[ARVADOS-DEV] updated: ec60d7fd235835947efd8dba97213015d37b036a

Git user git at public.curoverse.com
Thu Feb 25 11:16:23 EST 2016


Summary of changes:
 arvbox/bin/arvbox                                  |  7 +++--
 arvbox/lib/arvbox/docker/Dockerfile.base           |  5 +---
 arvbox/lib/arvbox/docker/Dockerfile.demo           |  3 +++
 arvbox/lib/arvbox/docker/Dockerfile.dev            |  3 +++
 .../{workbench => slurmctld}/log/main/.gitstub     |  0
 .../service/{workbench => slurmctld}/log/run       |  0
 arvbox/lib/arvbox/docker/service/slurmctld/run     | 31 ++++++++++++++++++++++
 .../{workbench => slurmd}/log/main/.gitstub        |  0
 .../docker/service/{workbench => slurmd}/log/run   |  0
 arvbox/lib/arvbox/docker/service/slurmd/run        |  6 +++++
 arvbox/lib/arvbox/docker/service/vm/run            | 14 +++++++++-
 arvbox/lib/arvbox/docker/service/vm/run-service    |  5 ----
 12 files changed, 60 insertions(+), 14 deletions(-)
 copy arvbox/lib/arvbox/docker/service/{workbench => slurmctld}/log/main/.gitstub (100%)
 copy arvbox/lib/arvbox/docker/service/{workbench => slurmctld}/log/run (100%)
 create mode 100755 arvbox/lib/arvbox/docker/service/slurmctld/run
 copy arvbox/lib/arvbox/docker/service/{workbench => slurmd}/log/main/.gitstub (100%)
 copy arvbox/lib/arvbox/docker/service/{workbench => slurmd}/log/run (100%)
 create mode 100755 arvbox/lib/arvbox/docker/service/slurmd/run

       via  ec60d7fd235835947efd8dba97213015d37b036a (commit)
       via  f03b4165fd33b2f8844a4bcda7f650a7023986f1 (commit)
       via  1aa0a5407d6a4e6b861d1fcf52d8268d62b9d6d4 (commit)
       via  e7ddc93ee0608266c34efbbfd4a84464eb8e81d2 (commit)
       via  e407a1d4db57c41cebebaf8f3d663785df8f5fb4 (commit)
      from  65a3779e6968835bc0b1fc1b103a408fd4eec4aa (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 ec60d7fd235835947efd8dba97213015d37b036a
Merge: 65a3779 f03b416
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Thu Feb 25 11:16:20 2016 -0500

    Merge branch 'arvbox-fixes' no issue #


commit f03b4165fd33b2f8844a4bcda7f650a7023986f1
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Thu Feb 25 11:15:47 2016 -0500

    Tweak slurm configuration to run as non-root user.

diff --git a/arvbox/lib/arvbox/docker/service/slurmctld/run b/arvbox/lib/arvbox/docker/service/slurmctld/run
index 7b3c6e1..bd75bd0 100755
--- a/arvbox/lib/arvbox/docker/service/slurmctld/run
+++ b/arvbox/lib/arvbox/docker/service/slurmctld/run
@@ -9,9 +9,11 @@ cat > /etc/slurm-llnl/slurm.conf  <<EOF
 ControlMachine=$HOSTNAME
 ControlAddr=$HOSTNAME
 AuthType=auth/munge
-DefaultStorageLoc=/var/log/slurm
+DefaultStorageLoc=/var/log/slurm-llnl
 SelectType=select/cons_res
+SelectTypeParameters=CR_CPU_Memory
 SlurmUser=arvbox
+SlurmdUser=arvbox
 SlurmctldPort=7002
 SlurmctldTimeout=300
 SlurmdPort=7003
diff --git a/arvbox/lib/arvbox/docker/service/slurmd/run b/arvbox/lib/arvbox/docker/service/slurmd/run
index 697f7a2..865a7e6 100755
--- a/arvbox/lib/arvbox/docker/service/slurmd/run
+++ b/arvbox/lib/arvbox/docker/service/slurmd/run
@@ -3,4 +3,4 @@
 exec 2>&1
 set -eux -o pipefail
 
-exec /usr/sbin/slurmd -v -D
+exec /usr/local/lib/arvbox/runsu.sh /usr/sbin/slurmd -v -D

commit 1aa0a5407d6a4e6b861d1fcf52d8268d62b9d6d4
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Thu Feb 25 11:14:21 2016 -0500

    Fix arvados-login-sync for vm account creation

diff --git a/arvbox/lib/arvbox/docker/service/vm/run b/arvbox/lib/arvbox/docker/service/vm/run
index b7fb9cc..0c10cb0 100755
--- a/arvbox/lib/arvbox/docker/service/vm/run
+++ b/arvbox/lib/arvbox/docker/service/vm/run
@@ -6,4 +6,16 @@ set -e
 git config --system "credential.http://$localip:${services[arv-git-httpd]}/.username" none
 git config --system "credential.http://$localip:${services[arv-git-httpd]}/.helper" '!cred(){ cat >/dev/null; if [ "$1" = get ]; then echo password=$ARVADOS_API_TOKEN; fi; };cred'
 
-exec /usr/local/lib/arvbox/runsu.sh $0-service
+/usr/local/lib/arvbox/runsu.sh $0-service
+
+cd /usr/src/arvados/services/login-sync
+
+export ARVADOS_API_HOST=$localip:${services[api]}
+export ARVADOS_API_HOST_INSECURE=1
+export ARVADOS_API_TOKEN=$(cat /var/lib/arvados/superuser_token)
+export ARVADOS_VIRTUAL_MACHINE_UUID=$(cat /var/lib/arvados/vm-uuid)
+
+while true ; do
+      bundle exec arvados-login-sync
+      sleep 120
+done
diff --git a/arvbox/lib/arvbox/docker/service/vm/run-service b/arvbox/lib/arvbox/docker/service/vm/run-service
index 5bb6825..fb209f5 100755
--- a/arvbox/lib/arvbox/docker/service/vm/run-service
+++ b/arvbox/lib/arvbox/docker/service/vm/run-service
@@ -34,8 +34,3 @@ if arv virtual_machine get --uuid $ARVADOS_VIRTUAL_MACHINE_UUID ; then
 else
     arv virtual_machine create --virtual-machine "$vm"
 fi
-
-while true ; do
-      bundle exec arvados-login-sync
-      sleep 120
-done

commit e7ddc93ee0608266c34efbbfd4a84464eb8e81d2
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Thu Feb 25 11:12:00 2016 -0500

    Generalize arvbox 'svrestart' to 'sv' no issue #

diff --git a/arvbox/bin/arvbox b/arvbox/bin/arvbox
index 7be361b..d790cb6 100755
--- a/arvbox/bin/arvbox
+++ b/arvbox/bin/arvbox
@@ -358,10 +358,9 @@ case "$subcmd" in
         fi
         ;;
 
-    svrestart)
+    sv)
         if test -n "$1" ; then
-            docker exec -ti $ARVBOX_CONTAINER sv restart "$1"
-            docker exec -ti $ARVBOX_CONTAINER sv restart ready
+            docker exec -ti $ARVBOX_CONTAINER sv "$1" "$2"
         else
             echo "Usage: $0 $subcmd <service>"
             echo "Available services:"
@@ -397,7 +396,7 @@ case "$subcmd" in
         echo "reset      delete arvbox arvados data (be careful!)"
         echo "destroy    delete all arvbox code and data (be careful!)"
         echo "log       <service> tail log of specified service"
-        echo "svrestart <service> restart specified service inside arvbox"
+        echo "sv        <start|stop|restart> <service> change state of service inside arvbox"
         echo "clone <from> <to>   clone an arvbox"
         ;;
 esac

commit e407a1d4db57c41cebebaf8f3d663785df8f5fb4
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Thu Feb 18 16:28:29 2016 -0500

    Run slurmctld and slurmd inside arvbox. refs #6518

diff --git a/arvbox/lib/arvbox/docker/Dockerfile.base b/arvbox/lib/arvbox/docker/Dockerfile.base
index 160afee..280ac68 100644
--- a/arvbox/lib/arvbox/docker/Dockerfile.base
+++ b/arvbox/lib/arvbox/docker/Dockerfile.base
@@ -10,7 +10,7 @@ RUN apt-get update && \
     pkg-config libattr1-dev python-llfuse python-pycurl \
     libwww-perl libio-socket-ssl-perl libcrypt-ssleay-perl \
     libjson-perl nginx gitolite3 lsof python-epydoc graphviz \
-    apt-transport-https ca-certificates
+    apt-transport-https ca-certificates slurm-wlm
 
 VOLUME /var/lib/docker
 VOLUME /var/log/nginx
@@ -38,8 +38,5 @@ ADD crunch-setup.sh gitolite.rc \
     application_yml_override.py \
     /usr/local/lib/arvbox/
 
-ADD service/ /var/lib/arvbox/service
-RUN rmdir /etc/service && ln -sf /var/lib/arvbox/service /etc
-
 # Start the supervisor.
 CMD ["/usr/local/bin/runsvinit"]
diff --git a/arvbox/lib/arvbox/docker/Dockerfile.demo b/arvbox/lib/arvbox/docker/Dockerfile.demo
index d3e36c6..1f13415 100644
--- a/arvbox/lib/arvbox/docker/Dockerfile.demo
+++ b/arvbox/lib/arvbox/docker/Dockerfile.demo
@@ -4,6 +4,9 @@ RUN cd /usr/src && \
     git clone https://github.com/curoverse/arvados.git && \
     git clone https://github.com/curoverse/sso-devise-omniauth-provider.git sso
 
+ADD service/ /var/lib/arvbox/service
+RUN rmdir /etc/service && ln -sf /var/lib/arvbox/service /etc
+
 RUN chown -R 1000:1000 /usr/src && /usr/local/lib/arvbox/createusers.sh
 
 RUN sudo -u arvbox /var/lib/arvbox/service/sso/run-service --only-deps
diff --git a/arvbox/lib/arvbox/docker/Dockerfile.dev b/arvbox/lib/arvbox/docker/Dockerfile.dev
index 5ec73bb..051c274 100644
--- a/arvbox/lib/arvbox/docker/Dockerfile.dev
+++ b/arvbox/lib/arvbox/docker/Dockerfile.dev
@@ -10,4 +10,7 @@ RUN set -e && \
  tar -C /usr/local -xjf /tmp/$PJS.tar.bz2 && \
  ln -s ../$PJS/bin/phantomjs /usr/local/bin/
 
+ADD service/ /var/lib/arvbox/service
+RUN rmdir /etc/service && ln -sf /var/lib/arvbox/service /etc
+
 RUN mkdir /etc/test-service && ln -sf /var/lib/arvbox/service/postgres /etc/test-service
diff --git a/arvbox/lib/arvbox/docker/service/slurmctld/log/main/.gitstub b/arvbox/lib/arvbox/docker/service/slurmctld/log/main/.gitstub
new file mode 100644
index 0000000..e69de29
diff --git a/arvbox/lib/arvbox/docker/service/slurmctld/log/run b/arvbox/lib/arvbox/docker/service/slurmctld/log/run
new file mode 120000
index 0000000..d6aef4a
--- /dev/null
+++ b/arvbox/lib/arvbox/docker/service/slurmctld/log/run
@@ -0,0 +1 @@
+/usr/local/lib/arvbox/logger
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/slurmctld/run b/arvbox/lib/arvbox/docker/service/slurmctld/run
new file mode 100755
index 0000000..7b3c6e1
--- /dev/null
+++ b/arvbox/lib/arvbox/docker/service/slurmctld/run
@@ -0,0 +1,29 @@
+#!/bin/bash
+
+exec 2>&1
+set -eux -o pipefail
+
+. /usr/local/lib/arvbox/common.sh
+
+cat > /etc/slurm-llnl/slurm.conf  <<EOF
+ControlMachine=$HOSTNAME
+ControlAddr=$HOSTNAME
+AuthType=auth/munge
+DefaultStorageLoc=/var/log/slurm
+SelectType=select/cons_res
+SlurmUser=arvbox
+SlurmctldPort=7002
+SlurmctldTimeout=300
+SlurmdPort=7003
+SlurmdSpoolDir=/var/tmp/slurmd.spool
+SlurmdTimeout=300
+StateSaveLocation=/var/tmp/slurm.state
+NodeName=$HOSTNAME
+PartitionName=compute State=UP Default=YES Nodes=$HOSTNAME
+EOF
+
+mkdir -p /var/run/munge
+
+/usr/sbin/munged -f
+
+exec /usr/sbin/slurmctld -v -D
diff --git a/arvbox/lib/arvbox/docker/service/slurmd/log/main/.gitstub b/arvbox/lib/arvbox/docker/service/slurmd/log/main/.gitstub
new file mode 100644
index 0000000..e69de29
diff --git a/arvbox/lib/arvbox/docker/service/slurmd/log/run b/arvbox/lib/arvbox/docker/service/slurmd/log/run
new file mode 120000
index 0000000..d6aef4a
--- /dev/null
+++ b/arvbox/lib/arvbox/docker/service/slurmd/log/run
@@ -0,0 +1 @@
+/usr/local/lib/arvbox/logger
\ No newline at end of file
diff --git a/arvbox/lib/arvbox/docker/service/slurmd/run b/arvbox/lib/arvbox/docker/service/slurmd/run
new file mode 100755
index 0000000..697f7a2
--- /dev/null
+++ b/arvbox/lib/arvbox/docker/service/slurmd/run
@@ -0,0 +1,6 @@
+#!/bin/bash
+
+exec 2>&1
+set -eux -o pipefail
+
+exec /usr/sbin/slurmd -v -D

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