Add helper scripts for creating and deleting large numbers of tecplot files

.github/workflows/unit_tests.yml

@@ -21,7 +21,7 @@ jobs:
   unit_test_and_docs:
     # Run on Ubuntu
     runs-on: ubuntu-latest
-    timeout-minutes: 30
+    timeout-minutes: 40
     # Necessary to prevent mpi tests failing due to lack of slots
     env:
       OMPI_MCA_btl: self,tcp

conda/build.sh

@@ -49,3 +49,7 @@ make default TACS_DIR=${TACS_DIR} \
              SO_LINK_FLAGS="${F5TOVTK_SLF}" SO_EXT=${SO_EXT};
 mv ./f5totec ${PREFIX}/bin;
 
+cd ${TACS_DIR}/extern
+mv ./f5convert ${PREFIX}/bin;
+mv ./f5clean ${PREFIX}/bin;
+

docs/source/install.rst

@@ -158,14 +158,19 @@ After compiling the C++ TACS library, go to the subdirectory ``tacs/extern/f5tov
 
 ``f5totec`` requires Tecplot's ``tecio`` library, the installation of which is described above.
 
+The ``extern`` directory also contains two bash scripts, ``f5convert`` and ``f5clean``, that can be used to convert and clean ``.f5`` files.
+``f5convert`` converts any ``.f5`` files that don't have an up-to-date ``.vtk`` or ``.plt`` file, and ``f5clean`` removes the ``.vtk`` or ``.plt`` file corresponding to each ``.f5`` file.
+Both scripts accept a ``-s`` flag that will also convert or clean the ``.f5`` files in any subdirectories that contain ``.f5`` files.
+Run ``f5convert -h`` or ``f5clean -h`` for more information.
 
-It is useful to put these utilities on your path if possible.
-I add the directory ``$HOME/bin`` to my ``PATH`` and then from the directory ``$HOME/bin`` execute
+Add the following lines to your ``.bashrc`` file to add the executables to your path:
 
 ::
 
-    ln -s $HOME/git/tacs/extern/f5tovtk
-    ln -s $HOME/git/tacs/extern/f5totec
+    export PATH="<path to the tacs directory>/extern/f5totec:$PATH"
+    export PATH="<path to the tacs directory>/extern/f5tovtk:$PATH"
+    export PATH="<path to the tacs directory>/extern:$PATH"
+
 
 Installing the python interface
 -------------------------------

extern/f5clean

@@ -0,0 +1,45 @@
+#!/bin/bash
+
+helpstring="
+
+This command will look for all .f5 files in the current directory and delete any files with the same name but a
+.plt, .szplt or .vtk extension, this is useful for clearing space on your filesystem by removing tecplot/paraview files
+that can be regenerated from the f5 files when needed. It is also safer than simply running 'rm *.plt *.szplt *.vtk' as
+it will only delete the files that can be regenerated from the f5 files.
+
+To clean up all files in the current directory:
+> `basename $0`
+
+To also run recursively in all subdirectories that contain .f5 files:
+> `basename $0` -s
+"
+
+if [ "$1" == "-h" ]; then
+    echo "$helpstring"
+    exit 0
+fi
+
+subdirs=false
+while [[ "$#" -gt 0 ]]; do case $1 in
+    -s|--subdirs) subdirs=true;;
+    *) echo "Unknown parameter passed: $1"; exit 1;;
+esac; shift; done
+
+f5clean_all() {
+    for f in *.f5; do
+        for extension in plt szplt vtk; do
+            fileName="${f%.*}.$extension"
+            [ -e $fileName ] && echo "deleting $fileName" && rm -f ./$fileName
+        done
+    done
+}
+
+
+if [ $subdirs = true ] ; then
+    RootDir=$(pwd)
+    find . -iname '*.f5' -printf '%h\n' | sort -u | while read i; do
+        cd "$i" && pwd && f5clean_all ; cd "$RootDir"
+    done
+else
+    f5clean_all
+fi

extern/f5convert

@@ -0,0 +1,127 @@
+#!/bin/bash
+
+helpstring="
+
+This command runs f5totec or f5tovtk in parallel on all .f5 files in the current directory
+
+Usage:
+
+To convert .f5 files in the current directory using all available procs:
+> `basename $0`
+
+By default, `basename $0` will ignore any .f5 files for which there is a corresponding .plt file newer than the .f5 file
+To convert all .f5 files overwriting existing files:
+> `basename $0` -r
+
+To run on N procs:
+> `basename $0` -n N
+
+To supress the echoing of which files will and won't be converted (does not supress f5totec's own output):
+> `basename $0` -q
+
+To also run recursively in all subdirectories that contain .f5 files:
+> `basename $0` -s
+
+To use f5tovtk instead of f5totec:
+> `basename $0` --vtk
+
+This script uses GNU parallel which can be installed on debian using:
+> sudo apt-get install parallel
+
+
+"
+
+if [ "$1" == "-h" ]; then
+    echo "$helpstring"
+    exit 0
+fi
+
+if ! command -v parallel &> /dev/null
+then
+    echo "parallel could not be found, please install it to use f5convert_all"
+    exit
+fi
+
+# Parse input options
+reconvert=false
+quiet=false
+vtk=false
+subdirs=false
+extra_args=""
+nprocs=+0
+while [[ "$#" -gt 0 ]]; do case $1 in
+    -n|--nprocs) nprocs=$2; shift;;
+    -q|--quiet) quiet=true; shift;;
+    -r|--reconvert) reconvert=true; shift;;
+    -s|--subdirs) subdirs=true; shift;;
+    --vtk) vtk=true;;
+    *) echo "Unknown parameter passed: $1"; exit 1;;
+esac; shift; done
+
+f5convert_all() {
+
+    reconvert=$1
+    quiet=$2
+    vtk=$3
+    nprocs=$4
+
+    for value in $reconvert $quiet $vtk $nprocs; do
+        echo $value
+    done
+
+    if [ $vtk = true ] ; then
+        convertCommand=f5tovtk
+    else
+        convertCommand=f5totec
+    fi
+
+    # Loop through all the f5 files in the current directory and figure out which ones to convert
+    filesToConvert=()
+    for f in *.f5;
+    do
+        if [ $reconvert = true ] || ([ "$vtk" = false ] && [ ! -f "${f%.*}.plt" ] && [ ! -f "${f%.*}.szplt" ]) || ([ "$vtk" = true ] && [ ! -f "${f%.*}.vtk" ]) ; then
+            # If there is not .plt/.szplt/.vtk file corresponding to the current .f5 or is user specified -r then convert the file
+            filesToConvert[${#filesToConvert[@]}]=$f
+            echo "$f" 'will be converted'
+        elif [ -f "${f%.*}.plt" ] && [ "$vtk" = false ] ; then
+            if [ "${f%.*}.plt" -ot "$f" ] ; then
+                # If there is a .plt file but it's older than the corresponding .f5 file then convert the .f5 file
+                echo "$f" 'will be converted as it is newer than' "${f%.*}.plt"
+                filesToConvert[${#filesToConvert[@]}]=$f
+            else
+                echo "$f" 'will not be converted as' "${f%.*}.plt" 'already exists, to force overwriting use the -r flag'
+            fi
+        elif [ -f "${f%.*}.szplt" ] && [ "$vtk" = false ]  ; then
+            if [ "${f%.*}.szplt" -ot "$f" ] ; then
+                # If there is a .szplt file but it's older than the corresponding .f5 file then convert the .f5 file
+                echo "$f" 'will be converted as it is newer than' "${f%.*}.szplt"
+                filesToConvert[${#filesToConvert[@]}]=$f
+            else
+                echo "$f" 'will not be converted as' "${f%.*}.szplt" 'already exists, to force overwriting use the -r flag'
+            fi
+        elif [ -f "${f%.*}.vtk" ] && [ "$vtk" = true ]  ; then
+            if [ "${f%.*}.vtk" -ot "$f" ] ; then
+                # If there is a .vtk file but it's older than the corresponding .f5 file then convert the .f5 file
+                echo "$f" 'will be converted as it is newer than' "${f%.*}.vtk"
+                filesToConvert[${#filesToConvert[@]}]=$f
+            else
+                echo "$f" 'will not be converted as' "${f%.*}.vtk" 'already exists, to force overwriting use the -r flag'
+            fi
+        fi
+    done
+
+    # Do the conversion
+    for f in "${filesToConvert[@]}";
+    do
+        echo "$f"
+    done | parallel --will-cite -j$nprocs $convertCommand {}
+}
+
+if [ $subdirs = true ] ; then
+    RootDir=$(pwd)
+    find . -iname '*.f5' -printf '%h\n' | sort -u | while read i; do
+        cd "$i" && pwd && f5convert_all $reconvert $quiet $vtk $nprocs ; cd "$RootDir"
+    done
+else
+    f5convert_all $reconvert $quiet $vtk $nprocs
+fi