Merge branch 'b1' of https://github.com/KylieGong/agui into b1

Makefile

@@ -1,4 +1,4 @@
-# See the INSTALL.md notes on how to use this Makefile
+# See the README.md notes on how to use this Makefile
 
 #
 SHELL = /bin/bash
@@ -15,13 +15,17 @@ GIT_DIRS = athena athenak
 
 # URLs that we'll need
 
+URL0  = https://github.com/teuben/Athena-Cversion
 URL1  = https://github.com/PrincetonUniversity/athena
 URL2  = https://gitlab.com/theias/hpc/jmstone/athena-parthenon/athenak
+URL2  = https://gitlab.com/theias/hpc/jmstone/athena-parthenon/athena-mini-k
+URL2  = https://github.com/teuben/Athena-miniK
 URL3  = https://github.com/teuben/nemo
 URL4  = https://github.com/teuben/tkrun
 URL5a = https://github.com/teuben/agui
 URL5b = https://github.com/anhhcao/agui
 URL5c = https://github.com/KylieGong/agui
+URL6  = https://github.com/teuben/pyThena
 
 # the ATHENA executable (from athena or athenak)
 # ATHENA = athena/bin/athena
@@ -60,84 +64,100 @@ branch:
 	-@for dir in $(GIT_DIRS); do\
 	(echo -n "$$dir: " ;cd $$dir; git branch --show-current); done
 
+athenac:
+	git clone $(URL0) -b teuben1 athenac
+	$(MAKE) build_athenac
 
 athena:
 	git clone $(URL1)
+	$(MAKE) build_athena
 
 athenak:
-	git clone --recursive $(URL2)
+	git clone --recursive $(URL2) athenak
 
 nemo:
 	git clone $(URL3)
 
+python: nemo anaconda3
+
+anaconda3:
+	nemo/src/scripts/install_anaconda3
+
 tkrun:
 	git clone $(URL4)
 
-## build:         build athenak
-build:	athenak
-	(mkdir -p athenak/build; cd athenak/build; cmake ..; make -j 4)
+## build_athenak:  build athenak
+build_athenak:	athenak
+	(mkdir -p athenak/build; cd athenak/build; cmake ..; make -j 8)
+
+# See also:   https://kokkos.github.io/kokkos-core-wiki/keywords.html#keywords-arch
+B_ARM = -D CMAKE_CXX_COMPILER=clang++-mp-15 -D CMAKE_C_COMPILER=clang-mp-15 -D Kokkos_ARCH_ARMV81=On
+arm:	athenak
+	(mkdir -p athenak/build; cd athenak/build; cmake $(B_ARM) ..; make -j 8)
+
+#PJT =  -D CMAKE_CXX_COMPILER=clang++ -D CMAKE_C_COMPILER=clang -D Kokkos_ARCH_INTEL_DG1=On
+#PJT =  -D Kokkos_ARCH_INTEL_DG1=On
+PJT =  -D Kokkos_ENABLE_OPENMP=On
+#PJT =  -D Athena_ENABLE_MPI=ON
+pjt:	athenak
+	(mkdir -p athenak/build; cd athenak/build; cmake $(PJT) ..; make -j 8)
 
-## build_athena   build athena++ for the linear_wave problem
+## build_athena    build athena++ for the linear_wave problem
 build_athena: athena
 	(cd athena; ./configure.py --prob linear_wave; make clean; make -j)
 
-## build_nemo:    build nemo
-build_nemo:	nemo
-	(cd nemo; ./configure ; make build check bench5)
+## build_athenac   build AthenaC for the linear_wave problem
+build_athenac: athenac
+	(cd athenac; autoconf;  ./configure; make all)
+
+## build_nemo:     build nemo - will also build classic tkrun
+build_nemo:    nemo
+	(cd nemo; ./configure ; make build check)
+
+## build_python:    build your private anaconda3
+build_python:  python
 
 # a few sample runs
 
-## run1:          example linear_wave_hydro
+##
+
+## run1:          example 1D linear_wave_hydro (athenak)   [ < 1sec  1069 cycles]
 run1:
-	$(ATHENA) -i athenak/inputs/tests/linear_wave_hydro.athinput -d run1
+	$(TIME) $(ATHENA) -i linear_wave_hydro.athinput -d run1
 	@echo ./animate1 base=run1/tab/LinWave xcol=x1v ycol=velx
-	# -> LinWave.hydro_w.00000.tab
 
-## run1:          example advect_hyd
+## run2:          example 2D orszag_tang (athenak) [ ~109"  1403 cycles]
 run2:
-	$(ATHENA) -i athenak/inputs/tests/advect_hyd.athinput        -d run2
+	$(TIME) $(ATHENA) -i orszag_tang.athinput      -d run2
 	@echo ./animate1 base=run2/tab/Advect xcol=x1v ycol=dens
-	# -> Advect.hydro_u.00000.tab
 
-run3:
-	$(ATHENA) -i athenak/inputs/tests/advect_mhd.athinput        -d run3
-	#  -> Advect.mhd_u.00000.tab
 
-run4:
-	$(ATHENA) -i athenak/inputs/tests/hohlraum_1d.athinput       -d run4
-	#  -> hohlraum_1d.rad_coord.00000.tab  
 
-run5:
-	$(ATHENA) -i athenak/inputs/tests/rad_linwave.athinput       -d run5
-	# -> rad_linwave.hydro_w.*.tab
-	# -> rad_linwave.rad_coord.*.tab
+#  We use past tense for old versions of athena :-)
+##  ran1 and ran2 are made by ATHENA++
+##  ran3 by good old AthenaC
+## ran1:          example athena++ linear_wave1d in vtk format
+ran1: athena
+	athena/bin/athena  -i inputs/hydro/athinput.linear_wave1d  -d ran1
+	@echo Results in ran1
 
-run6:
-	$(ATHENA) -i athenak/inputs/hydro/sod.athinput               -d run6
-	# -> Sod.hydro_w.00000.tab
-	#   base=run6/tab/Sod  xcol=3 ycol=4
-	#   base=run6/tab/Sod  xcol=3 ycol=5
-	#   base=run6/tab/Sod  xcol=3 ycol=6
+## ran2:          example athena++ linear_wave1d needed by some tests - will also build athena++
+ran2: athena
+	athena/bin/athena  -i inputs/hydro/athinput.linear_wave1d  -d ran2 output2/file_type=tab
+	@echo Results in ran2
 
-run7:
-	$(ATHENA) -i athenak/inputs/hydro/shu_osher.athinput         -d run7
-	#   THIS IS A KNOWN ERROR
+## ran3:          example AthenaC linear_wave1d needed by some tests - will also build athenac
+ran3: athenac
+	athenac/bin/athena  -i athenac/tst/1D-hydro/athinput.linear_wave1d  -d ran3
 
-run8:
-	$(ATHENA) -i athenak/inputs/hydro/viscosity.athinput         -d run8
-	#   ViscTest.hydro_w.00000.tab 
-	#   base=run8/tab/ViscTest xcol=3 ycol=6
 
 
-ran1: athena
-	(cd athena; bin/athena  -i inputs/hydro/athinput.linear_wave1d  -d ran1)
-	@echo Results in athena/ran1
-
-ran2: athena
-	(cd athena; bin/athena  -i inputs/hydro/athinput.linear_wave1d  -d ran2 output2/file_type=tab)
-	@echo Results in athena/ran2
+## 
 
+test0:
+	./z1.sh
 
+## test1:         old tkrun via arun1
 test1:
 	./arun1.py athinput.linear_wave1d > test1.sh
 	tkrun test1.sh
@@ -153,7 +173,8 @@ test3:
 test4:
 	python pysimplegui.py
 
-#bash format
+
+## test5:         native pyqt, tkrun style
 test5:
 	python pyqt.py testfile.sh
 
@@ -169,6 +190,43 @@ test7:
 test8:
 	python pyqt.py testfile4.csh
 
+## test7:         qooey, athena style
+test7:
+	./gooey_run2.py linear_wave_hydro.athinput
+
+# will try Qt first, else fall back to tkinter
+test8:
+	./pysg_run.py athinput.linear_wave1d
+
+test9: 	ran2
+	./plot1d.py -d ran2
+
+test10:
+	./pysg_run.py test.athinput
+
+test11:
+	./pyqt_run.py test.athinput
+
+# will run the plot when run is clicked
+## test12:        pyqt native, athena style
+test12:
+	./pyqt_run.py athinput.linear_wave1d
+
+## test13:        pysg, athena style
+test13: athena_problems.json
+	./pysg_menu.py
+
+## test14:        pyqt, athena style
+test14: athena_problems.json
+	./pyqt_menu.py
+
+## test15:        miniki version
+test15:
+	./pythena.py
+
+athena_problems.json:
+	./write_problems.py
+
 # collaborations
 agui_t:
 	git clone $(URL5a) agui_t
@@ -178,3 +236,10 @@ agui_a:
 
 agui_k:
 	git clone $(URL5c) agui_k
+
+# testing a pyThena from scratch:
+
+pythena:
+	rm -rf pyThena
+	git clone $(URL6)
+	(cd pyThena; make build_athenak; make run1; make test1)