source: issm/oecreview/Archive/24684-25833/ISSM-24823-24824.diff@ 25834

Last change on this file since 25834 was 25834, checked in by Mathieu Morlighem, 4 years ago

CHG: added 24684-25833
File size: 32.9 KB
RevLine 
[25834]1Index: ../trunk-jpl/jenkins/ross-debian_linux-codipack
2===================================================================
3--- ../trunk-jpl/jenkins/ross-debian_linux-codipack (revision 24823)
4+++ ../trunk-jpl/jenkins/ross-debian_linux-codipack (revision 24824)
5@@ -38,7 +38,7 @@
6 autotools install-debian-linux.sh
7 cmake install.sh
8 petsc install-3.12-linux.sh
9- gsl install-linux.sh
10+ gsl install.sh
11 triangle install-linux.sh
12 chaco install.sh
13 m1qn3 install.sh
14Index: ../trunk-jpl/jenkins/pine_island-mac-binaries-with_dakota
15===================================================================
16--- ../trunk-jpl/jenkins/pine_island-mac-binaries-with_dakota (revision 24823)
17+++ ../trunk-jpl/jenkins/pine_island-mac-binaries-with_dakota (revision 24824)
18@@ -28,8 +28,9 @@
19 --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \
20 --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \
21 --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \
22+ --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \
23+ --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \
24 --with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \
25- --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \
26 --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \
27 --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \
28 --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \
29@@ -50,7 +51,8 @@
30 autotools install.sh
31 cmake install.sh
32 petsc install-3.12-mac-static.sh
33- boost install-1.72-mac-static.sh
34+ gsl install-static.sh
35+ boost install-1.7-mac-static.sh
36 dakota install-6.2-mac-static.sh
37 triangle install-mac-static.sh
38 chaco install.sh
39Index: ../trunk-jpl/m4/issm_options.m4
40===================================================================
41--- ../trunk-jpl/m4/issm_options.m4 (revision 24823)
42+++ ../trunk-jpl/m4/issm_options.m4 (revision 24824)
43@@ -536,8 +536,12 @@
44 DAKOTAFLAGS=""
45
46 dnl NOTE:
47- dnl - See $ISSM_DIR/dakota/build/src/Makefile.export.Dakota for the
48- dnl flags needed by your combination of Boost and Dakota versions
49+ dnl - See,
50+ dnl
51+ dnl $ISSM_DIR/externalpackages/dakota/build/src/Makefile.export.Dakota
52+ dnl
53+ dnl for the flags needed by your combination of Boost and Dakota
54+ dnl versions
55 dnl - We know $DAKOTA_ROOT cannot be empty at this point, so no need to
56 dnl check again in the following conditionals
57 dnl
58@@ -567,14 +571,10 @@
59 AC_DEFINE([DAKOTA_HAVE_MPI], [1], [enabling Dakota with MPI])
60 elif test "${DAKOTA_VERSION}" == "6.1" || test "${DAKOTA_VERSION}" == "6.2"; then
61 if test "${BOOST_VERSION_MAJOR}" == "1"; then
62- if test "${BOOST_VERSION_MINOR}" == "55"; then
63- DAKOTAFLAGS="-DDISABLE_DAKOTA_CONFIG_H -DBOOST_MULTI_INDEX_DISABLE_SERIALIZATION -DDAKOTA_PLUGIN -DBOOST_DISABLE_ASSERTS -DDAKOTA_HAVE_BOOST_FS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DDAKOTA_UTILIB -DHAVE_ADAPTIVE_SAMPLING -DHAVE_CONMIN -DDAKOTA_DDACE -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL"
64- DAKOTALIB="-L${DAKOTA_ROOT}/lib -ldakota_src -ldream -lfsudace -lddace -lnomad -lpecos_src -llhs -llhs_mods -loptpp -lsurfpack -lconmin -ldakota_src_fortran -llhs_mod -lncsuopt -lsurfpack_fortran -lteuchos -lamplsolver -lcport -ldfftpack -lfsudace -lhopspack -lnidr -lpecos -lpsuade -lsparsegrid -L${BOOST_ROOT}/lib -lboost_serialization -lboost_signals -lboost_regex -lboost_filesystem -lboost_system ${BLASLAPACKLIB}"
65- elif test "${BOOST_VERSION_MINOR}" = "72"; then
66- DAKOTAFLAGS="-DHAVE_CONFIG_H -DHAVE_CONFIG_H -DDISABLE_DAKOTA_CONFIG_H -DBOOST_DISABLE_ASSERTS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DHAVE_ADAPTIVE_SAMPLING -DHAVE_ESM -DHAVE_CONMIN -DHAVE_DDACE -DHAVE_DREAM -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_NOMAD -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL"
67- dnl See $ISSM_DIR/dakota/build/src/Makefile.export.Dakota -> Dakota_LIBRARIES
68- DAKOTALIB="-L${DAKOTA_ROOT}/lib -ldakota_src -ldakota_src_fortran -lnidr -lteuchos -lpecos -lpecos_src -llhs -llhs_mods -llhs_mod -ldfftpack -lsparsegrid -lsurfpack -lsurfpack -lsurfpack_fortran -lconmin -lddace -ldream -lfsudace -lhopspack -lncsuopt -lcport -lnomad -loptpp -lpsuade -lamplsolver -L${BOOST_ROOT}/lib -lboost_filesystem -lboost_program_options -lboost_regex -lboost_serialization -lboost_system ${BLASLAPACKLIB}"
69- fi
70+ DAKOTAFLAGS="-DHAVE_CONFIG_H -DHAVE_CONFIG_H -DDISABLE_DAKOTA_CONFIG_H -DBOOST_DISABLE_ASSERTS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DHAVE_ADAPTIVE_SAMPLING -DHAVE_ESM -DHAVE_QUESO -DHAVE_QUESO_GPMSA -DHAVE_CONMIN -DHAVE_DDACE -DHAVE_DREAM -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_NOMAD -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL"
71+ DAKOTALIB="-L${DAKOTA_ROOT}/lib -ldakota_src -ldakota_src_fortran -lnidr -lteuchos -lpecos -lpecos_src -llhs -llhs_mods -llhs_mod -ldfftpack -lsparsegrid -lsurfpack -lsurfpack -lsurfpack_fortran -lqueso -lconmin -lddace -ldream -lfsudace -lhopspack -lncsuopt -lcport -lnomad -loptpp -lpsuade -lamplsolver"
72+ DAKOTALIB+=" -L${BOOST_ROOT}/lib -lboost_filesystem -lboost_program_options -lboost_regex -lboost_serialization -lboost_system"
73+ DAKOTALIB+=" ${BLASLAPACKLIB}"
74 fi
75 AC_DEFINE([DISABLE_DAKOTA_CONFIG_H], [1], [disabling DAKOTA_CONFIG_H])
76 AC_DEFINE([DAKOTA_HAVE_MPI], [1], [enabling Dakota with MPI])
77@@ -606,11 +606,7 @@
78 if test "${BOOST_VERSION_MAJOR}" == "1"; then
79 DAKOTAFLAGS="-DHAVE_CONFIG_H -DHAVE_CONFIG_H -DDISABLE_DAKOTA_CONFIG_H -DBOOST_DISABLE_ASSERTS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DHAVE_ADAPTIVE_SAMPLING -DHAVE_ESM -DHAVE_QUESO -DHAVE_QUESO_GPMSA -DHAVE_CONMIN -DHAVE_DDACE -DHAVE_DREAM -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_NOMAD -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL"
80 DAKOTALIB="-L${DAKOTA_ROOT}/lib -ldakota_src -ldakota_src_fortran -lnidr -lteuchos -lpecos -lpecos_src -llhs -llhs_mods -llhs_mod -ldfftpack -lsparsegrid -lsurfpack -lsurfpack -lsurfpack_fortran -lqueso -lconmin -lddace -ldream -lfsudace -lhopspack -lncsuopt -lcport -lnomad -loptpp -lpsuade -lamplsolver"
81- if test "${BOOST_VERSION_MINOR}" == "55"; then
82- DAKOTALIB+=" -L${BOOST_ROOT}/lib -lboost_serialization -lboost_signals -lboost_regex -lboost_filesystem -lboost_system ${BLASLAPACKLIB}"
83- elif test "${BOOST_VERSION_MINOR}" = "72"; then
84- DAKOTALIB+=" -L${BOOST_ROOT}/lib -lboost_filesystem -lboost_program_options -lboost_regex -lboost_serialization -lboost_system"
85- fi
86+ DAKOTALIB+=" -L${BOOST_ROOT}/lib -lboost_filesystem -lboost_program_options -lboost_regex -lboost_serialization -lboost_system"
87 DAKOTALIB+=" ${BLASLAPACKLIB}"
88 fi
89 AC_DEFINE([DISABLE_DAKOTA_CONFIG_H], [1], [disabling DAKOTA_CONFIG_H])
90Index: ../trunk-jpl/externalpackages/dakota/install-6.2-macosx64.sh
91===================================================================
92--- ../trunk-jpl/externalpackages/dakota/install-6.2-macosx64.sh (revision 24823)
93+++ ../trunk-jpl/externalpackages/dakota/install-6.2-macosx64.sh (nonexistent)
94@@ -1,78 +0,0 @@
95-#!/bin/bash
96-set -eu
97-
98-# Constants
99-DAK_VER="6.2"
100-
101-# Some cleanup
102-rm -rf build
103-rm -rf install
104-rm -rf tests
105-rm -rf src
106-mkdir build install src
107-
108-# Download from ISSM server
109-$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/dakota-${DAK_VER}-public.src.tar.gz" "dakota-${DAK_VER}-public-src.tar.gz"
110-
111-# Untar
112-tar -zxvf dakota-${DAK_VER}-public-src.tar.gz
113-
114-# Move Dakota to src directory
115-mv dakota-${DAK_VER}.0.src/* src
116-rm -rf dakota-${DAK_VER}.0.src
117-
118-# Set up Dakota and CMake variables
119-DAK_PATH=$ISSM_DIR/externalpackages/dakota
120-
121-export DAK_BUILD=$DAK_PATH/build
122-export DAK_INSTALL=$DAK_PATH/install
123-export DAK_SRC=$DAK_PATH/src
124-export MPIHOME=$ISSM_DIR/externalpackages/mpich/install
125-export BOOST_ROOT=$ISSM_DIR/externalpackages/boost/install
126-
127-# Apply patches
128-cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake
129-patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/$DAK_VER/BuildDakotaCustom.cmake.mac.patch
130-patch $DAK_SRC/cmake/DakotaDev.cmake configs/$DAK_VER/DakotaDev.cmake.patch
131-patch $DAK_SRC/cmake/InstallDarwinDylibs.cmake configs/$DAK_VER/InstallDarwinDylibs.cmake.patch
132-patch $DAK_SRC/CMakeLists.txt configs/$DAK_VER/CMakeLists.txt.patch
133-patch src/src/NonDSampling.cpp configs/$DAK_VER/NonDSampling.cpp.patch
134-patch src/src/NonDLocalReliability.cpp configs/$DAK_VER/NonDLocalReliability.cpp.patch
135-patch src/packages/pecos/src/pecos_global_defs.hpp configs/$DAK_VER/pecos_global_defs.hpp.patch
136-
137-# Configure and build Dakota
138-cd $DAK_BUILD
139-cmake \
140- -C$DAK_SRC/cmake/BuildDakotaCustom.cmake \
141- -C$DAK_SRC/cmake/DakotaDev.cmake \
142- -DBOOST_ROOT:PATHNAME=$BOOST_ROOT \
143- -DBoost_NO_BOOST_CMAKE=TRUE \
144- -DBoost_NO_SYSTEM_PATHS=TRUE \
145- -DBoost_LIBRARY_DIRS:FILEPATH=$BOOST_ROOT/lib \
146- -DCMAKE_INSTALL_PREFIX=$DAK_INSTALL \
147- -DCMAKE_C_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicc \
148- -DCMAKE_CXX_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicxx \
149- -DCMAKE_Fortran_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpif77 \
150- -DCMAKE_CXX_FLAGS=-fdelayed-template-parsing \
151- -DHAVE_ACRO=off \
152- -DHAVE_JEGA=off \
153- $DAK_SRC
154-
155-if [ $# -eq 0 ];
156-then
157- make
158- make install
159-else
160- make -j $1
161- make -j $1 install
162-fi
163-
164-# Set paths and library paths
165-export PATH=$DAK_INSTALL/bin:$DAK_INSTALL/test:$PATH
166-
167-if [ -z ${DYLD_LIBRARY_PATH+x} ]
168-then
169- export DYLD_LIBRARY_PATH=$DAK_INSTALL/lib:$DAK_INSTALL/bin
170-else
171- export DYLD_LIBRARY_PATH=$DAK_INSTALL/lib:$DAK_INSTALL/bin:$DYLD_LIBRARY_PATH
172-fi
173
174Property changes on: ../trunk-jpl/externalpackages/dakota/install-6.2-macosx64.sh
175___________________________________________________________________
176Deleted: svn:executable
177## -1 +0,0 ##
178-*
179\ No newline at end of property
180Index: ../trunk-jpl/externalpackages/dakota/install-6.2-mac-static.sh
181===================================================================
182--- ../trunk-jpl/externalpackages/dakota/install-6.2-mac-static.sh (revision 24823)
183+++ ../trunk-jpl/externalpackages/dakota/install-6.2-mac-static.sh (revision 24824)
184@@ -56,6 +56,8 @@
185 -DBoost_NO_BOOST_CMAKE=TRUE \
186 -DHAVE_ACRO=OFF \
187 -DHAVE_JEGA=OFF \
188+ -DHAVE_QUESO=ON \
189+ -DDAKOTA_HAVE_GSL=ON \
190 -C${DAK_SRC}/cmake/BuildDakotaCustom.cmake \
191 -C${DAK_SRC}/cmake/DakotaDev.cmake \
192 ${DAK_SRC}
193Index: ../trunk-jpl/externalpackages/dakota/install-6.2-linux.sh
194===================================================================
195--- ../trunk-jpl/externalpackages/dakota/install-6.2-linux.sh (revision 24823)
196+++ ../trunk-jpl/externalpackages/dakota/install-6.2-linux.sh (revision 24824)
197@@ -11,7 +11,7 @@
198 #
199 export BLAS_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lfblas -L/usr/lib/x86_64-linux-gnu -lgfortran" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
200 export BOOST_ROOT=${ISSM_DIR}/externalpackages/boost/install
201-export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with Matlab's Boost (absolutely necessary for this version)
202+export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with MATLAB's Boost (absolutely necessary for this version)
203 #export CXXFLAGS='-std=c++11'
204 export DAK_BUILD=${DAK_ROOT}/build
205 export DAK_INSTALL=${DAK_ROOT}/install
206@@ -52,6 +52,7 @@
207 -DCMAKE_C_COMPILER=${MPI_HOME}/bin/mpicc \
208 -DCMAKE_CXX_COMPILER=${MPI_HOME}/bin/mpicxx \
209 -DCMAKE_Fortran_COMPILER=${MPI_HOME}/bin/mpif77 \
210+ -DBoost_NO_BOOST_CMAKE=TRUE \
211 -DHAVE_ACRO=OFF \
212 -DHAVE_JEGA=OFF \
213 -DHAVE_QUESO=ON \
214Index: ../trunk-jpl/externalpackages/dakota/install-6.2-mac.sh
215===================================================================
216--- ../trunk-jpl/externalpackages/dakota/install-6.2-mac.sh (revision 24823)
217+++ ../trunk-jpl/externalpackages/dakota/install-6.2-mac.sh (revision 24824)
218@@ -14,6 +14,7 @@
219 export DAK_BUILD=${DAK_ROOT}/build
220 export DAK_INSTALL=${DAK_ROOT}/install
221 export DAK_SRC=${DAK_ROOT}/src
222+export GSL_HOME=${ISSM_DIR}/externalpackages/gsl/install
223 export LAPACK_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lflapack -L/usr/local/Cellar/gcc/9.3.0/lib/gcc/9 -lgfortran" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
224
225 # Cleanup
226@@ -55,6 +56,8 @@
227 -DBoost_NO_BOOST_CMAKE=TRUE \
228 -DHAVE_ACRO=OFF \
229 -DHAVE_JEGA=OFF \
230+ -DHAVE_QUESO=ON \
231+ -DDAKOTA_HAVE_GSL=ON \
232 -C${DAK_SRC}/cmake/BuildDakotaCustom.cmake \
233 -C${DAK_SRC}/cmake/DakotaDev.cmake \
234 ${DAK_SRC}
235Index: ../trunk-jpl/externalpackages/boost/install-1.72-linux.sh
236===================================================================
237--- ../trunk-jpl/externalpackages/boost/install-1.72-linux.sh (revision 24823)
238+++ ../trunk-jpl/externalpackages/boost/install-1.72-linux.sh (nonexistent)
239@@ -1,48 +0,0 @@
240-#!/bin/bash
241-#set -eu # Do not `run set -eu` because it causes some targets to fail
242-
243-
244-# NOTE:
245-# - Stop after bootstrap step and run `b2 --debug-configuration` to figure
246-# out which paths Boost is using to include Python. Make sure that each of
247-# the listed paths is covered by Python. If not, you must create a symbolic
248-# link from $ISSM_DIR/externalpackages/python to the location of the file
249-# that Boost is expecting. There is no way to get the Boost to compile with
250-# Python otherwise.
251-#
252-
253-## Constants
254-#
255-VER="1_72_0"
256-
257-## Envrionment
258-#
259-#export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with Matlab's Boost
260-#export CXXFLAGS='-std=c++11'
261-
262-# Download source
263-$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz"
264-
265-# Unpack source
266-tar -zxvf boost_${VER}.tar.gz
267-
268-# Cleanup
269-rm -rf install src
270-mkdir install src
271-
272-# Move source into 'src' directory
273-mv boost_${VER}/* src/
274-rm -rf boost_${VER}
275-
276-# Configure
277-cd src
278-./bootstrap.sh \
279- --prefix="${ISSM_DIR}/externalpackages/boost/install" \
280- --with-python=python2.7 \
281- --with-python-root="${ISSM_DIR}/externalpackages/python/install"
282-
283-# Modify project config to enable MPI
284-printf "\n# Enable MPI\nusing mpi ;\n" >> project-config.jam
285-
286-# Compile and install
287-./b2 --toolset=gcc install
288
289Property changes on: ../trunk-jpl/externalpackages/boost/install-1.72-linux.sh
290___________________________________________________________________
291Deleted: svn:executable
292## -1 +0,0 ##
293-*
294\ No newline at end of property
295Index: ../trunk-jpl/externalpackages/boost/install-1.72-mac.sh
296===================================================================
297--- ../trunk-jpl/externalpackages/boost/install-1.72-mac.sh (revision 24823)
298+++ ../trunk-jpl/externalpackages/boost/install-1.72-mac.sh (nonexistent)
299@@ -1,47 +0,0 @@
300-#!/bin/bash
301-#set -eu # Do not `run set -eu` because it causes some targets to fail
302-
303-
304-## Constants
305-#
306-VER="1_72_0"
307-
308-## Environment
309-#
310-export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost"
311-
312-# Download source
313-$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz"
314-
315-# Unpack source
316-tar -zxvf boost_${VER}.tar.gz
317-
318-# Cleanup
319-rm -rf install src
320-mkdir install src
321-
322-# Move source into 'src' directory
323-mv boost_${VER}/* src/
324-rm -rf boost_${VER}
325-
326-# Configure
327-cd src
328-./bootstrap.sh \
329- --prefix=${BOOST_ROOT}/install \
330- --with-python=python2.7
331-
332-# Modify project config to enable MPI
333-printf "\n# Enable MPI\nusing mpi ;\n" >> project-config.jam
334-
335-# Compile and install
336-./b2 install
337-
338-# Copy binary to install directory
339-mkdir ${BOOST_ROOT}/install/bin
340-cp bjam ${BOOST_ROOT}/install/bin
341-
342-# Set install_name for all shared libraries
343-cd ${BOOST_ROOT}/install/lib
344-for name in *.dylib; do
345- install_name_tool -id ${BOOST_ROOT}/install/lib/${name} ${name}
346-done
347
348Property changes on: ../trunk-jpl/externalpackages/boost/install-1.72-mac.sh
349___________________________________________________________________
350Deleted: svn:executable
351## -1 +0,0 ##
352-*
353\ No newline at end of property
354Index: ../trunk-jpl/externalpackages/boost/install-1.72-linux-static.sh
355===================================================================
356--- ../trunk-jpl/externalpackages/boost/install-1.72-linux-static.sh (revision 24823)
357+++ ../trunk-jpl/externalpackages/boost/install-1.72-linux-static.sh (nonexistent)
358@@ -1,43 +0,0 @@
359-#!/bin/bash
360-#set -eu # Do not `run set -eu` because it causes some targets to fail
361-
362-
363-## Constants
364-#
365-VER="1_72_0"
366-
367-## Envrionment
368-#
369-export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost"
370-
371-# Download source
372-$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz"
373-
374-# Unpack source
375-tar -zxvf boost_${VER}.tar.gz
376-
377-# Cleanup
378-rm -rf install src
379-mkdir install src
380-
381-# Move source into 'src' directory
382-mv boost_${VER}/* src/
383-rm -rf boost_${VER}
384-
385-# Configure
386-cd src
387-./bootstrap.sh \
388- --prefix="${BOOST_ROOT}/install" \
389- --with-python=python2.7
390-
391-# Modify project config to enable MPI
392-printf "\n# Enable MPI\nusing mpi ;\n" >> project-config.jam
393-
394-# Compile and install
395-./b2 link=static install
396-
397-# Remove any dynamic libraries that may have been compiled
398-#
399-# TODO: Reconfigure so that dynamic libraries are not compiled at all
400-#
401-rm -f $(find ${BOOST_ROOT}/install/lib -name *.so*)
402
403Property changes on: ../trunk-jpl/externalpackages/boost/install-1.72-linux-static.sh
404___________________________________________________________________
405Deleted: svn:executable
406## -1 +0,0 ##
407-*
408\ No newline at end of property
409Index: ../trunk-jpl/externalpackages/boost/install-1.72-mac-static.sh
410===================================================================
411--- ../trunk-jpl/externalpackages/boost/install-1.72-mac-static.sh (revision 24823)
412+++ ../trunk-jpl/externalpackages/boost/install-1.72-mac-static.sh (nonexistent)
413@@ -1,43 +0,0 @@
414-#!/bin/bash
415-#set -eu # Do not `run set -eu` because it causes some targets to fail
416-
417-
418-## Constants
419-#
420-VER="1_72_0"
421-
422-## Environment
423-#
424-export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost"
425-
426-# Download source
427-$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz"
428-
429-# Unpack source
430-tar -zxvf boost_${VER}.tar.gz
431-
432-# Cleanup
433-rm -rf install src
434-mkdir install src
435-
436-# Move source into 'src' directory
437-mv boost_${VER}/* src/
438-rm -rf boost_${VER}
439-
440-# Configure
441-cd src
442-./bootstrap.sh \
443- --prefix=${BOOST_ROOT}/install \
444- --with-python=python2.7
445-
446-# Modify project config to enable MPI
447-printf "\n# Enable MPI\nusing mpi ;\n" >> project-config.jam
448-
449-# Compile and install
450-./b2 link=static install
451-
452-# Remove any dynamic libraries that may have been compiled
453-#
454-# TODO: Reconfigure so that dynamic libraries are not compiled at all
455-#
456-rm -f $(find ${BOOST_ROOT}/install/lib -name *.dylib)
457
458Property changes on: ../trunk-jpl/externalpackages/boost/install-1.72-mac-static.sh
459___________________________________________________________________
460Deleted: svn:executable
461## -1 +0,0 ##
462-*
463\ No newline at end of property
464Index: ../trunk-jpl/externalpackages/boost/install-1.55-linux-static.sh
465===================================================================
466--- ../trunk-jpl/externalpackages/boost/install-1.55-linux-static.sh (revision 24823)
467+++ ../trunk-jpl/externalpackages/boost/install-1.55-linux-static.sh (revision 24824)
468@@ -9,7 +9,7 @@
469 ## Environment
470 #
471 export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost"
472-export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with Matlab's Boost
473+export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with MATLAB's Boost
474
475 # Download source
476 $ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz"
477Index: ../trunk-jpl/externalpackages/boost/install-1.55-mac-static.sh
478===================================================================
479--- ../trunk-jpl/externalpackages/boost/install-1.55-mac-static.sh (revision 24823)
480+++ ../trunk-jpl/externalpackages/boost/install-1.55-mac-static.sh (revision 24824)
481@@ -38,7 +38,7 @@
482 printf "\n# Enable MPI\nusing mpi ;\n" >> project-config.jam
483
484 # Compile and install
485-./bjam toolset=darwin link=static install
486+./bjam link=static install
487
488 # Copy binary to install directory
489 mkdir ${BOOST_ROOT}/install/bin
490Index: ../trunk-jpl/externalpackages/boost/install-1.55-stallo.sh
491===================================================================
492--- ../trunk-jpl/externalpackages/boost/install-1.55-stallo.sh (revision 24823)
493+++ ../trunk-jpl/externalpackages/boost/install-1.55-stallo.sh (revision 24824)
494@@ -23,7 +23,7 @@
495
496 patch src/boost/mpl/aux_/config/adl.hpp ./configs/1.55/adl.hpp.patch
497
498-#Setting CXXFLAGS to deal with C++11 incompatibility with Matlab's Boost
499+#Setting CXXFLAGS to deal with C++11 incompatibility with MATLAB's Boost
500 #export PATH="/usr/bin":$PATH
501 export CXXFLAGS='-std=c++98'
502 export CC=mpicc
503Index: ../trunk-jpl/externalpackages/boost/install-1.55-linux.sh
504===================================================================
505--- ../trunk-jpl/externalpackages/boost/install-1.55-linux.sh (revision 24823)
506+++ ../trunk-jpl/externalpackages/boost/install-1.55-linux.sh (revision 24824)
507@@ -9,7 +9,7 @@
508 ## Environment
509 #
510 export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost"
511-export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with Matlab's Boost
512+export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with MATLAB's Boost
513
514 # Download source
515 $ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz"
516Index: ../trunk-jpl/externalpackages/boost/install-1.55-mac.sh
517===================================================================
518--- ../trunk-jpl/externalpackages/boost/install-1.55-mac.sh (revision 24823)
519+++ ../trunk-jpl/externalpackages/boost/install-1.55-mac.sh (revision 24824)
520@@ -38,7 +38,7 @@
521 printf "\n# Enable MPI\nusing mpi ;\n" >> project-config.jam
522
523 # Compile and install
524-./bjam toolset=darwin install
525+./bjam install
526
527 # Copy binary to install directory
528 mkdir ${BOOST_ROOT}/install/bin
529Index: ../trunk-jpl/externalpackages/boost/install-1.7-linux-static.sh
530===================================================================
531--- ../trunk-jpl/externalpackages/boost/install-1.7-linux-static.sh (nonexistent)
532+++ ../trunk-jpl/externalpackages/boost/install-1.7-linux-static.sh (revision 24824)
533@@ -0,0 +1,43 @@
534+#!/bin/bash
535+#set -eu # Do not `run set -eu` because it causes some targets to fail
536+
537+
538+## Constants
539+#
540+VER="1_73_0"
541+
542+## Envrionment
543+#
544+export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost"
545+
546+# Download source
547+$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz"
548+
549+# Unpack source
550+tar -zxvf boost_${VER}.tar.gz
551+
552+# Cleanup
553+rm -rf install src
554+mkdir install src
555+
556+# Move source into 'src' directory
557+mv boost_${VER}/* src/
558+rm -rf boost_${VER}
559+
560+# Configure
561+cd src
562+./bootstrap.sh \
563+ --prefix="${BOOST_ROOT}/install" \
564+ --with-python=python2.7
565+
566+# Modify project config to enable MPI
567+printf "\n# Enable MPI\nusing mpi ;\n" >> project-config.jam
568+
569+# Compile and install
570+./b2 link=static install
571+
572+# Remove any dynamic libraries that may have been compiled
573+#
574+# TODO: Reconfigure so that dynamic libraries are not compiled at all
575+#
576+rm -f $(find ${BOOST_ROOT}/install/lib -name *.so*)
577
578Property changes on: ../trunk-jpl/externalpackages/boost/install-1.7-linux-static.sh
579___________________________________________________________________
580Added: svn:executable
581## -0,0 +1 ##
582+*
583\ No newline at end of property
584Index: ../trunk-jpl/externalpackages/boost/install-1.7-mac-static.sh
585===================================================================
586--- ../trunk-jpl/externalpackages/boost/install-1.7-mac-static.sh (nonexistent)
587+++ ../trunk-jpl/externalpackages/boost/install-1.7-mac-static.sh (revision 24824)
588@@ -0,0 +1,43 @@
589+#!/bin/bash
590+#set -eu # Do not `run set -eu` because it causes some targets to fail
591+
592+
593+## Constants
594+#
595+VER="1_73_0"
596+
597+## Environment
598+#
599+export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost"
600+
601+# Download source
602+$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz"
603+
604+# Unpack source
605+tar -zxvf boost_${VER}.tar.gz
606+
607+# Cleanup
608+rm -rf install src
609+mkdir install src
610+
611+# Move source into 'src' directory
612+mv boost_${VER}/* src/
613+rm -rf boost_${VER}
614+
615+# Configure
616+cd src
617+./bootstrap.sh \
618+ --prefix=${BOOST_ROOT}/install \
619+ --with-python=python2.7
620+
621+# Modify project config to enable MPI
622+printf "\n# Enable MPI\nusing mpi ;\n" >> project-config.jam
623+
624+# Compile and install
625+./b2 link=static install
626+
627+# Remove any dynamic libraries that may have been compiled
628+#
629+# TODO: Reconfigure so that dynamic libraries are not compiled at all
630+#
631+rm -f $(find ${BOOST_ROOT}/install/lib -name *.dylib)
632
633Property changes on: ../trunk-jpl/externalpackages/boost/install-1.7-mac-static.sh
634___________________________________________________________________
635Added: svn:executable
636## -0,0 +1 ##
637+*
638\ No newline at end of property
639Index: ../trunk-jpl/externalpackages/boost/install-1.7-linux.sh
640===================================================================
641--- ../trunk-jpl/externalpackages/boost/install-1.7-linux.sh (nonexistent)
642+++ ../trunk-jpl/externalpackages/boost/install-1.7-linux.sh (revision 24824)
643@@ -0,0 +1,37 @@
644+#!/bin/bash
645+#set -eu # Do not `run set -eu` because it causes some targets to fail
646+
647+
648+## Constants
649+#
650+VER="1_73_0"
651+
652+## Envrionment
653+#
654+export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost"
655+
656+# Download source
657+$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz"
658+
659+# Unpack source
660+tar -zxvf boost_${VER}.tar.gz
661+
662+# Cleanup
663+rm -rf install src
664+mkdir install src
665+
666+# Move source into 'src' directory
667+mv boost_${VER}/* src/
668+rm -rf boost_${VER}
669+
670+# Configure
671+cd src
672+./bootstrap.sh \
673+ --prefix="${BOOST_ROOT}/install" \
674+ --with-python=python2.7
675+
676+# Modify project config to enable MPI
677+printf "\n# Enable MPI\nusing mpi ;\n" >> project-config.jam
678+
679+# Compile and install
680+./b2 install
681
682Property changes on: ../trunk-jpl/externalpackages/boost/install-1.7-linux.sh
683___________________________________________________________________
684Added: svn:executable
685## -0,0 +1 ##
686+*
687\ No newline at end of property
688Index: ../trunk-jpl/externalpackages/boost/install-1.7-mac.sh
689===================================================================
690--- ../trunk-jpl/externalpackages/boost/install-1.7-mac.sh (nonexistent)
691+++ ../trunk-jpl/externalpackages/boost/install-1.7-mac.sh (revision 24824)
692@@ -0,0 +1,43 @@
693+#!/bin/bash
694+#set -eu # Do not `run set -eu` because it causes some targets to fail
695+
696+
697+## Constants
698+#
699+VER="1_73_0"
700+
701+## Environment
702+#
703+export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost"
704+
705+# Download source
706+$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/boost_${VER}.tar.gz" "boost_${VER}.tar.gz"
707+
708+# Unpack source
709+tar -zxvf boost_${VER}.tar.gz
710+
711+# Cleanup
712+rm -rf install src
713+mkdir install src
714+
715+# Move source into 'src' directory
716+mv boost_${VER}/* src/
717+rm -rf boost_${VER}
718+
719+# Configure
720+cd src
721+./bootstrap.sh \
722+ --prefix=${BOOST_ROOT}/install \
723+ --with-python=python2.7
724+
725+# Modify project config to enable MPI
726+printf "\n# Enable MPI\nusing mpi ;\n" >> project-config.jam
727+
728+# Compile and install
729+./b2 install
730+
731+# Set install_name for all shared libraries
732+cd ${BOOST_ROOT}/install/lib
733+for name in *.dylib; do
734+ install_name_tool -id ${BOOST_ROOT}/install/lib/${name} ${name}
735+done
736
737Property changes on: ../trunk-jpl/externalpackages/boost/install-1.7-mac.sh
738___________________________________________________________________
739Added: svn:executable
740## -0,0 +1 ##
741+*
742\ No newline at end of property
743Index: ../trunk-jpl/externalpackages/gsl/install.sh
744===================================================================
745--- ../trunk-jpl/externalpackages/gsl/install.sh (nonexistent)
746+++ ../trunk-jpl/externalpackages/gsl/install.sh (revision 24824)
747@@ -0,0 +1,37 @@
748+#!/bin/bash
749+set -eu
750+
751+
752+# Constants
753+#
754+GSL_ROOT=${ISSM_DIR}/externalpackages/gsl
755+VER="1.15"
756+
757+# Cleanup=
758+rm -rf install src
759+mkdir install src
760+
761+# Download source
762+${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gsl-${VER}.tar.gz" "gsl-${VER}.tar.gz"
763+
764+# Unpack source
765+tar -zxvf gsl-${VER}.tar.gz
766+
767+# Move source to 'src' directory
768+mv gsl-${VER}/* src
769+rm -rf gsl-${VER}
770+
771+# Configure
772+cd src
773+./configure \
774+ --prefix="${GSL_ROOT}/install" \
775+ --disable-static
776+
777+# Compile and install
778+if [ $# -eq 0 ]; then
779+ make
780+ make install
781+else
782+ make -j $1
783+ make -j $1 install
784+fi
785
786Property changes on: ../trunk-jpl/externalpackages/gsl/install.sh
787___________________________________________________________________
788Added: svn:executable
789## -0,0 +1 ##
790+*
791\ No newline at end of property
792Index: ../trunk-jpl/jenkins/ross-debian_linux-binaries-with_dakota
793===================================================================
794--- ../trunk-jpl/jenkins/ross-debian_linux-binaries-with_dakota (revision 24823)
795+++ ../trunk-jpl/jenkins/ross-debian_linux-binaries-with_dakota (revision 24824)
796@@ -47,8 +47,8 @@
797 autotools install-debian-linux.sh
798 cmake install.sh
799 petsc install-3.12-linux-static.sh
800- gsl install-linux-static.sh
801- boost install-1.72-linux-static.sh
802+ gsl install-static.sh
803+ boost install-1.55-linux-static.sh
804 dakota install-6.2-linux-static.sh
805 triangle install-linux-static.sh
806 chaco install.sh
807Index: ../trunk-jpl/jenkins/pine_island-mac-dakota
808===================================================================
809--- ../trunk-jpl/jenkins/pine_island-mac-dakota (revision 24823)
810+++ ../trunk-jpl/jenkins/pine_island-mac-dakota (revision 24824)
811@@ -23,8 +23,9 @@
812 --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \
813 --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \
814 --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \
815+ --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \
816+ --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \
817 --with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \
818- --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \
819 --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \
820 --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \
821 --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \
822@@ -46,7 +47,8 @@
823 autotools install.sh
824 cmake install.sh
825 petsc install-3.12-mac.sh
826- boost install-1.72-mac.sh
827+ gsl install.sh
828+ boost install-1.7-mac.sh
829 dakota install-6.2-mac.sh
830 triangle install-mac.sh
831 chaco install.sh
832@@ -78,5 +80,5 @@
833 # - Error is large for test420
834 # - test701 is skipped because it uses full Stokes equations
835 #
836-MATLAB_NROPTIONS="'exclude',[234,243,420,435,444,445,701,702,703,'id',[IdFromString('Dakota')]"
837+MATLAB_NROPTIONS="'exclude',[234,243,420,435,444,445,701,702,703],'id',[IdFromString('Dakota')]"
838 PYTHON_NROPTIONS="--exclude 234 243 418 420 435 444 445 701 702 703 --include_name 'Dakota'"
839Index: ../trunk-jpl/jenkins/ross-debian_linux-dakota
840===================================================================
841--- ../trunk-jpl/jenkins/ross-debian_linux-dakota (revision 24823)
842+++ ../trunk-jpl/jenkins/ross-debian_linux-dakota (revision 24824)
843@@ -39,7 +39,7 @@
844 autotools install-debian-linux.sh
845 cmake install.sh
846 petsc install-3.12-linux.sh
847- gsl install-linux.sh
848+ gsl install.sh
849 boost install-1.55-linux.sh
850 dakota install-6.2-linux.sh
851 triangle install-linux.sh
852Index: ../trunk-jpl/externalpackages/dakota/install-6.2-linux-static.sh
853===================================================================
854--- ../trunk-jpl/externalpackages/dakota/install-6.2-linux-static.sh (revision 24823)
855+++ ../trunk-jpl/externalpackages/dakota/install-6.2-linux-static.sh (revision 24824)
856@@ -11,7 +11,7 @@
857 #
858 export BLAS_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lfblas -L/usr/lib/x86_64-linux-gnu -lgfortran" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
859 export BOOST_ROOT=${ISSM_DIR}/externalpackages/boost/install
860-export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with Matlab's Boost (absolutely necessary for this version)
861+export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with MATLAB's Boost (absolutely necessary for this version)
862 #export CXXFLAGS='-std=c++11'
863 export DAK_BUILD=${DAK_ROOT}/build
864 export DAK_INSTALL=${DAK_ROOT}/install
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