finish draft of queue templates

ntBre · Sep 15, 2024 · 28f2ed8 · 28f2ed8
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diff --git a/docs/examples/slurm_cfour.toml b/docs/examples/slurm_cfour.toml
@@ -0,0 +1,9 @@
+#!/bin/bash
+#SBATCH --job-name={{.filename}}
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=1
+#SBATCH -o {{.filename}}.out
+#SBATCH --no-requeue
+#SBATCH --mem=8gb
+
+CFOUR_CMD="cfour"
diff --git a/docs/examples/slurm_dftb.toml b/docs/examples/slurm_dftb.toml
@@ -0,0 +1,9 @@
+#!/bin/bash
+#SBATCH --job-name={{.filename}}
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=1
+#SBATCH -o {{.filename}}.out
+#SBATCH --no-requeue
+#SBATCH --mem=8gb
+
+DFTB_CMD="dftb+"
diff --git a/docs/index.html b/docs/index.html
@@ -9,6 +9,8 @@
 
 
 
+
+
 <!DOCTYPE html>
 <html lang="en">
   <head>
@@ -115,9 +117,9 @@ <h2>Table of Contents</h2>
 <li><a href="#local">Local</a></li>
 <ul>
 <li><a href="#mopac---">MOPAC   </a></li>
+<li><a href="#dftb+---">DFTB+   </a></li>
 <li><a href="#molpro---">Molpro   </a></li>
 <li><a href="#cfour---">CFOUR   </a></li>
-<li><a href="#dftb+---">DFTB+   </a></li>
 </ul>
 </ul>
 <li><a href="#derivative-types">Derivative Types</a></li>
@@ -1265,6 +1267,14 @@ <h5 id=molpro-><a href="#molpro-">Molpro </a></h5>
 	<p>
 
 	<h5 id=cfour-><a href="#cfour-">CFOUR </a></h5>
+	<p>
+	  This template and the following are pretty much the same, as were the
+	  previous two, so there's not much more to say. In general, the top portion
+	  of each template just consists of normal PBS directives with optional
+	  template parameters, followed by a single command or couple of commands
+	  (for MOPAC) to set the variable used by pbqff.
+	</p>
+
 	<pre><code>queue_template = """
 #!/bin/sh
 #PBS -N {{.basename}}
@@ -1308,16 +1318,92 @@ <h5 id=dftb+-><a href="#dftb+-">DFTB+ </a></h5>
 
 	<h4 id=slurm><a href="#slurm">Slurm</a></h4>
 
+	<p>
+	  The general approach for Slurm and the local queue is identical to PBS, so
+	  you may want to read the previous section even if you're intending to use
+	  one of these other queues. Here I will just present some example templates
+	  for quick reference.
+	</p>
+
 	<h5 id=mopac--><a href="#mopac--">MOPAC  </a></h5>
+
+	<p>
+	  This template and the Molpro one below are embedded directly from psqs,
+	  where the templates for pbqff are defined. psqs doesn't currently define
+	  default templates for CFOUR or DFTB+, so you'll have to provide
+	  a <code>queue_template</code> of your own for those programs.
+	</p>
+
+	<pre><code>#!/bin/bash
+#SBATCH --job-name=semp
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=1
+#SBATCH -o {{.filename}}.out
+#SBATCH --no-requeue
+#SBATCH --mem=1gb
+export LD_LIBRARY_PATH=/home/qc/mopac2016/
+export MOPAC_CMD=/home/qc/mopac2016/MOPAC2016.exe
+echo $SLURM_JOB_ID
+date
+hostname
+</code></pre>
 	<h5 id=molpro--><a href="#molpro--">Molpro  </a></h5>
+	<pre><code>#!/bin/bash
+#SBATCH --job-name={{.filename}}
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=1
+#SBATCH -o {{.filename}}.out
+#SBATCH --no-requeue
+#SBATCH --mem=8gb
+
+MOLPRO_CMD="/home/qc/bin/molpro2020.sh 1 1"
+</code></pre>
 	<h5 id=cfour--><a href="#cfour--">CFOUR  </a></h5>
+	<pre><code>#!/bin/bash
+#SBATCH --job-name={{.filename}}
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=1
+#SBATCH -o {{.filename}}.out
+#SBATCH --no-requeue
+#SBATCH --mem=8gb
+
+CFOUR_CMD="cfour"
+</code></pre>
 	<h5 id=dftb+--><a href="#dftb+--">DFTB+  </a></h5>
-
+	<pre><code>#!/bin/bash
+#SBATCH --job-name={{.filename}}
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=1
+#SBATCH -o {{.filename}}.out
+#SBATCH --no-requeue
+#SBATCH --mem=8gb
+
+DFTB_CMD="dftb+"
+</code></pre>
 	<h4 id=local><a href="#local">Local</a></h4>
+
+	<p>
+	  Like for Slurm, pbqff includes only two default templates for the local
+	  queue option, which is primarily used for testing. Because the local queue
+	  simply "submits" jobs using bash scripts rather than PBS or Slurm
+	  submission scripts, a local queue template can be much simpler than a PBS
+	  or Slurm template, essentially just defining the path to the executable to
+	  be run. Of course, you can add any additional commands you want, but this
+	  is all that pbqff requires.
+	</p>
+
 	<h5 id=mopac---><a href="#mopac---">MOPAC   </a></h5>
+	<pre><code>export MOPAC_CMD=/opt/mopac/mopac
+export LD_LIBRARY_PATH=/opt/mopac/ </code></pre>
+
+	<h5 id=dftb+---><a href="#dftb+---">DFTB+   </a></h5>
+	<pre><code>DFTB_CMD=/opt/dftb+/dftb+ </code></pre>
+
 	<h5 id=molpro---><a href="#molpro---">Molpro   </a></h5>
+	<pre><code>MOLPRO_CMD=molpro </code></pre>
+
 	<h5 id=cfour---><a href="#cfour---">CFOUR   </a></h5>
-	<h5 id=dftb+---><a href="#dftb+---">DFTB+   </a></h5>
+	<pre><code>CFOUR_CMD=cfour </code></pre>
 
 	<h3 id=derivative-types><a href="#derivative-types">Derivative Types</a></h3>
 	<!-- TODO -->

diff --git a/docs/template.html b/docs/template.html
@@ -9,6 +9,11 @@
 define({{head4}}, {{<h4 id=make_id($1)><a href="#make_id($1)">$1</a></h4>}})
 define({{head5}}, {{<h5 id=make_id($1)><a href="#make_id($1)">$1</a></h5>}})
 define({{code_block}}, {{<pre><code>include($1)</code></pre>}})
+define({{qcode_block}}, {{changequote({{`}}, {{'}})dnl
+code_block($1)dnl
+changequote(`{{', `}}')dnl}})
+define({{icode_block}}, {{<pre><code>dnl
+$1 </code></pre>}})
 define({{csv_table}}, {{syscmd({{./tables/convert.awk $1}})}})
 
 <!DOCTYPE html>
@@ -892,23 +897,76 @@ <h2>Table of Contents</h2>
 	<p>
 
 	head5(CFOUR )
+	<p>
+	  This template and the following are pretty much the same, as were the
+	  previous two, so there's not much more to say. In general, the top portion
+	  of each template just consists of normal PBS directives with optional
+	  template parameters, followed by a single command or couple of commands
+	  (for MOPAC) to set the variable used by pbqff.
+	</p>
+
 	code_block(examples/pbs_cfour.toml)
 
 	head5(DFTB+ )
 	code_block(examples/pbs_dftb.toml)
 
 	head4(Slurm)
 
+	<p>
+	  The general approach for Slurm and the local queue is identical to PBS, so
+	  you may want to read the previous section even if you're intending to use
+	  one of these other queues. Here I will just present some example templates
+	  for quick reference.
+	</p>
+
 	head5(MOPAC  )
+
+	<p>
+	  This template and the Molpro one below are embedded directly from psqs,
+	  where the templates for pbqff are defined. psqs doesn't currently define
+	  default templates for CFOUR or DFTB+, so you'll have to provide
+	  a <code>queue_template</code> of your own for those programs.
+	</p>
+
+	qcode_block(../../psqs/templates/slurm/mopac)
+
 	head5(Molpro  )
+	qcode_block(../../psqs/templates/slurm/molpro)
+
 	head5(CFOUR  )
+	qcode_block(examples/slurm_cfour.toml)
+
 	head5(DFTB+  )
+	qcode_block(examples/slurm_dftb.toml)
 
 	head4(Local)
+
+	<p>
+	  Like for Slurm, pbqff includes only two default templates for the local
+	  queue option, which is primarily used for testing. Because the local queue
+	  simply "submits" jobs using bash scripts rather than PBS or Slurm
+	  submission scripts, a local queue template can be much simpler than a PBS
+	  or Slurm template, essentially just defining the path to the executable to
+	  be run. Of course, you can add any additional commands you want, but this
+	  is all that pbqff requires.
+	</p>
+
 	head5(MOPAC   )
+	icode_block(
+export MOPAC_CMD=/opt/mopac/mopac
+export LD_LIBRARY_PATH=/opt/mopac/)
+
+	head5(DFTB+   )
+	icode_block(
+DFTB_CMD=/opt/dftb+/dftb+)
+
 	head5(Molpro   )
+	icode_block(
+MOLPRO_CMD=molpro)
+
 	head5(CFOUR   )
-	head5(DFTB+   )
+	icode_block(
+CFOUR_CMD=cfour)
 
 	head3(Derivative Types)
 	<!-- TODO -->

diff --git a/docs/toc.html b/docs/toc.html
@@ -48,9 +48,9 @@
 <li><a href="#local">Local</a></li>
 <ul>
 <li><a href="#mopac---">MOPAC   </a></li>
+<li><a href="#dftb+---">DFTB+   </a></li>
 <li><a href="#molpro---">Molpro   </a></li>
 <li><a href="#cfour---">CFOUR   </a></li>
-<li><a href="#dftb+---">DFTB+   </a></li>
 </ul>
 </ul>
 <li><a href="#derivative-types">Derivative Types</a></li>