Fine tuning your Cloud Setup
Last updated on 2023-05-04 | Edit this page
- Is my remote computer correctly configured?
- How do I keep my processing going when I leave?
- Check the available resources and file system on your remote machine
- Keep background processes working in the cloud with
Once you’re connected to your new remote instance, it’s a good idea to double check that the settings are what you wanted, and that everything is working smoothly before you start your project.
For this workshop, your instructor did all the verification before the workshop even started, but this is an important skill for when you start running your own instances.
When you connect, it is typical to receive a welcome screen. The Data Carpentry Amazon instances display this message upon connecting:
Welcome to Ubuntu 20.04.5 LTS (GNU/Linux 5.4.0-137-generic x86_64) * Documentation: https://help.ubuntu.com * Management: https://landscape.canonical.com * Support: https://ubuntu.com/advantage System information as of Wed 25 Jan 2023 05:17:10 AM UTC System load: 0.9 Processes: 204 Usage of /: 19.7% of 98.27GB Users logged in: 0 Memory usage: 6% IPv4 address for eth0: 172.31.23.125 Swap usage: 0% Get cloud support with Ubuntu Advantage Cloud Guest: http://www.ubuntu.com/business/services/cloud 0 updates can be applied immediately. New release '22.04.1 LTS' available. Run 'do-release-upgrade' to upgrade to it.
You should also have a blinking cursor awaiting your command
Now that we have connected here are a few commands that tell you a little about the machine you have connected to:
whoami- shows your username on computer you have connected to:
dcuser@ip-172-31-62-209 ~ $ whoami dcuser
df -h- shows space on hard drive
dcuser@ip-172-31-62-209 ~ $ df -h Filesystem Size Used Avail Use% Mounted on udev 2.0G 12K 2.0G 1% /dev tmpfs 396M 792K 395M 1% /run /dev/xvda1 99G 48G 47G 51% / none 4.0K 0 4.0K 0% /sys/fs/cgroup none 5.0M 0 5.0M 0% /run/lock none 2.0G 144K 2.0G 1% /run/shm none 100M 36K 100M 1% /run/user
Under the column ‘Mounted on’ row that has
/as the value shows the value for the main disk
cat /proc/cpuinfo- shows detail information on how many processors (CPUs) the machine has
dcuser@ip-172-31-62-209 ~ $ cat /proc/cpuinfo processor : 0 vendor_id : GenuineIntel cpu family : 6 model : 62 model name : Intel(R) Xeon(R) CPU E5-2670 v2 @ 2.50GHz stepping : 4 microcode : 0x415 cpu MHz : 2494.060 cache size : 25600 KB physical id : 0 siblings : 2 core id : 0 cpu cores : 2 apicid : 0 initial apicid : 0 fpu : yes fpu_exception : yes cpuid level : 13 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx rdtscp lm constant_tsc rep_good nopl xtopology eagerfpu pni pclmulqdq ssse3 cx16 pcid sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm xsaveopt fsgsbase smep erms bogomips : 4988.12 clflush size : 64 cache_alignment : 64 address sizes : 46 bits physical, 48 bits virtual power management: processor : 1 vendor_id : GenuineIntel cpu family : 6 model : 62 model name : Intel(R) Xeon(R) CPU E5-2670 v2 @ 2.50GHz stepping : 4 microcode : 0x415 cpu MHz : 2494.060 cache size : 25600 KB physical id : 0 siblings : 2 core id : 1 cpu cores : 2 apicid : 2 initial apicid : 2 fpu : yes fpu_exception : yes cpuid level : 13 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx rdtscp lm constant_tsc rep_good nopl xtopology eagerfpu pni pclmulqdq ssse3 cx16 pcid sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm xsaveopt fsgsbase smep erms bogomips : 4988.12 clflush size : 64 cache_alignment : 64 address sizes : 46 bits physical, 48 bits virtual power management:
tree -L 1- shows a tree view of the file system 1 level below your current location.
dcuser@ip-172-31-62-209 ~ $ tree -L 1 . ├── dc_sample_data ├── Desktop ├── Downloads ├── FastQC ├── openrefine-2.6-beta.1 ├── R └── Trimmomatic-0.32 7 directories, 0 files
Depending on how you connect to the cloud, you may have processes and
jobs that are running, and will need to continue running for some time.
If you are connecting to your cloud desktop via VNC, jobs you start will
continue to run. If you are connecting via SSH, if you end the SSH
connection (e.g. you exit your SSH session, you lose your connection to
the internet, you close your laptop, etc.), jobs that are still running
when you disconnect will be killed. There are a few ways to keep cloud
processes running in the background. Many times when we refer to a
background process we are talking about what is described
at this tutorial - running a command and returning to shell prompt.
Here we describe a program that will allow us to run our entire shell
and keep that process running even if we disconnect:
If you don’t have
tmux on your system, you should still be
able to use
screen. This is another program that has mostly
the same capabilities as
tmux. It’s a lot older, though, so
can be more clunky to use; however, it is likely to be available on any
cloud system you encounter.
screen, you open a
‘session’. A ‘session’ can be thought of as a window for
screen, you might open an terminal to
do one thing on the a computer and then open a new terminal to work on
another task at the command line.
As you work, an open session will stay active until you close this session. Even if you disconnect from your machine, the jobs you start in this session will run till completion.
For the following instructions use either
screen, not both!
You can start a session and give it a descriptive name:
$ tmux new -s session_name
$ screen -S session_name
This creates a session with the name
will stay active until you close it.
You can detach from a session by pressing on your keyboard:
control + bfollowed by
control + afollowed by
If you disconnect from your session, or from your ssh into a machine, you will need to reconnect to an existing session. You can see a list of existing sessions:
$ tmux list-sessions
$ screen -ls
To connect to an existing session:
$ tmux attach -t session_name
-toption = ‘target’
$ screen -r session_name
-roption = ‘resume a detached screen session’
tmux is not installed in most cloud Linux
instances. However when you start a new instance, you can install new
software packages using Package Managers like YUM (for Red Hat and
Centos instances) or APT (for Debian or Ubuntu instances).
Most common software tools will have a package named with the same
name, but this is not always the case. If you know the name of the
program you wish to install, but are not sure of the package name, you
can use the
apt program to search packages:
$ apt search tmux Sorting... Done Full Text Search... Done tmux/trusty,now 1.8-5 amd64 [installed] terminal multiplexer $
On our system, searching for tmux only gives one result, and it is already installed.
If you own, or at least have administrator privileges on an instance,
you can also use APT to install a package. First you would need the
package name, which is whatever is before the
/ in your
search result. In our example above with
tmux, we got
tmux/trusty,now 1.8-5 amd64 [installed]
which means that it is stored in APT as tmux.
Once you know the package name, you could install it using
Before installing or upgrading any system packages, you should always
update the local APT cache. That ensures you’ll install the latest
version. Note that the instructions now start with
which is short for ‘super user do’.
sudo is a program that
allows a user to users to run programs as an administrator without
logging off and then logging back in as the admin.
So, in this line:
$ sudo apt upgrade
we are first invoking
sudo, and then having the
sudo program run
apt upgrade. This way,
apt upgrade is run from the administrator account. You can
actually try to run that line if you want, you’ll be prompted to input
the administrator password:
$ sudo apt upgrade [sudo] password for dcuser:
Since we don’t have the adminstrator password, our request will be rejected:
dcuser@ip-172-31-26-134:~$ sudo apt upgrade password for dcuser: dcuser is not in the sudoers file. This incident will be reported. dcuser@ip-172-31-26-134:~$
If we did have the administrator password, we would have seen this:
$ sudo apt upgrade password for dcuser: Hit:1 http://au.archive.ubuntu.com/ubuntu xenial InRelease Get:2 http://au.archive.ubuntu.com/ubuntu xenial-updates InRelease [102 kB] ... Fetched 3,413 kB in 1s (2,233 kB/s) Reading package lists... Done
And one the cache is updated, we could have then requested that APT
install a program. To have APT find packages, we used
apt search, which told the program APT to run it’s
sub-program ‘search’ but to install packages, we need to use the
subprogram ‘install’. Confusingly, there is also an
program with an ‘install’ subprogram which does exactly the same thing,
in 99% of cases, it doesn’t matter whether you use
apt install or
As with the ‘upgrade’ command, this will require the administrator password that we don’t have, but on your own machine, you’d get output like this:
$ sudo apt install tmux password for dcuser: Reading package lists... Done Building dependency tree Reading state information... Done The following additional packages will be installed: libevent-2.0-5 libutempter0 The following NEW packages will be installed: libevent-2.0-5 libutempter0 tmux 0 to upgrade, 3 to newly install, 0 to remove and 0 not to upgrade. Need to get 345 kB of archives. After this operation, 949 kB of additional disk space will be used. Do you want to continue? [Y/n] y Get:1 http://mirror.overthewire.com.au/ubuntu xenial-updates/main amd64 libevent-2.0-5 amd64 2.0.21-stable-2ubuntu0.16.04.1 [114 kB] Get:2 http://mirror.overthewire.com.au/ubuntu xenial/main amd64 libutempter0 amd64 1.1.6-3 [7,898 B] Get:3 http://mirror.overthewire.com.au/ubuntu xenial/main amd64 tmux amd64 2.1-3build1 [223 kB] Fetched 345 kB in 0s (863 kB/s) (Reading database ... 130583 files and directories currently installed.) ... Setting up libevent-2.0-5:amd64 (2.0.21-stable-2ubuntu0.16.04.1) ... Setting up libutempter0:amd64 (1.1.6-3) ... Setting up tmux (2.1-3build1) ... Processing triggers for libc-bin (2.23-0ubuntu10) ...