Changeset 26343


Ignore:
Timestamp:
07/06/21 16:13:13 (4 years ago)
Author:
jdquinn
Message:

CHG: Adding jenkins script for Pleiades (can be run with jenkins.sh to automatically install packages, configure, and install); now checking first for VERSION file to get Dakota version; missing ParMETIS includes in Makefile.am; clean up

Location:
issm/trunk-jpl
Files:
1 added
7 edited

Legend:

Unmodified
Added
Removed

  • TabularUnified issm/trunk-jpl/configure.ac

    r26203 r26343  
    2626AM_INIT_AUTOMAKE([foreign])
    2727AC_CONFIG_HEADERS([./config.h])         # Config file must be config.h
    28 AM_SILENT_RULES([yes])                          # Do not show compilation command by default
     28AM_SILENT_RULES([yes])                          # Reduce compilation and linking output (comment this line out or set value to "no" for verbose output)
    2929AM_PROG_AR
    3030

  • TabularUnified issm/trunk-jpl/etc/environment.sh

    r26123 r26343  
    446446        export BOOST_DIR=${BOOST_ROOT}
    447447        export BOOSTROOT=${BOOST_ROOT}
    448         library_path_prepend "${BOOST_ROOT}/lib"
    449         ld_library_path_prepend "${BOOST_ROOT}/lib"
    450         dyld_library_path_prepend "${BOOST_ROOT}/lib"
    451         path_prepend "${BOOST_ROOT}/bin"
     448        library_path_append "${BOOST_ROOT}/lib"
     449        ld_library_path_append "${BOOST_ROOT}/lib"
     450        dyld_library_path_append "${BOOST_ROOT}/lib"
     451        path_append "${BOOST_ROOT}/bin"
    452452fi
    453453

  • TabularUnified issm/trunk-jpl/externalpackages/petsc/install-3.13-pleiades.sh

    r26239 r26343  
    66#
    77VER="3.13.6"
     8
     9PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS
     10PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed
    811
    912# Download source
    … …  
    3033        --prefix="${PREFIX}" \
    3134        --PETSC_DIR="${PETSC_DIR}" \
    32         --with-cc=icc --with-cxx=icpc --with-fc=ifort --with-f77=ifort\
    33         -COPTFLAGS="-g -O3 -axCORE-AVX2,AVX -xSSE4.2" -CXXOPTFLAGS="-g -O3 -axCORE-AVX2,AVX -xSSE4.2" -FOPTFLAGS="-g -O3 -axCORE-AVX2,AVX -xSSE4.2" \
     35        --with-cc=icc \
     36        --with-cpp=/usr/bin/cpp \
     37        --with-cxx=icpc \
     38        --with-fc=ifort \
     39        -COPTFLAGS="-g -O3 -axCORE-AVX2,AVX -xSSE4.2" \
     40        -CXXOPTFLAGS="-g -O3 -axCORE-AVX2,AVX -xSSE4.2" \
     41        -FOPTFLAGS="-g -O3 -axCORE-AVX2,AVX -xSSE4.2" \
    3442        --with-blas-lapack-dir="/nasa/intel/Compiler/2016.2.181/compilers_and_libraries_2016.2.181/linux/mkl/" \
     43        --with-scalapack-include=/nasa/intel/Compiler/2016.2.181/mkl/include \
     44        --with-scalapack-lib="/nasa/intel/Compiler/2016.2.181/mkl/lib/intel64/libmkl_scalapack_lp64.so /nasa/intel/Compiler/2016.2.181/mkl/lib/intel64/libmkl_blacs_sgimpt_lp64.so" \
    3545        --known-mpi-shared-libraries=1 \
     46        --with-gnu-compilers=0 \
     47        --with-vendor-compilers=intel \
    3648        --with-debugging=0 \
    3749        --with-valgrind=0 \
    3850        --with-x=0 \
    3951        --with-ssl=0 \
    40         --with-batch=1  \
     52        --with-batch=1 \
    4153        --with-shared-libraries=1 \
    4254        --download-metis=1 \
    4355        --download-parmetis=1 \
    4456        --download-mumps=1 \
    45         --download-scalapack=1
     57        --download-zlib=1
    4658
    4759# Compile and install

  • TabularUnified issm/trunk-jpl/m4/issm_options.m4

    r26337 r26343  
    612612                dnl     AC_DEFINE_UNQUOTED([_DAKOTA_VERSION_], ${DAKOTA_VERSION}, [Dakota version number])
    613613                dnl
    614                 DAKOTA_VERSION_OUTPUT=`${DAKOTA_ROOT}/bin/dakota -v`
    615                 if test -n "${DAKOTA_VERSION_OUTPUT}"; then
    616                         DAKOTA_VERSION=`echo ${DAKOTA_VERSION_OUTPUT} grep "Dakota version" | sed 's/Dakota version //' | sed 's/ .*//'`
    617                 elif test -f "${DAKOTA_ROOT}/VERSION"; then
     614                if test -f "${DAKOTA_ROOT}/VERSION"; then
    618615                        DAKOTA_VERSION=`cat ${DAKOTA_ROOT}/VERSION | grep 'DAKOTA Version' | sed 's/.*DAKOTA Version //' | sed 's/ .*//'`
    619                 elif test -f "${DAKOTA_ROOT}/../src/src/CommandLineHandler.C"; then
    620                         DAKOTA_VERSION=`cat ${DAKOTA_ROOT}/../src/src/CommandLineHandler.C | grep 'DAKOTA version' | grep 'release' | grep -v // | sed 's/.*DAKOTA version //' | sed 's/ .*//' `
    621                 elif test -f "${DAKOTA_ROOT}/../src/src/CommandLineHandler.cpp"; then
    622                         DAKOTA_VERSION=`cat ${DAKOTA_ROOT}/../src/src/CommandLineHandler.cpp | grep 'DAKOTA version' | grep 'release' | grep -v // | sed 's/.*DAKOTA version //' | sed 's/ .*//' `
    623616                else
    624                         AC_MSG_ERROR([Dakota CommandLineHandler.C or CommandLineHandler.cpp file not found to determine DAKOTA_VERSION!]);
     617                        DAKOTA_VERSION_OUTPUT=`${DAKOTA_ROOT}/bin/dakota -v`
     618                        if test -n "${DAKOTA_VERSION_OUTPUT}"; then
     619                                DAKOTA_VERSION=`echo ${DAKOTA_VERSION_OUTPUT} grep "Dakota version" | sed 's/Dakota version //' | sed 's/ .*//'`
     620                        elif test -f "${DAKOTA_ROOT}/../src/src/CommandLineHandler.C"; then
     621                                DAKOTA_VERSION=`cat ${DAKOTA_ROOT}/../src/src/CommandLineHandler.C | grep 'DAKOTA version' | grep 'release' | grep -v // | sed 's/.*DAKOTA version //' | sed 's/ .*//' `
     622                        elif test -f "${DAKOTA_ROOT}/../src/src/CommandLineHandler.cpp"; then
     623                                DAKOTA_VERSION=`cat ${DAKOTA_ROOT}/../src/src/CommandLineHandler.cpp | grep 'DAKOTA version' | grep 'release' | grep -v // | sed 's/.*DAKOTA version //' | sed 's/ .*//' `
     624                        else
     625                                AC_MSG_ERROR([Dakota CommandLineHandler.C or CommandLineHandler.cpp file not found to determine DAKOTA_VERSION!]);
     626                        fi
    625627                fi
    626628                AC_MSG_RESULT([${DAKOTA_VERSION}])

  • TabularUnified issm/trunk-jpl/src/c/Makefile.am

    r26252 r26343  
    1 AM_CPPFLAGS = @NEOPZINCL@ @DAKOTAINCL@ @SHAPELIBINCL@ @PETSCINCL@ @SLEPCINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @MEDIPACKINCL@ @MPIINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @TRIANGLEINCL@ @SPAIINCL@ @HYPREINCL@ @PROMETHEUSINCL@ @SUPERLUINCL@ @SPOOLESINCL@ @PASTIXINCL@ @MLINCL@ @TAOINCL@ @ADIC2INCL@ @ADOLCINCL@ @CODIPACKINCL@ @GSLINCL@ @BOOSTINCL@ @ANDROID_NDKINCL@ @METEOIOINCL@ @SNOWPACKINCL@ @PROJINCL@ @ESMFINCL@
     1AM_CPPFLAGS = @NEOPZINCL@ @DAKOTAINCL@ @SHAPELIBINCL@ @PETSCINCL@ @SLEPCINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @MEDIPACKINCL@ @MPIINCL@ @PARMETISINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @TRIANGLEINCL@ @SPAIINCL@ @HYPREINCL@ @PROMETHEUSINCL@ @SUPERLUINCL@ @SPOOLESINCL@ @PASTIXINCL@ @MLINCL@ @TAOINCL@ @ADIC2INCL@ @ADOLCINCL@ @CODIPACKINCL@ @GSLINCL@ @BOOSTINCL@ @ANDROID_NDKINCL@ @METEOIOINCL@ @SNOWPACKINCL@ @PROJINCL@ @ESMFINCL@
    22AM_FCFLAGS = @SEMICINCL@
    33
    … …  
    66EXEEXT=$(ISSMEXT)
    77
    8 #Library declaration {{{
     8# Library declaration {{{
    99if !WINDOWS
    1010lib_LTLIBRARIES = libISSMCore.la
    … …  
    2323#}}}
    2424
    25 #Core sources
     25# Core sources
    2626issm_sources =
    2727
    28 #BAMG sources {{{
     28# BAMG sources {{{
    2929if BAMG
    3030issm_sources += \
    … …  
    5757        ./modules/BamgTriangulatex/BamgTriangulatex.cpp
    5858
    59 #do not include AmrBamg with AD
     59# Do not include AmrBamg with AD
    6060if ADOLC
    6161issm_sources += \
    … …  
    7171endif
    7272#}}}
    73 #Core sources{{{
     73# Core sources {{{
    7474issm_sources += \
    7575        ./datastructures/DataSet.cpp \
    … …  
    344344        ./classes/Inputs/ArrayInput.cpp
    345345#}}}
    346 #ADJOINTMPI/MeDiPack sources {{{
     346# ADJOINTMPI/MeDiPack sources {{{
    347347if ADJOINTMPI
    348348issm_sources += ./toolkits/codipack/ampi_interface.cpp
    … …  
    351351issm_sources += ./toolkits/codipack/ampi_interface.cpp
    352352endif
    353 # }}}
    354 #DAKOTA sources {{{
     353#}}}
     354# DAKOTA sources {{{
    355355if DAKOTA
    356356issm_sources += \
    … …  
    369369endif
    370370#}}}
    371 #Petsc sources {{{
     371# PETSc sources {{{
    372372if PETSC
    373373issm_sources += \
    … …  
    391391endif
    392392#}}}
    393 #Mumps sources {{{
     393# MUMPS sources {{{
    394394if MUMPS
    395395issm_sources += ./toolkits/mumps/MumpsSolve.cpp
    396396endif
    397397#}}}
    398 #Gsl sources {{{
     398#GSL sources {{{
    399399if GSL
    400400issm_sources += ./toolkits/gsl/DenseGslSolve.cpp
    401401endif
    402402#}}}
    403 #proj sources {{{
     403# PROJ sources {{{
    404404if PROJ
    405405issm_sources += ./modules/CoordinateSystemTransformx/CoordinateSystemTransformx.cpp
    406406endif
    407407#}}}
    408 #Analyses{{{
     408# Analyses {{{
    409409if ADJOINTBALANCETHICKNESS
    410410issm_sources += ./analyses/AdjointBalancethicknessAnalysis.cpp
    … …  
    521521endif
    522522#}}}
    523 #Love sources (only if have fortran){{{
     523# Love sources (only if have Fortran) {{{
    524524if LOVE
    525525if FORTRAN
    … …  
    536536endif
    537537#}}}
    538 #Esa sources {{{
     538# Esa sources {{{
    539539if ESA
    540540issm_sources += \
    … …  
    543543endif
    544544#}}}
    545 #Oceansources {{{
     545# Ocean sources {{{
    546546if OCEAN
    547547issm_sources += ./modules/OceanExchangeDatax/OceanExchangeDatax.cpp
    548548endif
    549549#}}}
    550 #Sampling sources {{{
     550# Sampling sources {{{
    551551if SAMPLING
    552552issm_sources += \
    … …  
    554554        ./analyses/SamplingAnalysis.cpp
    555555endif
    556 # }}}
    557 #Slc sources {{{
     556#}}}
     557# SLC sources {{{
    558558if SEALEVELCHANGE
    559559issm_sources += \
    … …  
    563563        ./classes/SealevelGeometry.cpp
    564564
    565 #gia ivins physics (only if have fortran)
     565# GIA Ivins physics (only if have Fortran)
    566566if FORTRAN
    567567issm_sources += \
    … …  
    578578endif
    579579#}}}
    580 #Metis sources {{{
     580# METIS sources {{{
    581581if METIS
    582582issm_sources += ./toolkits/metis/patches/METIS_PartMeshNodalPatch.cpp
    583583endif
    584584#}}}
    585 #Esmf sources {{{
     585# Esmf sources {{{
    586586if ESMF
    587587issm_sources += ./main/esmfbinders.cpp
    588588endif
    589589#}}}
    590 #SEMIC sources {{{
     590# SEMIC sources {{{
    591591if SEMIC
    592592if FORTRAN
    … …  
    595595endif
    596596#}}}
    597 #Wrapper sources
    598 #Kml sources {{{
     597# Wrapper sources
     598# Kml sources {{{
    599599kml_sources = \
    600600        ./modules/Exp2Kmlx/Exp2Kmlx.cpp \
    … …  
    632632        ./kml/KMLFileReadUtils.cpp
    633633#}}}
    634 #NEOPZ sources {{{
     634# NEOPZ sources {{{
    635635neopz_sources = ./classes/AmrNeopz.cpp
    636636#}}}
    637 #Modules sources{{{
     637# Modules sources {{{
    638638modules_sources = \
    639639        ./shared/Threads/LaunchThread.cpp \
    … …  
    678678#}}}
    679679
    680 #kriging (WRAPPER and executable)
    681 #Kriging sources {{{
     680# Kriging (wrapper and executable)
     681# Kriging sources {{{
    682682if KRIGING
    683683issm_sources += \
    … …  
    697697endif
    698698#}}}
    699 #Library flags and sources {{{
     699# Library flags and sources {{{
    700700ALL_CXXFLAGS = $(CXXFLAGS) $(CXXOPTFLAGS)
    701701
    … …  
    711711if !WINDOWS
    712712if !STANDALONE_LIBRARIES
    713 libISSMCore_la_LIBADD = $(CHACOLIB) $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(HDF5LIB) $(TAOLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(SUPERLULIB) $(SPOOLESLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(SCOTCHLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(ADJOINTMPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(OSLIBS)
     713libISSMCore_la_LIBADD = $(CHACOLIB) $(DAKOTALIB) $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(HDF5LIB) $(TAOLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(SUPERLULIB) $(SPOOLESLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(SCOTCHLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(ADJOINTMPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(OSLIBS)
    714714if FORTRAN
    715715libISSMCore_la_LIBADD += $(FLIBS) $(FORTRANLIB)
    … …  
    785785
    786786if !MSYS2
    787 #Overload library, to overload any non-standard symbols. {{{
     787# Overload library, to overload any non-standard symbols {{{
    788788libISSMOverload_la_SOURCES = ./shared/String/ApiPrintf.cpp
    789789libISSMOverload_la_CFLAGS  = -D_C_ -fPIC $(COPTFLAGS) $(CFLAGS)
    … …  
    800800endif
    801801#}}}
    802 #Executable {{{
     802# Executable {{{
    803803if ANDROID
    804804if ANDROIDEXE
    … …  
    815815endif
    816816
    817 #Standard libraries
     817# Standard libraries
    818818LDADD = ./libISSMCore.la
    819819
    … …  
    826826endif
    827827
    828 #External packages
     828# External packages
    829829LDADD += $(CHACOLIB) $(DAKOTALIB) $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(NEOPZLIB) $(TAOLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(SUPERLULIB) $(SPOOLESLIB) $(BLACSLIB) $(HDF5LIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(SCOTCHLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(AMPILIB) $(ADJOINTMPILIB) $(ADOLCLIB) $(MPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(PROJLIB) $(ESMFLIB) $(OSLIBS)
    830830

  • TabularUnified issm/trunk-jpl/src/wrappers/javascript/Makefile.am

    r26036 r26343  
    1 AM_CPPFLAGS = @DAKOTAINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @CODIPACKINCL@
     1AM_CPPFLAGS = @DAKOTAINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @PARMETISINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @CODIPACKINCL@
    22AUTOMAKE_OPTIONS = subdir-objects
    33

  • TabularUnified issm/trunk-jpl/src/wrappers/matlab/Makefile.am

    r26140 r26343  
    1 AM_CPPFLAGS = @NEOPZINCL@ @DAKOTAINCL@ @MATLABINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @MEDIPACKINCL@ @CODIPACKINCL@ @PROJINCL@
     1AM_CPPFLAGS = @NEOPZINCL@ @DAKOTAINCL@ @MATLABINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @PARMETISINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @MEDIPACKINCL@ @CODIPACKINCL@ @PROJINCL@
    22AUTOMAKE_OPTIONS = subdir-objects
    33
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