Merging the work of Yehor's thesis inot the main branch from ets_json_params

.gitignore

@@ -9,6 +9,8 @@ externals/*
 !Makefile.libbds
 !chease-patch.diff
 !gem-tmppatch.diff
+!gem0-ra0patch.diff
+!bohmgb-coefftypes-patch.diff
 
 usr/*
 

Makefile

@@ -21,6 +21,10 @@ export LIB_CONSTANTS = ${PWD}/ual/lib/${SYS}/constants
 export INC_XML = ${PWD}/ual/include/${SYS}/xml
 export LIB_XML = ${PWD}/ual/lib/${SYS}/xml
 
+export INC_JSON=../../json-fortran/build
+export LIB_JSON=../../json-fortran/build/lib
+export LIB_JSON_FILE=../../json-fortran/build/lib/libjsonfortran.so
+
 export DATAVERSION = 4.10b.10
 
 include config
@@ -30,6 +34,12 @@ export MAINMAKE=yes
 SVNURL_GFORGE = https://gforge-next.eufus.eu/svn
 SVNURL_SOLPS  = https://solps-mdsplus.aug.ipp.mpg.de/repos
 
+SVNADR_EPFL = https://spcsvn.epfl.ch/repos/
+
+GITLABADR_PSNC = gitlab.eufus.psnc.pl
+GITLABURL_PSNC = https://${GITLABADR_PSNC}
+GITLABADR_EPFL = gitlab.epfl.ch
+
 ################################################################################
 # global rules                                                                 #
 ################################################################################
@@ -44,7 +54,7 @@ all: kernels
 	@echo -e "\033[35m\033[1m ==== Full Build Completed ==== \033[0m"
 
 
-codes: libbds bdseq bohmgb ets gem chease dfefi imp4dv gem0 
+codes: libbds bdseq bohmgb ets gem chease imp4dv gem0 
 #orb5
 
 
@@ -113,10 +123,11 @@ libbds: ual get-libbds
 get-libbds:
 	@if [ ! -d "externals/libbds" ]; then \
 	  echo "Checking out libbds..."; \
-		svn co $(SVNURL_GFORGE)/libbds/tags/4.10b externals/libbds; \
+		# svn co $(SVNURL_GFORGE)/libbds/tags/4.10b externals/libbds; \
+		git clone git@${GITLABADR_PSNC}:ets/libbds.git --branch 4.10b --single-branch externals/libbds ; \
 	else  \
 		echo "Updating libbds..."; \
-		svn up externals/libbds; \
+		# svn up externals/libbds; \
 	fi
 
 clean-libbds:
@@ -136,10 +147,12 @@ ets: ual libbds get-ets
 get-ets:
 	@if [ ! -d "externals/ets" ]; then \
 	  echo "Checking out ets..."; \
-		svn co $(SVNURL_GFORGE)/ets/tags/4.10b.10_8 externals/ets; \
+		# svn co $(SVNURL_GFORGE)/ets/tags/4.10b.10_8 externals/ets; \
+		# git clone ${GITLABURL_PSNC}/ets/ets5sources.git externals/ets; \
+		(git clone git@${GITLABADR_PSNC}:ets/ets5sources.git --branch tags/4.10b.10_8 --single-branch externals/ets;) \
 	else  \
 		echo "Updating ets..."; \
-		svn up externals/ets; \
+		# svn up externals/ets; \
 	fi
 
 clean-ets:
@@ -159,12 +172,28 @@ bohmgb: ual libbds get-bohmgb
 get-bohmgb:
 	@if [ ! -d "externals/bohmgb" ]; then \
 	  echo "Checking out bohmgb..."; \
-		svn co $(SVNURL_GFORGE)/modtransp/tags/4.10b/bohmgb externals/bohmgb; \
+		if [ ! -d "externals/modtransp" ]; then \
+			echo "Modtransp is not yet cloned..."; \
+			git clone git@${GITLABADR_PSNC}:/ets/modtransp.git externals/modtransp ; \
+		else \
+			echo "Modtransp is already cloned..."; \
+		fi ; \
+		cp -r externals/modtransp/bohmgb externals/bohmgb ; \
+	echo "Copied bohmgb sourse..."  ; \
 	else  \
 		echo "Updating bohmgb..."; \
-		svn up externals/bohmgb; \
+		# # svn up externals/bohmgb; \
 	fi
 
+patch-bohmgb:
+# patch to change turbulent coefficients type declarations 
+	@grep -q R8 externals/bohmgb/include/bohmgb_coeff.h90 \
+	&& echo -e "\033[32m\033[1m -- ALREADY PATCHED -- \033[0m" \
+	|| (echo -e "\033[36m\033[1m ++++ Patch BohmGB sources ++++ \033[0m"; \
+	(patch -R -p0 -i externals/bohmgb-coefftypes-patch.diff \
+	&& echo -e "\033[32m\033[1m -- OK -- \033[0m") \
+	|| echo -e "\033[31m\033[1m -- FAIL -- \033[0m")
+
 clean-bohmgb:
 	@echo -e "\033[36m\033[1m ++++ Clean BOHMGB ++++ \033[0m"; \
 	($(MAKE) --no-print-directory -C externals -f Makefile.bohmgb clean \
@@ -173,21 +202,47 @@ clean-bohmgb:
 
 
 # gem0 #########################################################################
-gem0: ual libbds get-gem0
+# patch to force gem0 to read ra0 param from the xml file
+gem0: ual libbds get-gem0 patch-gem0
 	@echo -e "\033[36m\033[1m ++++ Build GEM0 ++++ \033[0m"; \
+	cp gem.F90.gem0_modified externals/gem0/main/gem.F90; \
 	($(MAKE) --no-print-directory -C externals -f Makefile.gem0 \
 	&& echo -e "\033[32m\033[1m -- OK -- \033[0m") \
 	|| echo -e "\033[31m\033[1m -- FAIL -- \033[0m"
 
 get-gem0:
+#TODO what is -r : version? git counterpart of revision? looks like not all commits were transfered...
 	@if [ ! -d "externals/gem0" ]; then \
 	  echo "Checking out gem0..."; \
-		svn co $(SVNURL_GFORGE)/modtransp/trunk/gem0 externals/gem0 -r 119; \
+		if [ ! -d "externals/modtransp" ]; then \
+			echo "Modtransp is not yet cloned..."; \
+			git clone git@${GITLABADR_PSNC}:/ets/modtransp.git externals/modtransp ; \
+		else \
+			echo "Modtransp is already cloned..." ; \
+		fi ; \
+		cp -r externals/modtransp/gem0 externals/gem0; \
+		echo "Copied gem0 source..." ; \
 	else  \
 		echo "Updating gem0..."; \
-		svn up externals/gem0 -r 119; \
+		# # svn up externals/gem0 -r 119; \
 	fi
 
+patch-gem0: 
+	@grep -q ra0 externals/gem0/main/gem.F90 \
+	&& echo -e "\033[32m\033[1m -- ALREADY PATCHED -- \033[0m" \
+	|| (echo -e "\033[36m\033[1m ++++ Patch GEM0 sources ++++ \033[0m"; \
+	(patch -p0 -i externals/gem0-ra0patch.diff \
+	&& echo -e "\033[32m\033[1m -- OK -- \033[0m") \
+	|| echo -e "\033[31m\033[1m -- FAIL -- \033[0m")
+
+revert-gem0:
+	@echo -e "\033[36m\033[1m ++++ Revert GEM0 sources ++++ \033[0m"; \
+	(svn revert externals/gem0/main/* \
+        && svn revert externals/gem0/inputs/* \
+        && svn revert externals/gem0/include/* \
+	&& echo -e "\033[32m\033[1m -- OK -- \033[0m") \
+	|| echo -e "\033[31m\033[1m -- FAIL -- \033[0m"
+
 clean-gem0:
 	@echo -e "\033[36m\033[1m ++++ Clean GEM0 ++++ \033[0m"; \
 	($(MAKE) --no-print-directory -C externals -f Makefile.gem0 clean \
@@ -205,10 +260,11 @@ bdseq: ual libbds get-bdseq
 get-bdseq:
 	@if [ ! -d "externals/bdseq" ]; then \
 	  echo "Checking out bdseq..."; \
-		svn co $(SVNURL_GFORGE)/bdseq/tags/4.10b externals/bdseq; \
+		# svn co $(SVNURL_GFORGE)/bdseq/tags/4.10b externals/bdseq; \
+		git clone git@${GITLABADR_PSNC}:ets/bdseq.git --branch 4.10b --single-branch externals/bdseq ;  \
 	else  \
 		echo "Updating bdseq..."; \
-		svn up externals/bdseq; \
+		# svn up externals/bdseq; \
 	fi
 
 clean-bdseq:
@@ -234,7 +290,7 @@ revert-gem:
 	&& echo -e "\033[32m\033[1m -- OK -- \033[0m") \
 	|| echo -e "\033[31m\033[1m -- FAIL -- \033[0m"
 
-gem: ual libbds get-gem patch-gem
+gem: ual libbds patch-gem # ual libbds get-gem patch-gem
 	@echo -e "\033[36m\033[1m ++++ Build GEM ++++ \033[0m"; \
 	($(MAKE) --no-print-directory -C externals -f Makefile.gem \
 	&& echo -e "\033[32m\033[1m -- OK -- \033[0m") \
@@ -255,6 +311,14 @@ clean-gem: revert-gem
 	&& echo -e "\033[32m\033[1m -- OK -- \033[0m") \
 	|| echo -e "\033[31m\033[1m -- FAIL -- \033[0m"
 
+compile-gem: ual libbds clean-gem patch-gem
+	@echo -e "\033[36m\033[1m ++++ Build GEM (change main function and MPI topology init; outputs in Energy(); w/o getting from a repository) ++++ \033[0m"; \
+	#cp mppein.h90.modified externals/gem/include/mppein.h90 ;\ 
+	cp gem.F90.modified externals/gem/actor/gem.F90 ;\
+	#cp energy.F90.modified externals/gem/main/energy.F90 ;\ 
+	($(MAKE) --no-print-directory -C externals -f Makefile.gem \
+	&& echo -e "\033[32m\033[1m -- OK -- \033[0m") \
+	|| echo -e "\033[31m\033[1m -- FAIL -- \033[0m"
 
 # dfefi (version from IPP repos) ###############################################
 dfefi: ual libbds get-dfefi
@@ -266,10 +330,11 @@ dfefi: ual libbds get-dfefi
 get-dfefi:
 	@if [ ! -d "externals/dfefi" ]; then \
 	  echo "Checking out dfefi..."; \
-		svn co $(SVNURL_SOLPS)/dFEFI/trunk externals/dfefi; \
+		# svn co $(SVNURL_SOLPS)/dFEFI/trunk externals/dfefi; \
+		git clone ${GITLABURL_PSNC}/... externals/dfefi; \
 	else  \
 		echo "Updating dfefi..."; \
-		svn up externals/dfefi; \
+		# svn up externals/dfefi; \
 	fi
 
 clean-dfefi:
@@ -282,17 +347,24 @@ clean-dfefi:
 # imp4dv #######################################################################
 imp4dv: ual libbds get-imp4dv
 	@echo -e "\033[36m\033[1m ++++ Build IMP4DV ++++ \033[0m"; \
+	cp imp4dv.f90.modified externals/imp4dv/main/imp4dv.f90; \
 	($(MAKE) --no-print-directory -C externals -f Makefile.imp4dv \
 	&& echo -e "\033[32m\033[1m -- OK -- \033[0m") \
 	|| echo -e "\033[31m\033[1m -- FAIL -- \033[0m"
 
 get-imp4dv:
 	@if [ ! -d "externals/imp4dv" ]; then \
 	  echo "Checking out imp4dv..."; \
-		svn co $(SVNURL_GFORGE)/modtransp/trunk/imp4dv externals/imp4dv; \
+		if [ ! -d "externals/modtransp" ]; then \
+			echo "Modtransp is not yet cloned..."; \
+			git clone git@${GITLABADR_PSNC}:/ets/modtransp.git externals/modtransp ; \
+		else \
+			echo "Modtransp is already cloned..."; \
+		fi ; \
+		cp -r externals/modtransp/imp4dv externals/imp4dv ; \
 	else  \
 		echo "Updating imp4dv..."; \
-		svn up externals/imp4dv; \
+		# # svn up externals/imp4dv; \
 	fi
 
 clean-imp4dv:
@@ -320,13 +392,17 @@ strip-chease:
 	externals/chease/src-f90/xml2eg.f90 \
 	externals/chease/src-f90/xml2eg_c.c \
 	externals/chease/src-f90/xml_file_reader.f90;	\
-	mv externals/chease/src-f90/energy.f90 externals/chease/src-f90/energy_chease.f90; \
-	sed -i "s/ENERGY/ENERGY_CHEASE/g" externals/chease/src-f90/energy_chease.f90; \
-	sed -i "s/ENERGY/ENERGY_CHEASE/g" externals/chease/src-f90/stepon.f90;\
-	sed -i "s/energy/energy_chease/g" externals/chease/src-f90/Makefile \
+	if [ ! -f "externals/chease/src-f90/energy_chease.f90" ]; then \
+	  mv externals/chease/src-f90/energy.f90 externals/chease/src-f90/energy_chease.f90; \
+	  sed -i "s/ENERGY/ENERGY_CHEASE/g" externals/chease/src-f90/energy_chease.f90; \
+	  sed -i "s/ENERGY/ENERGY_CHEASE/g" externals/chease/src-f90/stepon.f90;\
+	  sed -i "s/energy/energy_chease/g" externals/chease/src-f90/Makefile; \
+	fi  \
 	&& echo -e "\033[32m\033[1m -- OK -- \033[0m") \
 	|| echo -e "\033[31m\033[1m -- FAIL -- \033[0m") \
 	|| echo -e "\033[32m\033[1m -- ALREADY STRIPPED -- \033[0m" 
+
+	#NB: Chease has to be cleaned before every build due to the current sed set-up
 
 revert-chease:
 	@echo -e "\033[36m\033[1m ++++ Revert CHEASE makefiles ++++ \033[0m"; \
@@ -345,10 +421,12 @@ chease: ual get-chease strip-chease patch-chease
 get-chease:
 	@if [ ! -d "externals/chease" ]; then \
 	  echo "Checking out chease..."; \
-		svn co $(SVNURL_GFORGE)/chease/chease/tags/4.10b.10_CHEASEv12_9 externals/chease; \
+		# svn co $(SVNURL_GFORGE)/chease/chease/tags/4.10b.10_CHEASEv12_9 externals/chease; \
+		# git clone git@${GITLABADR_EPFL}:spc/chease.git --branch 4.10b.10_CHEASEv12_9 --single-branch externals/chease ; \
+		svn co ${SVNADR_EPFL}/CHEASE/chease/tags/4.10b.10_CHEASEv12_9 externals/chease; \
 	else  \
 		echo "Updating chease..."; \
-		svn up externals/chease; \
+		# svn up externals/chease; \
 	fi
 
 clean-chease: revert-chease

archive_slurm.sh

@@ -0,0 +1,43 @@
+#!/bin/bash -l
+
+## job name
+#SBATCH --job-name=ARCHIVE_FILES_
+
+## stdout and stderr files
+#SBATCH --output=archive-out.%j
+#SBATCH --error=archive-err.%j
+
+## wall time in format (HOURS):MINUTES:SECONDS
+#SBATCH --time=24:00:00
+
+## number of nodes and tasks per node
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=40
+###SBATCH --ntasks-per-core=1
+###SBATCH --cpus-per-task=8
+
+#SBATCH --partition=medium
+###SBATCH --qos=
+
+#SBATCH --profile=all
+###SBATCH --oversubscribe
+
+## grant
+###SBATCH --account=
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=yyudin@ipp.mpg.de
+
+#############################################
+
+export DIR_BASE=VARY_1FT_GEM_NT_
+export DIR_NAME=akgbbn1a
+
+
+echo 'Archiving files in '${DIR_BASE}${DIR_NAME}
+
+tar -czvf  /r/y/yyudin/${DIR_BASE}${DIR_NAME}.tar.gz /ptmp/yyudin/${DIR_BASE}${DIR_NAME}/runs/dat/9/
+
+tar -ztvf  /r/y/yyudin/${DIR_BASE}${DIR_NAME}.tar.gz &> log_${DIR_NAME}.txt
+
+echo 'Finished archiving'
+

check_resolutions.sh

@@ -0,0 +1,14 @@
+#!/bin/bash -l
+
+n_list=(1 4 5 8 16 32)
+
+for n in ${!n_list[@]}; do
+
+	# TODO: substitute expression with a variable in sed
+      	sed "s/<npess> .* <\/npess>/<npess> \${n} <\/npess>/g" gem.xml > gem.xml.new.${n}
+
+	# TODO: substitute expression with a result of an arithmetic operation in sed
+	sed "s/srun .* .\/COBRA\//srun -n \$((\${n}*8))/g" gem_test_batch.sh > gem_test_batch.sh.new.${n} 
+
+done
+

config

@@ -335,13 +335,16 @@ ifeq ($(SYS),COBRA)
 export CC = icc
 export CCFLAGS = -g -O3 -fPIC
 export FC90= ifort
-export FC90FLAGS = -g -O3 -fPIC 
+#export FC90FLAGS = -g -O3 -fPIC 
+export FC90FLAGS = -g -O2 -fPIC
+#export FC90FLAGS = -g -O0 -traceback -fPIC # for debugging
 export FC77 = ifort
 export FC77FLAGS = ${FC90FLAGS}
 export MPIF90 = mpiifort
 export MPIFLAGS = ${FC90FLAGS}
 export FPP = fpp
-export FPPFLAGS =  
+#export FPPFLAGS =  
+export FPPFLAGS = -traceback
 export LD = ifort
 export LDFLAGS =