ports/166726: New port: science/fvcom
Jason Bacon
jwbacon at tds.net
Sat Apr 7 14:20:02 UTC 2012
>Number: 166726
>Category: ports
>Synopsis: New port: science/fvcom
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: change-request
>Submitter-Id: current-users
>Arrival-Date: Sat Apr 07 14:20:01 UTC 2012
>Closed-Date:
>Last-Modified:
>Originator: Jason Bacon
>Release: 9.0-RELEASE
>Organization:
Acadix Consulting, LLC
>Environment:
FreeBSD sculpin.jbacon.dyndns.org 9.0-RELEASE FreeBSD 9.0-RELEASE #0: Tue Jan 3 07:46:30 UTC 2012 root at farrell.cse.buffalo.edu:/usr/obj/usr/src/sys/GENERIC amd64
>Description:
FVCOM is a prognostic, unstructured-grid, finite-volume, free-surface, 3-D
primitive equation coastal ocean circulation model developed by UMASSD-WHOI
joint efforts.
WWW: http://fvcom.smast.umassd.edu/FVCOM/index.html
>How-To-Repeat:
>Fix:
Patch attached with submission follows:
# This is a shell archive. Save it in a file, remove anything before
# this line, and then unpack it by entering "sh file". Note, it may
# create directories; files and directories will be owned by you and
# have default permissions.
#
# This archive contains:
#
# fvcom
# fvcom/pkg-descr
# fvcom/Makefile
# fvcom/distinfo
# fvcom/files
# fvcom/files/patch-Makefile
# fvcom/files/patch-mod_lag.F
# fvcom/files/patch-METIS_source-makefile
#
echo c - fvcom
mkdir -p fvcom > /dev/null 2>&1
echo x - fvcom/pkg-descr
sed 's/^X//' >fvcom/pkg-descr << '501d1001d556af2daebd2f403497aef9'
XFVCOM is a prognostic, unstructured-grid, finite-volume, free-surface, 3-D
Xprimitive equation coastal ocean circulation model developed by UMASSD-WHOI
Xjoint efforts.
X
XWWW: http://fvcom.smast.umassd.edu/FVCOM/index.html
501d1001d556af2daebd2f403497aef9
echo x - fvcom/Makefile
sed 's/^X//' >fvcom/Makefile << '3d1abee2278bf98e801d51be8ba19aaf'
X# New ports collection makefile for: fvcom
X# Date created: 2012-03-13
X# Whom: Jason Bacon <bacon at sculpin.jbacon.dyndns.org>
X#
X# $FreeBSD$
X#
X
XPORTNAME= fvcom
XPORTVERSION= 2.7.1
XCATEGORIES= science
XMASTER_SITES= http://fvcom.smast.umassd.edu/FVCOM/index.html/
XDISTNAME= sourcecode1
X
XMAINTAINER= jwbacon at tds.net
XCOMMENT= Unstructured Grid Finite Volume Coastal Ocean Model
X
X# Check netcdf lib for Fortran support!
XLIB_DEPENDS= netcdff:${PORTSDIR}/science/netcdf-ftn \
X lapack:${PORTSDIR}/math/lapack \
X blas:${PORTSDIR}/math/lapack
X
XUSE_FORTRAN= yes
XWRKSRC= ${WRKDIR}/FVCOM2.7.1/FVCOM_source
X
X.include <bsd.port.pre.mk>
X
XPLIST_FILES= bin/${PORTNAME}${PKGNAMESUFFIX}
X
X.if !defined(PACKAGE_BUILDING) && \
X !exists(${DISTDIR}/${DISTNAME}${EXTRACT_SUFX})
Xpre-everything::
X @${PRINTF} "\nPlease register at http://fvcom.smast.umassd.edu/FVCOM/index.html in order to download the source code ${DISTNAME}${EXTRACT_SUFX} and place it in ${DISTDIR}.\n\n" | ${FMT}
X @${FALSE}
X.endif
X
Xpost-extract:
X ${MV} ${WRKSRC}/makefile ${WRKSRC}/Makefile
X
Xpre-build:
X (cd ${WRKSRC}/../METIS_source && make)
X
Xdo-install:
X ${INSTALL_PROGRAM} ${WRKSRC}/fvcom \
X ${PREFIX}/bin/${PORTNAME}${PKGNAMESUFFIX}
X
X.include <bsd.port.post.mk>
3d1abee2278bf98e801d51be8ba19aaf
echo x - fvcom/distinfo
sed 's/^X//' >fvcom/distinfo << '1750b572474787a27a71c1f5812ed6cb'
XSHA256 (sourcecode1.tar.gz) = b687fccef91e37b3b98554bd80bfbf6f857703cd9bdfde166b502bee7473b7ad
XSIZE (sourcecode1.tar.gz) = 6162463
1750b572474787a27a71c1f5812ed6cb
echo c - fvcom/files
mkdir -p fvcom/files > /dev/null 2>&1
echo x - fvcom/files/patch-Makefile
sed 's/^X//' >fvcom/files/patch-Makefile << '7a11eb13c22c448423d3cc8714c8143e'
X--- Makefile.orig 2009-09-22 14:45:57.000000000 -0500
X+++ Makefile 2012-03-31 21:58:24.000000000 -0500
X@@ -17,7 +17,7 @@
X # UNCOMMENT TO SELECT DOUBLE PRECISION
X #--------------------------------------------------------------------------
X
X-# FLAG_1 = -DDOUBLE_PRECISION
X+ FLAG_1 = -DDOUBLE_PRECISION
X
X #--------------------------------------------------------------------------
X # SPHERICAL SELECT SPHERICAL COORDINATES FOR INTEGRATION
X@@ -35,7 +35,7 @@
X # UNCOMMENT TO INCLUDE FLOODYING/DRYING
X #--------------------------------------------------------------------------
X
X-# FLAG_3 = -DWET_DRY
X+ FLAG_3 = -DWET_DRY
X
X #--------------------------------------------------------------------------
X # MULTI_PROCESSOR INCLUDES PARALLELIZATION WITH MPI
X@@ -45,13 +45,14 @@
X # UNCOMMENT TO INCLUDE MPI PARALLEL CAPABILITY
X #--------------------------------------------------------------------------
X
X- FLAG_4 = -DMULTIPROCESSOR
X+# FLAG_4 = -DMULTIPROCESSOR
X
X # For em64t computers at SMAST (guppy)
X # PARLIB = -L/hosts/salmon01/data00/medm/em64t/lib64 -lmetis
X
X # For i386 computers at SMAST (salmon and minke)
X # PARLIB = -L/hosts/salmon01/data00/medm/lib -lmetis
X+# PARLIB = -L${LOCALBASE}/lib -lmetis
X PARLIB = -L../METIS_source -lmetis
X
X # For Typhoeus and Hydra
X@@ -67,7 +68,7 @@
X # UNCOMMENT TO INCLUDE WATER QUALITY MODEL
X #--------------------------------------------------------------------------
X
X-# FLAG_5 = -DWATER_QUALITY
X+ FLAG_5 = -DWATER_QUALITY
X
X #--------------------------------------------------------------------------
X # NETCDF OUTPUT DUMP OUTPUT INTO NETCDF FILES (yes/no)
X@@ -79,8 +80,10 @@
X # UNCOMMENT TO INCLUDE NETCDF OUTPUT CAPABILITY
X #--------------------------------------------------------------------------
X FLAG_6 = -DNETCDF_IO
X- IOLIBS = -L/hosts/mao/usr/medm/install/netcdf/3.6.3/em64t/lib -lnetcdf
X- IOINCS = -I/hosts/mao/usr/medm/install/netcdf/3.6.3/em64t/include
X+# FreeBSD ports netcdf fortran support is separate from the standard
X+# netcdf library. Must have both -lnetcdff and -lnetcdf
X+ IOLIBS = -L${LOCALBASE}/lib -lnetcdff -lnetcdf
X+ IOINCS = -I${LOCALBASE}/include
X
X # For em64t computers at SMAST (guppy)
X # IOLIBS = -L/hosts/salmon01/data00/medm/em64t/lib64 -lnetcdf
X@@ -107,7 +110,7 @@
X # UNCOMMENT TO INCLUDE DATA ASSIMILATION
X #--------------------------------------------------------------------------
X
X-# FLAG_7 = -DNG_OI_ASSIM
X+ FLAG_7 = -DNG_OI_ASSIM
X
X # For Build on em64t computer (Guppy)
X # OILIB = -L/usr/X11R6/lib64 -L/usr/local/lib64 -lmkl_lapack -lmkl_em64t -lguide -lpthread
X@@ -381,15 +384,15 @@
X #--------------------------------------------------------------------------
X # Intel/MPI Compiler Definitions (SMAST)
X #--------------------------------------------------------------------------
X- CPP = /usr/bin/cpp
X- CPPFLAGS = $(DEF_FLAGS) -DINTEL
X- FC = mpif90
X- DEBFLGS = #-check all
X+# CPP = /usr/bin/cpp
X+# CPPFLAGS = $(DEF_FLAGS) -DINTEL
X+# FC = mpif90
X+# DEBFLGS = #-check all
X # Use 'OPT = -O0 -g' for fast compile to test the make
X # Use 'OPT = -xP' for fast run on em64t (Hydra, Typhoeus and Guppy)
X # Use 'OPT = -xN' for fast run on em64t (Salmon and Minke)
X # OPT = -O0 -g
X- OPT = -xP
X+# OPT = -xP
X # OPT = -xN
X
X # Do not set static for use with visit!
X@@ -398,12 +401,11 @@
X #--------------------------------------------------------------------------
X # gfortran defs
X #--------------------------------------------------------------------------
X-# CPP = /usr/bin/cpp
X-# CPPFLAGS = $(DEF_FLAGS) -DGFORTRAN
X-# FC = gfortran -O3
X-# DEBFLGS =
X-# OPT =
X-# CLIB =
X+ CPP = cpp
X+ CPPFLAGS = $(DEF_FLAGS) -DGFORTRAN
X+ DEBFLGS = -g
X+ OPT = -O
X+ CLIB =
X #--------------------------------------------------------------------------
X # absoft / mac os x defs
X #--------------------------------------------------------------------------
X@@ -448,7 +450,8 @@
X #--------------------------------------------------------------------------
X # CAT Preprocessing Flags
X #--------------------------------------------------------------------------
X- CPPARGS = $(CPPFLAGS) $(DEF_FLAGS) $(FLAG_1) $(FLAG_2) \
X+ CPPARGS = $(CPPFLAGS) $(DEF_FLAGS) $(PORT_CPP_FLAGS) \
X+ $(FLAG_1) $(FLAG_2) \
X $(FLAG_3) $(FLAG_4) $(FLAG_5) $(FLAG_6) \
X $(FLAG_7) $(FLAG_8) $(FLAG_9) $(FLAG_10) \
X $(FLAG_11) $(FLAG_12) $(FLAG_13) $(FLAG_14) \
X@@ -463,7 +466,7 @@
X
X LIBS = $(PV3LIB) $(CLIB) $(PARLIB) $(IOLIBS) \
X $(MPILIB) $(GOTMLIB) $(KFLIB) $(BIOLIB) \
X- $(OILIB) $(VISITLIB) $(PETSC_LIB)
X+ $(OILIB) $(VISITLIB) $(PETSC_LIB) -llapack -lblas
X
X INCS = $(IOINCS) $(GOTMINCS) $(BIOINCS) $(VISITINC) $(PETSC_FC_INCLUDES)
X
X@@ -539,6 +542,8 @@
X # Linking Directives
X #--------------------------------------------------------------------------
X
X+all: $(EXEC)
X+
X $(EXEC): $(OBJS)
X $(FC) $(FFLAGS) $(VISOPT) $(LDFLAGS) $(OBJS) $(LIBS) -o $(EXEC)
X
7a11eb13c22c448423d3cc8714c8143e
echo x - fvcom/files/patch-mod_lag.F
sed 's/^X//' >fvcom/files/patch-mod_lag.F << 'd8371a56de761b2d4eda9bf0140f9f2d'
X--- mod_lag.F.orig 2008-07-25 16:44:11.000000000 -0500
X+++ mod_lag.F 2012-03-31 21:57:17.000000000 -0500
X@@ -212,7 +212,12 @@
X !Lagrangian particle associated scalar
X character(len=80) :: lag_scal_choice
X integer, parameter:: n_scal_choice = 6
X- character(len=80) :: scal_choices(n_scal_choice) = (/"s1","t1","rho1","km","kh","user_defined"/)
X+ character(len=80) :: scal_choices(n_scal_choice) = (/ "s1 ", &
X+ "t1 ", &
X+ "rho1 ", &
X+ "km ", &
X+ "kh ", &
X+ "user_defined"/)
X logical :: scal_choice_valid
X
X
d8371a56de761b2d4eda9bf0140f9f2d
echo x - fvcom/files/patch-METIS_source-makefile
sed 's/^X//' >fvcom/files/patch-METIS_source-makefile << 'f5c8dc15368582156cc71b54398a43e3'
X--- ../METIS_source/makefile.orig 2012-03-31 22:00:57.000000000 -0500
X+++ ../METIS_source/makefile 2012-03-31 22:01:01.000000000 -0500
X@@ -2,7 +2,7 @@
X AR = ar rv
X RANLIB = ranlib
X # add path to c compiler
X-CC = icc
X+CC = gcc
X # add c compiler optimization flags
X OPTFLAGS = -O2
X CFLAGS = $(COPTIONS) $(OPTFLAGS) $(INCLUDES)
f5c8dc15368582156cc71b54398a43e3
exit
>Release-Note:
>Audit-Trail:
>Unformatted:
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