM64)
+# ===================================
+
+
+
+#set -x  # print commands and their arguments as they are executed
+
+export BBS_DEBUG="0"
+
+export BBS_NODE_HOSTNAME="kunpeng1"
+export BBS_USER="biocbuild"
+export BBS_WORK_TOPDIR="/home/biocbuild/bbs-3.17-bioc"
+export BBS_R_HOME="$BBS_WORK_TOPDIR/R"
+export BBS_NB_CPU=8         # 8 cores are available
+# export BBS_BUILD_NB_CPU=26  # 8 cores are available
+# export BBS_CHECK_NB_CPU=30  # 8 cores are available
+
+# Central build node is nebbiolo1 at DFCI.
+#export BBS_CENTRAL_RHOST="nebbiolo1"
+export BBS_CENTRAL_RHOST="localhost"
+export BBS_RSH_CMD="ssh -F /home/biocbuild/.ssh/config"
+#export BBS_CENTRAL_ROOT_URL="http://155.52.207.165"
+export BBS_CENTRAL_ROOT_URL="http://$BBS_CENTRAL_RHOST"
+export BBS_PRODUCT_TRANSMISSION_MODE="asynchronous"
+
+
+
+# Shared settings (by all Unix nodes).
+
+wd0=$(pwd)
+cd ..
+. ./config.sh
+cd "$wd0"
+
+
+
+# -----------------------------------------------------------------------------
+# The variables below control postrun.sh so only need to be defined on the
+# central node
+
+# Control propagation:
+#export BBS_OUTGOING_MAP="source:nebbiolo1/buildsrc win.binary:palomino3/buildbin mac.binary:merida1/buildbin"
+#export BBS_FINAL_REPO="file://home/biocpush/PACKAGES/$BBS_BIOC_VERSION/bioc"
+
+# Control generation of the report:
+#export BBS_REPORT_NODES="nebbiolo1 palomino3:bin merida1:bin"
+export BBS_REPORT_NODES="kunpeng1"
+export BBS_REPORT_PATH="$BBS_CENTRAL_RDIR/report"
+export BBS_REPORT_CSS="$BBS_HOME/$BBS_BIOC_VERSION/report.css"
+export BBS_REPORT_BGIMG="$BBS_HOME/images/DEVEL3b.png"
+export BBS_REPORT_JS="$BBS_HOME/$BBS_BIOC_VERSION/report.js"
+#export BBS_REPORT_MOTD="Happy new year to all Bioconductor developers!"
+
+# Control where to publish the report:
+#export BBS_PUBLISHED_REPORT_RELATIVEURL="checkResults/$BBS_BIOC_VERSION/$BBS_BUILDTYPE-LATEST/"
+#export BBS_PUBLISHED_REPORT_DEST_DIR="[email protected]:/extra/www/bioc/$BBS_PUBLISHED_REPORT_RELATIVEURL"
+
+
+# -----------------------------------------------------------------------------
+# The variables below control stage7-notify.sh so only need to be defined on
+# the central node
+
+# TODO: when BBS_NOTIFY_NODES is not defined then take all the build nodes
+#export BBS_NOTIFY_NODES="nebbiolo1"
+#export BBS_PUBLISHED_REPORT_URL="https://master.bioconductor.org/$BBS_PUBLISHED_REPORT_RELATIVEURL"
+

3.17/bioc/kunpeng1/postrun.sh

@@ -0,0 +1,44 @@
+#!/bin/bash
+
+echo ""
+echo "======================================================================="
+this_script=$(basename "$0")
+echo "<<< Now starting $this_script at $(date) >>>"
+echo "-------------------"
+
+# Adapted from : http://stackoverflow.com/a/246128/320399
+script_dir=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
+. "${script_dir}"/config.sh
+
+cd "$BBS_CENTRAL_RDIR"
+
+# Remove target repo (no-vignettes source packages). It's no longer
+# needed so we can make room before we generate the HTML report below
+# and before we propagate packages (this will be done later by the
+# updateReposPkgs-bioc.sh script that we run from the biocpush
+# account). Can help significantly if the machine has limited disk capacity.
+rm -rf src
+
+# Fix perms
+chmod -R +r .
+find products-in -type d -exec chmod 755 {} \;
+
+set -e # Exit immediately if a simple command exits with a non-zero status.
+
+$BBS_PYTHON_CMD $BBS_HOME/BBS-make-BUILD_STATUS_DB.py
+
+if [ -n "$BBS_OUTGOING_MAP" ]; then
+    $BBS_PYTHON_CMD $BBS_HOME/BBS-make-OUTGOING.py
+    $BBS_PYTHON_CMD $BBS_HOME/BBS-make-PROPAGATION_STATUS_DB.py
+fi
+
+# Generate the HTML report
+$BBS_PYTHON_CMD $BBS_HOME/BBS-report.py simple-layout
+REPORT_DIRNAME=$(dirname "$BBS_REPORT_PATH")
+REPORT_BASENAME=$(basename "$BBS_REPORT_PATH")
+cd "$REPORT_DIRNAME"
+$BBS_TAR_CMD zcf "$REPORT_BASENAME.tgz" "$REPORT_BASENAME"
+mv "$REPORT_BASENAME.tgz" "$BBS_REPORT_PATH"
+
+# Publish it (no more --delete here, too dangerous!)
+$BBS_RSYNC_CMD -ave 'ssh -o StrictHostKeyChecking=no' "$BBS_REPORT_PATH/" "$BBS_PUBLISHED_REPORT_DEST_DIR/"

3.17/bioc/kunpeng1/prerun.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+. ./config.sh
+
+$BBS_PYTHON_CMD $BBS_HOME/BBS-prerun.py

3.17/bioc/kunpeng1/run.sh

@@ -0,0 +1,12 @@
+#!/bin/bash
+
+. ./config.sh
+
+. $BBS_HOME/utils/clean-before-run.sh
+
+$BBS_PYTHON_CMD $BBS_HOME/BBS-run.py
+
+# We have to use brute force because some R processes might still be running
+# in the background. This will kick out the user BBS is running as!
+sleep 60  # wait 1 min before the kill
+kill -9 -1

3.18/bioc/kunpeng1/config.sh

@@ -0,0 +1,71 @@
+#!/usr/bin/env bash
+# ===================================
+# Settings for kunpeng1 (Linux ARM64)
+# ===================================
+
+
+
+#set -x  # print commands and their arguments as they are executed
+
+export BBS_DEBUG="0"
+
+export BBS_NODE_HOSTNAME="kunpeng1"
+export BBS_USER="biocbuild"
+export BBS_WORK_TOPDIR="/home/biocbuild/bbs-3.18-bioc"
+export BBS_R_HOME="/home/biocbuild/R/R-4.3.0-bin"
+export R_LIBS="$BBS_R_HOME/site-library"
+export BBS_NB_CPU=24         # 32 cores are available
+export BBS_BUILD_NB_CPU=10   # 32 cores are available
+export BBS_CHECK_NB_CPU=10   # 32 cores are available
+
+# Central build node is nebbiolo1 at DFCI.
+#export BBS_CENTRAL_RHOST="nebbiolo1"
+export BBS_CENTRAL_RHOST="localhost"
+export BBS_RSH_CMD="ssh -F /home/biocbuild/.ssh/config"
+#export BBS_CENTRAL_ROOT_URL="http://155.52.207.165"
+export BBS_CENTRAL_ROOT_URL="http://$BBS_CENTRAL_RHOST"
+export BBS_PRODUCT_TRANSMISSION_MODE="asynchronous"
+
+export BBS_BUILD_TIMEOUT=2400
+export BBS_CHECK_TIMEOUT=2400
+
+# Shared settings (by all Unix nodes).
+
+wd0=$(pwd)
+cd ..
+. ./config.sh
+cd "$wd0"
+
+
+
+# -----------------------------------------------------------------------------
+# The variables below control postrun.sh so only need to be defined on the
+# central node
+
+# Control propagation:
+#export BBS_OUTGOING_MAP="source:nebbiolo1/buildsrc win.binary:palomino3/buildbin mac.binary:merida1/buildbin"
+#export BBS_FINAL_REPO="file://home/biocpush/PACKAGES/$BBS_BIOC_VERSION/bioc"
+
+# Control generation of the report:
+#export BBS_REPORT_NODES="nebbiolo1 palomino3:bin merida1:bin"
+export BBS_REPORT_NODES="kunpeng1"
+export BBS_REPORT_PATH="$BBS_CENTRAL_RDIR/report"
+export BBS_REPORT_CSS="$BBS_HOME/$BBS_BIOC_VERSION/report.css"
+export BBS_REPORT_BGIMG="$BBS_HOME/images/DEVEL3b.png"
+export BBS_REPORT_JS="$BBS_HOME/$BBS_BIOC_VERSION/report.js"
+#export BBS_REPORT_MOTD="Happy new year to all Bioconductor developers!"
+
+# Control where to publish the report:
+#export BBS_PUBLISHED_REPORT_RELATIVEURL="checkResults/$BBS_BIOC_VERSION/$BBS_BUILDTYPE-LATEST/"
+#export BBS_PUBLISHED_REPORT_DEST_DIR="[email protected]:/extra/www/bioc/$BBS_PUBLISHED_REPORT_RELATIVEURL"
+
+
+# -----------------------------------------------------------------------------
+# The variables below control stage7-notify.sh so only need to be defined on
+# the central node
+
+# TODO: when BBS_NOTIFY_NODES is not defined then take all the build nodes
+#export BBS_NOTIFY_NODES="nebbiolo1"
+#export BBS_PUBLISHED_REPORT_URL="https://master.bioconductor.org/$BBS_PUBLISHED_REPORT_RELATIVEURL"
+
+

3.18/bioc/kunpeng1/postrun.sh

@@ -0,0 +1,44 @@
+#!/bin/bash
+
+echo ""
+echo "======================================================================="
+this_script=$(basename "$0")
+echo "<<< Now starting $this_script at $(date) >>>"
+echo "-------------------"
+
+# Adapted from : http://stackoverflow.com/a/246128/320399
+script_dir=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
+. "${script_dir}"/config.sh
+
+cd "$BBS_CENTRAL_RDIR"
+
+# Remove target repo (no-vignettes source packages). It's no longer
+# needed so we can make room before we generate the HTML report below
+# and before we propagate packages (this will be done later by the
+# updateReposPkgs-bioc.sh script that we run from the biocpush
+# account). Can help significantly if the machine has limited disk capacity.
+rm -rf src
+
+# Fix perms
+chmod -R +r .
+find products-in -type d -exec chmod 755 {} \;
+
+set -e # Exit immediately if a simple command exits with a non-zero status.
+
+$BBS_PYTHON_CMD $BBS_HOME/BBS-make-BUILD_STATUS_DB.py
+
+if [ -n "$BBS_OUTGOING_MAP" ]; then
+    $BBS_PYTHON_CMD $BBS_HOME/BBS-make-OUTGOING.py
+    $BBS_PYTHON_CMD $BBS_HOME/BBS-make-PROPAGATION_STATUS_DB.py
+fi
+
+# Generate the HTML report
+$BBS_PYTHON_CMD $BBS_HOME/BBS-report.py simple-layout
+REPORT_DIRNAME=$(dirname "$BBS_REPORT_PATH")
+REPORT_BASENAME=$(basename "$BBS_REPORT_PATH")
+cd "$REPORT_DIRNAME"
+$BBS_TAR_CMD zcf "$REPORT_BASENAME.tgz" "$REPORT_BASENAME"
+mv "$REPORT_BASENAME.tgz" "$BBS_REPORT_PATH"
+
+# Publish it (no more --delete here, too dangerous!)
+$BBS_RSYNC_CMD -ave 'ssh -o StrictHostKeyChecking=no' "$BBS_REPORT_PATH/" "$BBS_PUBLISHED_REPORT_DEST_DIR/"

3.18/bioc/kunpeng1/prerun.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+. ./config.sh
+
+$BBS_PYTHON_CMD $BBS_HOME/BBS-prerun.py

3.18/bioc/kunpeng1/run.sh

@@ -0,0 +1,12 @@
+#!/bin/bash
+
+. ./config.sh
+
+. $BBS_HOME/utils/clean-before-run.sh
+
+$BBS_PYTHON_CMD $BBS_HOME/BBS-run.py
+
+# We have to use brute force because some R processes might still be running
+# in the background. This will kick out the user BBS is running as!
+sleep 60  # wait 1 min before the kill
+kill -9 -1

nodes/kunpeng1/local-settings.sh

@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+# =========================================
+# Local settings for kunpeng1 (Linux ARM64)
+# =========================================
+
+
+if [ -z "$BBS_HOME" ]; then
+    export BBS_HOME="/home/biocbuild/BBS"
+fi
+
+export BBS_PYTHON_CMD="/usr/bin/python3"
+
+export BBS_SSH_CMD="/usr/bin/ssh"
+export BBS_RSYNC_CMD="/usr/bin/rsync"
+
+# Needed only on a node capable of running STAGE1 (STAGE1 is supported on
+# Linux only)
+#export BBS_SVN_CMD="/usr/bin/svn"
+export BBS_TAR_CMD="/usr/bin/tar"
+export BBS_GIT_CMD="/usr/bin/git"
+export BBS_CURL_CMD="/usr/bin/curl"
+

nodes/nodespecs.py

@@ -58,5 +58,10 @@
                    'Arch'    : "x86_64",
                    'Platform': "x86_64-linux-gnu",
                    'pkgType' : "source",
-                   'encoding': "utf_8"}
+                   'encoding': "utf_8"},
+    'kunpeng1':   {'OS'      : "Linux (Ubuntu 22.04.1 LTS)",
+                   'Arch'    : "aarch64",
+                   'Platform': "aarch64-linux-gnu",
+                   'pkgType' : "source",
+                   'encoding': "utf_8"},
 }