Initial commit

aliases-functions/job-aliases.csh

@@ -0,0 +1,3 @@
+alias job-cpu 'sacct -o jobid,jobname,ncpus,elapsed,mincpu,cputime%12 -j'
+alias job-disk 'sacct -o jobid,jobname,elapsed,maxdiskread,maxdiskwrite -j'
+alias job-mem 'sacct -o jobid,jobname,maxvmsize,maxrss,averss,maxpages -j'

aliases-functions/job-aliases.sh

@@ -0,0 +1,3 @@
+alias job-cpu='sacct -o jobid,jobname,ncpus,elapsed,mincpu,cputime%12 -j'
+alias job-disk='sacct -o jobid,jobname,elapsed,maxdiskread,maxdiskwrite -j'
+alias job-mem='sacct -o jobid,jobname,maxvmsize,maxrss,averss,maxpages -j'

aliases-functions/stail

@@ -0,0 +1,47 @@
+#!/bin/csh
+
+    # Validate input.
+    if ($# < 1) then
+	echo "Usage: $argv[0] SLURM_SUBMISSION_FILE"
+	exit 1
+    else if (! -e $argv[1]) then
+	echo "Usage: $argv[0] SLURM_SUBMISSION_FILE"
+	exit 1
+    endif
+    # Submit job using `sbatch`.
+    set sbatch_out = `sbatch $argv[1]`
+    # Exit if submission is unsuccessful.
+    if (-z "$sbatch_out") then
+        exit 1
+    endif
+    echo $sbatch_out
+    # Grab job metadata.
+    set job_id = `echo $sbatch_out | awk '{ print $NF }'`
+    set out_file = `scontrol -ao show job $job_id | sed -E 's#.* StdOut=([^ ]+).*#\1#'`
+    # Wait for the job to start running or fail.
+    set message = "Waiting for job $job_id"
+    foreach i (`seq 1 120`)
+        set state = `\sacct -PXnj $job_id -o state`
+        if ("$state" == "PENDING") then
+            if ("$message" != "") then
+                echo "$message"
+                set message = ""
+            endif
+        else if ("$state" == "RUNNING") then
+            echo "Job $job_id is running.  Showing output file $out_file (hit Ctrl + C to exit):\
+"
+            tail -f $out_file
+            break
+        else if ("$state" == "FAILED") then
+            echo "Error: Job $job_id failed.  Showing end of output file $out_file :\
+"
+            tail $out_file
+            break
+        else if ("$state" == "COMPLETED") then
+            echo "Job $job_id completed.  Showing end of output file $out_file :\
+"
+            tail $out_file
+	    break
+        endif
+        sleep 1
+    end

aliases-functions/watch-sbatch.sh

@@ -0,0 +1,44 @@
+function stail() {
+    # Validate input.
+    if ! [[ -e "$1" ]]; then
+	echo "Usage: ${FUNCNAME} SLURM_SUBMISSION_FILE"
+	return 1
+    fi
+    # Submit job using `sbatch`.
+    sbatch_out=$(sbatch $1)
+    # Exit if submission is unsuccessful.
+    if [[ -z "$sbatch_out" ]]; then
+        return 1
+    fi
+    echo $sbatch_out
+    # Grab job metadata.
+    job_id=${sbatch_out##* }
+    out_file=$(scontrol -ao show job $job_id | sed -E 's#.* StdOut=([^ ]+).*#\1#')
+    # Wait for the job to start running or fail.
+    message="Waiting for job $job_id"
+    for i in {1..120}; do
+        state=$(command sacct -PXnj $job_id -o state)
+        if [[ "$state" == "PENDING" ]]; then
+            if ! [[ -z "$message" ]]; then
+                echo "$message"
+                message=
+            fi
+        elif [[ "$state" == "RUNNING" ]]; then
+            echo "Job $job_id is running.  Showing output file $out_file (hit Ctrl + C to exit):
+"
+            tail -f $out_file
+            break
+        elif [[ "$state" == "FAILED" ]]; then
+            echo "Error: Job $job_id failed.  Showing end of output file $out_file :
+"
+            tail $out_file
+            break
+        elif [[ "$state" == "COMPLETED" ]]; then
+            echo "Job $job_id completed.  Showing end of output file $out_file :
+"
+            tail $out_file
+	    break
+        fi
+        sleep 1
+    done
+}

install-apps/R-commands.R

@@ -0,0 +1,7 @@
+# The usual `install.packages("rPython")` doesn't work because we also
+# need to interactively at least once tell R to use the user library
+# and to select a mirror.
+
+dir.create(Sys.getenv("R_LIBS_USER"), recursive = TRUE)
+.libPaths(Sys.getenv("R_LIBS_USER"))
+install.packages("rPython", repos = "http://cran.us.r-project.org")

install-apps/R-example

@@ -0,0 +1,5 @@
+source /etc/profile.d/modules.sh # Needed for bash
+module purge
+module load r/3.1.1
+Rscript R-commands.R
+# Then we will setup the paths

install-apps/python-example

@@ -0,0 +1,5 @@
+source /etc/profile.d/modules.sh # Needed for bash
+module purge
+module load python/2.7.6
+pip install --user cutadapt
+# Then we will setup the paths

slurm-troubleshooting/bash-debug.slurm

@@ -0,0 +1,7 @@
+#!/bin/bash -x
+# Submit a 1 minute job.
+#SBATCH --partition=phi
+#SBATCH --time=1:00
+
+scontrol show job $SLURM_JOB_ID
+hostname

slurm-troubleshooting/bash-fail.slurm

@@ -0,0 +1,6 @@
+#!/bin /bash
+# Submit a 1 minute job.
+#SBATCH --partition=phi
+#SBATCH --time=1:00
+
+hostname

slurm-troubleshooting/bash-pending.slurm

@@ -0,0 +1,6 @@
+#!/bin/bash
+# Submit a 1 hour job.
+#SBATCH --partition=debug
+#SBATCH --time=1:00:00
+
+hostname

slurm-troubleshooting/bash-success.slurm

@@ -0,0 +1,6 @@
+#!/bin/bash
+# Submit a 1 minute job.
+#SBATCH --partition=phi
+#SBATCH --time=1:00
+
+hostname