Add singularity installation scripts.

3 files changed, 91 insertions, 0 deletions

diff --git a/singularity-head-deploy.sh b/singularity-head-deploy.sh
new file mode 100755
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--- /dev/null
+++ b/singularity-head-deploy.sh
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+#! /bin/sh -xe
+
+##
+## singularity deployment on octopus01 (the head node)
+##
+
+## Install singularity in the same way as the worker nodes.
+./singularity-worker-deploy.sh $(guix build -f singularity.scm)
+
+# Register garbage collector root to prevent `guix gc' from garbage
+# collecting singularity.
+sudo ln --force --symbolic /usr/local/bin/singularity /var/guix/gcroots
diff --git a/singularity-worker-deploy.sh b/singularity-worker-deploy.sh
new file mode 100755
index 0000000..d709758
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+++ b/singularity-worker-deploy.sh
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+#! /bin/sh -xe
+
+##
+## singularity deployment on octopus worker nodes
+##
+
+case $1 in
+    "")
+	echo "Usage: $0 SINGULARITY_STORE_ITEM"
+	exit 1
+	;;
+    *)
+	singularity=$1
+	echo $singularity
+	;;
+esac
+
+# Symlink singularity executable.
+sudo ln --force --symbolic $singularity/bin/singularity /usr/local/bin/singularity
+
+# To set up singularity, we imitate what the Guix
+# singularity-service-type does.
+
+# Install setuid binaries.
+sudo mkdir -p /usr/local/libexec/singularity/bin
+for program in action mount start;
+do
+    sudo cp $singularity/libexec/singularity/bin/$program-suid /usr/local/libexec/singularity/bin/singularity-$program-helper
+    sudo chmod u+s /usr/local/libexec/singularity/bin/singularity-$program-helper
+done
+
+# Create the directories that Singularity 2.6 expects to find.
+for directory in container final overlay session;
+do
+    sudo mkdir -p /var/singularity/mnt/$directory
+    sudo chmod 755 /var/singularity/mnt/$directory
+done
diff --git a/singularity.scm b/singularity.scm
new file mode 100644
index 0000000..9a4c0ce
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+++ b/singularity.scm
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+(use-modules (gnu packages linux)
+             (guix download)
+             (guix packages))
+
+(package
+  (inherit singularity)
+  (version (package-version singularity))
+  (source (origin
+            (inherit (package-source singularity))
+            (snippet
+             '(begin
+                ;; We put the singularity setuid binaries under
+                ;; /usr/local. The Guix package puts it under
+                ;; /run/privileged/bin. But, we cannot do that since
+                ;; /run is mounted noexec on octopus.
+                (substitute* (find-files "libexec/cli" "\\.exec$")
+                  (("\\$SINGULARITY_libexecdir/singularity/bin/([a-z]+)-suid"
+                    _ program)
+                   (string-append "/usr/local/libexec/singularity/bin/singularity-"
+                                  program "-helper")))
+
+                ;; The remaining snippet code below is copied from the
+                ;; Guix package.
+                
+                ;; Do not create directories in /var.
+                (substitute* "Makefile.in"
+                  (("\\$\\(MAKE\\) .*install-data-hook") ""))
+
+                ;; The original source overrides PATH so that it
+                ;; points to /bin, /usr/local/bin, etc., which
+                ;; obviously doesn't work on Guix System. Leave PATH
+                ;; unchanged so we refer to the installed Coreutils,
+                ;; grep, etc.
+                (substitute* "bin/singularity.in"
+                  (("^PATH=.*" all)
+                   (string-append "#" all "\n")))
+
+                ;; These squashfs mount options are apparently no
+                ;; longer supported since Linux-libre 5.4.5.
+                (substitute* "src/lib/image/squashfs/mount.c"
+                  (("\"errors=remount-ro\"")
+                   "NULL")))))))