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1.Load all necessary system modules on mahuika
ssh mahuika
 
melody.zhu@mahuika02 ~> vim machine_env.sh
# content of machine_ev.sh
# all needed system modules for building GMT. Maybe overkill but no harm.
module load GCC/7.1.0
module load FFTW/3.3.5-gimkl-2017a
module load GEOS/3.6.1-gimkl-2017a
module load GDAL/2.2.2-gimkl-2017a-GEOS-3.5.1
module load PROJ/4.9.3-gimkl-2017a
module load HDF/4.2.13-gimkl-2017a
module load HDF5/1.8.18-gimkl-2017a
module load netcdf/gcc/64/4.4.0
module load libpng/1.6.28-gimkl-2017a
module load libreadline/6.3-gimkl-2017a
module load libpmi
module load imkl/2017.6.256-gimpi-2017a
module load lapack/gcc/64/3.7.0

 
# load all modules 
melody.zhu@mahuika02 ~> source machine_env.sh

melody.zhu@mahuika02 ~> module list
Currently Loaded Modules:
  1) craype-broadwell            6) FFTW/3.3.5-gimkl-2017a           11) KEALib/1.4.6-gimkl-2017a      16) GEOS/3.5.1-gimkl-2017a                       21) XZ/5.2.3-gimkl-2017a               26) HDF/4.2.13-gimkl-2017a
  2) craype-network-infiniband   7) expat/2.2.0-gimkl-2017a          12) LibTIFF/4.0.7-gimkl-2017a     17) ncurses/6.0-gimkl-2017a                      22) libxml2/2.9.4-gimkl-2017a          27) HDF5/1.8.18-gimkl-2017a
  3) slurm/17.11.7               8) libjpeg-turbo/1.5.1-gimkl-2017a  13) PROJ/4.9.3-gimkl-2017a        18) libreadline/6.3-gimkl-2017a                  23) PCRE/8.40-gimkl-2017a              28) netcdf/gcc/64/4.4.0
  4) gimpi/2017a                 9) OpenJPEG/2.3.0-gimkl-2017a       14) libgeotiff/1.4.2-gimkl-2017a  19) SQLite/3.16.2-gimkl-2017a                    24) PostgreSQL/9.6.2-gimkl-2017a       29) lapack/gcc/64/3.7.0
  5) gimkl/2017a                10) Szip/2.1-gimkl-2017a             15) FreeXL/1.0.2-gimkl-2017a      20) libspatialite/4.3.0a-gimkl-2017a-GEOS-3.5.1  25) GDAL/2.2.2-gimkl-2017a-GEOS-3.5.1


 

 

2. Build GMT  http://gmt.soest.hawaii.edu/projects/gmt/wiki/BuildingGMT#Building-GMT-from-source

  • Get the latest GMT source code from Github

    melody.zhu@mahuika02 ~> git clone https://github.com/GenericMappingTools/gmt.git
  • Get GSHHG (coastlines, rivers, and political boundaries; filename: gshhg-gmt-x.x.x.tar.gz) from the download page or ftp://ftp.soest.hawaii.edu/gshhg and extract the files.
  • Get DCW (country polygons; filename: dcw-gmt-x.x.x.tar.gz) from the download page or ftp://ftp.soest.hawaii.edu/dcw and extract the files.

  • In the source tree copycmake/ConfigUserTemplate.cmake to cmake/ConfigUser.cmake and edit the file according to your demands. 

  • Example:

     melody.zhu@mahuika02 ~/gmt> vim cmake/ConfigUser.cmake 
    #
    #
    # Copyright (c) 1991-2018 by P. Wessel, W. H. F. Smith, R. Scharroo, J. Luis and F. Wobbe
    # See LICENSE.TXT file for copying and redistribution conditions.
    #
    # This program is free software; you can redistribute it and/or modify it
    # under the terms of the GNU Lesser General Public License as published by the
    # Free Software Foundation; version 3 or any later version.
    #
    # This program is distributed in the hope that it will be useful, but WITHOUT
    # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
    # FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License
    # for more details.
    #
    # Contact info: gmt.soest.hawaii.edu
    # ----------------------------------------------------------------------------
    # Use this file to override variables in 'ConfigDefault.cmake' on a per-user
    # basis.  First copy 'ConfigUserTemplate.cmake' to 'ConfigUser.cmake', then
    # edit 'ConfigUser.cmake'.  'ConfigUser.cmake' is not version controlled
    # (currently listed in svn:ignore property)
    #
    # Note: CMake considers an empty string, "FALSE", "OFF", "NO", or any string
    # ending in "-NOTFOUND" to be false (this happens to be case-insensitive, so
    # "False", "off", "no", and "something-NotFound" are all false).  Other values
    # are true.  Thus it does not matter whether you use TRUE and FALSE, ON and
    # OFF, or YES and NO for your booleans.
    ##
    ## Section 1: Installation paths
    ##
    # ============================================================================
    # Basic setup begins here.  All settings are optional.  In most cases, setting
    # CMAKE_INSTALL_PREFIX should be all you need to do in order to build GMT with
    # reasonable defaults enabled.  Note: If you need to specify directory names
    # with spaces (e.g., on Windows) then you must put them in quotes.
    # ============================================================================
    # Installation path (usually defaults to /usr/local) [auto]:
    #set (CMAKE_INSTALL_PREFIX "/home/melody.zhu/bin/gmt")
    # Set install name suffix used for directories and gmt executables
    # [undefined]:
    #set (GMT_INSTALL_NAME_SUFFIX "suffix")
    # Install into traditional directory structure. Disable to install a
    # distribution type directory structure (doc and share separated) [on]:
    #set (GMT_INSTALL_TRADITIONAL_FOLDERNAMES OFF)
    # Install convenience links for GMT modules. Disable to install only the main
    # gmt program and access modules as "gmt modulename options" [TRUE]:
    #set (GMT_INSTALL_MODULE_LINKS FALSE)
    # Make executables relocatable on supported platforms (relative RPATH) [FALSE]:
    #set (GMT_INSTALL_RELOCATABLE TRUE)
    # Exclude optional GDAL, PCRE, PCRE2, FFTW3, LAPACK, BLAS, ZLIB dependencies even if you have them installed [FALSE]
    #set (GMT_EXCLUDE_GDAL TRUE)
    #set (GMT_EXCLUDE_PCRE TRUE)
    #set (GMT_EXCLUDE_PCRE2 TRUE)
    #set (GMT_EXCLUDE_FFTW3 TRUE)
    #set (GMT_EXCLUDE_LAPACK TRUE)
    #set (GMT_EXCLUDE_BLAS TRUE)
    #set (GMT_EXCLUDE_ZLIB TRUE)
    # ============================================================================
    # Advanced configuration begins here.  Usually it is not necessary to edit any
    # settings below.  You should know what you are doing if you do though.  Note:
    # installation paths are relative to ${CMAKE_INSTALL_PREFIX} unless absolute
    # path is given.
    # ============================================================================
    # Set binary installation path [bin]:
    #set (GMT_BINDIR "bin")
    # Set library installation path [lib or lib64]:
    #set (GMT_LIBDIR "lib")
    # Set include installation path [include/gmt${GMT_INSTALL_NAME_SUFFIX}]:
    #set (GMT_INCLUDEDIR "include/gmt")
    # Set share installation path [share or share/gmt${GMT_INSTALL_NAME_SUFFIX}]:
    #set (GMT_DATADIR "share/gmt")
    # Set doc installation path [share/doc or
    # share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}]:
    #set (GMT_DOCDIR "share/doc/gmt")
    # Set manpage installation path [share/man or
    # share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}/man]:
    #set (GMT_MANDIR "share/doc/gmt/man")
    # Install documentation files from this external location instead of creating
    # new PDF and HTML documents from scratch [${GMT_SOURCE_DIR}/doc_release]:
    #set (GMT_INSTALL_EXTERNAL_DOC OFF)
    # Install manual pages from this external location instead of creating the
    # manpages from scratch [${GMT_SOURCE_DIR}/man_release]:
    #set (GMT_INSTALL_EXTERNAL_MAN OFF)
    ##
    ## Section 2: Build dependencies (should only be needed if CMake cannot
    ## automatically detect the rights version or path.)
    ##
    # Set URL to GMT Data server [auto]:
    #set (GMT_DATA_URL "data_server_url")
    # Set path to GSHHG Shoreline Database [auto]:
    set (GSHHG_ROOT "/home/melody.zhu/gshhg-gmt-2.3.7")
    # Copy GSHHG files to $/coast [FALSE]:
    set (COPY_GSHHG TRUE)
    # Set path to DCW Digital Chart of the World for GMT [auto]:
    set (DCW_ROOT "/home/melody.zhu/dcw-gmt-1.1.4")
    # Copy DCW files to $/dcw [FALSE]:
    set (COPY_DCW TRUE)
    # FOR WINDOWS ONLY
    # Set path to location where the gmtmex is located.
    #set (GMTMEX_PATH "C:/progs_cygw/GMTdev/gmtmex/${GMTver}")
    # Set location of NetCDF (can be root directory, path to header file or path
    # to nc-config) [auto]:
    set (NETCDF_ROOT "/cm/shared/apps/netcdf/gcc/64/4.4.0/lib/pkgconfig")
    # Set location of GDAL (can be root directory, path to header file or path to
    # gdal-config) [auto]:
    #set (GDAL_ROOT "gdal_install_prefix")
    # Set location of PCRE (can be root directory, path to header file or path to
    # pcre-config) [auto]:
    #set (PCRE_ROOT "pcre_install_prefix")
    # Alternatively, set location of PCRE2 (can be root directory, path to header file or path to
    # pcre2-config) [auto]:
    #set (PCRE2_ROOT "pcre2_install_prefix")
    # Set location of single precision FFTW (can be root directory or path to
    # header file) [auto]:
    #set (FFTW3_ROOT "fftw_install_prefix")
    # Set location of ZLIB (can be root directory or path to header file) [auto]:
    set (ZLIB_ROOT "/home/melody.zhu/bin/zlib/lib/libz.so")
    # Set location of CURL (can be root directory or path to header file) [auto]:
    set (CURL_DIR "/home/melody.zhu/bin/curl/lib/libcurl.so")
    # Set location of GLIB component gthread [auto].  This is an optional (and
    # experimental) option which you need to enable:
    #set (GMT_USE_THREADS TRUE)
    # If pkg-config is not installed (e.g. on Windows) you need to specify these:
    #set (GLIB_INCLUDE_DIR c:/path/to/glib-dev/include/glib-2.0)
    #set (GLIB_LIBRARIES c:/path/to/glib-dev/lib/glib-2.0.lib)
    # Set location of pthreads-win32 (only Windows); needs GMT_USE_THREADS:
    #set (PTHREADS_WIN32_ROOT c:/prefix/of/pthreads-win32)
    #set (GMT_USE_THREADS TRUE)
    # Set LAPACK location. Use this when want to link with LAPACK and it's not found automatically
    #set (LAPACK_LIBRARY "V:/lapack-3.5.0/build/lib/liblapack.lib")
    #set (BLAS_LIBRARY "V:/lapack-3.5.0/build/lib/libblas.lib")
    ##
    ## Section 3: GMT features
    ##
    # Enforce GPL or LGPL conformity. Use this to disable routines that cannot be
    # redistributed under the terms of the GPL or LGPL such as Shewchuk's
    # triangulation (valid values are GPL, LGPL and off) [off]:
    #set (LICENSE_RESTRICTED GPL)
    # Allow building of OpenMP if compiler supports it
    # set (GMT_ENABLE_OPENMP TRUE)
    # Configure default units (possible values are SI and US) [SI]:
    #set (UNITS "US")
    # Enable building of shared libraries [TRUE] (disable to use static libraries;
    # not recommended; on non-x86 architectures uncomment the next option as well):
    #set (BUILD_SHARED_LIBS FALSE)
    # Create position independent code on all targets [auto] (needed for static
    # build on non-x86:
    #set (CMAKE_POSITION_INDEPENDENT_CODE TRUE)
    # Build GMT shared lib with supplemental modules [TRUE]:
    #set (BUILD_SUPPLEMENTS FALSE)
    # Build/Install GMT Developer include files [TRUE]:
    # This installs the extra include files and configured files needed by 3rd-party
    # developers.  Until we build a separate gmt-devel we include them in the main
    # Distribution.
    #set (BUILD_DEVELOPER FALSE)
    ##
    ## Section 4: Advanced tweaking
    ##
    #
    # Testing and development
    #
    # Enable running examples/tests with "ctest" or "make check" (out-of-source).
    # Need to set either DO_EXAMPLES, DO_TESTS or both and uncomment the following
    # line.
    #enable_testing()
    #set (DO_EXAMPLES TRUE)
    #set (DO_TESTS TRUE)
    #set (DO_ANIMATIONS TRUE)
    # Auto-convert classic scripts to modern during testing:
    #set (MODERNIZE_TESTS TRUE)
    # Number of parallel test jobs with "make check":
    #set (N_TEST_JOBS 4)
    # Location of optional third-party files used by test suite available from
    # svn://gmtserver.soest.hawaii.edu/gmt-data [${GMT_SOURCE_DIR}/test/data]
    #set (GMT_TEST_DATA "test_data_path")
    # Enable this option to run GMT programs from within ${GMT_BINARY_DIR} without
    # installing or setting GMT_SHAREDIR and GMT_USERDIR first. This is required
    # for testing [OFF]:
    #set (SUPPORT_EXEC_IN_BINARY_DIR ON)
    # List extra sub-dirs of 'src' with a CMakeList.txt to build non-module codes
    # that link against the full gmt libs (not just the API; for building codes
    # that only need the GMT API, see the gmt-custom project).
    #set (EXTRA_BUILD_DIRS apidemo)
    #set (DO_API_TESTS ON)
    # Directory in which to install the release sources per default
    # [${GMT_BINARY_DIR}/gmt-${GMT_PACKAGE_VERSION}]:
    #set (GMT_RELEASE_PREFIX "release-src-prefix")
    # If set to false, image conversion from PS images to PNG and PDF does
    # not depend on the gmt binary target. Note: "make gmt" is then required
    # before docs_depends [TRUE].
    #set (GMT_DOCS_DEPEND_ON_GMT FALSE)
    #
    # Debugging
    #
    # Set build type can be: empty, Debug, Release, RelWithDebInfo or MinSizeRel
    # [Release]:
    #set (CMAKE_BUILD_TYPE Debug)
    # Extra debugging for developers:
    #if ( CMAKE_GENERATOR STREQUAL "Xcode" )
    ##	So Xcode can find the supplemental plug-ins during debug sessions
    #	add_definitions(-DXCODER)
    #   add_definitions(-DDEBUG_MODERN)			# To set PPID == 0 during Xcode test
    #	message("Add Xcode definition for GMT")
    #endif()
    #add_definitions(-DDEBUG)
    #add_definitions(-DMEMDEBUG) # Turn on memory tracking see gmt_support.c for extra info
    #set (CMAKE_C_FLAGS "-Wall -Wdeclaration-after-statement") # recommended even for release build
    #set (CMAKE_C_FLAGS "-Wextra ${CMAKE_C_FLAGS}")            # extra warnings
    #set (CMAKE_C_FLAGS_DEBUG -ggdb3)                          # gdb debugging symbols
    #set (CMAKE_LINK_DEPENDS_DEBUG_MODE TRUE)                  # debug link dependencies
    if (HAVE_OPENMP)
    	set (CMAKE_C_FLAGS_RELEASE "-ggdb3 -O2 -Wuninitialized -flax-vector-conversions")  # check uninitialized variables
    else (HAVE_OPENMP)
    	set (CMAKE_C_FLAGS_RELEASE "-ggdb3 -O2 -Wuninitialized")  # check uninitialized variables
    endif (HAVE_OPENMP)
    #
    # System specific tweaks
    #
    # This is for GCC on Solaris to avoid "relocations remain against allocatable
    # but non-writable sections" problems:
    #set (USER_GMTLIB_LINK_FLAGS -mimpure-text)
    # This may be needed to enable strdup and extended math functions with GCC and
    # Suncc on Solaris:
    #set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -D__EXTENSIONS__")
    # Do not warn when building with Windows SDK or Visual Studio Express:
    #set (CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS_NO_WARNINGS ON)
    # Manually select runtime library when compiling with Windows SDK or Visual
    # Studio Express:
    #set (CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS c:/Windows/System32/msvcr100.dll)
    # If your NetCDF library is static (not recommended, applies to Windows only)
    #set (NETCDF_STATIC TRUE)
    # If want to rename the DLLs to something else than the default (e.g. to
    # append the bitness - Windows only)
    # WARNING: if using this option it is mandatory that the suffix starts with an underscore.
    #if (WIN32)
    # set (BITAGE 32)
    # # Detect if we are building a 32 or 64 bits version
    # if (CMAKE_SIZEOF_VOID_P EQUAL 8)
    #   set (BITAGE 64)
    # endif ()
    # set (GMT_DLL_RENAME gmt_w${BITAGE})
    # set (PSL_DLL_RENAME psl_w${BITAGE})
    #endif(WIN32)
    # On Windows Visual C 2012 needs _ALLOW_KEYWORD_MACROS to build
    #if(MSVC11)
    #  add_definitions(/D_ALLOW_KEYWORD_MACROS)
    #endif(MSVC11)
    # vim: textwidth=78 noexpandtab tabstop=2 softtabstop=2 shiftwidth=2
    
    

       

Building GMT from source

 

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