From owner-freebsd-ports-bugs@FreeBSD.ORG Sat Apr 7 14:20:02 2012 Return-Path: Delivered-To: freebsd-ports-bugs@hub.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [69.147.83.52]) by hub.freebsd.org (Postfix) with ESMTP id 0FB91106566B for ; Sat, 7 Apr 2012 14:20:02 +0000 (UTC) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (freefall.freebsd.org [IPv6:2001:4f8:fff6::28]) by mx1.freebsd.org (Postfix) with ESMTP id D8DF38FC12 for ; Sat, 7 Apr 2012 14:20:01 +0000 (UTC) Received: from freefall.freebsd.org (localhost [127.0.0.1]) by freefall.freebsd.org (8.14.5/8.14.5) with ESMTP id q37EK1tq070680 for ; Sat, 7 Apr 2012 14:20:01 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.14.5/8.14.5/Submit) id q37EK1Fc070679; Sat, 7 Apr 2012 14:20:01 GMT (envelope-from gnats) Resent-Date: Sat, 7 Apr 2012 14:20:01 GMT Resent-Message-Id: <201204071420.q37EK1Fc070679@freefall.freebsd.org> Resent-From: FreeBSD-gnats-submit@FreeBSD.org (GNATS Filer) Resent-To: freebsd-ports-bugs@FreeBSD.org Resent-Reply-To: FreeBSD-gnats-submit@FreeBSD.org, Jason Bacon Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id 8E6E21065674 for ; Sat, 7 Apr 2012 14:11:14 +0000 (UTC) (envelope-from nobody@FreeBSD.org) Received: from red.freebsd.org (red.freebsd.org [IPv6:2001:4f8:fff6::22]) by mx1.freebsd.org (Postfix) with ESMTP id 798AF8FC1F for ; Sat, 7 Apr 2012 14:11:14 +0000 (UTC) Received: from red.freebsd.org (localhost [127.0.0.1]) by red.freebsd.org (8.14.4/8.14.4) with ESMTP id q37EBEKX085843 for ; Sat, 7 Apr 2012 14:11:14 GMT (envelope-from nobody@red.freebsd.org) Received: (from nobody@localhost) by red.freebsd.org (8.14.4/8.14.4/Submit) id q37EBEAN085839; Sat, 7 Apr 2012 14:11:14 GMT (envelope-from nobody) Message-Id: <201204071411.q37EBEAN085839@red.freebsd.org> Date: Sat, 7 Apr 2012 14:11:14 GMT From: Jason Bacon To: freebsd-gnats-submit@FreeBSD.org X-Send-Pr-Version: www-3.1 Cc: Subject: ports/166726: New port: science/fvcom X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.5 Precedence: list List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 07 Apr 2012 14:20:02 -0000 >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@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 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@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= ${WRKDIR}/FVCOM2.7.1/FVCOM_source X X.include X XPLIST_FILES= bin/${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}${PKGNAMESUFFIX} X X.include 3d1abee2278bf98e801d51be8ba19aaf echo x - fvcom/distinfo sed 's/^X//' >fvcom/distinfo << '1750b572474787a27a71c1f5812ed6cb' XSHA256 (sourcecode1.tar.gz) = b687fccef91e37b3b98554bd80bfbf6f857703cd9bdfde166b502bee7473b7ad XSIZE (sourcecode1.tar.gz) = 6162463 1750b572474787a27a71c1f5812ed6cb echo c - fvcom/files mkdir -p fvcom/files > /dev/null 2>&1 echo x - fvcom/files/patch-Makefile sed 's/^X//' >fvcom/files/patch-Makefile << '7a11eb13c22c448423d3cc8714c8143e' X--- Makefile.orig 2009-09-22 14:45:57.000000000 -0500 X+++ Makefile 2012-03-31 21:58:24.000000000 -0500 X@@ -17,7 +17,7 @@ X # UNCOMMENT TO SELECT DOUBLE PRECISION X #-------------------------------------------------------------------------- X X-# FLAG_1 = -DDOUBLE_PRECISION X+ FLAG_1 = -DDOUBLE_PRECISION X X #-------------------------------------------------------------------------- X # SPHERICAL SELECT SPHERICAL COORDINATES FOR INTEGRATION X@@ -35,7 +35,7 @@ X # UNCOMMENT TO INCLUDE FLOODYING/DRYING X #-------------------------------------------------------------------------- X X-# FLAG_3 = -DWET_DRY X+ FLAG_3 = -DWET_DRY X X #-------------------------------------------------------------------------- X # MULTI_PROCESSOR INCLUDES PARALLELIZATION WITH MPI X@@ -45,13 +45,14 @@ X # UNCOMMENT TO INCLUDE MPI PARALLEL CAPABILITY X #-------------------------------------------------------------------------- X X- FLAG_4 = -DMULTIPROCESSOR X+# FLAG_4 = -DMULTIPROCESSOR X X # For em64t computers at SMAST (guppy) X # PARLIB = -L/hosts/salmon01/data00/medm/em64t/lib64 -lmetis X X # For i386 computers at SMAST (salmon and minke) X # PARLIB = -L/hosts/salmon01/data00/medm/lib -lmetis X+# PARLIB = -L${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: