Merge branch '19095-singularity-bugfix'

fixes #19095

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

diff --git a/doc/admin/upgrading.html.textile.liquid b/doc/admin/upgrading.html.textile.liquid
index 226c8667d67a710283c436db321dc1f26246593d..227a8cf07bd8945c0e442b864821c67d4a1b5424 100644 (file)
--- a/doc/admin/upgrading.html.textile.liquid
+++ b/doc/admin/upgrading.html.textile.liquid
@@ -32,6 +32,10 @@ h2(#main). development main (as of 2022-04-08)
 
 "previous: Upgrading to 2.4.0":#v2_4_0
 
+h3. Now recommending Singularity 3.9.9
+
+The compute image "build script":{{site.baseurl}}/install/crunch2-cloud/install-compute-node.html now installs Singularity 3.9.9 instead of 3.7.4. The newer version includes a bugfix that should resolve "intermittent loopback device errors":https://dev.arvados.org/issues/18489 when running containers.
+
 h2(#v2_4_0). v2.4.0 (2022-04-08)
 
 "previous: Upgrading to 2.3.1":#v2_3_1

diff --git a/doc/architecture/singularity.html.textile.liquid b/doc/architecture/singularity.html.textile.liquid
index 9a82cd93d60e1fdb718ae14833686369ce7d060f..8ebc6f73df6af90866f1d4f31f20968f18830a4b 100644 (file)
--- a/doc/architecture/singularity.html.textile.liquid
+++ b/doc/architecture/singularity.html.textile.liquid
@@ -32,4 +32,4 @@ Arvados @Singularity@ support is a work in progress. These are the current limit
 * Even when using the Singularity runtime, users' container images are expected to be saved in Docker format. Specifying a @.sif@ file as an image when submitting a container request is not yet supported.
 * Arvados' Singularity implementation does not yet limit the amount of memory available in a container. Each container will have access to all memory on the host where it runs, unless memory use is restricted by Slurm/LSF.
 * The Docker ENTRYPOINT instruction is ignored.
-* Arvados is tested with Singularity version 3.7.4. Other versions may not work.
+* Arvados is tested with Singularity version 3.9.9. Other versions may not work.

diff --git a/doc/install/crunch2/install-compute-node-singularity.html.textile.liquid b/doc/install/crunch2/install-compute-node-singularity.html.textile.liquid
index e61b6cbe3783b192325b77c1454747abcc128a1e..2afdf8a919150e62b3464e58b8637e6045bf4398 100644 (file)
--- a/doc/install/crunch2/install-compute-node-singularity.html.textile.liquid
+++ b/doc/install/crunch2/install-compute-node-singularity.html.textile.liquid
@@ -36,13 +36,13 @@ This page describes how to configure a compute node so that it can be used to ru
 
 h2(#singularity). Set up Singularity
 
-Follow the "Singularity installation instructions":https://sylabs.io/guides/3.7/user-guide/quick_start.html. Make sure @singularity@ and @mksquashfs@ are working:
+Follow the "Singularity installation instructions":https://sylabs.io/guides/3.9/user-guide/quick_start.html. Make sure @singularity@ and @mksquashfs@ are working:
 
 <notextile>
 <pre><code>$ <span class="userinput">singularity version</span>
-3.7.4
+3.9.9
 $ <span class="userinput">mksquashfs -version</span>
-mksquashfs version 4.3-git (2014/06/09)
+mksquashfs version 4.4 (2019/08/29)
 [...]
 </code></pre>
 </notextile>
@@ -56,20 +56,3 @@ Then update @Containers.RuntimeEngine@ in your cluster configuration:
 </notextile>
 
 {% include 'singularity_mksquashfs_configuration' %}
-
-h2(#singularity_loop_device_errors). Singularity loop device errors
-
-With singularity v3.9.1 and earlier, containers may fail intermittently at startup with an error message similar to the following in the container log's @stderr.txt@ (line breaks added):
-
-<notextile>
-<pre><code>FATAL:   container creation failed:
- mount /proc/self/fd/3->/usr/local/var/singularity/mnt/session/rootfs error:
- while mounting image /proc/self/fd/3:
- failed to find loop device:
- could not attach image file to loop device:
- failed to set loop flags on loop device:
- resource temporarily unavailable
-</code></pre>
-</notextile>
-
-This problem is addressed in singularity v3.9.2. For details, please see "Arvados issue #18489":https://dev.arvados.org/issues/18489 and "singularity PR #458":https://github.com/sylabs/singularity/pull/458.

diff --git a/lib/install/deps.go b/lib/install/deps.go
index 62b295a1f1dca79b58d6fe4cab0f98c6b9be8b7f..cdf28e09c69c23bd9259710380fdbaa8476101bf 100644 (file)
--- a/lib/install/deps.go
+++ b/lib/install/deps.go
@@ -34,7 +34,7 @@ const goversion = "1.17.7"
 const (
        rubyversion             = "2.7.5"
        bundlerversion          = "2.2.19"
-       singularityversion      = "3.7.4"
+       singularityversion      = "3.9.9"
        pjsversion              = "1.9.8"
        geckoversion            = "0.24.0"
        gradleversion           = "5.3.1"
@@ -138,7 +138,6 @@ func (inst *installCommand) RunCommand(prog string, args []string, stdin io.Read
                pkgs = append(pkgs,
                        "dpkg-dev",
                        "eatmydata", // install it for later steps, even if we're not using it now
-                       "rsync",
                )
        }
 
@@ -185,6 +184,7 @@ func (inst *installCommand) RunCommand(prog string, args []string, stdin io.Read
                        "r-cran-markdown",
                        "r-cran-roxygen2",
                        "r-cran-xml",
+                       "rsync",
                        "sudo",
                        "uuid-dev",
                        "wget",

diff --git a/tools/compute-images/scripts/base.sh b/tools/compute-images/scripts/base.sh
index 2bc41e34737801baa2ef3862403209326a54a4a6..c9fd0945d2927157b46a0ba5bd4232f2a120b8e5 100644 (file)
--- a/tools/compute-images/scripts/base.sh
+++ b/tools/compute-images/scripts/base.sh
@@ -120,7 +120,7 @@ rm -rf /var/lib/arvados/go/
 curl -s https://storage.googleapis.com/golang/go${GOVERSION}.linux-amd64.tar.gz | tar -C /var/lib/arvados -xzf -
 ln -sf /var/lib/arvados/go/bin/* /usr/local/bin/
 
-singularityversion=3.7.4
+singularityversion=3.9.9
 curl -Ls https://github.com/sylabs/singularity/archive/refs/tags/v${singularityversion}.tar.gz | tar -C /var/lib/arvados -xzf -
 cd /var/lib/arvados/singularity-${singularityversion}