Initial conversion for NERSC

Author: Trevor Keller

MAINTENANCE.md

@@ -38,9 +38,8 @@ of the HPC Carpentry community.
 
 ### Slack
 
-The main Carpentries Slack channel is reachable at
-[swcarpentry.slack.com][swc-slack]. To become a member, you can
-trigger in invitation from [here][slack-invite].
+HPC Carpentry participates in the The Carpentries' Slack channel.
+Click through for a [Slack invite][slack-invite].
 
 You can go directly to the HPC Carpentry sub-channel at
 [#hpc-carpentry][hpc-slack]. These are the things to bookmark —
@@ -91,8 +90,8 @@ assigned to `CHECKERS` near the bottom of `bin/lesson_check.py`.
 [project-github]: https://github.com/hpc-carpentry
 [coord-repo]: https://github.com/hpc-carpentry/coordination
 [mainsite-repo]: https://github.com/hpc-carpentry/hpc-carpentry.org
-[swc-slack]: https://swcarpentry.slack.com
-[hpc-slack]: https://swcarpentry.slack.com/#hpc-carpentry
-[slack-invite]: https://swc-slack-invite.herokuapp.com
+[swc-slack]: https://carpentries.slack.com
+[hpc-slack]: https://carpentries.slack.com/#hpc-carpentry
+[slack-invite]: https://slack-invite.carpentries.org/
 [topicbox]: https://carpentries.topicbox.com
 [zenodo]: https://zenodo.org/

config.yaml

@@ -1,7 +1,7 @@
 #------------------------------------------------------------
 # Values for this lesson.
 #------------------------------------------------------------
-
+---
 # Which carpentry is this (swc, dc, lc, or cp)?
 # swc: Software Carpentry
 # dc: Data Carpentry
@@ -17,7 +17,7 @@ carpentry: 'cp'
 # carpentry_description: "Custom Carpentry"
 
 # Overall title for pages.
-title: 'Introduction to High-Performance Computing'
+title: 'Introduction to High-Performance Computing at NERSC'
 
 # Date the lesson was created (YYYY-MM-DD, this is empty by default)
 created: 2017-03-24
@@ -33,7 +33,7 @@ life_cycle: 'alpha'
 license: 'CC-BY 4.0'
 
 # Link to the source repository for this lesson
-source: 'https://github.com/ocaisa/probable-pancake'
+source: 'https://github.com/hpc-workshops/nersc-hpc-intro'
 
 # Default branch of your lesson
 branch: 'main'
@@ -94,7 +94,7 @@ profiles:
 # sandpaper and varnish versions) should live
 
 
-carpentry_description: Lesson Description
-url: 'https://ocaisa.github.io/probable_pancake'
+carpentry_description: "HPC Intro at NERSC"
+url: 'https://hpc-workshops.github.io/perlmutter-hpc-intro'
 analytics: carpentries
 lang: en

episodes/12-cluster.Rmd

@@ -75,7 +75,7 @@ sends back. We will use the Secure SHell protocol (or SSH) to open an encrypted
 network connection between two machines, allowing you to send & receive text
 and data without having to worry about prying eyes.
 
-![Connect to cluster](fig/connect-to-remote.svg){alt-text="Connect to cluster"}
+![Connect to cluster](fig/connect-to-remote.svg){alt="Connect to cluster"}
 
 Make sure you have a SSH client installed on your laptop. Refer to the
 [setup](../index.md) section for more details. SSH clients are

episodes/epcc_config.yaml …CC_ARCHER2_slurm/lesson_config_epcc.yamlepisodes/epcc_config.yaml renamed to episodes/files/snippets/EPCC_ARCHER2_slurm/lesson_config_epcc.yaml episodes/epcc_config.yaml renamed to episodes/files/snippets/EPCC_ARCHER2_slurm/lesson_config_epcc.yaml

@@ -0,0 +1,54 @@
+# ----------------
+# NERSC Perlmutter
+# ----------------
+# If you need an account, please visit <nersc.gov>
+#
+# Compute responsibly.
+---
+snippets: "NERSC_Perlmutter_slurm"
+
+local:
+  prompt: "local:~$"
+  bash_shebang: "#!/bin/bash"
+
+remote:
+  name: "Perlmutter"
+  host_id: "Perlmutter"
+  login: "saul.nersc.gov"
+  host: "saul"
+  node: "pm001"
+  location: "saul.nersc.gov"
+  homedir: "/home"
+  user: "user"
+  prompt: 'remote:~$'
+  prompt_work: "user@saul:/work/user"
+  module_python3: "Python"
+  bash_shebang: "#!/bin/bash"
+
+sched:
+  name: "Slurm"
+  reservation: "trn010"
+  submit:
+    name: "sbatch"
+    options: ""
+  queue:
+    debug: "smnode"
+    testing: "cpubase_bycore_b1"
+  status: "squeue"
+  flag:
+    user: "-u user"
+    interactive: "--pty /bin/bash"
+    histdetail: "-l -j"
+    name: "--job-id="
+    time: "--time="
+    queue: "--constraint="
+    nodes: "--nodes="
+    tasks: "--ntasks="
+  del: "scancel"
+  interactive: "srun"
+  info: "sinfo"
+  comment: "#SBATCH"
+  hist: "sacct -u user"
+  hist_filter: ""
+  partition: "cpu"
+  qos: "debug"

episodes/lesson_config_hpcc.yaml …agicCastle_slurm/lesson_config_hpcc.yamlepisodes/lesson_config_hpcc.yaml renamed to episodes/files/snippets/HPCC_MagicCastle_slurm/lesson_config_hpcc.yaml episodes/lesson_config_hpcc.yaml renamed to episodes/files/snippets/HPCC_MagicCastle_slurm/lesson_config_hpcc.yaml

@@ -0,0 +1,6 @@
+```output
+PARTITION          AVAIL  TIMELIMIT  NODES  STATE NODELIST
+cpubase_bycore_b1*    up   infinite      4   idle node[1-2],smnode[1-2]
+node                  up   infinite      2   idle node[1-2]
+smnode                up   infinite      2   idle smnode[1-2]
+```

episodes/files/snippets/NERSC_Perlmutter_slurm/_config_options.yml

@@ -0,0 +1,12 @@
+::: challenge
+
+## Explore a Worker Node
+
+Finally, let's look at the resources available on the worker nodes
+where your jobs will actually run. Try running this command to see
+the name, CPUs and memory available on one of the worker nodes:
+
+```bash
+`r config$remote$prompt` sinfo -o "%n %c %m" | column -t
+```
+:::

episodes/files/snippets/NERSC_Perlmutter_slurm/cluster/queue-info.Rmd

@@ -0,0 +1,21 @@
+```
+~~~ /cvmfs/pilot.eessi-hpc.org/2020.12/software/x86_64/amd/zen2/modules/all ~~~
+  Bazel/3.6.0-GCCcore-x.y.z              NSS/3.51-GCCcore-x.y.z
+  Bison/3.5.3-GCCcore-x.y.z              Ninja/1.10.0-GCCcore-x.y.z
+  Boost/1.72.0-gompi-2020a               OSU-Micro-Benchmarks/5.6.3-gompi-2020a
+  CGAL/4.14.3-gompi-2020a-Python-3.x.y   OpenBLAS/0.3.9-GCC-x.y.z
+  CMake/3.16.4-GCCcore-x.y.z             OpenFOAM/v2006-foss-2020a
+
+[removed most of the output here for clarity]
+
+  Where:
+   L:        Module is loaded
+   Aliases:  Aliases exist: foo/1.2.3 (1.2) means that "module load foo/1.2"
+             will load foo/1.2.3
+   D:        Default Module
+
+Use "module spider" to find all possible modules and extensions.
+Use "module keyword key1 key2 ..." to search for all possible modules matching
+any of the "keys".
+```
+{: .output}

episodes/files/snippets/NERSC_Perlmutter_slurm/cluster/specific-node-info.Rmd

@@ -0,0 +1,4 @@
+```
+No Modulefiles Currently Loaded.
+```
+{: .output}