source: issm/oecreview/Archive/18296-19100/ISSM-18339-18340.diff

Last change on this file was 19102, checked in by Mathieu Morlighem, 10 years ago

NEW: added 18296-19100
File size: 11.9 KB
RevLine 
[19102]1Index: ../trunk-jpl/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.pfe.patch
2===================================================================
3--- ../trunk-jpl/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.pfe.patch (revision 0)
4+++ ../trunk-jpl/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.pfe.patch (revision 18340)
5@@ -0,0 +1,6 @@
6+156c153,155
7+< # TODO: Can't this be integrated into the following logic?
8+---
9+> # TODO: Can't this be integrated into the following logic?
10+> set(BLAS_LIBS "-L/nasa/intel/mkl/10.0.011/lib/em64t/ -lmkl -lmkl_lapack -liomp5 -lpthread")
11+> set(LAPACK_LIBS "-L/nasa/intel/mkl/10.0.011/lib/em64t/ -lmkl -lmkl_lapack -liomp5 -lpthread")
12Index: ../trunk-jpl/externalpackages/dakota/install-5.3.1-pleiades.sh
13===================================================================
14--- ../trunk-jpl/externalpackages/dakota/install-5.3.1-pleiades.sh (revision 0)
15+++ ../trunk-jpl/externalpackages/dakota/install-5.3.1-pleiades.sh (revision 18340)
16@@ -0,0 +1,51 @@
17+#!/bin/bash
18+set -eu
19+
20+#Some cleanup
21+rm -rf Dakota
22+rm -rf src
23+rm -rf build
24+rm -rf install
25+mkdir src build install
26+
27+#Download from ISSM server
28+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/dakota-5.3.1-public-src.tar.gz' 'dakota-5.3.1-public-src.tar.gz'
29+
30+#Untar
31+tar -zxvf dakota-5.3.1-public-src.tar.gz
32+
33+#Move Dakota to src directory
34+mv dakota-5.3.1.src/* src
35+rm -rf dakota-5.3.1.src
36+
37+#Set up Dakota cmake variables and config
38+export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src
39+export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build
40+cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake
41+patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/5.3.1/BuildDakotaCustom.cmake.patch
42+patch $DAK_SRC/cmake/DakotaDev.cmake configs/5.3.1/DakotaDev.cmake.patch
43+patch $DAK_SRC/CMakeLists.txt configs/5.3.1/CMakeLists.txt.pfe.patch
44+
45+#Apply patches
46+patch src/src/ParallelLibrary.cpp configs/5.3.1/ParallelLibrary.cpp.patch
47+patch src/src/ParallelLibrary.hpp configs/5.3.1/ParallelLibrary.hpp.patch
48+patch src/src/NonDSampling.cpp configs/5.3.1/NonDSampling.cpp.patch
49+patch src/src/NonDLocalReliability.cpp configs/5.3.1/NonDLocalReliability.cpp.patch
50+patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.3.1/pecos_global_defs.hpp.patch
51+
52+#Configure dakota
53+cd $DAK_BUILD
54+cmake -C $DAK_SRC/cmake/BuildDakotaCustom.cmake -C $DAK_SRC/cmake/DakotaDev.cmake $DAK_SRC
55+cd ..
56+
57+#Compile and install dakota
58+cd $DAK_BUILD
59+if [ $# -eq 0 ];
60+then
61+ make
62+ make install
63+else
64+ make -j $1
65+ make -j $1 install
66+fi
67+cd ..
68
69Property changes on: ../trunk-jpl/externalpackages/dakota/install-5.3.1-pleiades.sh
70___________________________________________________________________
71Added: svn:executable
72## -0,0 +1 ##
73+*
74\ No newline at end of property
75Index: ../trunk-jpl/externalpackages/petsc/install-3.4-pleiades-intel2012.0.032-mpt.2.06rp16
76===================================================================
77--- ../trunk-jpl/externalpackages/petsc/install-3.4-pleiades-intel2012.0.032-mpt.2.06rp16 (revision 18339)
78+++ ../trunk-jpl/externalpackages/petsc/install-3.4-pleiades-intel2012.0.032-mpt.2.06rp16 (revision 18340)
79@@ -1,61 +0,0 @@
80-#!/bin/bash
81-
82-#Some cleanup
83-rm -rf install petsc-3.4.2 src
84-mkdir install src
85-
86-#Download from ISSM server
87-$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.4.2.tar.gz' 'petsc-3.4.2.tar.gz'
88-
89-#Untar and move petsc to install directory
90-tar -zxvf petsc-3.4.2.tar.gz
91-mv petsc-3.4.2/* src/
92-rm -rf petsc-3.4.2
93-
94-#configure
95-cd src
96-./config/configure.py \
97- --prefix="$ISSM_DIR/externalpackages/petsc/install" \
98- --PETSC_ARCH="$ISSM_ARCH" \
99- --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
100- --with-batch=1 \
101- --with-debugging=0 \
102- --with-shared-libraries=1 \
103- --known-mpi-shared-libraries=1 \
104- --with-mpi=1 \
105- --with-mpi-lib="/nasa/sgi/mpt/2.06rp16/lib/libmpi.so" \
106- --with-mpi-include="/nasa/sgi/mpt/2.06rp16/include" \
107- --with-blas-lapack-dir="/nasa/intel/Compiler/2012.0.032/composer_xe_2011_sp1/mkl/lib/intel64" \
108- --download-scalapack=yes \
109- --download-blacs=yes \
110- --download-mumps=yes \
111- --download-metis=yes \
112- --download-parmetis=yes \
113- --download-trilinos=yes \
114- --download-euclid=yes \
115- --download-hypre=yes \
116- --COPTFLAGS="-lmpi -O3" \
117- --FOPTFLAGS="-lmpi -O3" \
118- --CXXOPTFLAGS="-lmpi -O3"
119-
120-#prepare script to reconfigure petsc
121-cat > script.queue << EOF
122-#PBS -S /bin/bash
123-#PBS -l select=1:ncpus=1:model=wes
124-#PBS -l walltime=200
125-#PBS -W group_list=s1010
126-#PBS -m e
127-
128-. /usr/share/modules/init/bash
129-module load comp-intel/2012.0.032
130-module load mpi-sgi/mpt.2.06rp16
131-
132-export PATH="$PATH:."
133-export MPI_GROUP_MAX=64
134-mpiexec -np 1 ./conftest-linux-gnu-ia64-intel.py
135-EOF
136-
137-#print instructions
138-echo "== Now: cd src/ "
139-echo "== qsub -q devel script.queue "
140-echo "== Then run reconfigure script generated by PETSc and follow instructions"
141Index: ../trunk-jpl/externalpackages/petsc/install-3.4-pleiades-intel2012.0.032-mpt.2.06rp16.sh
142===================================================================
143--- ../trunk-jpl/externalpackages/petsc/install-3.4-pleiades-intel2012.0.032-mpt.2.06rp16.sh (revision 0)
144+++ ../trunk-jpl/externalpackages/petsc/install-3.4-pleiades-intel2012.0.032-mpt.2.06rp16.sh (revision 18340)
145@@ -0,0 +1,61 @@
146+#!/bin/bash
147+
148+#Some cleanup
149+rm -rf install petsc-3.4.2 src
150+mkdir install src
151+
152+#Download from ISSM server
153+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.4.2.tar.gz' 'petsc-3.4.2.tar.gz'
154+
155+#Untar and move petsc to install directory
156+tar -zxvf petsc-3.4.2.tar.gz
157+mv petsc-3.4.2/* src/
158+rm -rf petsc-3.4.2
159+
160+#configure
161+cd src
162+./config/configure.py \
163+ --prefix="$ISSM_DIR/externalpackages/petsc/install" \
164+ --PETSC_ARCH="$ISSM_ARCH" \
165+ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
166+ --with-batch=1 \
167+ --with-debugging=0 \
168+ --with-shared-libraries=1 \
169+ --known-mpi-shared-libraries=1 \
170+ --with-mpi=1 \
171+ --with-mpi-lib="/nasa/sgi/mpt/2.06rp16/lib/libmpi.so" \
172+ --with-mpi-include="/nasa/sgi/mpt/2.06rp16/include" \
173+ --with-blas-lapack-dir="/nasa/intel/Compiler/2012.0.032/composer_xe_2011_sp1/mkl/lib/intel64" \
174+ --download-scalapack=yes \
175+ --download-blacs=yes \
176+ --download-mumps=yes \
177+ --download-metis=yes \
178+ --download-parmetis=yes \
179+ --download-trilinos=yes \
180+ --download-euclid=yes \
181+ --download-hypre=yes \
182+ --COPTFLAGS="-lmpi -O3" \
183+ --FOPTFLAGS="-lmpi -O3" \
184+ --CXXOPTFLAGS="-lmpi -O3"
185+
186+#prepare script to reconfigure petsc
187+cat > script.queue << EOF
188+#PBS -S /bin/bash
189+#PBS -l select=1:ncpus=1:model=wes
190+#PBS -l walltime=200
191+#PBS -W group_list=s1010
192+#PBS -m e
193+
194+. /usr/share/modules/init/bash
195+module load comp-intel/2012.0.032
196+module load mpi-sgi/mpt.2.06rp16
197+
198+export PATH="$PATH:."
199+export MPI_GROUP_MAX=64
200+mpiexec -np 1 ./conftest-linux-gnu-ia64-intel.py
201+EOF
202+
203+#print instructions
204+echo "== Now: cd src/ "
205+echo "== qsub -q devel script.queue "
206+echo "== Then run reconfigure script generated by PETSc and follow instructions"
207
208Property changes on: ../trunk-jpl/externalpackages/petsc/install-3.4-pleiades-intel2012.0.032-mpt.2.06rp16.sh
209___________________________________________________________________
210Added: svn:executable
211## -0,0 +1 ##
212+*
213\ No newline at end of property
214Index: ../trunk-jpl/externalpackages/petsc/install-3.5-pleiades-intel2012.0.032-mpt.2.06rp16.sh
215===================================================================
216--- ../trunk-jpl/externalpackages/petsc/install-3.5-pleiades-intel2012.0.032-mpt.2.06rp16.sh (revision 0)
217+++ ../trunk-jpl/externalpackages/petsc/install-3.5-pleiades-intel2012.0.032-mpt.2.06rp16.sh (revision 18340)
218@@ -0,0 +1,62 @@
219+#!/bin/bash
220+set -eu
221+
222+#Some cleanup
223+rm -rf install petsc-3.5.1 src
224+mkdir install src
225+
226+#Download from ISSM server
227+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.5.1.tar.gz' 'petsc-3.5.1.tar.gz'
228+
229+#Untar and move petsc to install directory
230+tar -zxvf petsc-3.5.1.tar.gz
231+mv petsc-3.5.1/* src/
232+rm -rf petsc-3.5.1
233+
234+#configure
235+cd src
236+./config/configure.py \
237+ --prefix="$ISSM_DIR/externalpackages/petsc/install" \
238+ --PETSC_ARCH="$ISSM_ARCH" \
239+ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
240+ --with-batch=1 \
241+ --with-debugging=0 \
242+ --with-shared-libraries=1 \
243+ --known-mpi-shared-libraries=1 \
244+ --with-mpi=1 \
245+ --with-mpi-lib="/nasa/sgi/mpt/2.06rp16/lib/libmpi.so" \
246+ --with-mpi-include="/nasa/sgi/mpt/2.06rp16/include" \
247+ --with-blas-lapack-dir="/nasa/intel/Compiler/2012.0.032/composer_xe_2011_sp1/mkl/lib/intel64" \
248+ --download-scalapack=yes \
249+ --download-mumps=yes \
250+ --download-metis=yes \
251+ --download-parmetis=yes \
252+ --download-trilinos=yes \
253+ --download-euclid=yes \
254+ --download-hypre=yes \
255+ --COPTFLAGS="-lmpi -O3" \
256+ --FOPTFLAGS="-lmpi -O3" \
257+ --CXXOPTFLAGS="-lmpi -O3"
258+
259+#prepare script to reconfigure petsc
260+cat > script.queue << EOF
261+#PBS -S /bin/bash
262+#PBS -l select=1:ncpus=1:model=wes
263+#PBS -l walltime=200
264+#PBS -W group_list=s1010
265+#PBS -m e
266+
267+. /usr/share/modules/init/bash
268+module load comp-intel/2012.0.032
269+module load math/intel_mkl_64_10.0.011
270+module load mpi-sgi/mpt.2.06rp16
271+
272+export PATH="$PATH:."
273+export MPI_GROUP_MAX=64
274+mpiexec -np 1 ./conftest-linux-gnu-ia64-intel.py
275+EOF
276+
277+#print instructions
278+echo "== Now: cd src/ "
279+echo "== qsub -q devel script.queue "
280+echo "== Then run reconfigure script generated by PETSc and follow instructions"
281
282Property changes on: ../trunk-jpl/externalpackages/petsc/install-3.5-pleiades-intel2012.0.032-mpt.2.06rp16.sh
283___________________________________________________________________
284Added: svn:executable
285## -0,0 +1 ##
286+*
287\ No newline at end of property
288Index: ../trunk-jpl/externalpackages/boost/install-1.55-pleiades.sh
289===================================================================
290--- ../trunk-jpl/externalpackages/boost/install-1.55-pleiades.sh (revision 0)
291+++ ../trunk-jpl/externalpackages/boost/install-1.55-pleiades.sh (revision 18340)
292@@ -0,0 +1,47 @@
293+#!/bin/bash
294+set -eu
295+
296+#Note of caution: stop after boostrap phase, and run
297+#bjam --debug-configuration, to figure out which paths boost is using to include
298+#python. make sure everyone of these paths is covered by python. If not, just make
299+#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY
300+#to get the boost library to include python support without doing that.
301+
302+#Some cleanup
303+rm -rf install boost_1_55_0 src
304+mkdir install src
305+
306+#Download from ISSM server
307+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/boost_1_55_0.tar.gz' 'boost_1_55_0.tar.gz'
308+
309+#Untar
310+tar -zxvf boost_1_55_0.tar.gz
311+
312+#Move boost into install directory
313+mv boost_1_55_0/* src
314+rm -rf boost_1_55_0
315+
316+#patch src/boost/atomic/detail/cas128strong.hpp ./configs/1.55/cas128strong.hpp.patch
317+#patch src/boost/atomic/detail/gcc-atomic.hpp ./configs/1.55/gcc-atomic.hpp.patch
318+#patch src/tools/build/v2/user-config.jam ./configs/1.55/user-config.jam.patch
319+#patch src/tools/build/v2/tools/darwin.jam ./configs/1.55/darwin.jam.patch
320+#patch src/tools/build/v2/tools/darwin.py ./configs/1.55/darwin.py.patch
321+
322+#Configure and compile
323+cd src
324+./bootstrap.sh \
325+ --prefix="$ISSM_DIR/externalpackages/boost/install" \
326+ --with-python=python2.7 \
327+ --with-python-root="$ISSM_DIR/externalpackages/python/install" \
328+ --with-toolset=intel-linux
329+
330+#Compile boost
331+# Need gcc with iconv installed in a location that has been added to your path
332+./b2 toolset=intel-linux cxxflags=-static-libstdc++ linkflags=-static-libstdc++ threading=multi install
333+#./bjam install
334+
335+#./b2 toolset=clang cxxflags=-stdlib=libstdc++ linkflags=-stdlib=libstdc++ -j2 variant=release link=static threading=multi instal
336+
337+#put bjam into install also:
338+mkdir ../install/bin
339+cp bjam ../install/bin
340
341Property changes on: ../trunk-jpl/externalpackages/boost/install-1.55-pleiades.sh
342___________________________________________________________________
343Added: svn:executable
344## -0,0 +1 ##
345+*
346\ No newline at end of property
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