From 2fafd58626c8d67b6e4df5e537ae0ac7d6a97060 Mon Sep 17 00:00:00 2001
From: Achim Gsell <achim.gsell@psi.ch>
Date: Wed, 11 Jul 2018 10:56:06 +0200
Subject: [PATCH] ioapi added

---
 HDF5/ioapi/build                              |  60 ++++
 HDF5/ioapi/files/Makefile.pncf.sed.patch      | 271 ++++++++++++++++++
 HDF5/ioapi/files/Makeinclude.OSX_x86_gfortmpi |  46 +++
 HDF5/ioapi/files/variants                     |   1 +
 HDF5/ioapi/modulefile                         |  19 ++
 5 files changed, 397 insertions(+)
 create mode 100755 HDF5/ioapi/build
 create mode 100644 HDF5/ioapi/files/Makefile.pncf.sed.patch
 create mode 100644 HDF5/ioapi/files/Makeinclude.OSX_x86_gfortmpi
 create mode 100644 HDF5/ioapi/files/variants
 create mode 100644 HDF5/ioapi/modulefile

diff --git a/HDF5/ioapi/build b/HDF5/ioapi/build
new file mode 100755
index 0000000..6838d9e
--- /dev/null
+++ b/HDF5/ioapi/build
@@ -0,0 +1,60 @@
+#!/usr/bin/env modbuild
+
+pbuild::set_download_url "https://gitlab.psi.ch/Pmodules/download/raw/master/$P-$V.tar.gz"
+
+pbuild::add_to_group 'HDF5'
+pbuild::compile_in_sourcetree
+pbuild::add_patch 'files/Makefile.pncf.sed.patch'
+
+pbuild::add_docfile README.txt
+pbuild::add_docfile V32-CHANGES.txt
+pbuild::add_docfile VERSION.txt
+pbuild::add_docfile HTML/gpl.txt
+
+echo $SRC_DIR
+
+pbuild::post_prep() {
+	find "${SRC_DIR}" -name "*.mod" -exec rm {} \;
+	find "${SRC_DIR}" -name "*.o" -exec rm {} \;
+}
+
+pbuild::pre_configure() {
+	config_args=()
+	config_args+=( "BASEDIR=${SRC_DIR}" )
+	config_args+=( "CPLMODE=pncf" )
+	config_args+=( "INSTALL=${PREFIX}" )
+	config_args+=( "NCFLIBS=-lpnetcdf -lnetcdf -lnetcdff -lgfortran" )
+
+	case "${OS}" in
+	"Darwin" )
+		config_args+=( "BIN=OSX_x86_gfortmpi" )
+		;;
+	* )
+		echo "OS not supported!" 1>&2
+		exit 1
+		;;
+	esac
+}
+
+pbuild::pre_configure_Darwin() {
+	cd "${SRC_DIR}"
+	cp Makefile.template Makefile
+	cp -av "${BUILDBLOCK_DIR}/files/Makeinclude.OSX_x86_gfortmpi" "ioapi"
+}
+
+pbuild::configure() {
+	cd "${SRC_DIR}"
+	make "${config_args[@]}" configure
+}
+
+pbuild::build() {
+	make "${config_args[@]}" all
+}
+
+pbuild::install() {
+	mkdir -p "${PREFIX}"
+	make "${config_args[@]}" install
+}
+
+pbuild::make_all
+
diff --git a/HDF5/ioapi/files/Makefile.pncf.sed.patch b/HDF5/ioapi/files/Makefile.pncf.sed.patch
new file mode 100644
index 0000000..c6b21e5
--- /dev/null
+++ b/HDF5/ioapi/files/Makefile.pncf.sed.patch
@@ -0,0 +1,271 @@
+Only in src/: .configure
+Only in src/: .prep
+Only in src/: Linux2_x86_64
+Only in src/: Makefile
+Only in src/: OSX_x86_gfortmpi
+Only in src/ioapi: Makefile
+Only in src/ioapi: Makeinclude.OSX_x86_gfortmpi
+Only in ioapi-3.2/ioapi: bilin.o
+Only in ioapi-3.2/ioapi: bmatvec.o
+Only in ioapi-3.2/ioapi: bufint3.o
+Only in ioapi-3.2/ioapi: cbarnes1.o
+Only in ioapi-3.2/ioapi: cbarnesN.o
+Only in ioapi-3.2/ioapi: check3.o
+Only in ioapi-3.2/ioapi: check3c.o
+Only in ioapi-3.2/ioapi: chkbuf3.o
+Only in ioapi-3.2/ioapi: chkfil3.o
+Only in ioapi-3.2/ioapi: ckdesc3.o
+Only in ioapi-3.2/ioapi: ckfile3.o
+Only in ioapi-3.2/ioapi: ckgeom.o
+Only in ioapi-3.2/ioapi: ckname.o
+Only in ioapi-3.2/ioapi: cktflag3.o
+Only in ioapi-3.2/ioapi: close3.o
+Only in ioapi-3.2/ioapi: close3c.o
+Only in ioapi-3.2/ioapi: crdict3.o
+Only in ioapi-3.2/ioapi: crlf.o
+Only in ioapi-3.2/ioapi: crtbuf3.o
+Only in ioapi-3.2/ioapi: crtfil3.o
+Only in ioapi-3.2/ioapi: crtkf.o
+Only in ioapi-3.2/ioapi: currec.o
+Only in ioapi-3.2/ioapi: currstep.o
+Only in ioapi-3.2/ioapi: currstepc.o
+Only in ioapi-3.2/ioapi: daymon.o
+Only in ioapi-3.2/ioapi: daymonc.o
+Only in ioapi-3.2/ioapi: dble2real.o
+Only in ioapi-3.2/ioapi: dbllist.o
+Only in ioapi-3.2/ioapi: ddtvar3.o
+Only in ioapi-3.2/ioapi: ddtvar3c.o
+Only in ioapi-3.2/ioapi: ddtvar3v.o
+Only in ioapi-3.2/ioapi: desc3.o
+Only in ioapi-3.2/ioapi: desc3c.o
+Only in ioapi-3.2/ioapi: dmatvec.o
+Only in ioapi-3.2/ioapi: dscgrid.o
+Only in ioapi-3.2/ioapi: dscgridc.o
+Only in ioapi-3.2/ioapi: dt2str.o
+Only in ioapi-3.2/ioapi: dt2strc.o
+Only in ioapi-3.2/ioapi: envgets.o
+Only in ioapi-3.2/ioapi: filchk3.o
+Only in ioapi-3.2/ioapi: filchk3c.o
+Only in ioapi-3.2/ioapi: find1.o
+Only in ioapi-3.2/ioapi: find2.o
+Only in ioapi-3.2/ioapi: find3.o
+Only in ioapi-3.2/ioapi: find4.o
+Only in ioapi-3.2/ioapi: findc.o
+Only in ioapi-3.2/ioapi: findr1.o
+Only in ioapi-3.2/ioapi: findr2.o
+Only in ioapi-3.2/ioapi: findr3.o
+Only in ioapi-3.2/ioapi: findr4.o
+Only in ioapi-3.2/ioapi: findsc.o
+diff -ur ioapi-3.2/ioapi/fixed_src/STATE3.EXT src/ioapi/fixed_src/STATE3.EXT
+--- ioapi-3.2/ioapi/fixed_src/STATE3.EXT	2017-06-20 20:00:05.000000000 +0200
++++ src/ioapi/fixed_src/STATE3.EXT	2018-07-09 16:29:26.000000000 +0200
+@@ -11,8 +11,11 @@
+ !....................................................................
+ !  INCLUDE FILE  STATE3.EXT
+ !
++!   PRIVATE!
++!       For internal I/O API use only.
++!       Do not use in model or other application code.
+ !
+-!  DO NOT EDIT !!
++!   DO NOT EDIT !!
+ !
+ !       The EDSS/Models-3 I/O API depends in an essential manner
+ !       upon the contents of this INCLUDE file.  ANY CHANGES are
+Only in ioapi-3.2/ioapi: flush3.o
+Only in ioapi-3.2/ioapi: gcd.o
+Only in ioapi-3.2/ioapi: gctp.o
+Only in ioapi-3.2/ioapi: get_endian.o
+Only in ioapi-3.2/ioapi: getdate.o
+Only in ioapi-3.2/ioapi: getdble.o
+Only in ioapi-3.2/ioapi: getdfile.o
+Only in ioapi-3.2/ioapi: getdfilec.o
+Only in ioapi-3.2/ioapi: getdttime.o
+Only in ioapi-3.2/ioapi: getefile.o
+Only in ioapi-3.2/ioapi: getefilec.o
+Only in ioapi-3.2/ioapi: getffile.o
+Only in ioapi-3.2/ioapi: getmenu.o
+Only in ioapi-3.2/ioapi: getnum.o
+Only in ioapi-3.2/ioapi: getreal.o
+Only in ioapi-3.2/ioapi: getstr.o
+Only in ioapi-3.2/ioapi: getyn.o
+Only in ioapi-3.2/ioapi: grdchk3.o
+Only in ioapi-3.2/ioapi: gridops.o
+Only in ioapi-3.2/ioapi: hhmmss.o
+Only in ioapi-3.2/ioapi: hhmmssc.o
+Only in ioapi-3.2/ioapi: index1.o
+Only in ioapi-3.2/ioapi: init3.o
+Only in ioapi-3.2/ioapi: init3c.o
+Only in ioapi-3.2/ioapi: initblk3.o
+Only in ioapi-3.2/ioapi: initlog3.o
+Only in ioapi-3.2/ioapi: inqatt3.o
+Only in ioapi-3.2/ioapi: inqatt3c.o
+Only in ioapi-3.2/ioapi: interp3.o
+Only in ioapi-3.2/ioapi: interp3c.o
+Only in ioapi-3.2/ioapi: intg2real.o
+Only in ioapi-3.2/ioapi: intlist.o
+Only in ioapi-3.2/ioapi: iobin3.o
+Only in ioapi-3.2/ioapi: iocpl.o
+Only in ioapi-3.2/ioapi: iocplf2c.o
+Only in ioapi-3.2/ioapi: ioparms3.o
+Only in ioapi-3.2/ioapi: isdstime.o
+Only in ioapi-3.2/ioapi: jstep3.o
+Only in ioapi-3.2/ioapi: julian.o
+Only in ioapi-3.2/ioapi: julianc.o
+Only in ioapi-3.2/ioapi: junit.o
+Only in ioapi-3.2/ioapi: kfindx.o
+Only in ioapi-3.2/ioapi: kfopen.o
+Only in ioapi-3.2/ioapi: kfread.o
+Only in ioapi-3.2/ioapi: kfwrite.o
+Only in ioapi-3.2/ioapi: lambert.o
+Only in ioapi-3.2/ioapi: lblank.o
+Only in ioapi-3.2/ioapi: len2.o
+Only in ioapi-3.2/ioapi: ll2utm.o
+Only in ioapi-3.2/ioapi: locat1.o
+Only in ioapi-3.2/ioapi: locat2.o
+Only in ioapi-3.2/ioapi: locat3.o
+Only in ioapi-3.2/ioapi: locat4.o
+Only in ioapi-3.2/ioapi: locatc.o
+Only in ioapi-3.2/ioapi: locatr1.o
+Only in ioapi-3.2/ioapi: locatr2.o
+Only in ioapi-3.2/ioapi: locatr3.o
+Only in ioapi-3.2/ioapi: locatr4.o
+Only in ioapi-3.2/ioapi: locatsc.o
+Only in ioapi-3.2/ioapi: lustr.o
+Only in ioapi-3.2/ioapi: m3abort.o
+Only in ioapi-3.2/ioapi: m3err.o
+Only in ioapi-3.2/ioapi: m3errc.o
+Only in ioapi-3.2/ioapi: m3exit.o
+Only in ioapi-3.2/ioapi: m3exitc.o
+Only in ioapi-3.2/ioapi: m3mesgc.o
+Only in ioapi-3.2/ioapi: m3msg2.o
+Only in ioapi-3.2/ioapi: m3utilio.mod
+Only in ioapi-3.2/ioapi: m3utilio.o
+Only in ioapi-3.2/ioapi: m3warn.o
+Only in ioapi-3.2/ioapi: m3warnc.o
+Only in ioapi-3.2/ioapi: mmddyy.o
+Only in ioapi-3.2/ioapi: mmddyyc.o
+Only in ioapi-3.2/ioapi: modatts3.mod
+Only in ioapi-3.2/ioapi: modatts3.o
+Only in ioapi-3.2/ioapi: modgctp.mod
+Only in ioapi-3.2/ioapi: modgctp.o
+Only in ioapi-3.2/ioapi: modmpasfio.mod
+Only in ioapi-3.2/ioapi: modmpasfio.o
+Only in ioapi-3.2/ioapi: modncfio.mod
+Only in ioapi-3.2/ioapi: modncfio.o
+Only in ioapi-3.2/ioapi: modpdata.mod
+Only in ioapi-3.2/ioapi: modpdata.o
+Only in ioapi-3.2/ioapi: modwrfio.mod
+Only in ioapi-3.2/ioapi: modwrfio.o
+Only in ioapi-3.2/ioapi: name2fid.o
+Only in ioapi-3.2/ioapi: nameval.o
+Only in ioapi-3.2/ioapi: nextime.o
+Only in ioapi-3.2/ioapi: nextimec.o
+Only in ioapi-3.2/ioapi: open3.o
+Only in ioapi-3.2/ioapi: open3c.o
+Only in ioapi-3.2/ioapi: opnfil3.o
+Only in ioapi-3.2/ioapi: opnkf.o
+Only in ioapi-3.2/ioapi: opnlist3.o
+Only in ioapi-3.2/ioapi: opnlog3.o
+Only in ioapi-3.2/ioapi: pcoef.o
+Only in ioapi-3.2/ioapi: pgrdsum.o
+Only in ioapi-3.2/ioapi: pmatvec.o
+Only in ioapi-3.2/ioapi: pn_crtfil3.o
+Only in ioapi-3.2/ioapi: pn_opnfil3.o
+Only in ioapi-3.2/ioapi: pn_wrvars.o
+Only in ioapi-3.2/ioapi: poly.o
+Only in ioapi-3.2/ioapi: promptdfile.o
+Only in ioapi-3.2/ioapi: promptffile.o
+Only in ioapi-3.2/ioapi: promptgrid.o
+Only in ioapi-3.2/ioapi: promptmfile.o
+Only in ioapi-3.2/ioapi: rdatt3.o
+Only in ioapi-3.2/ioapi: rdatt3c.o
+Only in ioapi-3.2/ioapi: rdbndary.o
+Only in ioapi-3.2/ioapi: rdbuf3.o
+Only in ioapi-3.2/ioapi: rdcustom.o
+Only in ioapi-3.2/ioapi: rddict3.o
+Only in ioapi-3.2/ioapi: rdgrdded.o
+Only in ioapi-3.2/ioapi: rdgrnest.o
+Only in ioapi-3.2/ioapi: rdiddata.o
+Only in ioapi-3.2/ioapi: rdprofil.o
+Only in ioapi-3.2/ioapi: rdsmatrx.o
+Only in ioapi-3.2/ioapi: rdtflag.o
+Only in ioapi-3.2/ioapi: rdvars.o
+Only in ioapi-3.2/ioapi: read3.o
+Only in ioapi-3.2/ioapi: read3c.o
+Only in ioapi-3.2/ioapi: read4d.o
+Only in ioapi-3.2/ioapi: read4dc.o
+Only in ioapi-3.2/ioapi: readsmet.o
+Only in ioapi-3.2/ioapi: realist.o
+Only in ioapi-3.2/ioapi: rmfile.o
+Only in ioapi-3.2/ioapi: runspec.o
+Only in ioapi-3.2/ioapi: scanint.o
+Only in ioapi-3.2/ioapi: sec2time.o
+Only in ioapi-3.2/ioapi: sec2timec.o
+Only in ioapi-3.2/ioapi: secsdiff.o
+Only in ioapi-3.2/ioapi: secsdiffc.o
+Only in ioapi-3.2/ioapi: setsphere.o
+Only in ioapi-3.2/ioapi: shut3.o
+Only in ioapi-3.2/ioapi: shut3c.o
+Only in ioapi-3.2/ioapi: skipl.o
+Only in ioapi-3.2/ioapi: sleep3.o
+Only in ioapi-3.2/ioapi: smatvec.o
+Only in ioapi-3.2/ioapi: sortic.o
+Only in ioapi-3.2/ioapi: sortir.o
+Only in ioapi-3.2/ioapi: sortis.o
+Only in ioapi-3.2/ioapi: splitline.o
+Only in ioapi-3.2/ioapi: str2dble.o
+Only in ioapi-3.2/ioapi: str2int.o
+Only in ioapi-3.2/ioapi: str2real.o
+Only in ioapi-3.2/ioapi: strlist.o
+Only in ioapi-3.2/ioapi: sync3.o
+Only in ioapi-3.2/ioapi: sync3c.o
+Only in ioapi-3.2/ioapi: syncfid.o
+Only in ioapi-3.2/ioapi: synchtao.o
+Only in ioapi-3.2/ioapi: systemf.o
+Only in ioapi-3.2/ioapi: time2sec.o
+Only in ioapi-3.2/ioapi: time2secc.o
+Only in ioapi-3.2/ioapi: trimlen.o
+Only in ioapi-3.2/ioapi: ungridb.o
+Only in ioapi-3.2/ioapi: ungridi.o
+Only in ioapi-3.2/ioapi: upcase.o
+Only in ioapi-3.2/ioapi: utm2ll.o
+Only in ioapi-3.2/ioapi: wkday.o
+Only in ioapi-3.2/ioapi: wkdayc.o
+Only in ioapi-3.2/ioapi: wratt3.o
+Only in ioapi-3.2/ioapi: wratt3c.o
+Only in ioapi-3.2/ioapi: wrbndary.o
+Only in ioapi-3.2/ioapi: wrbuf3.o
+Only in ioapi-3.2/ioapi: wrcustom.o
+Only in ioapi-3.2/ioapi: wrdict3.o
+Only in ioapi-3.2/ioapi: wrgrdded.o
+Only in ioapi-3.2/ioapi: wrgrnest.o
+Only in ioapi-3.2/ioapi: wriddata.o
+Only in ioapi-3.2/ioapi: write3.o
+Only in ioapi-3.2/ioapi: write3c.o
+Only in ioapi-3.2/ioapi: write4d.o
+Only in ioapi-3.2/ioapi: write4dc.o
+Only in ioapi-3.2/ioapi: wrmpigrd.o
+Only in ioapi-3.2/ioapi: wrpatch.o
+Only in ioapi-3.2/ioapi: wrprofil.o
+Only in ioapi-3.2/ioapi: wrsmatrx.o
+Only in ioapi-3.2/ioapi: wrtflag.o
+Only in ioapi-3.2/ioapi: wrvars.o
+Only in ioapi-3.2/ioapi: xtbuf3.o
+Only in ioapi-3.2/ioapi: xtract3.o
+Only in ioapi-3.2/ioapi: xtract3c.o
+Only in ioapi-3.2/ioapi: year4.o
+Only in ioapi-3.2/ioapi: yr2day.o
+Only in src/m3tools: Makefile
+diff -ur ioapi-3.2/m3tools/Makefile.pncf.sed src/m3tools/Makefile.pncf.sed
+--- ioapi-3.2/m3tools/Makefile.pncf.sed	2017-10-21 03:37:21.000000000 +0200
++++ src/m3tools/Makefile.pncf.sed	2018-07-09 18:01:58.000000000 +0200
+@@ -99,7 +99,7 @@
+ insertgrid      jul2greg        juldate         juldiff         julshift        \
+ kfxtract        latlon          m3agmax         m3agmask        m3cple          \
+ m3combo         m3diff          m3edhdr         m3fake          m3hdr           \
+-m3interp        m3mask          m3merge         m3pair          m3probe         \
++m3interp        m3merge         m3pair          m3probe         \
+ m3stat          m3totxt         m3tproc         m3tshift        m3wndw          \
+ m3xtract        mtxblend        mtxbuild        mtxcalc         mtxcple         \
+ presterp        presz           projtool        selmrg2d        timeshift       \
diff --git a/HDF5/ioapi/files/Makeinclude.OSX_x86_gfortmpi b/HDF5/ioapi/files/Makeinclude.OSX_x86_gfortmpi
new file mode 100644
index 0000000..c2dbaaa
--- /dev/null
+++ b/HDF5/ioapi/files/Makeinclude.OSX_x86_gfortmpi
@@ -0,0 +1,46 @@
+# Version "$Id: Makeinclude.Linux2_x86_64gfortmpi 1 2017-06-10 18:05:20Z coats $"
+#
+#  Build MPI/PnetCDF distributed-file support using "mpif90" and "mpcc",
+#  where compilers are built "on top of" Gnu compilers
+#
+#  12/2013 by CJC: Conditional preprocessor-code "-DNEED_ARGS=1"
+#  to implement  IARGC() and GETARG() for compilers
+#  ("gfortran" version 4.8 or later to be exact) that insist on
+#  enforcing F2003-only with no backwards nor industry-standards compatibility.
+#
+#  Remove "-DNEED_ARGS=1" from ARCHFLAGS for version 4.7.x and earlier
+#
+# Use "-march=native -mtune=native" if compile-platform and compute-platform
+# are the same.
+# Use "-Wall -Wsurprising" for full diagnostics.
+
+AR   = ar
+CC   = mpicc
+CXX  = mpiCC
+FC   = mpif90
+M4   = m4
+LINK = $(CC)
+
+## Module-include-directory command
+MODI = -I
+E132 = -ffixed-line-length-132
+
+MFLAGS    = -ffast-math -funroll-loops -m64  #  -Wall -Wsurprising -march=native -mtune=native
+
+OMPFLAGS  = -fopenmp
+OMPLIBS   = -fopenmp
+COPTFLAGS = -O3 ${MFLAGS}
+FOPTFLAGS = -O3 ${MFLAGS}
+FPPFLAGS  = -DF90=1 -DIOAPI_PNCF=1
+FSFLAGS   = -fno-automatic
+ARCHFLAGS = \
+ -DAUTO_ARRAYS=1 \
+ -DF90=1 -DFLDMN=1 \
+ -DFSTR_L=int \
+ -DIOAPI_NO_STDOUT=1 \
+ -DNEED_ARGS=1
+PARFLAGS  =
+ARCHLIB   = -dynamic -lm -lpthread -lc
+
+M4DEFFILE = $(PVM_ROOT)/conf/$(PVM_ARCH).m4
+PVMLIBS   = -lpvm3
diff --git a/HDF5/ioapi/files/variants b/HDF5/ioapi/files/variants
new file mode 100644
index 0000000..09884c3
--- /dev/null
+++ b/HDF5/ioapi/files/variants
@@ -0,0 +1 @@
+ioapi/3.2	unstable	gcc/7.3.0 openmpi/1.10.7 hdf5/1.10.1 netcdf/4.6.1 parallel-netcdf/1.9.0
diff --git a/HDF5/ioapi/modulefile b/HDF5/ioapi/modulefile
new file mode 100644
index 0000000..be7b1dd
--- /dev/null
+++ b/HDF5/ioapi/modulefile
@@ -0,0 +1,19 @@
+#%Module1.0
+
+module-whatis		"Models-3 Input/Output Applications Programming Interface"
+module-url		"https://www.cmascenter.org/ioapi/"
+module-license		"GNU GPLv2"
+module-maintainer	"Achim Gsell <achim.gsell@psi.ch>"
+
+module-help		"
+The Models-3 Input/Output Applications Programming Interface (I/O API) is
+a selective and direct-access programming interface to the data: you tell
+the system what variables and dates and times you're talking about and it
+figures all the stuff about record numbers, etc., for itself. Also, you
+don't have to read the data in consecutive order, or to write it in order,
+either -- you just ask for what you want, and the I/O API finds it for you
+(although there are moderate performance penalties for writing data out-of-
+order). The files are self-describing files -- that is, the file headers
+have all the dimensioning and descriptive information needed about the data
+in them. 
+"