diff --git a/java-restructuring b/java-restructuring
deleted file mode 160000
index b632d5e696ebe7487a2584d7a42960c5f684cb43..0000000000000000000000000000000000000000
--- a/java-restructuring
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit b632d5e696ebe7487a2584d7a42960c5f684cb43
diff --git a/common-functions.rc b/models/common-functions.rc
similarity index 100%
rename from common-functions.rc
rename to models/common-functions.rc
diff --git a/models/mitgcm/dotPic-single-fileConverter.sh b/models/dotPic-single-fileConverter.sh
similarity index 100%
rename from models/mitgcm/dotPic-single-fileConverter.sh
rename to models/dotPic-single-fileConverter.sh
diff --git a/models/mitgcm/logback.xml b/models/logback.xml
similarity index 100%
rename from models/mitgcm/logback.xml
rename to models/logback.xml
diff --git a/models/make-tables-and-images.sh b/models/make-tables-and-images.sh
new file mode 100755
index 0000000000000000000000000000000000000000..f596c19087dc5c540db47700f39175245af95714
--- /dev/null
+++ b/models/make-tables-and-images.sh
@@ -0,0 +1,48 @@
+#!/bin/bash
+
+export BASE_DIR=$(cd "$(dirname "$0")"; pwd)
+
+. "${BASE_DIR}/../common-functions.rc"
+
+if [ -f "$BASE_DIR/config" ] ; then
+ . $BASE_DIR/config
+else
+ echo "Config file not found."
+fi
+
+export JAVA_OPTS="-Dlogback.configurationFile=${BASE_DIR}/logback.xml"
+
+export JOB_FILE="${OPTIMIZATION_DATA}/list-of-tables-and-images.md"
+
+checkDirectory "Result directory" "${OPTIMIZATION_DATA}"
+checkFile "List of jobs" "${JOB_FILE}"
+
+IFS=$'\n'
+
+MODE="base"
+
+for LINE in `cat "${JOB_FILE}"` ; do
+ if [ $MODE == "base" ] ; then
+ information $LINE
+ JOB_DIRECTORY="${OPTIMIZATION_DATA}/$LINE.job"
+ NAME=$LINE
+ MODE="option"
+ elif [ $MODE == "option" ] ; then
+ FIRST_CHAR=`echo $LINE | sed 's/^\(.\).*$/\1/g'`
+ if [ "$FIRST_CHAR" == "-" ] ; then
+ OPT=`echo $LINE | sed 's/^- opt-//g'`
+ TABLE_CSV="${JOB_DIRECTORY}/original-model-optimized-$OPT.csv"
+ information " $OPT"
+ checkFile "diff file" "${TABLE_CSV}"
+ MERGE_MODEL="${JOB_DIRECTORY}/original-model-optimized-$OPT"
+ mkdir -p "${MERGE_MODEL}"
+ ${MOP} -e merged-$OPT-$NAME -i "${JOB_DIRECTORY}/original-model" "${JOB_DIRECTORY}/optimized-$OPT" -o "${MERGE_MODEL}" merge
+ else
+ information $LINE
+ JOB_DIRECTORY="${OPTIMIZATION_DATA}/$LINE.job"
+ NAME=$LINE
+ fi
+ fi
+done
+
+# end
diff --git a/models/mitgcm/combine-models.sh b/models/mitgcm/combine-models.sh
index fdf191526e3866f12c95361017ae97e6acc579a2..71b635eb919f57256d470e58c8ac45ccbd29ce94 100755
--- a/models/mitgcm/combine-models.sh
+++ b/models/mitgcm/combine-models.sh
@@ -2,7 +2,7 @@
export BASE_DIR=$(cd "$(dirname "$0")"; pwd)
-. "${BASE_DIR}/../../common-functions.rc"
+. "${BASE_DIR}/../common-functions.rc"
if [ "$1" != "" ] ; then
export EXPERIMENT_NAME="$1"
@@ -26,7 +26,7 @@ fi
checkMode "$2"
-export JAVA_OPTS="-Dlogback.configurationFile=${BASE_DIR}/logback.xml"
+export JAVA_OPTS="-Dlogback.configurationFile=${BASE_DIR}/../logback.xml"
# variables
export MODEL_DATA_PATH="${DATA_PATH}/mitgcm/${EXPERIMENT_NAME}"
diff --git a/models/mitgcm/compare-models.sh b/models/mitgcm/compare-models.sh
index b5e0dd1e6461f75576eb75644afecd8ee291d7e0..9c3a7c7602cee00b3eca7e1749ea835c7c364872 100755
--- a/models/mitgcm/compare-models.sh
+++ b/models/mitgcm/compare-models.sh
@@ -2,7 +2,7 @@
export BASE_DIR=$(cd "$(dirname "$0")"; pwd)
-. "${BASE_DIR}/../../common-functions.rc"
+. "${BASE_DIR}/../common-functions.rc"
if [ -f "${BASE_DIR}/../config" ] ; then
. "${BASE_DIR}/../config"
@@ -17,7 +17,7 @@ else
exit 1
fi
-export JAVA_OPTS="-Dlogback.configurationFile=${BASE_DIR}/logback.xml"
+export JAVA_OPTS="-Dlogback.configurationFile=${BASE_DIR}/../logback.xml"
checkExecutable "Restructuring" "${RESTRUCTURING}"
checkDirectory "Result directory" "${OPTIMIZATION_DATA}"
@@ -46,7 +46,7 @@ for JOB_DIRECTORY in `find "${OPTIMIZATION_DATA}" -name '*mitgcm*job'` ; do
"${RESTRUCTURING}" -i "${ORIGINAL}" $LIST -o "${JOB_DIRECTORY}" -e compare -s kuhn
for K in $LIST ; do
OPTIMIZED=`basename $K`
- "${DELTA}" -i "${JOB_DIRECTORY}/original-model-${OPTIMIZED}.xmi" -o "${JOB_DIRECTORY}/original-model-${OPTIMIZED}" &
+ "${DELTA}" -i "${JOB_DIRECTORY}/original-model-${OPTIMIZED}.xmi" -o "${JOB_DIRECTORY}/original-model-${OPTIMIZED}"
done
fi
done
diff --git a/models/mitgcm/compute-statistics.sh b/models/mitgcm/compute-statistics.sh
index c982345416f7ce98dc681c61b18b4364740e670c..7b883828467880daf6b8f1356996518c6b3d7eb9 100755
--- a/models/mitgcm/compute-statistics.sh
+++ b/models/mitgcm/compute-statistics.sh
@@ -2,7 +2,7 @@
export BASE_DIR=$(cd "$(dirname "$0")"; pwd)
-. "${BASE_DIR}/../../common-functions.rc"
+. "${BASE_DIR}/../common-functions.rc"
if [ "$1" != "" ] ; then
export EXPERIMENT_NAME="$1"
@@ -26,7 +26,7 @@ fi
checkMode $2
-export JAVA_OPTS="-Dlogback.configurationFile=${BASE_DIR}/logback.xml"
+export JAVA_OPTS="-Dlogback.configurationFile=${BASE_DIR}/../logback.xml"
# variables
export MODEL_DATA_PATH="${DATA_PATH}/mitgcm/${EXPERIMENT_NAME}"
diff --git a/models/mitgcm/console-logger.xml b/models/mitgcm/console-logger.xml
deleted file mode 100644
index 961d6ab729df1eeeae21864be3ec04ab71325939..0000000000000000000000000000000000000000
--- a/models/mitgcm/console-logger.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<configuration>
- <appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
- <encoder>
- <pattern>%d{HH:mm:ss.SSS} [%thread] %-5level %logger{36} - %msg%n</pattern>
- </encoder>
- </appender>
-
- <root level="info">
- <appender-ref ref="STDOUT" />
- </root>
-</configuration>
diff --git a/models/mitgcm/prepare-models-for-inspection.sh b/models/mitgcm/prepare-models-for-inspection.sh
index 41d943446f97ea941d4cdd8f8278d527be35207a..f7c58fd75873f4c8615431a64efc0c9141c3f584 100755
--- a/models/mitgcm/prepare-models-for-inspection.sh
+++ b/models/mitgcm/prepare-models-for-inspection.sh
@@ -2,7 +2,7 @@
export BASE_DIR=$(cd "$(dirname "$0")"; pwd)
-. "${BASE_DIR}/../../common-functions.rc"
+. "${BASE_DIR}/../common-functions.rc"
if [ -f "${BASE_DIR}/../config" ] ; then
. "${BASE_DIR}/../config"
@@ -17,7 +17,7 @@ else
exit 1
fi
-export JAVA_OPTS="-Dlogback.configurationFile=${BASE_DIR}/logback.xml"
+export JAVA_OPTS="-Dlogback.configurationFile=${BASE_DIR}/../logback.xml"
checkExecutable "Merge model" "${MOP}"
checkExecutable "Relabel" "${RELABEL}"
diff --git a/models/mitgcm/run-all.sh b/models/mitgcm/run-all.sh
new file mode 100755
index 0000000000000000000000000000000000000000..2a43d3e8df1a25caaaca24ee4bc3a3a1fbcf5569
--- /dev/null
+++ b/models/mitgcm/run-all.sh
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+for I in call dataflow both ; do
+ for J in global_ocean.cs32x15 tutorial_barotropic_gyre tutorial_global_oce_biogeo ; do
+ $1 $J $I
+ done
+done
+
+# end
diff --git a/models/mitgcm/run-architecture-analysis.sh b/models/mitgcm/run-architecture-analysis.sh
index c6b863536b97e7516a14bcf9fa61cba013cbe5b8..a3d6a1f229dedc78e76bf53aeca8bcb1a5f0a9d2 100755
--- a/models/mitgcm/run-architecture-analysis.sh
+++ b/models/mitgcm/run-architecture-analysis.sh
@@ -2,7 +2,7 @@
export BASE_DIR=$(cd "$(dirname "$0")"; pwd)
-. "${BASE_DIR}/../../common-functions.rc"
+. "${BASE_DIR}/../common-functions.rc"
if [ "$1" != "" ] ; then
export EXPERIMENT_NAME="$1"
@@ -24,7 +24,7 @@ else
exit 1
fi
-export JAVA_OPTS="-Dlogback.configurationFile=${BASE_DIR}/logback.xml"
+export JAVA_OPTS="-Dlogback.configurationFile=${BASE_DIR}/../logback.xml"
information "++++++++++++++++++++++++++++++++++++++"
information "Configuration ${EXPERIMENT_NAME}"
diff --git a/models/mitgcm/run-dynamic-analysis.sh b/models/mitgcm/run-dynamic-analysis.sh
index e29d0f0832fbbf631be108def3eae32cc231528f..b3b3544267b8af55a5a9eab869b30a237fdecd8f 100755
--- a/models/mitgcm/run-dynamic-analysis.sh
+++ b/models/mitgcm/run-dynamic-analysis.sh
@@ -2,7 +2,7 @@
export BASE_DIR=$(cd "$(dirname "$0")"; pwd)
-. "${BASE_DIR}/../../common-functions.rc"
+. "${BASE_DIR}/../common-functions.rc"
if [ "$1" != "" ] ; then
export EXPERIMENT_NAME="$1"
@@ -40,7 +40,7 @@ STATIC_MODULE_MAP="${MODEL_DATA_PATH}/module-file-map.csv"
# check tools and executables
checkExecutable "dynamic architecture analysis" "${DAR}"
-checkExecutable "maa" "${MAA}"
+checkExecutable "Model architecture analysis" "${MAA}"
checkExecutable "Executable" "${EXECUTABLE}"
checkExecutable "addr2line" "${ADDR2LINE}"
diff --git a/models/mitgcm/run-dynamic-observation.sh b/models/mitgcm/run-dynamic-observation.sh
index c3b09e9e0a732d97f412e75d50a615b5645d81b7..02ba6341c82176cd476d55071730a436276af4fb 100755
--- a/models/mitgcm/run-dynamic-observation.sh
+++ b/models/mitgcm/run-dynamic-observation.sh
@@ -2,7 +2,7 @@
export BASE_DIR=$(cd "$(dirname "$0")"; pwd)
-. "${BASE_DIR}/../../common-functions.rc"
+. "${BASE_DIR}/../common-functions.rc"
if [ "$1" != "" ] ; then
EXPERIMENT_NAME="$1"
diff --git a/models/mitgcm/run-static-analysis.sh b/models/mitgcm/run-static-analysis.sh
index f46c3c2fc618a252894344ffde84f16b5bd3b1dd..edffa816c8f23bf0335c20197c1e9d8f628f50be 100755
--- a/models/mitgcm/run-static-analysis.sh
+++ b/models/mitgcm/run-static-analysis.sh
@@ -2,7 +2,7 @@
export BASE_DIR=$(cd "$(dirname "$0")"; pwd)
-. "${BASE_DIR}/../../common-functions.rc"
+. "${BASE_DIR}/../common-functions.rc"
if [ "$1" != "" ] ; then
export EXPERIMENT_NAME="$1"
@@ -27,6 +27,7 @@ else
fi
# variables
+export JAVA_OPTS="-Dlogback.configurationFile=${BASE_DIR}/../logback.xml"
export MODEL_DATA_PATH="${DATA_PATH}/mitgcm/${EXPERIMENT_NAME}"
STATIC_FILE_MODEL="${MODEL_DATA_PATH}/static-plain-$MODE-file"
diff --git a/models/mitgcm/run-static-code-processing.sh b/models/mitgcm/run-static-code-processing.sh
index 43fc12ee9e84b07f215ce2c4ec57bf146e7b2835..6642e23b91c636a3b21008bca7b3a0a4dd573c97 100755
--- a/models/mitgcm/run-static-code-processing.sh
+++ b/models/mitgcm/run-static-code-processing.sh
@@ -2,7 +2,7 @@
export BASE_DIR=$(cd "$(dirname "$0")"; pwd)
-. "${BASE_DIR}/../../common-functions.rc"
+. "${BASE_DIR}/../common-functions.rc"
if [ "$1" != "" ] ; then
EXPERIMENT_NAME="$1"
@@ -24,6 +24,7 @@ else
exit 1
fi
+export JAVA_OPTS="-Dlogback.configurationFile=${BASE_DIR}/../logback.xml"
export MODEL_DATA_PATH="${DATA_PATH}/mitgcm/${EXPERIMENT_NAME}"
# inputs
diff --git a/models/uvic/combine-models.sh b/models/uvic/combine-models.sh
index 0d73b326187e446fe2faf3f1d379c085bb93751f..21c8056632652862b8deb878575de8f3e3fc0ac0 100755
--- a/models/uvic/combine-models.sh
+++ b/models/uvic/combine-models.sh
@@ -2,7 +2,7 @@
export BASE_DIR=$(cd "$(dirname "$0")"; pwd)
-. "${BASE_DIR}/../../common-functions.rc"
+. "${BASE_DIR}/../common-functions.rc"
if [ "$1" != "" ] ; then
export EXPERIMENT_NAME="$1"
@@ -26,7 +26,7 @@ fi
checkMode "$2"
-export JAVA_OPTS="-Dlogback.configurationFile=${BASE_DIR}/logback.xml"
+export JAVA_OPTS="-Dlogback.configurationFile=${BASE_DIR}/../logback.xml"
# variables
export MODEL_DATA_PATH="${DATA_PATH}/uvic"
diff --git a/models/uvic/compare-models.sh b/models/uvic/compare-models.sh
index edaeddce8f92dd509eefc0c18124f980854a3469..3d86e9536ce2b7a114c1c8605c18b93362e0ae4e 100755
--- a/models/uvic/compare-models.sh
+++ b/models/uvic/compare-models.sh
@@ -2,7 +2,7 @@
export BASE_DIR=$(cd "$(dirname "$0")"; pwd)
-. "${BASE_DIR}/../../common-functions.rc"
+. "${BASE_DIR}/../common-functions.rc"
if [ -f "${BASE_DIR}/../config" ] ; then
. "${BASE_DIR}/../config"
@@ -17,7 +17,7 @@ else
exit 1
fi
-export JAVA_OPTS="-Dlogback.configurationFile=${BASE_DIR}/logback.xml"
+export JAVA_OPTS="-Dlogback.configurationFile=${BASE_DIR}/../logback.xml"
checkExecutable "Restructuring" "${RESTRUCTURING}"
checkDirectory "Result directory" "${OPTIMIZATION_DATA}"
diff --git a/models/uvic/compute-statistics.sh b/models/uvic/compute-statistics.sh
index 42320eab1625ac076878d4a8394d3182419ac38e..859d5b3d94924f80355f422c9b8125c9d49b3f2e 100755
--- a/models/uvic/compute-statistics.sh
+++ b/models/uvic/compute-statistics.sh
@@ -2,7 +2,7 @@
export BASE_DIR=$(cd "$(dirname "$0")"; pwd)
-. "${BASE_DIR}/../../common-functions.rc"
+. "${BASE_DIR}/../common-functions.rc"
if [ "$1" != "" ] ; then
export EXPERIMENT_NAME="$1"
@@ -26,6 +26,8 @@ fi
checkMode $2
+export JAVA_OPTS="-Dlogback.configurationFile=${BASE_DIR}/../logback.xml"
+
# variables
export MODEL_DATA_PATH="${DATA_PATH}/uvic"
diff --git a/models/uvic/linux_amd64_gfortran_kieker b/models/uvic/linux_amd64_gfortran_kieker
deleted file mode 100644
index cb21aed1277de3dcfa9bdfccc3f231cb06dcdf17..0000000000000000000000000000000000000000
--- a/models/uvic/linux_amd64_gfortran_kieker
+++ /dev/null
@@ -1,184 +0,0 @@
-#!/bin/bash
-
-# Build options for gfortran compiler (GNU) on Linux AMD64 platform
-#
-# Tested with gcc-gfortran v4.1.x as shipped with Fedora Core 6,7,8
-# with gcc-gfortran v4.3.x as shipped with Fedora Core 9,10
-#
-# OpenMP : Tested on dickens with gcc-gfortran v4.3.2 as shipped with FC 10
-# on baudelaire with gcc-gfortran v4.4.5 as shipped with FC 13
-# on danton with gcc-gfortran v4.5.1 as shipped with FC 14
-# with gcc-gfortran v4.7.x as shipped with FC 17
-# with gcc-gfortran v4.8.1 as shipped with FC 19
-# on acesgrid with gcc-gfortran v4.6.0 as shipped with FC 15
-#
-# MPI : Tested on acesgrid (Fedora Core 15), using:
-# module load gcc (Version 4.6.0)
-# and with mpich1:
-# module load mvapich
-# or with mpich2:
-# module load mvapich2
-# or with openmpi:
-# module load openmpi
-# and on baudelaire.csail.mit.edu (FC13), using:
-# export MPI_GCC_DIR=/srv/software/gcc/gcc-packages/gcc-4.4.5/mpich2/mpich2-1.3
-# export MPI_INC_DIR=$MPI_GCC_DIR/include
-# export PATH=$MPI_GCC_DIR/bin:$PATH
-#
-# and on IRIDIS at Southampton
-# http://www.southampton.ac.uk/isolutions/computing/hpc/iridis/
-# with
-# module load openmpi/1.4.3/gcc-4.3.3
-# and
-# export MPI_INC_DIR=$MPIROOT/include
-
-#-------
-# run with OpenMP: needs to set environment var. OMP_NUM_THREADS
-# and generally, needs to increase the thread stack-size:
-# - sh,bash:
-# > export OMP_NUM_THREADS=2
-# > export GOMP_STACKSIZE=400m
-# - csh,tcsh:
-# > setenv OMP_NUM_THREADS 2
-# > setenv GOMP_STACKSIZE 400m
-#-------
-
-if test "x$MPI" = xtrue ; then
- CC=${CC:=mpicc}
- FC=${FC:=mpif77}
- F90C=${F90C:=mpif90}
-else
- CC=gcc
- FC=gfortran
- F90C=gfortran
-fi
-
-DEFINES='-DWORDLENGTH=4 -DNML_TERMINATOR'
-EXTENDED_SRC_FLAG='-ffixed-line-length-132'
-F90FIXEDFORMAT='-ffixed-form'
-GET_FC_VERSION="--version"
-OMPFLAG='-fopenmp'
-
-NOOPTFLAGS='-O0'
-NOOPTFILES=''
-
-CFLAGS='-O0'
-#- Requires gfortran from 2006 onwards for -fconvert=big-endian
-FFLAGS="$FFLAGS -fconvert=big-endian -fimplicit-none"
-#- for big setups, compile & link with "-fPIC" or set memory-model to "medium":
-#CFLAGS="$CFLAGS -fPIC"
-#FFLAGS="$FFLAGS -fPIC"
-#- with FC 19, need to use this without -fPIC (which cancels -mcmodel option):
- CFLAGS="$CFLAGS -mcmodel=medium"
- FFLAGS="$FFLAGS -mcmodel=medium"
-#- might want to use '-fdefault-real-8' for fizhi pkg:
-#FFLAGS="$FFLAGS -fdefault-real-8 -fdefault-double-8"
-
-if test "x$IEEE" = x ; then #- with optimisation:
- #- full optimisation
- FOPTIM='-O3 -funroll-loops'
- NOOPTFILES="$NOOPTFILES ini_masks_etc.F"
- #- can use -O2 (safe optimisation) to avoid Pb with some gcc version of -O3:
- #FOPTIM='-O2 -funroll-loops'
-else
- # these may also be useful, but require specific gfortran versions:
- # -Wnonstd-intrinsics for gfortran <= 4.3
- # -Wintrinsics-std for gfortran >= 4.4
- # -Wno-tabs for gfortran >= 4.3
- # -Wno-unused-dummy-argument for gfortran >= 4.6
- #FFLAGS="$FFLAGS -Waliasing -Wampersand -Wsurprising -Wline-truncation"
- #- or simply:
- FFLAGS="$FFLAGS -Wall"
- #- to get plenty of warnings: -Wall -Wextra (older form: -Wall -W) or:
- #FFLAGS="$FFLAGS -Wconversion -Wimplicit-interface -Wunused-labels"
- if test "x$DEVEL" = x ; then #- no optimisation + IEEE :
- FOPTIM='-O0'
- else #- development/check options:
- FOPTIM='-O0 -g -fbounds-check'
- FOPTIM="$FOPTIM -ffpe-trap=invalid,zero,overflow -finit-real=inf"
- fi
-fi
-
-F90FLAGS=$FFLAGS
-F90OPTIM=$FOPTIM
-
-INCLUDEDIRS=''
-INCLUDES=''
-LIBS=''
-
-if [ "x$NETCDF_ROOT" != x ] ; then
- INCLUDEDIR="${NETCDF_ROOT}/include"
- INCLUDES="-I${NETCDF_ROOT}/include"
- LIBDIR="${NETCDF_ROOT}/lib"
- LIBS="-L${NETCDF_ROOT}/lib"
-elif [ "x$NETCDF_HOME" != x ]; then
- INCLUDEDIR="${NETCDF_HOME}/include"
- INCLUDES="-I${NETCDF_HOME}/include"
- LIBDIR="${NETCDF_HOME}/lib"
- LIBS="-L${NETCDF_HOME}/lib"
-elif [ "x$NETCDF_INC" != x -a "x$NETCDF_LIB" != x ]; then
- NETCDF_INC=`echo $NETCDF_INC | sed 's/-I//g'`
- NETCDF_LIB=`echo $NETCDF_LIB | sed 's/-L//g'`
- INCLUDEDIR="${NETCDF_INC}"
- INCLUDES="-I${NETCDF_INC}"
- LIBDIR="${NETCDF_LIB}"
- LIBS="-L${NETCDF_LIB}"
-elif [ "x$NETCDF_INCDIR" != x -a "x$NETCDF_LIBDIR" != x ]; then
- INCLUDEDIR="${NETCDF_INCDIR}"
- INCLUDES="-I${NETCDF_INCDIR}"
- LIBDIR="${NETCDF_LIBDIR}"
- LIBS="-L${NETCDF_LIBDIR}"
-elif [[ -n $( nf-config --includedir ) && ($? == 0) ]] ; then
- # NETCDF env variables are not set, trying nf-config instead
- INCLUDEDIR=$( nf-config --includedir )
- INCLUDES="-I$INCLUDEDIR"
- LIBS=$( nf-config --flibs )
-elif test -d /usr/include/netcdf-3 ; then
- INCLUDES='-I/usr/include/netcdf-3'
- LIBS='-L/usr/lib/netcdf-3 -L/usr/lib64/netcdf-3'
-elif test -d /usr/include/netcdf ; then
- INCLUDES='-I/usr/include/netcdf'
-elif test -d /usr/local/netcdf ; then
- INCLUDES='-I/usr/local/netcdf/include'
- LIBS='-L/usr/local/netcdf/lib'
-elif test -d /usr/local/include/netcdf.inc ; then
- INCLUDES='-I/usr/local/include'
- LIBS='-L/usr/local/lib64'
-elif test -d /usr/include/netcdf.inc ; then
- INCLUDES='-I/usr/include'
- LIBS='-L/usr/lib64'
-fi
-
-if [ -n "$MPI_HOME" -a -z "$MPI_INC_DIR" ]; then
- MPI_INC_DIR="$MPI_HOME/include"
-fi
-
-if [ "x$MPI" = xtrue ] ; then
- if [ -z "$MPI_INC_DIR" ] ; then
- # MPI env variables are not set, trying pkg-config insteal
- if [[ -n $( pkg-config --cflags-only-I ompi ) && ($? == 0) ]] ; then
- MPI_INC_DIR=$(pkg-config --cflags-only-I ompi | awk '{ print $1 }' | sed -e "s/-I//" )
- else
- echo MPI_HOME is not set and pkg-config not available, aborting
- exit 1
- fi
- fi
- if [ -n "$MPI_INC_DIR" ] ; then
- # only fill this if we can find MPI, otherwise triggers netcdf error
- INCLUDES+=" -I$MPI_INC_DIR"
- INCLUDEDIRS+=" $MPI_INC_DIR"
- #- used for parallel (MPI) DIVA
- MPIINCLUDEDIR="$MPI_INC_DIR"
- else
- echo could not set MPI_INC_DIR, aborting
- exit 1
- fi
-fi
-
-# Kieker setup
-FOPTIM=""
-F90OPTIM=""
-
-FFLAGS="$FFLAGS -finstrument-functions -g"
-CFLAGS="$CFLAGS -finstrument-functions -g"
-LIBS="$LIBS -L/usr/lib/x86_64-linux-gnu -L/home/reiner/Projects/Kieker/kieker-lang-pack-c/libkieker/.libs -lkieker -ldl"
diff --git a/models/uvic/prepare-models-for-inspection.sh b/models/uvic/prepare-models-for-inspection.sh
index c5dee62de2d4b0db2881f154c3b5520f8ee1120d..978c535631cceffd08c64bd5d910ab805b91b340 100755
--- a/models/uvic/prepare-models-for-inspection.sh
+++ b/models/uvic/prepare-models-for-inspection.sh
@@ -2,7 +2,7 @@
export BASE_DIR=$(cd "$(dirname "$0")"; pwd)
-. "${BASE_DIR}/../../common-functions.rc"
+. "${BASE_DIR}/../common-functions.rc"
if [ -f "${BASE_DIR}/../config" ] ; then
. "${BASE_DIR}/../config"
@@ -17,7 +17,7 @@ else
exit 1
fi
-export JAVA_OPTS="-Dlogback.configurationFile=${BASE_DIR}/logback.xml"
+export JAVA_OPTS="-Dlogback.configurationFile=${BASE_DIR}/../logback.xml"
checkExecutable "Merge model" "${MOP}"
checkExecutable "Relabel" "${RELABEL}"
diff --git a/models/uvic/run-architecture-analysis.sh b/models/uvic/run-architecture-analysis.sh
index c6b863536b97e7516a14bcf9fa61cba013cbe5b8..a3d6a1f229dedc78e76bf53aeca8bcb1a5f0a9d2 100755
--- a/models/uvic/run-architecture-analysis.sh
+++ b/models/uvic/run-architecture-analysis.sh
@@ -2,7 +2,7 @@
export BASE_DIR=$(cd "$(dirname "$0")"; pwd)
-. "${BASE_DIR}/../../common-functions.rc"
+. "${BASE_DIR}/../common-functions.rc"
if [ "$1" != "" ] ; then
export EXPERIMENT_NAME="$1"
@@ -24,7 +24,7 @@ else
exit 1
fi
-export JAVA_OPTS="-Dlogback.configurationFile=${BASE_DIR}/logback.xml"
+export JAVA_OPTS="-Dlogback.configurationFile=${BASE_DIR}/../logback.xml"
information "++++++++++++++++++++++++++++++++++++++"
information "Configuration ${EXPERIMENT_NAME}"
diff --git a/models/uvic/run-dynamic-analysis.sh b/models/uvic/run-dynamic-analysis.sh
index fceb6e2ef1f7833dee67d28d1e06d8f3ecedda83..9ad42bf0570113d035df5b07350d930d93fb82f5 100755
--- a/models/uvic/run-dynamic-analysis.sh
+++ b/models/uvic/run-dynamic-analysis.sh
@@ -2,7 +2,7 @@
export BASE_DIR=$(cd "$(dirname "$0")"; pwd)
-. "${BASE_DIR}/../../common-functions.rc"
+. "${BASE_DIR}/../common-functions.rc"
if [ "$1" != "" ] ; then
export EXPERIMENT_NAME="$1"
@@ -62,7 +62,6 @@ checkDirectory "Interface 2-level model" "${INTERFACE_2_LEVEL_MODEL}" recreate
# run
information "Dynamic architecture analysis - file based components"
-
"${DAR}" -a "${ADDR2LINE}" -c -e "${EXECUTABLE}" -E "${EXPERIMENT_NAME}-dynamic-call" -i "${KIEKER_LOG}" -m file-mode -o "${DYNAMIC_FILE_MODEL}" -s elf -l dynamic
information "Dynamic architecture analysis - map based components"
@@ -70,7 +69,6 @@ information "Dynamic architecture analysis - map based components"
"${DAR}" -a "${ADDR2LINE}" -c -e "${EXECUTABLE}" -E "${EXPERIMENT_NAME}-dynamic-call" -i "${KIEKER_LOG}" -m map-mode -o "${DYNAMIC_MAP_MODEL}" -s elf -l dynamic -M "${STATIC_MODULE_MAP}"
information "2 level map and file-based info"
-
"${MAA}" -g "${STATIC_MODULE_MAP}" -i "${DYNAMIC_FILE_MODEL}" -o "${DYNAMIC_2_LEVEL_MODEL}" -gs ";" -E "${EXPERIMENT_NAME}-dynamic-plain-call-2-level"
information "Compute interface models"
diff --git a/models/uvic/run-dynamic-observation.sh b/models/uvic/run-dynamic-observation.sh
index f70cc37bb48c2660e9b93374cb84a83b0f985464..a947e860fcb553b0dbddcd572e5bbb85244bd46a 100755
--- a/models/uvic/run-dynamic-observation.sh
+++ b/models/uvic/run-dynamic-observation.sh
@@ -2,7 +2,7 @@
export BASE_DIR=$(cd "$(dirname "$0")"; pwd)
-. "${BASE_DIR}/../../common-functions.rc"
+. "${BASE_DIR}/../common-functions.rc"
if [ -f "${BASE_DIR}/../config" ] ; then
. "${BASE_DIR}/../config"
diff --git a/models/uvic/run-static-analysis.sh b/models/uvic/run-static-analysis.sh
index 74219abb559d2b82c1ec3b3d94319cbdfacc1f7a..a52e62fe7b22ee16ce47dad32ec439d94da49959 100755
--- a/models/uvic/run-static-analysis.sh
+++ b/models/uvic/run-static-analysis.sh
@@ -2,7 +2,7 @@
export BASE_DIR=$(cd "$(dirname "$0")"; pwd)
-. "${BASE_DIR}/../../common-functions.rc"
+. "${BASE_DIR}/../common-functions.rc"
if [ "$1" != "" ] ; then
export EXPERIMENT_NAME="$1"
@@ -27,6 +27,7 @@ else
fi
# variables
+export JAVA_OPTS="-Dlogback.configurationFile=${BASE_DIR}/../logback.xml"
export MODEL_DATA_PATH="${DATA_PATH}/uvic"
STATIC_FILE_MODEL="${MODEL_DATA_PATH}/static-plain-$MODE-file"
diff --git a/models/uvic/run-static-code-processing.sh b/models/uvic/run-static-code-processing.sh
index 5f20d3e9af0a868c976e622ccfb5f75d73a55cf6..9a8fc84ec3c66f58159f7451737aa2111e26d7bf 100755
--- a/models/uvic/run-static-code-processing.sh
+++ b/models/uvic/run-static-code-processing.sh
@@ -2,7 +2,7 @@
export BASE_DIR=$(cd "$(dirname "$0")"; pwd)
-. "${BASE_DIR}/../../common-functions.rc"
+. "${BASE_DIR}/../common-functions.rc"
if [ -f "${BASE_DIR}/../config" ] ; then
. "${BASE_DIR}/../config"
@@ -17,6 +17,7 @@ else
exit 1
fi
+export JAVA_OPTS="-Dlogback.configurationFile=${BASE_DIR}/../logback.xml"
export MODEL_DATA_PATH="${DATA_PATH}/uvic"
# inputs
diff --git a/python-coupling-analysis b/python-coupling-analysis
deleted file mode 160000
index 59c79f24f720002d7bd9a2e0ef0a2eab5c0d3656..0000000000000000000000000000000000000000
--- a/python-coupling-analysis
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 59c79f24f720002d7bd9a2e0ef0a2eab5c0d3656