GNU Make notes

15 files changed, 236 insertions, 0 deletions

diff --git a/examples/dragmap/Makefile b/examples/dragmap/Makefile
new file mode 100644
index 0000000..31dd118
--- /dev/null
+++ b/examples/dragmap/Makefile
@@ -0,0 +1,6 @@
+include config.mk
+$(info    BOOST_ROOT is $(BOOST_ROOT))
+$(info    BOOST_INCLUDEDIR is $(BOOST_INCLUDEDIR))
+$(info    BOOST_LIBRARYDIR is $(BOOST_LIBRARYDIR))
+$(info    CPPFLAGS is $(CPPFLAGS))
+$(info    LDFLAGS is $(LDFLAGS))
diff --git a/examples/dragmap/README.md b/examples/dragmap/README.md
new file mode 100644
index 0000000..29ba382
--- /dev/null
+++ b/examples/dragmap/README.md
@@ -0,0 +1,47 @@
+# README
+
+Trying to build [DRAGMAP](https://github.com/Illumina/DRAGMAP) using updated
+[Boost libraries](https://www.boost.org/). But the building process seems to be
+using the outdated system Boost libraries in `/usr/include/boost/`. This is because I keep getting these errors:
+
+    /usr/include/boost/program_options/detail/value_semantic.hpp:170: undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)'
+
+Here I examine the behaviour of the following environment variables:
+
+* `BOOST_ROOT`
+* `BOOST_INCLUDEDIR`
+* `BOOST_LIBRARYDIR`
+
+The required Boost libraries are:
+
+    BOOST_LIBRARIES := system filesystem date_time thread iostreams regex program_options
+
+They reside in `/usr/include/boost169/boost/`; for example:
+
+    /usr/include/boost169/boost/system
+    /usr/include/boost169/boost/filesystem
+
+Use `./run.sh` to run all the test scripts.
+
+## Notes
+
+* The `CPPFLAGS` macro is the one to use to specify `#include` directories.
+* The `LDFLAGS` is normally set to contain options that are passed through to
+  the linker (so may include required libraries).
+
+[Probably the same
+problem](https://stackoverflow.com/questions/62280304/yum-using-boost-1-69-instead-of-default-1-53-version-on-centos)
+but I do not want to manually manipulate the symlinks by changing:
+
+    /lib64/libboost_system.so -> libboost_system.so.1.53.0
+
+to:
+
+    /lib64/libboost_system.so -> libboost_system.so.1.69.0
+
+## Fix
+
+Do not include `boost` in the DIR. For example:
+
+    export BOOST_INCLUDEDIR=/usr/include/boost169
+    export BOOST_LIBRARYDIR=/usr/lib64/boost169
diff --git a/examples/dragmap/config.mk b/examples/dragmap/config.mk
new file mode 100755
index 0000000..433163a
--- /dev/null
+++ b/examples/dragmap/config.mk
@@ -0,0 +1,15 @@
+BOOST_LIBRARIES := system filesystem date_time thread iostreams regex program_options
+
+ifneq (,$(BOOST_ROOT))
+BOOST_INCLUDEDIR?=$(BOOST_ROOT)/include
+BOOST_LIBRARYDIR?=$(BOOST_ROOT)/lib
+endif # ifneq (,$(BOOST_ROOT))
+
+ifneq (,$(BOOST_INCLUDEDIR))
+CPPFLAGS += -I $(BOOST_INCLUDEDIR)
+endif
+
+ifneq (,$(BOOST_LIBRARYDIR))
+LDFLAGS += -L $(BOOST_LIBRARYDIR)
+endif
+LDFLAGS += $(BOOST_LIBRARIES:%=-lboost_%)
diff --git a/examples/dragmap/run.sh b/examples/dragmap/run.sh
new file mode 100755
index 0000000..dcb38fd
--- /dev/null
+++ b/examples/dragmap/run.sh
@@ -0,0 +1,11 @@
+#!/usr/bin/env bash
+
+>&2 echo -e "Running test1\n"
+./test1.sh
+>&2 echo
+>&2 echo -e "Running test2\n"
+./test2.sh
+>&2 echo
+>&2 echo -e "Running test3\n"
+./test3.sh
+>&2 echo
diff --git a/examples/dragmap/test1.sh b/examples/dragmap/test1.sh
new file mode 100755
index 0000000..d9eae58
--- /dev/null
+++ b/examples/dragmap/test1.sh
@@ -0,0 +1,3 @@
+#!/usr/bin/env bash
+
+make
diff --git a/examples/dragmap/test2.sh b/examples/dragmap/test2.sh
new file mode 100755
index 0000000..8bbc6ff
--- /dev/null
+++ b/examples/dragmap/test2.sh
@@ -0,0 +1,5 @@
+#!/usr/bin/env bash
+
+export BOOST_ROOT=/usr/include/boost169/boost/
+
+make
diff --git a/examples/dragmap/test3.sh b/examples/dragmap/test3.sh
new file mode 100755
index 0000000..99aca0d
--- /dev/null
+++ b/examples/dragmap/test3.sh
@@ -0,0 +1,7 @@
+#!/usr/bin/env bash
+
+export BOOST_ROOT=/usr/include/boost169/
+export BOOST_INCLUDEDIR=/usr/include/boost169
+export BOOST_LIBRARYDIR=/usr/lib64/boost169
+
+make
diff --git a/examples/sge/Makefile b/examples/sge/Makefile
new file mode 100644
index 0000000..e0baff6
--- /dev/null
+++ b/examples/sge/Makefile
@@ -0,0 +1,25 @@
+.PHONY: all
+SHELL := /bin/bash
+
+FILES := a.txt b.txt c.txt d.txt
+all: $(FILES) merged.txt 3.txt
+
+%.txt:
+	@echo "Generating: $@"
+	sleep 5
+	echo $(basename $@) > $@
+
+merged.txt: $(FILES)
+	cat $^ | sort > $@
+
+1.txt: job1.sh
+	qsub $<
+
+2.txt: job2.sh 1.txt
+	qsub -hold_jid job1 $<
+
+3.txt: job3.sh 2.txt
+	qsub -hold_jid job2 $<
+
+clean:
+	rm -rf *.txt *.log
diff --git a/examples/sge/job1.sh b/examples/sge/job1.sh
new file mode 100755
index 0000000..4c72eb2
--- /dev/null
+++ b/examples/sge/job1.sh
@@ -0,0 +1,14 @@
+#!/usr/bin/env bash
+#$ -S /bin/bash
+#$ -N job1
+#$ -q all.q
+#$ -cwd
+#$ -l h_rt=01:00:00
+#$ -l h_rss=30720M,mem_free=30720M
+#$ -j y
+#$ -o job1.log
+
+export LANGUAGE=en_AU.UTF-8
+
+sleep 10
+echo job1 > 1.txt
diff --git a/examples/sge/job2.sh b/examples/sge/job2.sh
new file mode 100755
index 0000000..fcd80d7
--- /dev/null
+++ b/examples/sge/job2.sh
@@ -0,0 +1,15 @@
+#!/usr/bin/env bash
+#$ -S /bin/bash
+#$ -N job2
+#$ -q all.q
+#$ -cwd
+#$ -l h_rt=01:00:00
+#$ -l h_rss=30720M,mem_free=30720M
+#$ -j y
+#$ -o job2.log
+
+export LANGUAGE=en_AU.UTF-8
+
+sleep 10
+cat 1.txt > 2.txt
+echo job2 >> 2.txt
diff --git a/examples/sge/job3.sh b/examples/sge/job3.sh
new file mode 100755
index 0000000..7243049
--- /dev/null
+++ b/examples/sge/job3.sh
@@ -0,0 +1,15 @@
+#!/usr/bin/env bash
+#$ -S /bin/bash
+#$ -N job3
+#$ -q all.q
+#$ -cwd
+#$ -l h_rt=01:00:00
+#$ -l h_rss=30720M,mem_free=30720M
+#$ -j y
+#$ -o job3.log
+
+export LANGUAGE=en_AU.UTF-8
+
+sleep 10
+cat 2.txt > 3.txt
+echo job3 >> 3.txt
diff --git a/examples/sge/submit.sh b/examples/sge/submit.sh
new file mode 100644
index 0000000..8adee71
--- /dev/null
+++ b/examples/sge/submit.sh
@@ -0,0 +1,10 @@
+#!/usr/bin/env bash
+#$ -S /bin/bash
+#$ -N make_job
+#$ -q all.q
+#$ -pe make 4
+#$ -cwd
+#$ -j y
+#$ -o make_job.log
+
+make -j $NSLOTS
diff --git a/examples/visual/Makefile b/examples/visual/Makefile
new file mode 100644
index 0000000..6352ecb
--- /dev/null
+++ b/examples/visual/Makefile
@@ -0,0 +1,28 @@
+# Simple Makefile Example
+
+# Default target
+all: build test clean
+
+# Build target
+build: compile link
+	@echo "Building the project..."
+
+# Compile target
+compile: init
+	@echo "Compiling source files..."
+
+# Link target
+link: init
+	@echo "Linking objects..."
+
+# Test target
+test: build
+	@echo "Running tests..."
+
+# Clean target
+clean:
+	@echo "Cleaning up..."
+
+# Init target (independent target)
+init:
+	@echo "Initializing the build environment..."
diff --git a/examples/visual/README.md b/examples/visual/README.md
new file mode 100644
index 0000000..f497901
--- /dev/null
+++ b/examples/visual/README.md
@@ -0,0 +1,35 @@
+# README
+
+Creates a graph of dependencies from GNU-Make using [make2graph](https://github.com/lindenb/makefile2graph).
+
+```console
+git clone https://github.com/lindenb/makefile2graph.git
+cd makefile2graph
+make
+./make2graph --version
+```
+```
+1.5.0
+```
+
+Install `graphviz`.
+
+```console
+sudo apt update
+sudo apt install -y graphviz
+```
+
+`make`
+
+* -B, --always-make
+    * Unconditionally make all targets.
+* -n, --just-print, --dry-run, --recon
+    * Print the commands that would be executed, but do not execute them (except in certain circumstances).
+* -d
+    * Print debugging information in addition to normal processing.
+
+```console
+make -Bnd | ./make2graph | dot -Tpng -o out.png
+```
+
+![](out.png)
diff --git a/examples/visual/out.png b/examples/visual/out.png
new file mode 100644
index 0000000..becc47e
--- /dev/null
+++ b/examples/visual/out.png