Remove default petsc path in the Makefile and istallation

[aguspesce]

In the Makefile and installation instruction, I removed the default path to $HOME/petsc.

• Remove the default path for pests at ~
• Add instruction to add a symlinks of mpirun
• Add instruction to create an env variable for PETSC_DIR before build Mandyoc

[aguspesce]

@victorsacek and @rafaelmds.
Maybe this PR can be a starting point to fix part of #46 and #52. What do you think?

[rafaelmds]

@aguspesce, here some suggestions for Makefile file after some testing:

• I had some problems with the make install command, so I've tweaked it a bit by adding the file name and making sure the dest dir exists. Before, it was creating the mandyoc binary as ~/.local/bin.
• added clean to override petsc default rule
• added check for PETSC_DIR

It's working fine on my environment (with either PETSC_ARCH set or unset).
Will test on docker that is using petsc with "prefix type" installation.

I found it easier to attach a patch (instead of using the github suggestion), so you can apply and test it as well.

diff --git a/Makefile b/Makefile
index e415590..37ab8e1 100644
--- a/Makefile
+++ b/Makefile
@@ -1,3 +1,7 @@
+ifndef PETSC_DIR
+$(error PETSC_DIR environment variable is not set. Please, set/export it before continue.)
+endif
+
 include ${PETSC_DIR}/lib/petsc/conf/variables
 include ${PETSC_DIR}/lib/petsc/conf/rules
 
@@ -23,25 +27,25 @@ BIN_DIR = bin
 MANDYOC = $(BIN_DIR)/mandyoc
 LOCAL_BIN = $(HOME)/.local/bin
 
-.PHONY: help all install clear test
+.PHONY: help all install clear clean test
 
 help:
 	@echo ""
 	@echo "Commands:"
 	@echo ""
-	@echo "  all		Build Mandyoc"
+	@echo "  all		Build Mandyoc."
 	@echo "  install	Install MANDYOC in ~/.local/bin/"
 	@echo "  test		Run the MANDYOC tests using 1 core. It takes several minutes."
-	@echo "  clear		Removes the files produced when building MANDYOC"
+	@echo "  clear		Removes the files produced when building MANDYOC."
 	@echo ""
 
 all: $(MANDYOC)
 	@echo ""
 	@echo "Mandyoc built in bin/"
 
-install: $(MANDYOC)
+install: $(MANDYOC) | $(LOCAL_BIN)
 	@echo ""
-	install $< $(LOCAL_BIN)
+	install $< $(LOCAL_BIN)/mandyoc
 
 test:
 	@echo "Run MANDYOC test may take several minutes..."
@@ -49,14 +53,16 @@ test:
 	pytest -v test/testing_result.py
 
 clear:
-	rm $(SRC)/*.o
+	rm -f $(SRC)/*.o
 	rm -rf $(BIN_DIR)
 
+clean:: clear
+
 %.o: %.cpp
 	${PCC} -Wall -fdiagnostics-color -c $< -o $@ ${INCFLAGS}
 
-$(BIN_DIR):
-	mkdir $@
+$(BIN_DIR) $(LOCAL_BIN):
+	mkdir -p $@
 
 $(MANDYOC): ${OBJECTS} | $(BIN_DIR)
 	-${CLINKER} -o $@ ${OBJECTS} ${PETSC_LIB}

[aguspesce]

@rafaelmds I added your suggestion and improve the names of the directory variables:

PREFIX = $(HOME)/.local
BINDIR = $(PREFIX)/bin
BUILDDIR = bin
MANDYOC = $(BUILDDIR)/mandyoc

But I didn't add this line:

$(BIN_DIR) $(LOCAL_BIN):
  mkdir -p $@

Because it is not correct for Makefile to create a folder on the user's system. If the user doesn't have the ~/.local/bin it's a good idea to create it.
We need to add all this information about the ~/.local/bin and the PETSC_SIR variable in the documentation

[rafaelmds]

I agree @aguspesce, best not to automatically/programmactically create that folder.

But I didn't add this line:

$(BIN_DIR) $(LOCAL_BIN):
  mkdir -p $@

Because it is not correct for Makefile to create a folder on the user's system. If the user doesn't have the ~/.local/bin it's a good idea to create it. We need to add all this information about the ~/.local/bin and the PETSC_SIR variable in the documentation

If user doesn't have ~/.local/bin dir, this is the error:

make: *** No rule to make target '/home/rafael/.local/bin', needed by 'install'.  Stop.

This is because $(BINDIR) appears in rule requirements:

install: $(MANDYOC) | $(BINDIR)

If we remove $(BINDIR), I think the error points better to the problem:

install bin/mandyoc /home/rafael/.local/bin/mandyoc
install: cannot create regular file '/home/rafael/.local/bin/mandyoc': No such file or directory
make: *** [Makefile:47: install] Error 1

[aguspesce]

Ok @rafaelmds! Now I understand the situation.

I will remove BINDIR as a requirement, so the code will be:

install: $(MANDYOC):
     install $< $(BINDIR)/mandyoc

[rafaelmds]

I noticed there is no entry for src/*.o in .gitignore file.
I think we could add it in this PR as well.

[rafaelmds]

@jamisonassuncao We are almost ready with this new Makefile. Could you test on macos and give your feedback?

[rafaelmds]

@aguspesce

I tested on macos as well, and just have the "problem" with make install due missing ~/.local/bin folder.

I suggest the following modification to print a message to the user to create the folder.

diff --git a/Makefile b/Makefile
index 70b8504..1afd806 100644
--- a/Makefile
+++ b/Makefile
@@ -44,7 +44,12 @@ help:
 all: $(MANDYOC)
 
 install: $(MANDYOC)
+ifeq ($(shell [ -d $(BINDIR) ] && echo 1 || echo 0 ), 1)
 	install $< $(BINDIR)/mandyoc
+else
+	@echo -e "\nDirectory \"$(BINDIR)\" does not exists."
+	@echo -e "Please, create this directory before continue.\n"
+endif
 
 test:
 	@echo "Run MANDYOC test may take several minutes..."

[aguspesce]

@aguspesce

I tested on macos as well, and just have the "problem" with make install due missing ~/.local/bin folder.

I suggest the following modification to print a message to the user to create the folder.

diff --git a/Makefile b/Makefile
index 70b8504..1afd806 100644
--- a/Makefile
+++ b/Makefile
@@ -44,7 +44,12 @@ help:
 all: $(MANDYOC)
 
 install: $(MANDYOC)
+ifeq ($(shell [ -d $(BINDIR) ] && echo 1 || echo 0 ), 1)
 	install $< $(BINDIR)/mandyoc
+else
+	@echo -e "\nDirectory \"$(BINDIR)\" does not exists."
+	@echo -e "Please, create this directory before continue.\n"
+endif
 
 test:
 	@echo "Run MANDYOC test may take several minutes..."

I understand the problem, but create the founder is not the solution because you need to add it to the PATH.
So maybe it is better to keep it simple. What do you think about this:

1. Add a variable in the Makefile with the install path (say INSTALL_PATH)
2. Set it to a default location in the repo, like ~/.local/bin
3. Tell users to set the location they want when installing by running make INSTALL_PATH="~/bin" install.

[rafaelmds]

Thats fine!

[rafaelmds]

I think we can merge, right? @aguspesce

[aguspesce]

@rafaelmds, I think that it is ok!