GSI Fundamentals (1): Setup and Compilation
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1 2012 GSI Summer Tutorial, Boulder, CO GSI Fundamentals (1): Setup and Compilation Donald Stark Na-onal Center for Atmospheric Research (NCAR) The Developmental Testbed Center (DTC) Wednesday 21 August, 2012
2 Outline GSI fundamentals (1): Setup and Compilation Where to get the code Directory structure Unpacking, setup, & build Por-ng build to new plaoorms GSI fundamentals (2): Run and Namelist GSI fundamentals (3): Diagnos-cs GSI fundamentals (4): Applica-ons This talk is tailored based on Chapter 2 of the GSI User s Guide for Community Release V3.1 2
3 Downloading the Source Code All of the GSI source code can be obtained from: hup:// GSI/users/downloads/index.php 3
4 Downloading Source code 4
5 Unpack Downloads Two tar files comgsi_v3.1.tar.gz CRTM_Coefficients tar.gz Unpack source code & CRTM coefficients gunzip *.tar.gz tar xvf comgsi_v3.1.tar tar xvf CRTM_Coefficients tar 5
6 Supported Platforms Platform IBM Linux Mac Darwin F compiler xlf Intel (ifort) Intel (ifort) PGI (pgf90) PGI (pgf90) PGI (pgf90) C compiler xlc Intel (icc) Gnu (gcc) PGI (pgcc) Gnu (gcc) PGI (pgcc) 6
7 System Requirements FORTRAN 90+ compiler C compiler Perl Gnu Make NetCDF V3.6+, & V4+ Linear algebra library (ESSL or LAPACK/BLAS) MPI V1.2+ & OpenMP 7
8 Tour of the Directory Structure Inside the top level of the comgsi_v3.1/ directory are four scripts and five directories. arch/ clean compile configure fix/ makefile run/ src/ u-l/ 8
9 Build Infrastructure Uses DTC Build system /arch directory contains rules & scripts for build. /arch/config.pl perl script for parsing system info & combining together configure.gsi file. /arch/preamble: uniform requirements for the code, such as word size, etc. /arch/configure.defaults default plaoorm seings /arch/postamble: standard make rules & dependencies./clean script to clean the build../configure script to create configura-on file configure.gsi; contains infoma-on on compiler, MPI, & paths../compile script to compile executable../makefile top level makefile for build. 9
10 The rest fix/ directory containing fixed files Background error covariance and observa-on errors CRTM coefficients moved to a separate directory due to size Observa-on data control files BUFR tables for BUFR/PrepBUFR files run/ run_gsi.ksh sample GSI run script run_gsi_angupdate.ksh sample satellite angle bias correc-on run script gsi.exe executable aker compiling src/ source directory libs/ supplemental library source code main/ main GSI source code u:l/ addi-onal GSI community tools 10
11 Supplemental Libraries (libs/) bacio/ NCEP BACIO library bufr/ NCEP BUFR library crtm_jcsda_2.0/ JCSDA Community Radia-ve Transfer Model gfsio/ UnformaUed Fortran record for GFS I/O gsdcloud/ GSD Cloud Analysis misc/ Misc addi-onal libraries nemsio/ Support for NEMS I/O sfcio/ NCEP GFS surface file I/O module sigio/ NCEP GFS atmospheric file I/O module sp/ NCEP spectral- grid transforms (global applica-on only) w3/ NCEP W3 library (date/-me manipula-on, GRIB) 11
12 12 Building GSI
13 Building GSI Build sequence./clean a Set library paths setenv WRF_DIR Location_of_WRF_directory setenv LAPACK (typically only needed for Linux w/intel)../configure Customize file configure.gsi if necessary./compile >& compile.log & Successful compila-on comgsi_v3.1/run/gsi.exe No Error informaion in compile.log 13
14 Clean Compilation To remove all object files and executables, type: clean To remove all built files, including the configure file, type: clean a A clean all needed if: Compila-on failed Want to change configura-on file 14
15 Diagnosing Build Issues How the build system works What to do when the build fails 15
16 GSI Build System Configuration stage./configure./configure.gsi./configure Generate local compile options Saves values in configure.gsi Compiling stage./makefile./src/ makefile src/main/ makefile_dtc src/libs/ makefile src/libs/lib1/ makefile src/libs/lib2/ makefile ü Run ü Run./compile Runs top level./makefile Which in turn runs./src/makefile, Which runs./src/main/makefile 16
17 How the build works Running./configure creates file configure.gsi by: Running the Perl script /arch/config.pl Script Config.pl queries the system & selects the appropriate entry from /arch/ configure.defaults Results are saved to configure.gsi. 17
18 Fixing Build Issues Most build problems are due to non- standard ins-lla-on of one of the following: compiler, MPI, or support libraries. Edit paths in the file configure.gsi to correctly reflect your system. When build succeeds, modify file arch/ configure.defaults to include new seings. Report issues to so they can be addressed in next release. 18
19 Fixing Build Issues (continued) The name or loca-on of your LAPACK library may differ from what the build assumes. See MYLIBsys You may also want to use different Fortran compiler flags: See FFLAGS_* You may also want to use different C compiler flags: See CFLAGS You may have a slightly different name for your compilers: See SFC, SF90, and SCC to specify your Fortran, Fortran90+, and C compilers. See the User s Guide for details 19
20 configure.gsi #### Architecture specific settings #### # Settings for Linux x86_64, PGI compilers (pgf90 & gcc) (dmpar,optimize)# LDFLAGS = -Wl,-noinhibit-exec COREDIR = /d1/stark/gsi/src/pgi/release_v3.1 INC_DIR = $(COREDIR)/include BYTE_ORDER = LITTLE_ENDIAN SFC = pgf90 SF90 = pgf90 -Mfree SCC = gcc INC_FLAGS = -module $(INC_DIR) -I $(INC_DIR) -I /usr/local/netcdf3-pgi/include FFLAGS_i4r4 = -i4 -r4 FFLAGS_i4r8 = -i4 -r8 FFLAGS_i8r8 = -i8 -r8 FFLAGS_DEFAULT = -Kieee -pc 64 -Ktrap=fp FFLAGS_DEBUG FFLAGS_OPT FFLAGS = -O0 -q -C = -O3 = -fast $(FFLAGS_DEFAULT) -DLANGUAGE_FORTRAN -DsysLinux $(INC_FLAGS) $(LDFLAGS) -DLINUX -DPGI # Library build flags FFLAGS_BACIO = -O3 $(FFLAGS_DEFAULT) ARFLAGS_BACIO = FFLAGS_BUFR = -O3 $(FFLAGS_DEFAULT) $(FFLAGS_i4r8) CFLAGS_BUFR = -O3 -DUNDERSCORE FFLAGS_CLOUD = -O3 $(FFLAGS_DEFAULT) FFLAGS_CRTM = -fast $(FFLAGS_DEFAULT) LFLAGS_CRTM = FFLAGS_GFSIO = -O3 $(FFLAGS_DEFAULT) $(FFLAGS_i4r4) ARFLAGS_GFSIO = 20
21 configure.gsi #### Architecture specific settings #### # Settings for Linux x86_64, PGI compilers (pgf90 & gcc) (dmpar,optimize)# LDFLAGS = -Wl,-noinhibit-exec COREDIR = /d1/stark/gsi/src/pgi/release_v3.1 INC_DIR = $(COREDIR)/include BYTE_ORDER = LITTLE_ENDIAN SFC = pgf90 SF90 = pgf90 -Mfree SCC = gcc INC_FLAGS = -module $(INC_DIR) -I $(INC_DIR) -I /usr/local/netcdf3-pgi/include FFLAGS_i4r4 = -i4 -r4 FFLAGS_i4r8 = -i4 -r8 FFLAGS_i8r8 = -i8 -r8 FFLAGS_DEFAULT = -Kieee -pc 64 -Ktrap=fp FFLAGS_DEBUG FFLAGS_OPT FFLAGS = -O0 -q -C = -O3 = -fast $(FFLAGS_DEFAULT) -DLANGUAGE_FORTRAN -DsysLinux $(INC_FLAGS) $(LDFLAGS) -DLINUX -DPGI # Library build flags FFLAGS_BACIO = -O3 $(FFLAGS_DEFAULT) ARFLAGS_BACIO = FFLAGS_BUFR = -O3 $(FFLAGS_DEFAULT) $(FFLAGS_i4r8) CFLAGS_BUFR = -O3 -DUNDERSCORE FFLAGS_CLOUD = -O3 $(FFLAGS_DEFAULT) FFLAGS_CRTM = -fast $(FFLAGS_DEFAULT) LFLAGS_CRTM = FFLAGS_GFSIO = -O3 $(FFLAGS_DEFAULT) $(FFLAGS_i4r4) ARFLAGS_GFSIO = 21
22 Paths & FFLAGS configure.gsi COREDIR = /d1/stark/gsi/src/pgi/release_v3.1 INC_DIR = $(COREDIR)/include BYTE_ORDER = LITTLE_ENDIAN SFC = pgf90 SF90 = pgf90 -Mfree SCC = gcc INC_FLAGS = -module $(INC_DIR) -I $(INC_DIR) -I / usr/local/netcdf3-pgi/include 22
23 Paths & FFLAGS configure.gsi COREDIR = /d1/stark/gsi/src/pgi/release_v3.1 INC_DIR = $(COREDIR)/include BYTE_ORDER = LITTLE_ENDIAN SFC = pgf90 SF90 = pgf90 -Mfree SCC = gcc INC_FLAGS = -module $(INC_DIR) -I $(INC_DIR) -I / usr/local/netcdf3-pgi/include 23
24 Paths & FFLAGS configure.gsi COREDIR = /d1/stark/gsi/src/pgi/release_v3.1 INC_DIR = $(COREDIR)/include BYTE_ORDER = LITTLE_ENDIAN SFC = pgf90 SF90 = pgf90 -Mfree SCC = gcc INC_FLAGS = -module $(INC_DIR) -I $(INC_DIR) -I / usr/local/netcdf3-pgi/include 24
25 Paths & FFLAGS configure.gsi COREDIR = /d1/stark/gsi/src/pgi/release_v3.1 INC_DIR = $(COREDIR)/include BYTE_ORDER = LITTLE_ENDIAN SFC = pgf90 SF90 = pgf90 -Mfree SCC = gcc INC_FLAGS = -module $(INC_DIR) -I $(INC_DIR) -I / usr/local/netcdf3-pgi/include 25
26 Paths & FFLAGS configure.gsi FFLAGS_DEFAULT = -Kieee -pc 64 -Ktrap=fp FFLAGS_DEBUG = -O0 -q -C FFLAGS_OPT = -O3 FFLAGS = -fast $(FFLAGS_DEFAULT) -DLANGUAGE_FORTRAN -DsysLinux $(INC_FLAGS) $(LDFLAGS) -DLINUX DPGI 26
27 configure.gsi #### Architecture specific settings #### # Settings for Linux x86_64, PGI compilers (pgf90 & gcc) (dmpar,optimize)# LDFLAGS = -Wl,-noinhibit-exec COREDIR = /d1/stark/gsi/src/pgi/release_v3.1 INC_DIR = $(COREDIR)/include BYTE_ORDER = LITTLE_ENDIAN SFC = pgf90 SF90 = pgf90 -Mfree SCC = gcc INC_FLAGS = -module $(INC_DIR) -I $(INC_DIR) -I /usr/local/netcdf3-pgi/include FFLAGS_i4r4 = -i4 -r4 FFLAGS_i4r8 = -i4 -r8 FFLAGS_i8r8 = -i8 -r8 FFLAGS_DEFAULT = -Kieee -pc 64 -Ktrap=fp FFLAGS_DEBUG FFLAGS_OPT FFLAGS = -O0 -q -C = -O3 = -fast $(FFLAGS_DEFAULT) -DLANGUAGE_FORTRAN -DsysLinux $(INC_FLAGS) $(LDFLAGS) -DLINUX -DPGI # Library build flags FFLAGS_BACIO = -O3 $(FFLAGS_DEFAULT) ARFLAGS_BACIO = FFLAGS_BUFR = -O3 $(FFLAGS_DEFAULT) $(FFLAGS_i4r8) CFLAGS_BUFR = -O3 -DUNDERSCORE FFLAGS_CLOUD = -O3 $(FFLAGS_DEFAULT) FFLAGS_CRTM = -fast $(FFLAGS_DEFAULT) LFLAGS_CRTM = FFLAGS_GFSIO = -O3 $(FFLAGS_DEFAULT) $(FFLAGS_i4r4) ARFLAGS_GFSIO = 27
28 Library Build FFLAGS configure.gsi # Library build flags FFLAGS_BACIO = -O3 $(FFLAGS_DEFAULT) ARFLAGS_BACIO = FFLAGS_BUFR = -O3 $(FFLAGS_DEFAULT) $(FFLAGS_i4r8) CFLAGS_BUFR = -O3 -DUNDERSCORE FFLAGS_CLOUD = -O3 $(FFLAGS_DEFAULT) FFLAGS_CRTM = -fast $(FFLAGS_DEFAULT) LFLAGS_CRTM = FFLAGS_GFSIO = -O3 $(FFLAGS_DEFAULT) $(FFLAGS_i4r4) 28
29 configure.gsi CPP = cpp CPP_FLAGS = -C -P -D$(BYTE_ORDER) -D_REAL8_ DWRF -DLINUX -DPGI CPP_F90FLAGS = -traditional-cpp -lang-fortran DM_FC DM_F90 DM_CC = mpif90 -f90=pgf90 = mpif90 -Mfree -f90=pgf90 = gcc CFLAGS = -O0 -DLINUX -DUNDERSCORE CFLAGS2 = -DLINUX -Dfunder -DFortranByte=char -DFortranInt=int -DFortranLlong='long long 29
30 Library Paths configure.gsi Main issues are: library paths are wrong library names are wrong MYLIBsys = -llapack -lblas NETCDF_PATH = -rpath,/usr/local/netcdf3pgi/lib 30
31 Support For more detailed informa-on on installa-on, please see: GSI User s Guide, Chapter 2 GSI/users/docs/index.php For further assistance contact: gsi_help@ucar.edu 31
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