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INSTALL
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INSTALL
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How to install JAGURS-D
June 24, 2015
[TOC]
1. Requirements
2. How to install
3. Special instructions for each platform
3.1. The Earth simulator and NEC SX
3.2. K computer
4. Troubleshooting
================================================================================
1. Requirements
JAGURS-D requires the followings.
- Fortran compiler supports Fortran 2003 standards
- C compiler
- GNU make
- NetCDF library (URL: http://www.unidata.ucar.edu/software/netcdf/)
If you need NetCDF4 functions (i.e. single record over 4 GByte),
more libraries (HDF5, cURL, etc...) may be required to link.
- FFT library
- ASL for the Earth simulator and NEC SX
- FFW3 (URL: http://www.fftw.org/) for others
(MKL FFTW3 interface is also okay)
- PROJ.4 library (URL: https://trac.osgeo.org/proj/)
Currently, only proj-4.9.1 is confirmed.
- [optional] MPI library
If MPI parallelization is required. (MPI=ON)
Note that GMT (URL: https://www.soest.hawaii.edu/gmt/) tools are actually
essential in front-end server (not necessary in computational server) to handle
input/output files.
================================================================================
2. How to install
About the following platforms, sample makefiles "Makefile.[platform]" exist.
In other platforms, you need to make makefile for your platform based on
existing samples.
SC_ICE: SGI Altix ICE X system
Intel Fortran/C++ compilers, SGI MPT and MKL FFTW3 interface are
utilized.
SX: Cross environment for the Earth simulator and NEC SX
K: Cross environment for K computer
Typically, you need to modify install path of each libraries.
NETCDF: Install path of NetCDF library
FFTW3_INCLUDE_DIR: FFTW3 include file path
FFTW3_LIB: Arguments to link FFTW3 library
(Typically, "-L${FFTW3_INSTALL_DIR}/lib -lfftw3")
PROJ4_DIR: Install path of PROJ.4 library
After necessary modifications are applied, type "make -f Makefile.[platform]"
in JAGURS-D_V???? directory.
================================================================================
3. Special instructions for each platform
--------------------------------------------------------------------------------
3.1. The Earth simulator and NEC SX
(1) How to install PROJ.4 library
Invoke the following commands on cross environment.
Here, PROJ.4 install path is ${PROJ4_DIR}.
$ tar -zxvf proj-4.9.1.tar.gz
$ cd proj-4.9.1
$ ./configure CC=sxcc CFLAGS=-size_t64 AR=sxar RANLIB=touch \
--host=x86_64-unknown-linux-gnu --target=sx8r-nec-superux \
--without-mutex --disable-shared --prefix=${PROJ4_DIR}
$ make
$ make install
--------------------------------------------------------------------------------
3.2. K computer
(1) How to install PROJ.4 library
Installation on own environment (computational node) with interactive mode is
highly recommended.
For example, invoke the following commands on cross/own environment.
Here, PROJ.4 install path is ${PROJ4_DIR}.
[fornt end]$ tar -zxvf proj-4.9.1.tar.gz
[fornt end]$ cd proj-4.9.1
[fornt end]$ pjsub --interact --rsc-list "node=1" --rsc-list "elapse=1:0:0" \
--sparam "wait-time=3600"
[computational node]$ . /work/system/Env_base
[computational node]$ ./configure --build=sparc64 --prefix=${PROJ4_DIR}
[computational node]$ make
[computational node]$ make install
[computational node]$ exit
================================================================================
4. Troubleshooting
--------------------------------------------------------------------------------
4.1. Undefined references to "nf_*_" (i.e. nf_create_, nf_def_dim_, etc...)
occurs and it fails in link.
Add "-lnetcdff" before "-lnetcdf" to LIBS variable in Makefile.
If you are trying to link NetCDF4, not only libnetcdf.so but also libnetcdff.so
(Fortran lapper library) have to be liked.
--------------------------------------------------------------------------------
4.2. PROJ.4 library is not found and it fails in execution with the message
like "./jagurs: error while loading shared libraries: libproj.so.9:
cannot open shared object file: No such file or directory".
Add the path to "${PROJ4_DIR}/lib" to the environment variable LD_LIBRARY_PATH.
In sh/bash, add the following line into your execution script.
export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${PROJ4_DIR}/lib"
================================================================================