From f018f83407309e769e0a18296f36ac3ac9be5260 Mon Sep 17 00:00:00 2001
From: Mike Smith <grimbough@gmail.com>
Date: Wed, 11 Oct 2017 10:40:12 +0200
Subject: [PATCH] changed user names
---
cluster_setup/README.md | 4 ++--
cluster_setup/cloud_cluster_setup.md | 24 ++++++++++++++++++++++++
cluster_setup/user_delete.sh | 2 +-
cluster_setup/user_setup.sh | 20 ++++++++++----------
4 files changed, 37 insertions(+), 13 deletions(-)
diff --git a/cluster_setup/README.md b/cluster_setup/README.md
index b2199ff..df7bc24 100644
--- a/cluster_setup/README.md
+++ b/cluster_setup/README.md
@@ -4,6 +4,6 @@ This folder contains instructions and files for setting up the example cluster u
# Cluster infrastructure
-The cluster we're using is running on the Heidelberg installation of the de.NBI cloud. The current design is to create a 4 node cluster (1 controller, 3 compute nodes), with varying hardware specifications for each node so we can demonstrate resource managment.
+The cluster we're using is running on the Heidelberg installation of the [de.NBI cloud](https://www.denbi.de/cloud-overview/cloud-hd). The current design is to create a 4 node cluster (1 controller, 3 compute nodes), with varying hardware specifications for each node so we can demonstrate resource managment.
-Job scheduling is doing using [https://slurm.schedmd.com/](SLURM) since it is (a) free and (b) mirrors the infrastructure we're currently using at EMBL.
+Job scheduling is doing using [SLURM](https://slurm.schedmd.com/) since it is (a) free and (b) mirrors the infrastructure we're currently using at EMBL.
diff --git a/cluster_setup/cloud_cluster_setup.md b/cluster_setup/cloud_cluster_setup.md
index 78e845a..22c6de8 100644
--- a/cluster_setup/cloud_cluster_setup.md
+++ b/cluster_setup/cloud_cluster_setup.md
@@ -1,5 +1,7 @@
## Generate _ubuntu_ user SSH keys
+We only need to do the is on the Master, since the home drive will be shared with the compute nodes
+
```
ssh-keygen -t rsa -N "" -f $HOME/.ssh/id_rsa
cat $HOME/.ssh/id_rsa.pub >> $HOME/.ssh/authorized_keys
@@ -21,7 +23,12 @@ sudo service nfs-kernel-server start
```
sudo apt-get update
sudo apt-get install nfs-common
+
+## add a line to automatically mount the shared home directory
sudo cat '10.0.0.8:/home /home nfs auto,noatime,nolock,bg,nfsvers=4,intr,tcp,actimeo=1800 0 0' >> /etc/fstab
+
+## restart the machine
+sudo shutdown -r now
```
@@ -31,17 +38,34 @@ sudo cat '10.0.0.8:/home /home nfs auto,noatime,nolock,bg,nfsvers=4,intr,tc
```
sudo apt-get install slurm-wlm
+
+## enable use of cgroups for process tracking and resource management
sudo bash -c 'echo CgroupAutomount=yes >> /etc/slurm-llnl/cgroup.conf'
sudo chown slurm:slurm /etc/slurm-llnl/cgroup.conf
+sudo sed -i 's/GRUB_CMDLINE_LINUX=""/GRUB_CMDLINE_LINUX="cgroup_enable=memory swapaccount=1"/g' /etc/default/grub
+sudo update-grub
+
+## put munge key in home directory so we can share it with the nodes
sudo cp /etc/munge/munge.key $HOME/
+
+## download slurm.conf file (may require some editing of IP addresses etc)
+sudo wget https://raw.githubusercontent.com/grimbough/embl_swc_hpc/oct2017/cluster_setup/slurm.conf -O /etc/slurm-llnl/slurm.conf -o /dev/null
+sudo chown slurm:slurm /etc/slurm-llnl/slurm.conf
```
### Node
```
+## install slurm worker daemon
sudo apt-get install slurmd
+
+## enable use of cgroups for process tracking and resource management
sudo bash -c 'echo CgroupAutomount=yes >> /etc/slurm-llnl/cgroup.conf'
sudo chown slurm:slurm /etc/slurm-llnl/cgroup.conf
+sudo sed -i 's/GRUB_CMDLINE_LINUX=""/GRUB_CMDLINE_LINUX="cgroup_enable=memory swapaccount=1"/g' /etc/default/grub
+sudo update-grub
+
+## copy the shared munge key and restart the service to start using it
sudo cp /home/ubuntu/munge.key /etc/munge/munge.key
sudo service munge restart
```
diff --git a/cluster_setup/user_delete.sh b/cluster_setup/user_delete.sh
index d30afb5..822795d 100644
--- a/cluster_setup/user_delete.sh
+++ b/cluster_setup/user_delete.sh
@@ -5,5 +5,5 @@ n=40
for i in `seq -w 1 ${n}`
do
echo $i;
- userdel -rf test${i}
+ userdel -rf user${i}
done;
diff --git a/cluster_setup/user_setup.sh b/cluster_setup/user_setup.sh
index bc2e6ef..25a02d5 100644
--- a/cluster_setup/user_setup.sh
+++ b/cluster_setup/user_setup.sh
@@ -1,5 +1,5 @@
#!/bin/bash
-## script to create 40 users called testXX with a default password
+## script to create 40 users called userXX with a default password
## and setup up ssh logins without asking for passwords & host checking
n=40
@@ -7,20 +7,20 @@ for i in `seq -w 1 ${n}`
do
echo $i;
- ## create n new user called testXX and create default password
- adduser --gecos "" --disabled-password test${i}
- echo test${i}:SoftwareC | chpasswd
+ ## create n new user called userXX and create default password
+ adduser --gecos "" --disabled-password user${i}
+ echo user${i}:SoftwareC | chpasswd
## create somewhere to store ssh configuration
- mkdir -p /home/test${i}/.ssh
- echo 'Host *\n StrictHostKeyChecking no\n ForwardX11 yes' > /home/test${i}/.ssh/config
+ mkdir -p /home/user${i}/.ssh
+ printf "Host *\n StrictHostKeyChecking no\n ForwardX11 yes\n" > /home/user${i}/.ssh/config
## generate a ssh key & copy to the list of authorized keys
- ssh-keygen -f /home/test${i}/.ssh/id_rsa -t rsa -N ''
- cp /home/test${i}/.ssh/id_rsa.pub /home/test${i}/.ssh/authorized_keys
+ ssh-keygen -f /home/user${i}/.ssh/id_rsa -t rsa -N ''
+ cp /home/user${i}/.ssh/id_rsa.pub /home/user${i}/.ssh/authorized_keys
## set new user as owner
- chown -R test${i}:test${i} /home/test${i}/.ssh
- chmod 600 /home/test${i}/.ssh/config
+ chown -R user${i}:user${i} /home/user${i}/.ssh
+ chmod 600 /home/user${i}/.ssh/config
done
--
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