Merge branch '16669-oidc-access-token'

refs #16669

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

diff --git a/doc/_includes/_install_compute_docker.liquid b/doc/_includes/_install_compute_docker.liquid
index fd5d88a9c3804349d637b79bc002a55fdd1b025c..e3814b23c5ec8e5807633858cc454123558c1b53 100644 (file)
--- a/doc/_includes/_install_compute_docker.liquid
+++ b/doc/_includes/_install_compute_docker.liquid
@@ -10,18 +10,21 @@ Linux can report what compute resources are used by processes in a specific cgro
 
 To enable cgroups accounting, you must boot Linux with the command line parameters @cgroup_enable=memory swapaccount=1@.
 
+Currently Arvados is not compatible with the new cgroups accounting, also known as cgroups v2. Currently, all supported GNU/Linux distributions don't use cgroups v2 as default
+If you are using a distribution in the compute nodes that ships with cgroups v2 enabled, make sure to disable it by booting Linux with the command line parameters @systemd.unified_cgroup_hierarchy=0@.
+
 After making changes, reboot the system to make these changes effective.
 
 h3. Red Hat and CentOS
 
 <notextile>
-<pre><code>~$ <span class="userinput">sudo grubby --update-kernel=ALL --args='cgroup_enable=memory swapaccount=1'</span>
+<pre><code>~$ <span class="userinput">sudo grubby --update-kernel=ALL --args='cgroup_enable=memory swapaccount=1 systemd.unified_cgroup_hierarchy=0'</span>
 </code></pre>
 </notextile>
 
 h3. Debian and Ubuntu
 
-Open the file @/etc/default/grub@ in an editor.  Find where the string @GRUB_CMDLINE_LINUX@ is set.  Add @cgroup_enable=memory swapaccount=1@ to that string.  Save the file and exit the editor.  Then run:
+Open the file @/etc/default/grub@ in an editor.  Find where the string @GRUB_CMDLINE_LINUX@ is set.  Add @cgroup_enable=memory swapaccount=1 systemd.unified_cgroup_hierarchy=0@ to that string.  Save the file and exit the editor.  Then run:
 
 <notextile>
 <pre><code>~$ <span class="userinput">sudo update-grub</span>

diff --git a/doc/user/getting_started/setup-cli.html.textile.liquid b/doc/user/getting_started/setup-cli.html.textile.liquid
new file mode 100644 (file)
index 0000000..46ea770
--- /dev/null
+++ b/doc/user/getting_started/setup-cli.html.textile.liquid
@@ -0,0 +1,20 @@
+---
+layout: default
+navsection: userguide
+title: Getting started at the command line
+...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
+Many operations in Arvados can be performed using either the web Workbench or through command line tools.  Some operations can only be done using the command line.
+
+To use the command line tools, you can either log into an Arvados-managed VM instance where those tools are pre-installed, or install the Arvados tools on your own system.
+
+To log into an Arvados-managed VM, see instructions for "Webshell":{{site.baseurl}}/user/getting_started/vm-login-with-webshell.html or "Unix":{{site.baseurl}}/user/getting_started/ssh-access-unix.html or "Windows":{{site.baseurl}}/user/getting_started/ssh-access-windows.html .
+
+To install the Arvados tools on your own system, you should install the "Command line SDK":{{site.baseurl}}/sdk/cli/install.html (requires Ruby) and "Python SDK":{{site.baseurl}}/sdk/python/sdk-python.html (requires Python).  You may also want to install "arvados-cwl-runner":{{site.baseurl}}/sdk/python/arvados-cwl-runner.html to submit workflows and "arvados-fuse":{{site.baseurl}}/sdk/python/arvados-fuse.html to mount keep as a filesystem.
+
+Once you are logged in or have command line tools installed, see "getting an API token":{{site.baseurl}}/user/reference/api-tokens.html and "check your environment":{{site.baseurl}}/user/getting_started/check-environment.html .

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 7b81bfb447a54b15674095508f7a95b4ec21c1e1..72ef14f6731baf83de87df28534a5c76b5a7dc42 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -547,6 +547,17 @@ class RunnerContainer(Runner):
 
         logger.info("%s submitted container_request %s", self.arvrunner.label(self), response["uuid"])
 
+        workbench1 = self.arvrunner.api.config()["Services"]["Workbench1"]["ExternalURL"]
+        workbench2 = self.arvrunner.api.config()["Services"]["Workbench2"]["ExternalURL"]
+        url = ""
+        if workbench2:
+            url = "{}processes/{}".format(workbench2, response["uuid"])
+        elif workbench1:
+            url = "{}container_requests/{}".format(workbench1, response["uuid"])
+        if url:
+            logger.info("Monitor workflow progress at %s", url)
+
+
     def done(self, record):
         try:
             container = self.arvrunner.api.containers().get(

diff --git a/sdk/cwl/arvados_cwl/executor.py b/sdk/cwl/arvados_cwl/executor.py
index 947b630bab9d861deebf3772bb1ef53376fb2be4..f60c480873b833dca11b0dba1a6cc853f4c29e2c 100644 (file)
--- a/sdk/cwl/arvados_cwl/executor.py
+++ b/sdk/cwl/arvados_cwl/executor.py
@@ -524,7 +524,10 @@ The 'jobs' API is no longer supported.
     def arv_executor(self, updated_tool, job_order, runtimeContext, logger=None):
         self.debug = runtimeContext.debug
 
-        logger.info("Using cluster %s (%s)", self.api.config()["ClusterID"], self.api.config()["Services"]["Controller"]["ExternalURL"])
+        workbench1 = self.api.config()["Services"]["Workbench1"]["ExternalURL"]
+        workbench2 = self.api.config()["Services"]["Workbench2"]["ExternalURL"]
+        controller = self.api.config()["Services"]["Controller"]["ExternalURL"]
+        logger.info("Using cluster %s (%s)", self.api.config()["ClusterID"], workbench2 or workbench1 or controller)
 
         updated_tool.visit(self.check_features)
 
@@ -760,6 +763,8 @@ The 'jobs' API is no longer supported.
 
         if runtimeContext.submit and isinstance(tool, Runner):
             logger.info("Final output collection %s", tool.final_output)
+            if workbench2 or workbench1:
+                logger.info("Output at %scollections/%s", workbench2 or workbench1, tool.final_output)
         else:
             if self.output_name is None:
                 self.output_name = "Output of %s" % (shortname(tool.tool["id"]))