[ARVADOS] updated: 2.1.0-1031-g7ee7461f1

Mon Jul 5 20:56:04 UTC 2021

Summary of changes:
 .../install-dispatch.html.textile.liquid           | 114 +++++++++++++++++++++
 1 file changed, 114 insertions(+)
 create mode 100644 doc/install/crunch2-lsf/install-dispatch.html.textile.liquid

       via  7ee7461f1658535b736c9ffd055a1895aa70e284 (commit)
      from  51afdd46ed4732d38496f80f7c07e05cfa15094e (commit)

Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.


commit 7ee7461f1658535b736c9ffd055a1895aa70e284
Author: Tom Clegg <tom at curii.com>
Date:   Mon Jul 5 16:55:38 2021 -0400

    17756: Add arvados-dispatch-lsf install doc page.
    
    Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom at curii.com>

diff --git a/doc/install/crunch2-lsf/install-dispatch.html.textile.liquid b/doc/install/crunch2-lsf/install-dispatch.html.textile.liquid
new file mode 100644
index 000000000..0dd6a8b26
--- /dev/null
+++ b/doc/install/crunch2-lsf/install-dispatch.html.textile.liquid
@@ -0,0 +1,114 @@
+---
+layout: default
+navsection: installguide
+title: Install the LSF dispatcher
+...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
+{% include 'notebox_begin_warning' %}
+arvados-dispatch-lsf is only relevant for on premises clusters that will spool jobs to LSF. Skip this section if you are installing a cloud cluster.
+{% include 'notebox_end' %}
+
+Containers can be dispatched to an LSF cluster.  The dispatcher sends work to the cluster using LSF's @bsub@ command, so it works in a variety of LSF configurations.
+
+*LSF support is currently considered experimental.*
+
+Limitations include:
+* Arvados container priority is not propagated to LSF job priority. This can cause inefficient use of compute resources, and even deadlock if there are fewer compute nodes than concurrent Arvados workflows.
+* Combining LSF with docker may not work, depending on LSF configuration and user/group IDs (if LSF only sets up the configured user's primary group ID when executing the crunch-run process on a compute node, it may not have permission to connect to the docker daemon).
+
+In order to run containers, you must choose a user that has permission to set up FUSE mounts and run Singularity/Docker containers on each compute node.  This install guide refers to this user as the @crunch@ user.  We recommend you create this user on each compute node with the same UID and GID, and add it to the @fuse@ and @docker@ system groups to grant it the necessary permissions.  However, you can run the dispatcher under any account with sufficient permissions across the cluster.
+
+Set up all of your compute nodes "as you would for a SLURM cluster":../crunch2-slurm/install-compute-node.html.
+
+
+h2(#update-config). Update config.yml
+
+Arvados-dispatch-lsf reads the common configuration file at @/etc/arvados/config.yml at .
+
+Review the following configuration parameters and adjust as needed.
+
+
+h3(#BsubSudoUser). Containers.LSF.BsubSudoUser
+
+arvados-dispatch-lsf uses @sudo@ to execute @bsub@, for example @sudo -E -u crunch bsub [...]@. To use a user account other than @crunch@, configure @BsubSudoUser@:
+
+<notextile>
+<pre>    Containers:
+      LSF:
+        <code class="userinput">BsubSudoUser: <b>lsfuser</b>
+</code></pre>
+</notextile>
+
+Alternatively, you can arrange for the arvados-dispatch-lsf process to run as an unprivileged user that has a corresponding account on all compute nodes, and disable the use of @sudo@ by specifying an empty string:
+
+<notextile>
+<pre>    Containers:
+      LSF:
+        # Don't use sudo
+        <code class="userinput">BsubSudoUser: <b>""</b>
+</code></pre>
+</notextile>
+
+
+h3(#SbatchArguments). Containers.LSF.BsubArgumentsList
+
+When arvados-dispatch-lsf invokes @bsub@, you can add arguments to the command by specifying @BsubArgumentsList at .  You can use this to send the jobs to specific cluster partitions or add resource requests.  Set @BsubArgumentsList@ to an array of strings.  For example:
+
+<notextile>
+<pre>    Containers:
+      LSF:
+        <code class="userinput">BsubArgumentsList:
+          - <b>"-C"</b>
+          - <b>"0"</b></code>
+</pre>
+</notextile>
+
+
+h3(#PollPeriod). Containers.PollInterval
+
+arvados-dispatch-lsf polls the API server periodically for new containers to run.  The @PollInterval@ option controls how often this poll happens.  Set this to a string of numbers suffixed with one of the time units @s@, @m@, or @h at .  For example:
+
+<notextile>
+<pre>    Containers:
+      <code class="userinput">PollInterval: <b>10s</b>
+</code></pre>
+</notextile>
+
+
+h3(#ReserveExtraRAM). Containers.ReserveExtraRAM: Extra RAM for jobs
+
+Extra RAM to reserve (in bytes) on each LSF job submitted by Arvados, which is added to the amount specified in the container's @runtime_constraints at .  If not provided, the default value is zero.
+
+Supports suffixes @KB@, @KiB@, @MB@, @MiB@, @GB@, @GiB@, @TB@, @TiB@, @PB@, @PiB@, @EB@, @EiB@ (where @KB@ is 10[^3^], @KiB@ is 2[^10^], @MB@ is 10[^6^], @MiB@ is 2[^20^] and so forth).
+
+<notextile>
+<pre>    Containers:
+      <code class="userinput">ReserveExtraRAM: <b>256MiB</b></code>
+</pre>
+</notextile>
+
+
+h3(#CrunchRunCommand-network). Containers.CrunchRunArgumentList: Using host networking for containers
+
+Older Linux kernels (prior to 3.18) have bugs in network namespace handling which can lead to compute node lockups.  This by is indicated by blocked kernel tasks in "Workqueue: netns cleanup_net".   If you are experiencing this problem, as a workaround you can disable use of network namespaces by Docker across the cluster.  Be aware this reduces container isolation, which may be a security risk.
+
+<notextile>
+<pre>    Containers:
+      <code class="userinput">CrunchRunArgumentsList:
+        - <b>"-container-enable-networking=always"</b>
+        - <b>"-container-network-mode=host"</b></code>
+</pre>
+</notextile>
+
+{% assign arvados_component = 'arvados-dispatch-lsf' %}
+
+{% include 'install_packages' %}
+
+{% include 'start_service' %}
+
+{% include 'restart_api' %}

-----------------------------------------------------------------------


hooks/post-receive
-- 


