differences for PR #489

Author: actions-user

12-cluster.md

@@ -311,8 +311,7 @@ each resource is.
 The local filesystems (ext, tmp, xfs, zfs) will depend on whether you're
 on the same login node (or compute node, later on). Networked filesystems
 (beegfs, cifs, gpfs, nfs, pvfs) will be similar --- but may include
-yourUsername, depending on how it is [mounted](
-https://en.wikipedia.org/wiki/Mount_(computing)).
+`/usr`, depending on how it is [mounted](https://en.wikipedia.org/wiki/Mount_(computing)).
 :::
 
 ::: callout

13-scheduler.md

@@ -170,7 +170,7 @@ following the `#SBATCH` comment is interpreted as an
 instruction to the scheduler.
 
 Let's illustrate this by example. By default, a job's name is the name of the
-script, but the `-J` option can be used to change the
+script, but the `--job-name` option can be used to change the
 name of a job. Add an option to the script:
 
 ```bash
@@ -179,7 +179,7 @@ name of a job. Add an option to the script:
 
 ```bash
 #!/bin/bash
-#SBATCH -Jhello-world
+#SBATCH --job-namehello-world
 
 echo -n "This script is running on "
 hostname
@@ -253,7 +253,7 @@ for it on the cluster.
 
 ```bash
 #!/bin/bash
-#SBATCH -t 00:01 # timeout in HH:MM
+#SBATCH --time 00:01 # timeout in HH:MM
 
 echo -n "This script is running on "
 sleep 20 # time in seconds
@@ -282,8 +282,8 @@ wall time, and attempt to run a job for two minutes.
 
 ```bash
 #!/bin/bash
-#SBATCH -Jlong_job
-#SBATCH -t 00:01 # timeout in HH:MM
+#SBATCH --job-namelong_job
+#SBATCH --time 00:01 # timeout in HH:MM
 
 echo "This script is running on ... "
 sleep 240 # time in seconds

14-environment-variables.md

@@ -210,7 +210,7 @@ job was submitted.
 
 ```output
 #!/bin/bash
-#SBATCH -t 00:00:30
+#SBATCH --time 00:00:30
 
 echo -n "This script is running on "
 hostname

15-modules.md

@@ -381,7 +381,8 @@ compute node).
 ```output
 #!/bin/bash
 #SBATCH 
-r config$sched$comment` -t 00:00:30
+
+#SBATCH --time 00:00:30
 
 module load Python
 

17-parallel.md

@@ -172,8 +172,8 @@ Create a submission file, requesting one task on a single node, then launch it.
 
 ```bash
 #!/bin/bash
-#SBATCH -J solo-job
-#SBATCH -p cpubase_bycore_b1
+#SBATCH --job-name solo-job
+#SBATCH --partition cpubase_bycore_b1
 #SBATCH -N 1
 #SBATCH -n 1
 
@@ -294,8 +294,8 @@ Let's modify the job script to request more cores and use the MPI run-time.
 
 ```bash
 #!/bin/bash
-#SBATCH -J parallel-job
-#SBATCH -p cpubase_bycore_b1
+#SBATCH --job-name parallel-job
+#SBATCH --partition cpubase_bycore_b1
 #SBATCH -N 1
 #SBATCH -n 4
 
@@ -411,8 +411,8 @@ code gets.
 
 ```bash
 #!/bin/bash
-#SBATCH -J parallel-job
-#SBATCH -p cpubase_bycore_b1
+#SBATCH --job-name parallel-job
+#SBATCH --partition cpubase_bycore_b1
 #SBATCH -N 1
 #SBATCH -n 8
 

18-resources.md

@@ -87,7 +87,7 @@ To get info about a specific job (for example, 347087), we change command
 slightly.
 
 ```bash
-[yourUsername@login1 ~]$ sacct -u yourUsername -l -j 347087
+[yourUsername@login1 ~]$ sacct -u yourUsername --long --jobs 347087
 ```
 
 It will show a lot of info; in fact, every single piece of info collected on
@@ -96,7 +96,7 @@ information to `less` to make it easier to view (use the left and right arrow
 keys to scroll through fields).
 
 ```bash
-[yourUsername@login1 ~]$ sacct -u yourUsername -l -j 347087 | less -S
+[yourUsername@login1 ~]$ sacct -u yourUsername --long --jobs 347087 | less -S
 ```
 
 ::::::::::::::::::::::::::::::::::::::  discussion
@@ -132,7 +132,7 @@ get your job dispatched earlier.
 Edit `parallel_job.sh` to set a better time estimate. How close can
 you get?
 
-Hint: use `-t`.
+Hint: use `--time`.
 
 :::::::::::::::  solution
 
@@ -142,7 +142,7 @@ The following line tells Slurm that our job should
 finish within 2 minutes:
 
 ```bash
-#SBATCH -t 00:02:00
+#SBATCH --time 00:02:00
 ```
 
 :::::::::::::::::::::::::

config.yaml

@@ -7,6 +7,11 @@
 # chain-loader, per @tobyhodges' suggestion.
 #
 # Compute irresponsibly.
+#
+# Use the HPC_CARPENTRY_CUSTOMIZATION variable to invoke these:
+#
+# > HPC_CARPENTRY_CUSTOMIZATION=episodes/files/customization/Ghastly_Mistakes/_config_options.yml
+# > export HPC_CARPENTRY_CUSTOMIZATION
 ---
 
 snippets: "Ghastly_Mistakes"
@@ -22,7 +27,8 @@ remote:
   host: "castle"
   node: "turtle"
   location: "World 8-4"
-  homedir: "/darkland"
+  fs:
+    home: "/darkland"
   user: "luigi"
   module_python3: "Boa"
   prompt: "luigi@castle:~$"

files/customization/Ghastly_Mistakes/_config_options.yml

@@ -9,6 +9,11 @@
 # account, please visit <cluster.hpc-carpentry.org>.
 #
 # Compute responsibly.
+#
+# Use the HPC_CARPENTRY_CUSTOMIZATION variable to invoke these:
+#
+# > HPC_CARPENTRY_CUSTOMIZATION=episodes/files/customization/HPCC_MagicCastle_slurm/_config_options.yml
+# > export HPC_CARPENTRY_CUSTOMIZATION
 ---
 
 snippets: "HPCC_MagicCastle_slurm"
@@ -24,11 +29,14 @@ remote:
   host: "login1"
   node: "smnode1"
   location: "cluster.hpc-carpentry.org"
-  homedir: "/home"
   user: "yourUsername"
   module_python3: "Python"
   prompt: "[yourUsername@login1 ~]$"
   shebang: "#!/bin/bash"
+
+  fs:
+    home: "/home"
+
   modules:
     python: "Python"
 
@@ -45,10 +53,15 @@ sched:
   flag:
     user: "-u yourUsername"
     interactive: ""
-    histdetail: "-l -j"
-    name: "-J"
-    time: "-t"
-    queue: "-p"
+    histdetail: "--long --jobs"
+    name:    "--job-name"
+    account: "--account"
+    array:   "--array"
+    time:    "--time"
+    queue:   "--partition"
+    nodes:   "--nodes"
+    tasks:   "--tasks"
+    threads: "--cpus-per-task"
   del: "scancel"
   interactive: "srun"
   info: "sinfo"

files/customization/HPCC_MagicCastle_slurm/_config_options.yml

@@ -0,0 +1,33 @@
+```output
+      1 a
+      1 and
+      1 be
+      1 can
+      1 count
+      1 in
+      1 is
+      1 it
+      1 look
+      1 most
+      1 often
+      1 our
+      1 out
+      1 script
+      1 see
+      1 small
+      1 some
+      1 them
+      1 to
+      1 trying
+      1 useful
+      1 very
+      1 we
+      1 which
+      1 will
+      2 are
+      2 file
+      2 for
+      2 this
+      3 repeated
+      3 words
+```