Prepared wrappers for clang-format and clang-tidy compatibility with …

…CUDA / CUB headers and scripts to run formatting and checks on all source c++/cuda files. Formatted source c++/cuda files with clang-format. Checked with clang-tidy and made small fixes to solve warnings.
nest · Jan 23, 2024 · 4f0eb12 · 4f0eb12
1 parent ebc740d
commit 4f0eb12
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Showing 206 changed files with 17,283 additions and 15,278 deletions.
diff --git a/build_support/check_all_c_c++_cu_files.sh b/build_support/check_all_c_c++_cu_files.sh
@@ -0,0 +1,125 @@
+#!/bin/bash
+
+#
+#   This file is part of NEST GPU.
+#
+#  Copyright (C) 2021 The NEST Initiative
+#
+#  NEST GPU is free software: you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation, either version 2 of the License, or
+#  (at your option) any later version.
+#
+#  NEST GPU is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with NEST GPU.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+# With this script you can easily check all C/C++/CU files contained in
+# the src directory of NEST GPU. Internally it uses clang-tidy to do
+# the actual check.
+#
+
+function make_temp_dir {
+  # Create a temporary directory and store its name in a variable.
+  TEMPD=$(mktemp -d)
+
+  # Exit if the temp directory wasn't created successfully.
+  if [ ! -e "$TEMPD" ]; then
+    >&2 echo "Error: failed to create temp directory"
+    exit 1    
+  fi
+
+
+  # Make sure the temp directory gets removed on script exit.
+  trap "exit 1"           HUP INT PIPE QUIT TERM
+  trap 'rm -rf "$TEMPD"'  EXIT
+}
+
+if [ "$#" -ne 1 ]; then
+    echo "Usage: $0 <src-folder-path>"
+    exit 1
+fi
+
+CMD_DIR=$(dirname $(echo $0))
+CLANG_TIDY=${CMD_DIR}/clang-tidy-cuda.sh
+
+if [ ! -f $CLANG_TIDY ]; then
+    echo "Error: $CLANG_TIDY file not found in $CMD_DIR folder"
+    exit 1
+fi
+
+SRC_DIR=$1
+if [ -d "$SRC_DIR" ]; then 
+    if [ -L "$SRC_DIR" ]; then
+	# It is a symlink
+	echo "Error: cannot pass a symboloc link as source path"
+	exit 1
+    fi
+else
+    echo "Error: source path $SRC_DIR not found"
+    exit 1
+fi
+
+make_temp_dir
+CONF_DIR=${TEMPD}/config
+mkdir $CONF_DIR
+if [ ! -e "$CONF_DIR" ]; then
+    >&2 echo "Error: failed to create $CONF_DIR directory"
+    exit 1
+fi
+CONF_H=${CONF_DIR}/config.h
+:>$CONF_H
+if [ ! -f $CONF_H ]; then
+    echo "Error: cannot create temporary file $CONF_H"
+    exit 1
+fi
+
+
+cp $CLANG_TIDY $TEMPD
+CLANG_TIDY=$(basename $CLANG_TIDY)
+if [ ! -f $TEMPD/$CLANG_TIDY ]; then
+    echo "Error: cannot create temporary executable $CLANG_TIDY in folder $TEMPD"
+    exit 1
+fi
+
+pushd .
+cd $SRC_DIR
+
+for fn in $(ls *.cu *.cpp *.cc *.c *.cuh *.hpp *.h); do
+    cat $fn | sed 's://<BEGIN-CLANG-TIDY-SKIP>//:#if 0:;s://<END-CLANG-TIDY-SKIP>//:#endif:' > $TEMPD/$fn
+    if [ ! -f $TEMPD/$fn ]; then
+	echo "Error: cannot create file $TEMPD/$fn"
+	popd
+	exit 1
+    fi
+done
+
+
+cd $TEMPD
+
+PASSED_NUM=0
+for fn in $(ls *.cu *.cpp *.cc *.c | grep -v user_m); do
+    echo " - Check with $CLANG_TIDY C/C++/CUDA file: $fn"
+    #$TEMPD/$CLANG_TIDY --include-path=../../build_cmake/libnestutil/ $fn
+    echo "$TEMPD/$CLANG_TIDY --include-path=$CONF_DIR $fn"
+    $TEMPD/$CLANG_TIDY --include-path=$CONF_DIR $fn
+    if [ $? -eq 0 ]; then
+	echo PASSED
+	PASSED_NUM=$(($PASSED_NUM + 1))
+    else
+	popd
+	exit 1
+    fi
+
+done
+
+popd
+echo "Checked $PASSED_NUM files with clang-tidy-cuda.sh"
+echo "All tests PASSED"
+
+exit 0
diff --git a/build_support/clang-format-cuda.sh b/build_support/clang-format-cuda.sh
@@ -0,0 +1,35 @@
+#!/bin/bash
+
+if [ "$#" -ne 1 ]; then
+    echo "Usage: $0 input-file"
+    return
+fi
+
+if [ ! -f .clang-format ]; then
+    echo "Error: .clang-format file not found in current directory"
+    return
+fi
+
+if [ ! -f $1 ]; then
+    echo "Error: input file $1 not found"
+    return
+fi
+
+if grep -q '$$<' $1; then
+    echo 'Error: illegal character sequence in input file: "$$<"'
+    return
+fi
+if grep -q '$ >' $1; then
+    echo 'Error: illegal character sequence in input file: "$ >"'
+    return
+fi
+if grep -q '$>' $1; then
+    echo 'Error: illegal character sequence in input file: "$>"'
+    return
+fi
+
+cat $1 | sed 's/<<</$$</g;s/>>>/$ >/g;' > tmp1~
+clang-format -style=file:.clang-format tmp1~ > tmp2~
+cat tmp2~ | sed 's/$$</<<</g;s/$ >/>>>/g;s/$>/>>>/g;' > $1
+rm -f tmp1~
+rm -f tmp2~
diff --git a/build_support/clang-tidy-cuda.sh b/build_support/clang-tidy-cuda.sh
@@ -0,0 +1,145 @@
+#!/bin/bash
+
+#
+#   This file is part of NEST GPU.
+#
+#  Copyright (C) 2021 The NEST Initiative
+#
+#  NEST GPU is free software: you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation, either version 2 of the License, or
+#  (at your option) any later version.
+#
+#  NEST GPU is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with NEST GPU.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+cuda_default_path="/usr/local/cuda/include"
+
+if [ "$#" -eq 0 ]; then
+    echo "Usage: $0 [--include-path=INCLUDE_PATHS] [--cuda-path=CUDA_PATHS] [--mpi-path=MPI_PATHS] input-file"
+    echo "where INCLUDE_PATHS are optional header paths separated by colons,"
+    echo "CUDA_PATHS are the paths of CUDA headers separated by colons"
+    echo "(default: $cuda_default_path)"
+    echo "and MPI_PATHS are the paths of MPI headers separated by colons"
+    exit 0
+fi
+
+cuda_path=""
+mpi_path=""
+include_path=""
+
+for i in "$@"; do
+    case $i in
+	--include-path=*)
+	    include_path="${i#*=}"
+	    shift # past argument=value
+	    ;;
+	--cuda-path=*)
+	    cuda_path="${i#*=}"
+	    shift # past argument=value
+	    ;;
+	--mpi-path=*)
+	    mpi_path="${i#*=}"
+	    shift # past argument=value
+	    ;;
+	-*|--*)
+	    echo "Error: unknown option $i"
+	    exit 1
+	    ;;
+	*)
+	    ;;
+    esac
+done
+
+if [[ -n $1 ]]; then
+    echo "Input file: $1"
+else
+    echo "Error: input file not specified."
+    exit 1
+fi
+
+if [ ! -f $1 ]; then
+    echo "Error: input file $1 not found."
+    exit 1
+fi
+
+if [ "$include_path" != "" ]; then    
+    include_path=$(echo ":$include_path" | sed 's/::*/:/g;s/:$//;s/:/ -I /g')
+fi
+
+# Searches the paths of CUDA headers
+if [ "$cuda_path" == "" ]; then    
+    cuda_path=":/usr/local/cuda/include"
+else
+    cuda_path=$(echo ":$cuda_path" | sed 's/::*/:/g;s/:$//')
+fi
+
+cuda_path_spaced=$(echo $cuda_path | tr ':' ' ')
+cuda_err=1
+for dn in $cuda_path_spaced; do
+    if test -f "$dn/cuda.h" ; then
+	echo "cuda.h found in path $dn"
+	cuda_err=0
+	break
+    fi
+done
+
+if [ $cuda_err -eq 1 ]; then
+    echo "cuda.h not found in path(s) $cuda_path_spaced"
+    echo "You can specify path for CUDA headers with the option --cuda-path=CUDA_PATHS"
+    echo "where CUDA_PATHS are the paths of CUDA headers separated by colons"
+    echo "(default: $cuda_default_path)"
+    exit 1
+fi
+
+cuda_include=$(echo $cuda_path | sed 's/:/ -isystem /g')
+
+#cat $1 | sed 's://<BEGIN-CLANG-TIDY-SKIP>//:#if 0:;s://<END-CLANG-TIDY-SKIP>//:#endif:' > tmp~
+
+#cat ../build_cmake/compile_commands.json | sed "s:-Xcompiler=-fPIC::;s:-forward-unknown-to-host-compiler::;s:--compiler-options='.*'::;s:--generate-code=arch=compute_80,code=\[compute_80,sm_80\]::;s:--maxrregcount=55::" > compile_commands.json
+
+# Searches the paths of MPI headers
+if [ "$mpi_path" == "" ]; then    
+    mpi_include=$( \
+		   for l in  $(mpicc -showme); do \
+		       echo $l; \
+		   done | grep '^-I')
+    if [ "$mpi_include" == "" ]; then
+	echo "Error: cannot find MPI include paths"
+	echo "You can specify path for MPI headers with the option --mpi-path=MPI_PATHS"
+	echo "where MPI_PATHS are the paths of MPI headers separated by colons"
+	exit 1
+    fi
+    mpi_include=$(echo $mpi_include | sed 's/-I/ -isystem /g')
+    mpi_path_spaced=$(echo $mpi_include | sed 's/-I/ /g')
+else
+    mpi_path=$(echo ":$mpi_path" | sed 's/::*/:/g;s/:$//')
+    mpi_path_spaced=$(echo $mpi_path | tr ':' ' ')
+    mpi_include=$(echo $mpi_path | sed 's/:/ -isystem /g')
+fi
+
+mpi_err=1
+for dn in $mpi_path_spaced; do
+    if test -f "$dn/mpi.h" ; then
+	echo "mpi.h found in path $dn"
+	mpi_err=0
+	break
+    fi
+done
+
+if [ $mpi_err -eq 1 ]; then
+    echo "mpi.h not found in path(s) $mpi_path_spaced"
+    echo "You can specify path for MPI headers with the option --mpi-path=MPI_PATHS"
+    echo "where MPI_PATHS are the paths of MPI headers separated by colons"
+    exit 1
+fi
+
+echo "clang-tidy $1 -p . -- $include_path $mpi_include $cuda_include --no-cuda-version-check"
+
+clang-tidy $1 -p .  -- $include_path $mpi_include $cuda_include --no-cuda-version-check