Add a build node named taishan for 3.20 on Linux ARM64 (#432)

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

Author: martin-g

3.20/bioc/taishan/config.sh

@@ -0,0 +1,39 @@
+#!/usr/bin/env bash
+# ===================================
+# Settings for taishan (Linux ARM64)
+# ===================================
+
+
+
+#set -x  # print commands and their arguments as they are executed
+
+export BBS_DEBUG="0"
+
+export BBS_NODE_HOSTNAME="taishan"
+export BBS_USER="biocbuild"
+export BBS_WORK_TOPDIR="/home/biocbuild/bbs-3.20-bioc"
+export BBS_R_HOME="/home/biocbuild/R/R"
+export R_LIBS="$BBS_R_HOME/site-library"
+
+# kunpeng2 has 32 logical CPUs.
+export BBS_NB_CPU=25
+export BBS_BUILD_NB_CPU=16
+export BBS_CHECK_NB_CPU=22
+export BBS_EXTRA_CHECK_OPTIONS="--no-vignettes"
+
+# Central build node is bbscentral2 on Jetstream2.
+export BBS_CENTRAL_ROOT_URL="http://149.165.152.87"
+export BBS_PRODUCT_TRANSMISSION_MODE="none"
+
+# Source tarballs produced during STAGE3 won't be propagated
+# so we don't need to push them to the central builder.
+export DONT_PUSH_SRCPKGS="1"
+
+
+
+# Shared settings (by all Unix nodes).
+
+wd0=$(pwd)
+cd ..
+. ./config.sh
+cd "$wd0"

3.20/bioc/taishan/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 no-bin
+
+# 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/kunpeng2/local-settings.sh

@@ -19,14 +19,3 @@ export BBS_TAR_CMD="/usr/bin/tar"
 #export BBS_SVN_CMD="/usr/bin/svn"
 export BBS_GIT_CMD="/usr/bin/git"
 export BBS_CURL_CMD="/usr/bin/curl"
-
-
-# We need these because some of the libraries/dependecies are installed from source
-export LIBSBML_CFLAGS=$(pkg-config --cflags ~/libsbml-from-git/lib/pkgconfig/libsbml.pc)
-export LIBSBML_LIBS=$(pkg-config --libs ~/libsbml-from-git/lib/pkgconfig/libsbml.pc)
-export UDUNITS2_INCLUDE="/home/biocbuild/libudunits-2/include"
-export UDUNITS2_LIBS="/home/biocbuild/libudunits-2/lib"
-export OPEN_BABEL_HOME="/home/biocbuild/openbabel-3.1.1"
-export OPENBABEL_CFLAGS="-I$OPEN_BABEL_HOME/include/openbabel3 -L$OPEN_BABEL_HOME/lib"
-export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib64:$UDUNITS2_LIBS:/home/biocbuild/libsbml-from-git/lib:$OPEN_BABEL_HOME/lib
-export PATH=$PATH:/usr/lib64/openmpi/bin:/home/biocbuild/libudunits-2/bin:$HOME/.dotnet:$OPEN_BABEL_HOME/bin

nodes/nodespecs.py

@@ -70,7 +70,13 @@
                     'pkgType' : "mac.binary.big-sur-x86_64",
                     'encoding': "utf-8"},
     ## External nodes.
-    'kunpeng2':    {'OS'      : "Linux (openEuler 22.03 LTS-SP1)",
+    'kunpeng2':    {'OS'      : "Linux (openEuler 24.03 LTS)",
+                    'Arch'    : "aarch64",
+                    'Platform': "aarch64-linux-gnu",
+                    'pkgType' : "source",
+                    'encoding': "utf-8",
+                    'displayOnHTMLReport': "See Martin Grigorov's <a target=\"_blank\" href=\"https://bioconductor.github.io/biocblog/posts/2023-06-09-debug-linux-arm64-on-docker/\">blog post</a> for how to debug Linux ARM64 related issues on a x86_64 host."},
+    'taishan':     {'OS'      : "Linux (openEuler 24.03 LTS)",
                     'Arch'    : "aarch64",
                     'Platform': "aarch64-linux-gnu",
                     'pkgType' : "source",

nodes/taishan/local-settings.sh

@@ -0,0 +1,21 @@
+#!/usr/bin/env bash
+# =========================================
+# Local settings for taishan (openEuler 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"
+export BBS_TAR_CMD="/usr/bin/tar"
+
+# Needed only on a node capable of running STAGE1 (STAGE1 is supported on
+# Linux only)
+#export BBS_SVN_CMD="/usr/bin/svn"
+export BBS_GIT_CMD="/usr/bin/git"
+export BBS_CURL_CMD="/usr/bin/curl"