Merge branch 'develop' of git.mpimet.mpg.de:cdo into develop

Makefile.in

-# Makefile.in generated by automake 1.14 from Makefile.am.
+# Makefile.in generated by automake 1.15 from Makefile.am.
 # @configure_input@
 
-# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+# Copyright (C) 1994-2014 Free Software Foundation, Inc.
 
 # This Makefile.in is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -14,7 +14,17 @@
 
 @SET_MAKE@
 VPATH = @srcdir@
-am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__is_gnu_make = { \
+  if test -z '$(MAKELEVEL)'; then \
+    false; \
+  elif test -n '$(MAKE_HOST)'; then \
+    true; \
+  elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \
+    true; \
+  else \
+    false; \
+  fi; \
+}
 am__make_running_with_option = \
   case $${target_option-} in \
       ?) ;; \
@@ -78,19 +88,6 @@ POST_UNINSTALL = :
 build_triplet = @build@
 host_triplet = @host@
 subdir = .
-DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
-	$(top_srcdir)/configure $(am__configure_deps) \
-	$(top_srcdir)/config/mkinstalldirs $(srcdir)/cdo.spec.in \
-	$(srcdir)/cdo.settings.in AUTHORS COPYING ChangeLog INSTALL \
-	NEWS README config/ar-lib config/compile config/config.guess \
-	config/config.sub config/depcomp config/install-sh \
-	config/missing config/mkinstalldirs config/ltmain.sh \
-	$(top_srcdir)/config/ar-lib $(top_srcdir)/config/compile \
-	$(top_srcdir)/config/config.guess \
-	$(top_srcdir)/config/config.sub \
-	$(top_srcdir)/config/install-sh $(top_srcdir)/config/ltmain.sh \
-	$(top_srcdir)/config/missing \
-	$(top_srcdir)/config/tap-driver.sh
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
 am__aclocal_m4_deps = $(top_srcdir)/m4/acx_options.m4 \
 	$(top_srcdir)/m4/ax_cxx_compile_stdcxx.m4 \
@@ -101,6 +98,8 @@ am__aclocal_m4_deps = $(top_srcdir)/m4/acx_options.m4 \
 	$(top_srcdir)/acinclude.m4 $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
+DIST_COMMON = $(srcdir)/Makefile.am $(top_srcdir)/configure \
+	$(am__configure_deps) $(am__DIST_COMMON)
 am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \
  configure.lineno config.status.lineno
 mkinstalldirs = $(SHELL) $(top_srcdir)/config/mkinstalldirs
@@ -163,6 +162,18 @@ ETAGS = etags
 CTAGS = ctags
 CSCOPE = cscope
 DIST_SUBDIRS = $(SUBDIRS)
+am__DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/cdo.settings.in \
+	$(srcdir)/cdo.spec.in $(top_srcdir)/config/ar-lib \
+	$(top_srcdir)/config/compile $(top_srcdir)/config/config.guess \
+	$(top_srcdir)/config/config.sub \
+	$(top_srcdir)/config/install-sh $(top_srcdir)/config/ltmain.sh \
+	$(top_srcdir)/config/missing \
+	$(top_srcdir)/config/mkinstalldirs \
+	$(top_srcdir)/config/tap-driver.sh AUTHORS COPYING ChangeLog \
+	INSTALL NEWS README config/ar-lib config/compile \
+	config/config.guess config/config.sub config/depcomp \
+	config/install-sh config/ltmain.sh config/missing \
+	config/mkinstalldirs
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 distdir = $(PACKAGE)-$(VERSION)
 top_distdir = $(distdir)
@@ -407,7 +418,6 @@ $(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am  $(am__confi
 	echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign Makefile'; \
 	$(am__cd) $(top_srcdir) && \
 	  $(AUTOMAKE) --foreign Makefile
-.PRECIOUS: Makefile
 Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	@case '$?' in \
 	  *config.status*) \
@@ -611,7 +621,7 @@ distdir: $(DISTFILES)
 	  ! -type d ! -perm -444 -exec $(install_sh) -c -m a+r {} {} \; \
 	|| chmod -R a+r "$(distdir)"
 dist-gzip: distdir
-	tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz
+	tardir=$(distdir) && $(am__tar) | eval GZIP= gzip $(GZIP_ENV) -c >$(distdir).tar.gz
 	$(am__post_remove_distdir)
 
 dist-bzip2: distdir
@@ -627,17 +637,17 @@ dist-xz: distdir
 	$(am__post_remove_distdir)
 
 dist-tarZ: distdir
-	@echo WARNING: "Support for shar distribution archives is" \
-	               "deprecated." >&2
+	@echo WARNING: "Support for distribution archives compressed with" \
+		       "legacy program 'compress' is deprecated." >&2
 	@echo WARNING: "It will be removed altogether in Automake 2.0" >&2
 	tardir=$(distdir) && $(am__tar) | compress -c >$(distdir).tar.Z
 	$(am__post_remove_distdir)
 
 dist-shar: distdir
-	@echo WARNING: "Support for distribution archives compressed with" \
-		       "legacy program 'compress' is deprecated." >&2
+	@echo WARNING: "Support for shar distribution archives is" \
+	               "deprecated." >&2
 	@echo WARNING: "It will be removed altogether in Automake 2.0" >&2
-	shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz
+	shar $(distdir) | eval GZIP= gzip $(GZIP_ENV) -c >$(distdir).shar.gz
 	$(am__post_remove_distdir)
 
 dist-zip: distdir
@@ -655,7 +665,7 @@ dist dist-all:
 distcheck: dist
 	case '$(DIST_ARCHIVES)' in \
 	*.tar.gz*) \
-	  GZIP=$(GZIP_ENV) gzip -dc $(distdir).tar.gz | $(am__untar) ;;\
+	  eval GZIP= gzip $(GZIP_ENV) -dc $(distdir).tar.gz | $(am__untar) ;;\
 	*.tar.bz2*) \
 	  bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\
 	*.tar.lz*) \
@@ -665,22 +675,23 @@ distcheck: dist
 	*.tar.Z*) \
 	  uncompress -c $(distdir).tar.Z | $(am__untar) ;;\
 	*.shar.gz*) \
-	  GZIP=$(GZIP_ENV) gzip -dc $(distdir).shar.gz | unshar ;;\
+	  eval GZIP= gzip $(GZIP_ENV) -dc $(distdir).shar.gz | unshar ;;\
 	*.zip*) \
 	  unzip $(distdir).zip ;;\
 	esac
 	chmod -R a-w $(distdir)
 	chmod u+w $(distdir)
-	mkdir $(distdir)/_build $(distdir)/_inst
+	mkdir $(distdir)/_build $(distdir)/_build/sub $(distdir)/_inst
 	chmod a-w $(distdir)
 	test -d $(distdir)/_build || exit 0; \
 	dc_install_base=`$(am__cd) $(distdir)/_inst && pwd | sed -e 's,^[^:\\/]:[\\/],/,'` \
 	  && dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \
 	  && am__cwd=`pwd` \
-	  && $(am__cd) $(distdir)/_build \
-	  && ../configure --srcdir=.. --prefix="$$dc_install_base" \
+	  && $(am__cd) $(distdir)/_build/sub \
+	  && ../../configure \
 	    $(AM_DISTCHECK_CONFIGURE_FLAGS) \
 	    $(DISTCHECK_CONFIGURE_FLAGS) \
+	    --srcdir=../.. --prefix="$$dc_install_base" \
 	  && $(MAKE) $(AM_MAKEFLAGS) \
 	  && $(MAKE) $(AM_MAKEFLAGS) dvi \
 	  && $(MAKE) $(AM_MAKEFLAGS) check \
@@ -857,6 +868,8 @@ uninstall-am:
 	mostlyclean mostlyclean-generic mostlyclean-libtool pdf pdf-am \
 	ps ps-am tags tags-am uninstall uninstall-am
 
+.PRECIOUS: Makefile
+
 
 # Tell versions [3.59,3.63) of GNU make to not export all variables.
 # Otherwise a system limit (for SysV at least) may be exceeded.

src/Makefile.am

@@ -162,6 +162,7 @@ libcdo_la_SOURCES =            \
                uthash.h        \
                util.cc          \
                util.h          \
+			   varlist.h		\
                zaxis_print.cc   \
                zaxis.cc
 libcdo_la_SOURCES +=           \

src/Makefile.in

-# Makefile.in generated by automake 1.14 from Makefile.am.
+# Makefile.in generated by automake 1.15 from Makefile.am.
 # @configure_input@
-# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+# Copyright (C) 1994-2014 Free Software Foundation, Inc.
 # This Makefile.in is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -16,7 +16,17 @@
 VPATH = @srcdir@
-am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__is_gnu_make = { \
+  if test -z '$(MAKELEVEL)'; then \
+    false; \
+  elif test -n '$(MAKE_HOST)'; then \
+    true; \
+  elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \
+    true; \
+  else \
+    false; \
+  fi; \
+}
 am__make_running_with_option = \
   case $${target_option-} in \
       ?) ;; \
@@ -84,9 +94,6 @@ bin_PROGRAMS = cdo$(EXEEXT)
 noinst_PROGRAMS = cdotest$(EXEEXT)
 @ENABLE_ALL_STATIC_TRUE@am__append_2 = -all-static
 subdir = src
-DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
-	$(srcdir)/config.h.in $(top_srcdir)/config/mkinstalldirs \
-	$(top_srcdir)/config/depcomp
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
 am__aclocal_m4_deps = $(top_srcdir)/m4/acx_options.m4 \
 	$(top_srcdir)/m4/ax_cxx_compile_stdcxx.m4 \
@@ -97,6 +104,7 @@ am__aclocal_m4_deps = $(top_srcdir)/m4/acx_options.m4 \
 	$(top_srcdir)/acinclude.m4 $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
+DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON)
 mkinstalldirs = $(SHELL) $(top_srcdir)/config/mkinstalldirs
 CONFIG_HEADER = config.h
 CONFIG_CLEAN_FILES =
@@ -355,6 +363,9 @@ am__define_uniq_tagged_files = \
   done | $(am__uniquify_input)`
 ETAGS = etags
 CTAGS = ctags
+am__DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/config.h.in \
+	$(top_srcdir)/config/depcomp \
+	$(top_srcdir)/config/mkinstalldirs
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 ACLOCAL = @ACLOCAL@
 AMTAR = @AMTAR@
@@ -569,8 +580,8 @@ libcdo_la_SOURCES = array.h array.cc cdo_int.h compare.h \
 	remap_bicubic_scrip.cc remap_bilinear_scrip.cc stdnametable.cc \
 	stdnametable.h specspace.cc specspace.h statistic.cc \
 	statistic.h table.cc text.cc text.h timebase.h timer.cc \
-	userlog.cc uthash.h util.cc util.h zaxis_print.cc zaxis.cc \
-	json/jsmn.h json/jsmn.c kdtreelib/kdtree.h \
+	userlog.cc uthash.h util.cc util.h varlist.h zaxis_print.cc \
+	zaxis.cc json/jsmn.h json/jsmn.c kdtreelib/kdtree.h \
 	kdtreelib/kdtree_cartesian.cc kdtreelib/kdtree_common.cc \
 	kdtreelib/kdtree_spherical.cc kdtreelib/qsort.cc \
 	kdtreelib/pmergesort.cc kdtreelib/pqueue.cc kdtreelib/pqueue.h \
@@ -669,7 +680,6 @@ $(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am  $(am__confi
 	echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign src/Makefile'; \
 	$(am__cd) $(top_srcdir) && \
 	  $(AUTOMAKE) --foreign src/Makefile
-.PRECIOUS: Makefile
 Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	@case '$?' in \
 	  *config.status*) \
@@ -5037,6 +5047,8 @@ uninstall-am: uninstall-binPROGRAMS
 	pdf pdf-am ps ps-am tags tags-am uninstall uninstall-am \
 	uninstall-binPROGRAMS
+.PRECIOUS: Makefile
+
 #
 clean-local: clean-local-dirs
 .PHONY: clean-local-dirs

src/pipe.h

@@ -29,44 +29,10 @@
 
 #include <pthread.h>
 #include "pthread_debug.h"
+#include "pstream.h"
 
 #endif
 
-typedef struct {
-  bool        check_datarange;
-  int         gridsize;
-  int         datatype;
-  double      missval;
-  double      addoffset;
-  double      scalefactor;
-} varlist_t;
-
-
-typedef struct {
-  int            self;
-  int            mode;
-  int            fileID;
-  int            vlistID;
-  int            tsID;
-  int            filetype;
-  int            tsID0;
-  int            mfiles;
-  int            nfiles;
-  int            varID;           /* next varID defined with streamDefVar */
-  bool           ispipe;
-  bool           isopen;
-  char          *name;
-  char         **mfnames;
-  varlist_t     *varlist;
-#if defined(HAVE_LIBPTHREAD)
-  void          *argument;
-  struct pipe_s *pipe;
-  pthread_t     rthreadID; /* read  thread ID */
-  pthread_t     wthreadID; /* write thread ID */
-#endif
-} pstream_t;
-
-
 #if defined(HAVE_LIBPTHREAD)
 
 struct pipe_s {

src/process.cc

@@ -40,6 +40,7 @@
 #include "util.h"
 #include "pstream_int.h"
 #include "dmemory.h"
+#include "pthread.h"
 
 #if defined(HAVE_LIBPTHREAD)
 pthread_mutex_t processMutex = PTHREAD_MUTEX_INITIALIZER;
@@ -385,29 +386,6 @@ const char *processOperator(void)
   return Process[processID].xoperator;
 }
 
-static
-char *getOperatorArg(const char *xoperator)
-{
-  char *operatorArg = NULL;
-
-  if ( xoperator )
-    {
-      char *commapos = (char *)strchr(xoperator, ',');
-
-      if ( commapos )
-        {
-          size_t len = strlen(commapos+1);
-          if ( len )
-            {
-              operatorArg = (char*) Malloc(len+1);
-              strcpy(operatorArg, commapos+1);
-            }
-        }
-    }
-
-  return operatorArg;
-}
-
 static int skipInputStreams(int argc, char *argv[], int globArgc, int nstreams);
 
 static
@@ -1000,3 +978,36 @@ int cdoStreamNumber()
 
   return operatorStreamNumber(Process[processID].operatorName);
 }
+
+void print_process(int p_process_id)
+{
+#if defined(HAVE_LIBPTHREAD)
+  std::cout << " threadID        : " << Process[p_process_id].threadID                     <<  std::endl;
+  std::cout << " l_threadID      : " << Process[p_process_id].l_threadID                   <<  std::endl;
+#endif
+  std::cout << " nchild          : " << Process[p_process_id].nchild                       <<  std::endl;
+  std::cout << " nInStream       : " << Process[p_process_id].nInStream                    <<  std::endl;
+  std::cout << " nOutStream      : " << Process[p_process_id].nOutStream                   <<  std::endl;
+  for(int i = 0; i < Process[p_process_id].nInStream; i++){
+    std::cout << "    " << Process[p_process_id].inputStreams[i]  <<  std::endl;
+  }
+  for(int i = 0; i < Process[p_process_id].nOutStream; i++){
+    std::cout << "    " << Process[p_process_id].outputStreams[i] <<  std::endl;
+  }
+  std::cout << " s_utime         : " << Process[p_process_id].s_utime                      <<  std::endl;
+  std::cout << " s_stime         : " << Process[p_process_id].s_stime                      <<  std::endl;
+  std::cout << " a_utime         : " << Process[p_process_id].a_utime                      <<  std::endl;
+  std::cout << " a_stime         : " << Process[p_process_id].a_stime                      <<  std::endl;
+  std::cout << " cputime         : " << Process[p_process_id].cputime                      <<  std::endl;
+
+  std::cout << " nvals           : " << Process[p_process_id].nvals                        <<  std::endl;
+  std::cout << " nvars           : " << Process[p_process_id].nvars                        <<  std::endl;
+  std::cout << " ntimesteps      : " << Process[p_process_id].ntimesteps                   <<  std::endl;
+  std::cout << " streamCnt       : " << Process[p_process_id].streamCnt                    <<  std::endl;
+  std::cout << " streamNames     : " << Process[p_process_id].streamNames                  <<  std::endl;
+  std::cout << " xoperator       : " << Process[p_process_id].xoperator                    <<  std::endl;
+  std::cout << " operatorName    : " << Process[p_process_id].operatorName                 <<  std::endl;
+  std::cout << " operatorArg     : " << Process[p_process_id].operatorArg                  <<  std::endl;
+  std::cout << " oargc           : " << Process[p_process_id].oargc                        <<  std::endl;
+  std::cout << " noper           : " << Process[p_process_id].noper                        <<  std::endl;
+}

src/process.h

@@ -104,4 +104,5 @@ const char *processInqOpername(void);
 const char *processInqOpername2(int processID);
 const char *processInqPrompt(void);
 
+void print_process(int p_process_id);
 #endif  /* _PROCESS_H */

src/pstream.cc

@@ -290,12 +290,12 @@ static void createPipeName(char *pipename, int pnlen){
   snprintf(pipename, pnlen, "(pipe%d.%d)", processSelf() + 1, processInqChildNum() + 1);
 }
 
-static pthread_t pCreateReadThread(char *newarg, argument_t *argument, const char *operatorName){
+pthread_t pCreateReadThread(argument_t *argument){
   pthread_attr_t attr;
   int status = pthread_attr_init(&attr);
-  if ( status ) SysError("pthread_attr_init failed for '%s'", newarg+1);
+  if ( status ) SysError("pthread_attr_init failed for '%s'", argument->operatorName);
   status = pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
-  if ( status ) SysError("pthread_attr_setdetachstate failed for '%s'", newarg+1);
+  if ( status ) SysError("pthread_attr_setdetachstate failed for '%s'", argument->operatorName);
   /*
     param.sched_priority = 0;
     status = pthread_attr_setschedparam(&attr, &param);
@@ -320,11 +320,11 @@ static pthread_t pCreateReadThread(char *newarg, argument_t *argument, const cha
     }
 
   pthread_t thrID;
-  int rval = pthread_create(&thrID, &attr, operatorModule(operatorName), argument);
+  int rval = pthread_create(&thrID, &attr, operatorModule(argument->operatorName.c_str()), argument);
   if ( rval != 0 )
     {
       errno = rval;
-      SysError("pthread_create failed for '%s'", newarg+1);
+      SysError("pthread_create failed for '%s'", argument->operatorName);
     }
   return thrID;
 }
@@ -339,9 +339,10 @@ void pstreamOpenReadPipe(const argument_t *argument, pstream_t *pstreamptr)
   char *pipename = (char*) Malloc(pnlen);
   // struct sched_param param;
   
-  argument_t *newargument = (argument_t*) Malloc(sizeof(argument_t));
+  argument_t *newargument = new argument_t();
   newargument->argc = argument->argc + 1;
   newargument->argv = (char **) Malloc(newargument->argc*sizeof(char *));
+  newargument->operatorName = "";
   memcpy(newargument->argv, argument->argv, argument->argc*sizeof(char *));
 
   char *operatorArg  = argument->argv[0];
@@ -356,6 +357,7 @@ void pstreamOpenReadPipe(const argument_t *argument, pstream_t *pstreamptr)
 
   newargument->argv[argument->argc] = pipename;
   newargument->args = newarg;
+  newargument->operatorName = std::string(operatorName,strlen(operatorName));
   /*
     printf("pstreamOpenRead: new args >%s<\n", newargument->args);
     for ( int i = 0; i < newargument->argc; ++i )
@@ -370,7 +372,7 @@ void pstreamOpenReadPipe(const argument_t *argument, pstream_t *pstreamptr)
   if ( ! cdoSilentMode ){
     cdoPrint("Started child process \"%s\".", newarg+1);
   }
-  pCreateReadThread(newarg, newargument, operatorName);
+  pCreateReadThread(newargument);
   /* Free(operatorName); */
   processAddInputStream(pstreamID);
   /*      pipeInqInfo(pstreamID); */
@@ -887,7 +889,7 @@ void pstreamClose(int pstreamID)
 	      argument_t *argument = (argument_t *) (pstreamptr->argument);
 	      if ( argument->argv ) Free(argument->argv);
 	      if ( argument->args ) Free(argument->args);
-	      Free(argument);
+          delete(argument);
 	    }
 	  vlistDestroy(pstreamptr->vlistID);
 	  pthread_mutex_unlock(pipe->mutex);

src/pstream.h

@@ -19,9 +19,34 @@
 #define PSTREAM_H
 
 #include "pstream_write.h"
+#include "varlist.h"
 
 #include <sys/types.h> /* off_t */
 
+typedef struct {
+  int            self;
+  int            mode;
+  int            fileID;