From 28f2ed85c65bff9ac511178b70bc7f024438647f Mon Sep 17 00:00:00 2001 From: Brent Westbrook Date: Sun, 15 Sep 2024 13:01:51 -0400 Subject: [PATCH] finish draft of queue templates --- docs/examples/slurm_cfour.toml | 9 ++++ docs/examples/slurm_dftb.toml | 9 ++++ docs/index.html | 92 ++++++++++++++++++++++++++++++++-- docs/template.html | 60 +++++++++++++++++++++- docs/toc.html | 2 +- 5 files changed, 167 insertions(+), 5 deletions(-) create mode 100644 docs/examples/slurm_cfour.toml create mode 100644 docs/examples/slurm_dftb.toml diff --git a/docs/examples/slurm_cfour.toml b/docs/examples/slurm_cfour.toml new file mode 100644 index 00000000..8ecb307b --- /dev/null +++ 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 new file mode 100644 index 00000000..0a7f163b --- /dev/null +++ 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 index 73a248dc..03b74d39 100644 --- a/docs/index.html +++ b/docs/index.html @@ -9,6 +9,8 @@ + + @@ -115,9 +117,9 @@

Table of Contents

  • Local
  • Derivative Types
    • @@ -1265,6 +1267,14 @@
    Molpro

    CFOUR
    +

    + 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. +

    + 
    queue_template = """
 #!/bin/sh
 #PBS -N {{.basename}}
@@ -1308,16 +1318,92 @@ 
    DFTB+ 
    
 
 	
    Slurm
    
 
+	
    
+	  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.
+	
    
+
 	
    MOPAC  
    
+
+	
    
+	  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 queue_template of your own for those programs.
+	
    
+
+	
    #!/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
+
    
 	
    Molpro  
    
+	
    #!/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"
+
    
 	
    CFOUR  
    
+	
    #!/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"
+
    
 	
    DFTB+  
    
-
+	
    #!/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+"
+
    
 	
    Local
    
+
+	
    
+	  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.
+	
    
+
 	
    MOPAC   
    
+	
    export MOPAC_CMD=/opt/mopac/mopac
+export LD_LIBRARY_PATH=/opt/mopac/ 
    
+
+	
    DFTB+   
    
+	
    DFTB_CMD=/opt/dftb+/dftb+ 
    
+
 	
    Molpro   
    
+	
    MOLPRO_CMD=molpro 
    
+
 	
    CFOUR   
    
-	
    DFTB+   
    
+	
    CFOUR_CMD=cfour 
    
 
 	
    Derivative Types
    
 	
diff --git a/docs/template.html b/docs/template.html
index 55c37cd6..96b5def0 100644
--- a/docs/template.html
+++ b/docs/template.html
@@ -9,6 +9,11 @@
 define({{head4}}, {{
    $1
    }})
 define({{head5}}, {{
    $1
    }})
 define({{code_block}}, {{
    include($1)
    }})
+define({{qcode_block}}, {{changequote({{`}}, {{'}})dnl
+code_block($1)dnl
+changequote(`{{', `}}')dnl}})
+define({{icode_block}}, {{
    dnl
+$1 
    }})
 define({{csv_table}}, {{syscmd({{./tables/convert.awk $1}})}})
 
 
@@ -892,6 +897,14 @@ 
    Table of Contents
    
 	
    
 
 	head5(CFOUR )
+	
    
+	  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.
+	
    
+
 	code_block(examples/pbs_cfour.toml)
 
 	head5(DFTB+ )
@@ -899,16 +912,61 @@ 
    Table of Contents
    
 
 	head4(Slurm)
 
+	
    
+	  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.
+	
    
+
 	head5(MOPAC  )
+
+	
    
+	  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 queue_template of your own for those programs.
+	
    
+
+	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)
+
+	
    
+	  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.
+	
    
+
 	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)
 	
diff --git a/docs/toc.html b/docs/toc.html
index 77b70158..e0dca70f 100644
--- a/docs/toc.html
+++ b/docs/toc.html
@@ -48,9 +48,9 @@
 
  • Local
    • 
 
 
 
  • Derivative Types
    •