libgmt.so.5.1.1: undefined reference to `nc_set_chunk_cache'

kimyoungjin06

Hello!, I'm Ph. D. in NIMS.

I come back with another problem with external packages

ENVIRONMENT

Ubuntu 18.04
ISSM 4.15

PROBLEM

For example about GIA, I additionally install gmsh and gmt.
Among the installinggmt, I got following message

libgmt.so.5.1.1: undefined reference to `nc_set_chunk_cache'

I installed with following script

#### gmsh
cd $ISSM_DIR/externalpackages/gmsh
./install.sh

#### gmt
cd $ISSM_DIR/

#### zlib for netCDF
wget http://www.zlib.net/zlib-1.2.11.tar.gz
tar -xzvf zlib-1.2.11.tar.gz
cd zlib-1.2.11
./configure --prefix=/usr/local/zlib
sudo make
sudo make install

#### netCDF

cd $ISSM_DIR/../
wget https://github.com/Unidata/netcdf-c/archive/v4.7.3.tar.gz
tar -xzvf v4.7.3.tar.gz
cd netcdf-c-4.7.3

ZDIR=/usr/local
./configure --prefix=${ZDIR}
sudo ldconfig
./configure --prefix=${ZDIR} --disable-dap --disable-netcdf-4
make check
sudo make install

# Build and install HDF5
H5DIR=/usr/local
./configure --with-zlib=${ZDIR} --prefix=${H5DIR} --enable-hl --disable-dap --disable-netcdf-4
make check
sudo make install

# Build and install netCDF-4
NCDIR=/usr/local
CPPFLAGS='-I${H5DIR}/include -I${ZDIR}/include' LDFLAGS='-L${H5DIR}/lib -L${ZDIR}/lib' ./configure --prefix=${NCDIR} --disable-dap --disable-netcdf-4
make check
sudo make install  # or sudo make install

justinquinn

I believe that netcdf4 has to be enabled in order for most/all of the nc_* symbols to be defined.

kimyoungjin06

In installing HDF5, I get this configuation.
I Success installing netCDF.
But whether NetCDF-4/HDF-5 is enabled in this build is NO.
So, I check with HDF5 configuration result.
Why HDF5 can not recognize c++?
Is it correct?

SUMMARY OF THE HDF5 CONFIGURATION
	    =================================

General Information:
-------------------
                   HDF5 Version: 1.10.5
                  Configured on: Fri Dec  6 18:07:03 KST 2019
                  Configured by: adminn@adminn-System-Product-Name
                    Host system: x86_64-unknown-linux-gnu
              Uname information: Linux adminn-System-Product-Name 4.15.0-70-generic #79-Ubuntu SMP Tue Nov 12 10:36:11 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
                       Byte sex: little-endian
             Installation point: 

Compiling Options:
------------------
                     Build Mode: production
              Debugging Symbols: no
                        Asserts: no
                      Profiling: no
             Optimization Level: high

Linking Options:
----------------
                      Libraries: static, shared
  Statically Linked Executables: 
                        LDFLAGS: 
                     H5_LDFLAGS: 
                     AM_LDFLAGS:  -L/usr/local/lib
                Extra libraries: -ldl -lm 
                       Archiver: ar
                       AR_FLAGS: cr
                         Ranlib: ranlib

Languages:
----------
                              C: yes
                     C Compiler: /usr/bin/gcc
                       CPPFLAGS: 
                    H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L   -DNDEBUG -UH5_DEBUG_API
                    AM_CPPFLAGS: 
                        C Flags: 
                     H5 C Flags:  -std=c99  -pedantic -Wall -Wextra -Wbad-function-cast -Wc++-compat -Wcast-align -Wcast-qual -Wconversion -Wdeclaration-after-statement -Wdisabled-optimization -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-declarations -Wmissing-include-dirs -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wpacked -Wpointer-arith -Wredundant-decls -Wshadow -Wstrict-prototypes -Wswitch-default -Wswitch-enum -Wundef -Wunused-macros -Wunsafe-loop-optimizations -Wwrite-strings -finline-functions -s -Wno-inline -Wno-aggregate-return -Wno-missing-format-attribute -Wno-missing-noreturn -O
                     AM C Flags: 
               Shared C Library: yes
               Static C Library: yes


                        Fortran: no

                            C++: no

                           Java: no


Features:
---------
                   Parallel HDF5: no
Parallel Filtered Dataset Writes: no
              Large Parallel I/O: no
              High-level library: yes
                    Threadsafety: no
             Default API mapping: v110
  With deprecated public symbols: yes
          I/O filters (external): 
                             MPE: no
                      Direct VFD: no
                         dmalloc: no
  Packages w/ extra debug output: none
                     API tracing: no
            Using memory checker: no
 Memory allocation sanity checks: no
          Function stack tracing: no
       Strict file format checks: no
    Optimization instrumentation: no

justinquinn

kimyoungjin06 I am actually working on a related issue right now. Let me finish sorting it out and then I will post here the configuration that works for me. Thank you for your patience.

justinquinn

kimyoungjin06 Do you have a copy of trunk-jpl/ checked out? If so, svn up, then take a look at the configuration at jenkins/ross-debian_linux-solid_earth (I just committed a new version last night, can confirm it works for Debian Linux 10, and it should work for most flavors of Linux).

Some dependencies you should install first via apt or apt-get,

gfortran # Required for compiling certain external packages and some modules of ISSM core
git # Needed to install, in particular, SEMIC.
libsqlite3-dev # Dependency of PROJ
sqlite3 # Dependency of PROJ

kimyoungjin06

I got this message

$ svn --username anon --password anon checkout http://issm.ess.uci.edu/svn/issm/issm/trunk-jpl
svn: E170013: Unable to connect to a repository at URL 'http://issm.ess.uci.edu/svn/issm/issm/trunk-jpl'
svn: E175013: Access to '/svn/issm/issm/trunk-jpl' forbidden

And gfortran and git is already installed. And I additionally install libsqlite3-dev and sqlite3. But all configuration information is not changed.

justinquinn

kimyoungjin06 I forgot that you are probably accessing trunk with open credentials. I will post an updated configuration for you here later today.

justinquinn

kimyoungjin06 The following set up works for GMT + GMSH on Linux systems. Note that these installation scripts will be available in trunk/ after our next public release.

External Packages

I suggest that you use the following scripts, in order, to install the required external packages to their respective subdirectories under $ISSM_DIR/externalpackages/. As always, run source $ISSM_DIR/etc/environment.sh after each successful installation.

mpich/install.sh (if you are not using a different MPI implementation)

#!/bin/bash
set -eu


## Constants
#
VER="3.3"

# Download source
$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/mpich-${VER}.tar.gz" "mpich-${VER}.tar.gz"

# Unpack source
tar -zxvf  mpich-$VER.tar.gz

# Cleanup
rm -rf install src
mkdir install src

# Move source into 'src' directory
mv mpich-$VER/* src
rm -rf mpich-$VER

# Configure
cd src
./configure \
	--prefix="${ISSM_DIR}/externalpackages/mpich/install" \
	--enable-shared

# Compile and install
if [ $# -eq 0 ]; then
	make
	make install
else
	make -j $1
	make -j $1 install
fi

lapack/install.sh

#!/bin/bash
set -eu


# NOTE: This installation script will build both BLAS and LAPACK libraries
#

## Constants
#
VER="3.8.0"

# Download source
$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/lapack-${VER}.tar.gz" "lapack-${VER}.tar.gz"

# Unpack source
tar -zxvf lapack-$VER.tar.gz

# Cleanup
rm -rf build install src
mkdir build install install/lib src

# Move source to 'src' directory
mv lapack-$VER/* src
rm -rf lapack-$VER

# Configure
#
cd build
cmake \
	-DBUILD_SHARED_LIBS=ON \
	../src

# Compile
make

# Install
cd ..
cp ./build/lib/* ./install/lib

petsc/install.sh

#!/bin/bash
set -eu


## Constants
#
VER="3.7.6"

# Download source
$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"

# Unpack source
tar -zxvf  petsc-$VER.tar.gz

# Cleanup
rm -rf install src
mkdir install src

# Move source to 'src' directory
mv petsc-$VER/* src/
rm -rf petsc-$VER

# Configure
cd src
./config/configure.py \
	--prefix="${ISSM_DIR}/externalpackages/petsc/install" \
	--PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \
	--with-mpi-dir="${ISSM_DIR}/externalpackages/mpich/install" \
	--with-blas-lib="-L${ISSM_DIR}/externalpackages/lapack/install/lib -lblas" \
	--with-lapack-lib="-L${ISSM_DIR}/externalpackages/lapack/install/lib -llapack" \
	--with-debugging=0 \
	--with-valgrind=0 \
	--with-x=0 \
	--with-ssl=0 \
	--with-shared-libraries=1 \
	--download-metis=1 \
	--download-parmetis=1 \
	--download-scalapack=1 \
	--download-mumps=1

# Compile and install
if [ $# -eq 0 ]; then
	make
	make install
else
	make -j $1
	make -j $1 install
fi

boost/install.sh

#!/bin/bash
#set -eu
#unhook set -eu because some target do fail and it is not a big deal

#Note of caution:  stop after boostrap phase, and run 
#bjam --debug-configuration, to figure out which paths boost is using to include 
#python. make sure everyone of these paths is covered by python. If not, just make 
#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY 
#to get the boost library to include python support without doing that. 

#Some cleanup
rm -rf install boost_1_55_0 src
mkdir install src

#Download from ISSM server
$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/boost_1_55_0.tar.gz' 'boost_1_55_0.tar.gz'

#Untar 
tar -zxvf  boost_1_55_0.tar.gz

#Move boost into install directory
mv boost_1_55_0/* src
rm -rf boost_1_55_0

#Setting CXXFLAGS to deal with C++11 incompatibility with Matlab's Boost
export CXXFLAGS='-std=c++98'

#Configure and compile
cd src 
./bootstrap.sh \
	--prefix="$ISSM_DIR/externalpackages/boost/install" \
	--with-python=python2.7 \
	--with-python-root="$ISSM_DIR/externalpackages/python/install" 

#Compile boost
./bjam install

#put bjam into install also: 
mkdir ../install/bin
cp bjam ../install/bin

zlib/install.sh

#!/bin/bash
set -eu


# Constants
#
VER="1.2.11"

# Download source
$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/zlib-${VER}.tar.gz" "zlib-${VER}.tar.gz"

# Unpack source
tar -zxvf zlib-$VER.tar.gz

# Cleanup
rm -rf install src
mkdir install src

# Move source to 'src' directory
mv zlib-$VER/* src/
rm -rf zlib-$VER

# Configure
cd src
./configure \
 	--prefix="${ISSM_DIR}/externalpackages/zlib/install"

# Compile and install
if [ $# -eq 0 ]; then
	make
	make install
else
	make -j $1
	make -j $1 install
fi

hdf5/install.sh

#!/bin/bash
set -eu


## Constants
#
VER="1.10.5"
ZLIB_ROOT="${ISSM_DIR}/externalpackages/zlib/install"

# Download source
$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/hdf5-${VER}.tar.gz" "hdf5-${VER}.tar.gz"

# Untar source
tar -zxvf hdf5-$VER.tar.gz

# Cleanup
rm -rf install src
mkdir install src

# Move source to 'src' directory
mv hdf5-$VER/* src/
rm -rf hdf5-$VER

# Configure
cd src
./configure \
	--prefix="${ISSM_DIR}/externalpackages/hdf5/install" \
	--with-zlib=${ZLIB_ROOT} \
	--enable-hl

# Compile and install
#
if [ $# -eq 0 ]; then
	make
	make install
else
	make -j $1
	make -j $1 install
fi

curl/install.sh

#!/bin/bash
set -eu


## Constants
#
VER="7.67.0"

# Download source
$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/curl-${VER}.tar.gz" "curl-${VER}.tar.gz"

# Unpack source
tar -zxvf curl-$VER.tar.gz

# Cleanup
rm -rf install src
mkdir install src

# Move source to 'src' directory
mv curl-$VER/* src
rm -rf curl-$VER

# Configure
cd src
./configure \
	--prefix="${ISSM_DIR}/externalpackages/curl/install" \
	--disable-manual \
	--disable-verbose

# Compile and install
if [ $# -eq 0 ]; then
	make
	make install
else
	make -j $1
	make -j $1 install
fi

netcdf/install.sh

#!/bin/bash
set -eu


# Dependencies
# - hdf5 (1.8.9 / 1.10.1 or later, for netCDF-4 support)
# - zlib (1.2.5 or later, for netCDF-4 compression)
# - curl (7.18.0 or later, for DAP remote access client support)
#
# For most ISSM installations, only hdf5 will be necessary
#

# Constants
#
VER="4.7.2"
CURL_ROOT="${ISSM_DIR}/externalpackages/curl/install"
HDF5_ROOT="${ISSM_DIR}/externalpackages/hdf5/install"
ZLIB_ROOT="${ISSM_DIR}/externalpackages/zlib/install"

# Environment
#
export CPPFLAGS="-I${HDF5_ROOT}/include -I${ZLIB_ROOT}/include -I${CURL_ROOT}/include"
export LDFLAGS="-L${HDF5_ROOT}/lib -L${ZLIB_ROOT}/lib -L${CURL_ROOT}/lib"

# Download source
$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/netcdf-c-${VER}.tar.gz" "netcdf-c-${VER}.tar.gz"

# Unpack source
tar -zxvf netcdf-c-$VER.tar.gz

# Cleanup
rm -rf install src
mkdir install src

# Move source to 'src' directory
mv netcdf-c-$VER/* src/
rm -rf netcdf-c-$VER

# Configure
cd src
./configure \
 	--prefix="${ISSM_DIR}/externalpackages/netcdf/install" \
 	--disable-doxygen

# Compile and install
if [ $# -eq 0 ]; then
	make
	make install
else
	make -j $1
	make -j $1 install
fi

proj/install.sh

#!/bin/bash
set -eu


# Constants
#
VER="6.2.1"

## Environnment
#

# NOTE: On macOS, SQLite3 should be installed by default, but PROJ currently
#		requires,
#
#			SQLITE3_LIBS="-lsqlite3".
#
#		On Ubuntu Linux, install the SQLite3 binary, libraries and headers
#		with,
#
#			`apt-get install sqlite3 libsqlite3-dev`
#
export SQLITE3_LIBS="-lsqlite3"

# Cleanup
rm -rf install src
mkdir install src

# Download source
$ISSM_DIR/scripts/DownloadExternalPackage.sh "http://issm.jpl.nasa.gov/files/externalpackages/proj-${VER}.tar.gz" "proj-${VER}.tar.gz"

# Unpack source
tar -zxvf proj-$VER.tar.gz

# Move source into 'src' directory
mv proj-$VER/* src
rm -rf proj-$VER

# Configure
cd src
./configure \
	--prefix="${ISSM_DIR}/externalpackages/proj/install"

# Compile and install
if [ $# -eq 0 ]; then
	make
	make install
else
	make -j $1
	make -j $1 install
fi

gdal/install.sh

#!/bin/bash
set -eu


## TODO
#	- May want to supply path to Python instead of, effectively, using result of `which python`
#

## Constants
#
VER="3.0.2"
HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install"
NETCDF_ROOT="${ISSM_DIR}/externalpackages/petsc/install"
PROJ_ROOT="${ISSM_DIR}/externalpackages/proj/install"

# Cleanup
rm -rf install src
mkdir install src

# Download source
$ISSM_DIR/scripts/DownloadExternalPackage.sh "http://issm.jpl.nasa.gov/files/externalpackages/gdal-${VER}.tar.gz" "gdal-${VER}.tar.gz"

# Unpack source
tar -zxvf gdal-$VER.tar.gz

# Move source into 'src' directory
mv gdal-$VER/* src
rm -rf gdal-$VER

# Configure
cd src
./configure \
	--prefix="${ISSM_DIR}/externalpackages/gdal/install" \
	--with-python \
	--with-hdf5="${HDF5_ROOT}" \
	--with-netcdf="${NETCDF_ROOT}" \
	--with-proj="${PROJ_ROOT}"

# Compile and install
if [ $# -eq 0 ]; then
	make
	make install
else
	make -j $1
	make -j $1 install
fi

gshhg/install.sh

#!/bin/bash
set -eu


## Constants
#
VER="2.3.4"

# Cleanup
rm -rf install

# Download source
$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gshhg-gmt-${VER}.tar.gz" "gshhg-gmt-${VER}.tar.gz"

# Unpack source
tar -zxvf gshhg-gmt-${VER}.tar.gz

# Install
mv gshhg-gmt-${VER} install

gmt/configs/5.1/linux/cmake/ConfigUser.cmake

#
# $Id: ConfigUserTemplate.cmake 12904 2014-02-17 20:52:35Z fwobbe $
#
# Copyright (c) 1991-2014 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.
# ============================================================================

# Installation path (usually defaults to /usr/local) [auto]:
set (CMAKE_INSTALL_PREFIX "$ENV{ISSM_DIR}/externalpackages/gmt/install")

# 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) [TRUE]:
#set (GMT_INSTALL_RELOCATABLE FALSE)

# ============================================================================
# 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 path to GSHHG Shoreline Database [auto]:
set (GSHHG_ROOT "$ENV{ISSM_DIR}/externalpackages/gshhg/install")

# 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 "dcw-gmt_path")

# Copy DCW files to $/dcw [FALSE]:
#set (COPY_DCW TRUE)

# Set location of NetCDF (can be root directory, path to header file or path
# to nc-config) [auto]:
set (NETCDF_ROOT "$ENV{ISSM_DIR}/externalpackages/netcdf/install")

# Set location of GDAL (can be root directory, path to header file or path to
# gdal-config) [auto]:
set (GDAL_ROOT "$ENV{ISSM_DIR}/externalpackages/gdal/install")

# Set location of PCRE (can be root directory, path to header file or path to
# pcre-config) [auto]:
#set (PCRE_ROOT "pcre_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 "$ENV{ISSM_DIR}/externalpackages/zlib/install")

##
## 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)

# 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):
#set (BUILD_SHARED_LIBS FALSE)

# Build GMT shared lib with supplemental modules [TRUE]:
#set (BUILD_SUPPLEMENTS 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)
# Number of parallel test jobs with "make check":
#set (N_TEST_JOBS 4)

# 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 gmtextension project).
#set (EXTRA_BUILD_DIRS apidemo)

# 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:
#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_C_FLAGS_RELEASE "-ggdb3 -O2 -Wuninitialized")  # check uninitialized variables
#set (CMAKE_LINK_DEPENDS_DEBUG_MODE TRUE)                  # debug link dependencies

#
# 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)
#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

gmt/install.sh

#!/bin/bash
set -eu


# Constants
#
VER="5.1.1"

# Download source
$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmt-${VER}.tar.gz" "gmt-${VER}.tar.gz"

# Unpack source
tar -zxvf gmt-$VER.tar.gz

# Cleanup
rm -rf install src
mkdir install src

# Move source to 'src' directory
mv gmt-$VER/* src
rm -rf gmt-$VER

# Copy source customizations
cp configs/5.1/linux/cmake/ConfigUser.cmake src/cmake

# Configure
cd src
mkdir build
cd build
cmake ..

# Install
if [ $# -eq 0 ]; then
	make install
else
	make -j $1 install
fi

gmsh/install.sh

#!/bin/bash
set -eu


## Constants
#
VER="3.0.5"

# Cleanup
rm -rf install src
mkdir install src

# Download source
$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmsh-${VER}-source.tgz" "gmsh-${VER}-source.tgz"

# Untar source
tar -xvzf gmsh-$VER-source.tgz

# Move source to src directory
mv gmsh-$VER-source/* src
rm -rf gmsh-$VER-source

# Configure
cd install
cmake ../src \
	-DCMAKE_INSTALL_PREFIX="$ISSM_DIR/externalpackages/gmsh/install" \
	-DENABLE_MPI=1

# Compile and install
if [ $# -eq 0 ]; then
	make
	make install
else
	make -j $1
	make -j $1 install
fi

Configuration

Then, your configuration options would look something like,

--prefix=$ISSM_DIR \
--with-matlab-dir=$MATLAB_PATH \
--with-python-dir=/usr \
--with-python-numpy-dir=/usr/local/lib/python2.7/dist-packages/numpy \
--with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/8 -lgfortran" \
--with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \
--with-mpi-libflags="-L${ISSM_DIR}/externalpackages/mpich/install/lib -lmpi -lmpicxx -lmpifort" \
--with-blas-lapack-dir=$ISSM_DIR/externalpackages/lapack/install \
--with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \
--with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \
--with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \
--with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
--with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
--with-boost-dir=$ISSM_DIR/externalpackages/boost/install

Let me know if you run into any further issues.

kimyoungjin06

when the next public release is updated?
There are not yet zlib and proj.

kimyoungjin06

And, without install zlib, I got following message.

checking size of ssize_t... 8
checking size of void*... 8
checking for library containing deflate... no
configure: error: Can't find or link to the z library. Turn off netCDF-4 and      DAP clients with --disable-netcdf-4 --disable-dap, or see config.log for errors.

kimyoungjin06

I install zlib with original source.
And proj with proj4

And I get following error among installing gdal.

**make[2]: Entering directory '/home/adminn/issm/trunk/externalpackages/gdal/src/frmts/hdf5'
/bin/bash /home/adminn/issm/trunk/externalpackages/gdal/src/libtool --mode=compile --silent --tag=CXX g++ -I/home/adminn/issm/trunk/externalpackages/gdal/src/port -I/home/adminn/issm/trunk/externalpackages/gdal/src/gcore -I/home/adminn/issm/trunk/externalpackages/gdal/src/alg -I/home/adminn/issm/trunk/externalpackages/gdal/src/ogr -I/home/adminn/issm/trunk/externalpackages/gdal/src/ogr/ogrsf_frmts -I/home/adminn/issm/trunk/externalpackages/gdal/src/gnm -I/home/adminn/issm/trunk/externalpackages/gdal/src/apps -DHAVE_AVX_AT_COMPILE_TIME -DHAVE_SSSE3_AT_COMPILE_TIME -DHAVE_SSE_AT_COMPILE_TIME -g -O2  -Wall -Wextra -Winit-self -Wunused-parameter -Wformat -Werror=format-security -Wno-format-nonliteral -Wlogical-op -Wshadow -Werror=vla -Wdate-time -Wnull-dereference -Wduplicated-cond -Wfloat-conversion -Wmissing-declarations -Wnon-virtual-dtor -Woverloaded-virtual -fno-operator-names -Wzero-as-null-pointer-constant -Wsuggest-override -Wimplicit-fallthrough   -DGNM_ENABLED -I/home/adminn/issm/trunk/externalpackages/gdal/src/port -I/home/adminn/issm/trunk/externalpackages/petsc/install  -DGDAL_COMPILATION -c -o ../o/hdf5dataset.lo hdf5dataset.cpp
In file included from hdf5dataset.cpp:34:0:
hdf5_api.h:43:10: fatal error: hdf5.h: No such file or directory
 #include "hdf5.h"
          ^~~~~~~~
compilation terminated.
../../GDALmake.opt:637: recipe for target '../o/hdf5dataset.lo' failed
make[2]: *** [../o/hdf5dataset.lo] Error 1
make[2]: Leaving directory '/home/adminn/issm/trunk/externalpackages/gdal/src/frmts/hdf5'
GNUmakefile:15: recipe for target 'hdf5-install-obj' failed
make[1]: *** [hdf5-install-obj] Error 2
make[1]: Leaving directory '/home/adminn/issm/trunk/externalpackages/gdal/src/frmts'
GNUmakefile:103: recipe for target 'frmts-target' failed
make: *** [frmts-target] Error 2

justinquinn

kimyoungjin06 The next public release will likely be some time in the next 30 days.

Regarding PROJ/zlib, you are absolutely right: for now, you will have to mkdir $ISSM_DIR/proj $ISSM_DIR/zlib.

Regarding HDF5, if you look at $ISSM_DIR/etc/environment.sh, the path to the HDF5 include folder should be appended to CPATH. Did you source $ISSM_DIR/etc/environment.sh before attempting to install GDAL?

kimyoungjin06

I try! but I cannot success compilation with source $ISSM_DIR/etc/environment.sh in every time after install each external package.

$ find ../ -name "hdf5.h"
../hdf5/src/src/hdf5.h
../hdf5/install/include/hdf5.h