Commit 90db646f authored by Philip Carns's avatar Philip Carns
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start filling in JLSE instructions

parent 41dd9ab1
# Mochi Boot Camp Session 2: Hands-on
## Logging on to JLSE
Begin by SSH'ing to the JLSE login node:
Make sure to use the ssh key that you set up when you registered for your
account. Once you connect to login.jlse, it will present you with the
following prompt:
Duo Authentication Required.
Duo two-factor login for carns
Enter a passcode or select one of the following options:
1. Duo Push to XXX-XXX-9834
Passcode or option (1-1):
Prese '1' to be prompted for MFA authentication from the Duo app on your
The login node is where you will generally be compiling and installing
software prior to running it on a compute node. Importantly, the login node
has external Internet connectivity, but the compute nodes do not.
Next make a subdirectory for your bootcamp exercises and clone the bootcamp
git repository.
mkdir ~/bootcamp
cd ~/bootcamp
git clone
At this point, you can continue following directions online or by looking at
this file in `~/bootcamp/mochi-boot-camp/session2/`.
## Installing Spack
The easiest way to download and compile Mochi components is via the [Spack
package manager]( Begin by cloning the spack repository
from github, and then adding spack to your environment:
cd ~/bootcamp
git clone
. ~/bootcamp/spack/share/spack/
At this point, the `spack` command line tool is available to you, but we
need just a few more steps to configure it ideally for this envionment.
First run `spack compiler find` to see what compilers are available by
[carns@jlselogin2 bootcamp]$ spack compiler find
==> Added 1 new compiler to /home/carns/.spack/linux/compilers.yaml
==> Compilers are defined in the following files:
You can see in this case that it only found `gcc 4.8.5`, which will work,
but is quite old. There are newer compilers available in the JLSE
environment that you can use in slack by putting them in your path and
re-running spack compiler find (you will not need to modify your path when
you log in in the future; spack will store the location of the compiler in
it's persistent configuration):
[carns@jlselogin2 bootcamp]$ export PATH="/soft/compilers/gcc/8.2.0/linux-rhel7-x86_64/bin/:$PATH"
[carns@jlselogin2 bootcamp]$ spack compiler find
==> Added 1 new compiler to /home/carns/.spack/linux/compilers.yaml
==> Compilers are defined in the following files:
## Adding the Mochi software repository to Spack
Many of the Mochi software components have not yet been upstreamed to the
Spack package manager. They are available as a separate software repository
that can be added to spack.
[carns@jlselogin2 bootcamp]$ cd ~/bootcamp
[carns@jlselogin2 bootcamp]$ git clone
Cloning into 'sds-repo'...
remote: Enumerating objects: 268, done.
remote: Counting objects: 100% (268/268), done.
remote: Compressing objects: 100% (121/121), done.
remote: Total 1426 (delta 152), reused 191 (delta 102)
Receiving objects: 100% (1426/1426), 174.53 KiB | 0 bytes/s, done.
Resolving deltas: 100% (828/828), done.
[carns@jlselogin2 bootcamp]$ spack repo add sds-repo
==> Added repo with namespace 'sds'.
## Customizing Spack for the JLSE environment
At this point you can install any Mochi software component, but it will
likely download and compile more packages than are strictly necessary, which
is time consuming. At this point we will install a `packages.yaml` file
that customizes Spack by informing if of system packages that it should
reuse, and specifies a subset of network transports to use for Mochi.
We have provided a pre-configured `packages.yaml` file for this purpose in
the JLSE environment. It primarily does the following:
* informs Spack to use already available software for certain common system
packages (Spack by default will build these packages itself)
* Configure the Mercury RPC package to not configure support for any
external network fabric packages (we will just use shared memory for this
week's experiments)
You can activate this configuration for your account by doing the following:
cp ~/bootcamp/mochi-boot-camp/s2-hands-on/packages.yaml ~/.spack/linux/
At this point you are ready to install and run Mochi software!
## General spack usage for package management
The following are the most important commands to know:
* `spack spec <package>` to see what will be installed if you were to
install it (including dependencies and version numbers)
* `spack install <package>` to install a package
* `spack load -r <package>` to load the package into your environment
* `module list` to observe what modules you have loaded
## Installing your first Mochi components
Run the following to download, compile, and install Margo:
spack install margo
This will take a few minutes and will install all of the necessary
dependencies, including Mercury and Argobots.
## Running a hands on example
TODO: Phil handle JLSE setup/documentation
TODO: make content here first with step by step, details, packages.yaml,
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