Add configure-time checking and override for external packing.

.gitignore

@@ -10,6 +10,8 @@ gmon.out
 /aclocal.m4
 /configure
 /config
+!/config/checksrc
+!/config/checkdoc
 config.h
 config.log
 config.status

config/checkdoc/test_mpi_pack_external_1.txt

+Your MPI installation has a serious defect in its implementation of
+external32 packing of data. This is the only serialization guaranteed
+to be portable across different MPI communicators. You can elect to
+use the regular data packing routines instead, for which such
+portability is not guaranteed, but often works in practice with the
+configure argument --without-mpi-pack-external. Alternatively you can
+ignore the result of this test with the --without-regard-for-quality
+option but this will probably result in a non-working YAC build,
+i.e. multiple tests will fail.

config/checkdoc/test_mpi_pack_external_2.txt

+test_mpi_pack_external_1.txt
\ No newline at end of file

config/checksrc/test_mpi_pack_external_1.c

+#include <mpi.h>
+#include <stdlib.h>
+#include <stdio.h>
+
+static void mpi_err_handler(int error_code, MPI_Comm comm);
+
+char const * datarep = "external32";
+
+#define UINT_COUNT (2)
+#define DBLE_COUNT (24)
+
+int main(void) {
+
+  MPI_Init(NULL, NULL);
+
+  unsigned * uint_data = calloc(UINT_COUNT, sizeof(*uint_data));
+  double * dble_data = calloc(DBLE_COUNT, sizeof(*dble_data));
+
+  MPI_Aint uint_pack_size, dble_pack_size;
+
+  mpi_err_handler(MPI_Pack_external_size(datarep, UINT_COUNT, MPI_UNSIGNED,
+                                         &uint_pack_size), MPI_COMM_WORLD);
+  mpi_err_handler(MPI_Pack_external_size(datarep, DBLE_COUNT, MPI_DOUBLE,
+                                         &dble_pack_size), MPI_COMM_WORLD);
+
+  MPI_Aint pack_size = uint_pack_size + dble_pack_size;
+
+  void * pack_buffer = malloc(pack_size);
+  MPI_Aint position = 0;
+
+#ifndef WITHOUT_PACK_EXTERNAL
+#define BUG
+#ifdef BUG
+  mpi_err_handler(MPI_Pack_external(datarep, uint_data, UINT_COUNT,
+                                    MPI_UNSIGNED, pack_buffer, pack_size,
+                                    &position), MPI_COMM_WORLD);
+  mpi_err_handler(MPI_Pack_external(datarep, dble_data, DBLE_COUNT, MPI_DOUBLE,
+                                    pack_buffer, pack_size, &position),
+                  MPI_COMM_WORLD);
+#else // NO_BUG
+  mpi_err_handler(MPI_Pack_external(datarep, dble_data, DBLE_COUNT, MPI_DOUBLE,
+                                    pack_buffer, pack_size, &position),
+                  MPI_COMM_WORLD);
+  mpi_err_handler(MPI_Pack_external(datarep, uint_data, UINT_COUNT,
+                                    MPI_UNSIGNED, pack_buffer, pack_size,
+                                    &position), MPI_COMM_WORLD);
+#endif // NO_BUG
+#endif // WITHOUT_PACK_EXTERNAL
+
+  free(pack_buffer);
+  free(dble_data);
+  free(uint_data);
+
+  MPI_Finalize();
+
+  return EXIT_SUCCESS;
+}
+
+//taken from http://beige.ucs.indiana.edu/I590/node85.html
+static void mpi_err_handler(int error_code, MPI_Comm comm) {
+
+   if (error_code != MPI_SUCCESS) {
+
+      int rank;
+
+      MPI_Comm_rank(comm, &rank);
+
+      char error_string[1024];
+      int length_of_error_string, error_class;
+
+      MPI_Error_class(error_code, &error_class);
+      MPI_Error_string(error_class, error_string, &length_of_error_string);
+      fprintf(stderr, "%3d: %s\n", rank, error_string);
+      MPI_Error_string(error_code, error_string, &length_of_error_string);
+      fprintf(stderr, "%3d: %s\n", rank, error_string);
+      MPI_Abort(comm, error_code);
+   }
+}

config/checksrc/test_mpi_pack_external_2.c

+#include <mpi.h>
+#include <stdlib.h>
+#include <stdio.h>
+
+static void mpi_err_handler(int error_code, MPI_Comm comm);
+
+char const * datarep = "external32";
+
+int main(void) {
+
+  int exit_code = EXIT_SUCCESS;
+
+  MPI_Init(NULL, NULL);
+
+#ifndef WITHOUT_PACK_EXTERNAL
+
+  int send_data[2] = {93184, -9023};
+  int recv_data[2];
+
+  MPI_Aint pack_size;
+  mpi_err_handler(MPI_Pack_external_size(datarep, 2, MPI_INT, &pack_size),
+                  MPI_COMM_WORLD);
+
+  char * buffer = malloc(pack_size);
+  MPI_Aint position = 0;
+
+  mpi_err_handler(MPI_Pack_external(datarep, send_data, 2, MPI_INT, buffer,
+                                    pack_size, &position), MPI_COMM_WORLD);
+  position = 0;
+  mpi_err_handler(MPI_Unpack_external(datarep, buffer, pack_size, &position,
+                                      recv_data, 2, MPI_INT), MPI_COMM_WORLD);
+
+  free(buffer);
+
+  if ((send_data[0] != recv_data[0]) || (send_data[1] != recv_data[1]))
+    exit_code = EXIT_FAILURE;
+
+#endif // WITHOUT_PACK_EXTERNAL
+
+  MPI_Finalize();
+
+  return exit_code;
+}
+
+//taken from http://beige.ucs.indiana.edu/I590/node85.html
+static void mpi_err_handler(int error_code, MPI_Comm comm) {
+
+   if (error_code != MPI_SUCCESS) {
+
+      int rank;
+
+      MPI_Comm_rank(comm, &rank);
+
+      char error_string[1024];
+      int length_of_error_string, error_class;
+
+      MPI_Error_class(error_code, &error_class);
+      MPI_Error_string(error_class, error_string, &length_of_error_string);
+      fprintf(stderr, "%3d: %s\n", rank, error_string);
+      MPI_Error_string(error_code, error_string, &length_of_error_string);
+      fprintf(stderr, "%3d: %s\n", rank, error_string);
+      MPI_Abort(comm, error_code);
+   }
+}

configure.ac

@@ -52,10 +52,36 @@ AS_IF([test x"$enable_MPI" = xno],
   ])
 AS_IF([test x"$enable_MPI" = xyes],
   [AC_DEFINE([USE_MPI],[1],[use MPI parallel process environment])
-   AC_CHECK_PROGS([MPI_LAUNCH],[mpirun mpiexec],[])
-   AS_IF([test x$MPI_LAUNCH = x],
-     [AC_MSG_FAILURE([MPI launcher (MPI_LAUNCH) not found])])
-   AC_SUBST([HAVE_MPI],[1])],
+   AC_SUBST([HAVE_MPI],[1])
+   saved_CFLAGS=$CFLAGS
+   saved_FCFLAGS=$FCFLAGS
+   saved_LIBS=$LIBS
+   CFLAGS="$CFLAGS $MPI_C_INCLUDE"
+   FCFLAGS="$FCFLAGS $MPI_FC_INCLUDE"
+   LIBS="$LIBS $MPI_C_LIB"
+   ACX_MPIRUN
+   # check MPI defects
+   AC_ARG_WITH([regard-for-quality],
+     [AS_HELP_STRING([--without-regard-for-quality],
+        [ignore results of checks for known defects @<:@default: abort on error@:>@])],
+     [],[with_regard_for_quality=yes])
+   AC_ARG_WITH([pack-external],
+     [AS_HELP_STRING([--without-pack-external],
+        [use MPI_Pack (not guaranteed to work) instead of MPI_Pack_external @<:@default: yes, use MPI_Pack_external@:>@])],,[with_pack_external=yes])
+   AS_IF([test x"$with_pack_external" = xyes],,
+     [CPPFLAGS="${CPPFLAGS+$CPPFLAGS }-DWITHOUT_PACK_EXTERNAL"])
+   ACX_MPI_DEFECTS(,,
+     [ACX_MPI_DEFECTS_DOCUMENT
+      AS_CASE(["$acx_subtestname"],[test_mpi_pack_external_*],
+        [AC_MSG_ERROR([Warning, known problem with MPI_Pack_external detected, please look into the description in config/checkdoc/${acx_subtestname}.txt!])])
+      AS_IF([test "$with_regard_for_quality" != no],
+        [AC_MSG_FAILURE([test for known defect $subtestname failed, re-configure with --without-regard-for-quality in case you must use the given MPI implementation, but some tests might fail])])])
+AS_IF([test "x$MPI_LAUNCH" = xtrue],
+  [AC_MSG_WARN([MPI launch command unavailable])])
+FCFLAGS=$saved_FCFLAGS
+CFLAGS=$saved_CFLAGS
+LIBS=$saved_LIBS
+   ],
   [MPI_LAUNCH="`pwd`/util/serialrun"
    AC_SUBST([MPI_LAUNCH])
    AC_SUBST([HAVE_MPI],[0])])

m4/acx_mpi_defects.m4

+dnl acx_mpi_defects.m4 --- check whether MPI has one or more of
+dnl                        several known defects
+dnl
+dnl Copyright  (C)  2014  Thomas Jahns <jahns@dkrz.de>
+dnl
+dnl Keywords: configure configure.ac autoconf MPI mpirun mpiexec
+dnl Author: Thomas Jahns <jahns@dkrz.de>
+dnl Maintainer: Thomas Jahns <jahns@dkrz.de>
+dnl URL: https://www.dkrz.de/redmine/projects/show/scales-ppm
+dnl
+dnl Redistribution and use in source and binary forms, with or without
+dnl modification, are  permitted provided that the following conditions are
+dnl met:
+dnl
+dnl Redistributions of source code must retain the above copyright notice,
+dnl this list of conditions and the following disclaimer.
+dnl
+dnl Redistributions in binary form must reproduce the above copyright
+dnl notice, this list of conditions and the following disclaimer in the
+dnl documentation and/or other materials provided with the distribution.
+dnl
+dnl Neither the name of the DKRZ GmbH nor the names of its contributors
+dnl may be used to endorse or promote products derived from this software
+dnl without specific prior written permission.
+dnl
+dnl THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+dnl IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+dnl TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+dnl PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+dnl OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+dnl EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+dnl PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+dnl PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+dnl LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+dnl NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+dnl SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+dnl
+dnl
+dnl ACX_MPI_DEFECTS([TEST-SOURCE-DIR=config/checksrc],
+dnl                 [ACTION-IF-CHECK-SUCCEEDS],
+dnl                 [ACTION-IF-CHECK-FAILED=AC_MSG_FAILURE])
+dnl
+dnl Requires MPI_LAUNCH program. Also CC/FC must be setup to
+dnl build MPI programs.
+dnl Builds and runs simple programs from TEST-SOURCE-DIR, each of which
+dnl should represent a test for a known defect that affects the library
+dnl code.
+dnl Each test is built according to it's file suffix as either Fortran
+dnl or C MPI program.
+dnl Within ACTION-IF-CHECK-SUCCEEDS and ACTION-IF-CHECK-FAILED,
+dnl the following variables are set to test-specific values:
+dnl acx_subtestname = base file name of the test
+dnl acx_mpi_check_src = path to check source file
+dnl acx_suffix = file suffix of source file
+dnl
+dnl Each test source may contain zero or more of the following stanzas
+dnl acx_mpirun_num_tasks = N
+dnl   specify number of tasks N (positive integer) to run this test with
+dnl TODO: extend for F77 and C++
+AC_DEFUN([ACX_MPI_DEFECTS],
+  [AS_IF([test x"$MPI_LAUNCH" = xtrue],
+     [AC_MSG_NOTICE([Skipping tests for known MPI defects: MPI launcher unavailable])],
+     [AC_MSG_CHECKING([MPI for known defects])
+      AC_MSG_RESULT([])
+      for acx_mpi_check_src in "$srcdir/m4_ifval([$1],[$1],[config/checksrc])/"* ; do
+        acx_suffix=`echo "$acx_mpi_check_src" | sed 's/^.*\.\(@<:@^.@:>@*\)$/\1/'`
+        acx_subtestname=`echo "$acx_mpi_check_src" | sed 's/^.*\/\(@<:@^\/@:>@*\)\.@<:@^.@:>@*/\1/'`
+        AS_CASE([$acx_suffix],
+          [c],
+          [cat confdefs.h "$acx_mpi_check_src" >conftest."$acx_suffix"
+           AC_LANG_PUSH([C])],
+          [f90|F90],[cat "$acx_mpi_check_src" >conftest."$acx_suffix"
+           AC_LANG_PUSH([Fortran])],
+          [AC_MSG_FAILURE([Unexpected language in MPI check: ${acx_subtestname}.${acx_suffix}])])
+        AC_MSG_CHECKING([$acx_subtestname])
+        acx_mpirun_num_tasks=`sed -n '/acx_mpirun_num_tasks *= *\(@<:@0-9@:>@*\)/{
+s/.*acx_mpirun_num_tasks *= *\(@<:@0-9@:>@*\).*/\1/
+p
+q
+}
+' "$acx_mpi_check_src"`
+        AS_IF([test `expr "$acx_mpirun_num_tasks" : "@<:@0-9@:>@@<:@0-9@:>@*$"` -gt 0 \
+               && test "$acx_mpirun_num_tasks" -gt 0],,
+          [acx_mpirun_num_tasks=1])
+        AC_LINK_IFELSE(,
+          [acx_mpirun_num_tasks="$MPI_LAUNCH -n $acx_mpirun_num_tasks ./conftest$EXEEXT"
+           AC_TRY_EVAL([acx_mpirun_num_tasks])
+           AS_IF([test $ac_status -eq 0],
+             [AC_MSG_RESULT([okay])m4_ifval([$2],[
+              $2])],
+             [AC_MSG_RESULT([error])
+              m4_ifval([$3],[$3],
+                [AC_MSG_FAILURE([chosen MPI has known error $acx_subtestname])])])],
+          [AC_MSG_RESULT([error])
+           m4_ifval([$3],[$3],
+             [AC_MSG_RESULT([chosen MPI has known error $acx_subtestname])])])
+        AS_CASE([$acx_suffix],
+          [f90|F90],[AC_LANG_POP([Fortran])],
+          [c],[AC_LANG_POP([C])])
+      done
+      ASX_VAR_UNSET([acx_mpirun_num_tasks])
+      ASX_VAR_UNSET([acx_mpi_check_src])
+      ASX_VAR_UNSET([acx_suffix])
+      ASX_VAR_UNSET([acx_subtestname])
+     ])])
+dnl dump text documentation of defect test to stderr
+dnl ACX_MPI_DEFECTS_DOCUMENT([TEST-DOC-DIR=config/checkdoc])
+AC_DEFUN([ACX_MPI_DEFECTS_DOCUMENT],
+  [AS_IF([test -r "$srcdir/m4_ifval([$1],[$1],[config/checkdoc])/${acx_subtestname}.txt"],
+             [cat "$srcdir/m4_ifval([$1],[$1],[config/checkdoc])/${acx_subtestname}.txt" >&2])])
+dnl
+dnl Local Variables:
+dnl mode: autoconf
+dnl license-project-url: "https://www.dkrz.de/redmine/projects/show/scales-ppm"
+dnl license-default: "bsd"
+dnl End:

m4/acx_mpirun.m4

+dnl acx_mpirun.m4 --- check whether launching MPI programs works
+dnl
+dnl Copyright  (C)  2014  Thomas Jahns <jahns@dkrz.de>
+dnl
+dnl Keywords: configure configure.ac autoconf MPI mpirun mpiexec
+dnl Author: Thomas Jahns <jahns@dkrz.de>
+dnl Maintainer: Thomas Jahns <jahns@dkrz.de>
+dnl URL: https://www.dkrz.de/redmine/projects/show/scales-ppm
+dnl
+dnl Redistribution and use in source and binary forms, with or without
+dnl modification, are  permitted provided that the following conditions are
+dnl met:
+dnl
+dnl Redistributions of source code must retain the above copyright notice,
+dnl this list of conditions and the following disclaimer.
+dnl
+dnl Redistributions in binary form must reproduce the above copyright
+dnl notice, this list of conditions and the following disclaimer in the
+dnl documentation and/or other materials provided with the distribution.
+dnl
+dnl Neither the name of the DKRZ GmbH nor the names of its contributors
+dnl may be used to endorse or promote products derived from this software
+dnl without specific prior written permission.
+dnl
+dnl THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+dnl IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+dnl TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+dnl PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+dnl OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+dnl EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+dnl PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+dnl PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+dnl LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+dnl NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+dnl SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+dnl
+dnl
+dnl ACX_MPIRUN([NUM_TASKS=4],[ACTION-IF-WORKING],
+dnl            [ACTION-IF-RUN-FAILS=AC_MSG_FAILURE],
+dnl            [ACTION-IF-BUILD-FAILS=AC_MSG_FAILURE])
+dnl
+dnl First determines mpi launcher program (and sets MPI_LAUNCH to its path),
+dnl then builds and runs simple program with 4 tasks
+dnl (or NUM_TASKS if specified).
+dnl MPI_LAUNCH is either set to a valid MPI launcher program path (unless
+dnl cross-compiling, because it can't be tested then) or true (when it
+dnl doesn't work).
+dnl
+dnl TODO: instead of setting C language, perform test for active AC_LANG
+AC_DEFUN([ACX_MPIRUN],
+  [AC_PATH_PROGS([MPI_LAUNCH],[mpirun mpiexec],[true])
+   AC_ARG_VAR([MPI_LAUNCH],[absolute path to launcher for MPI programs, must be working unless configuring in cross-compilation mode])
+   AS_IF([test x"$cross_compiling" = xno -a x"$MPI_LAUNCH" != xtrue],
+     [AC_MSG_CHECKING([if $MPI_LAUNCH works])
+      AC_LANG_PUSH([C])
+      AC_LINK_IFELSE([AC_LANG_SOURCE([
+@%:@include <stdio.h>
+@%:@include <stdlib.h>
+
+@%:@include <mpi.h>
+
+@%:@define xmpi(ret)           \\
+  do {                      \\
+    if (ret != MPI_SUCCESS) \\
+      exit(EXIT_FAILURE);   \\
+  } while (0)
+
+int
+main(int argc, char **argv)
+{
+  xmpi(MPI_Init(&argc, &argv));
+  char *numarg = argv@<:@1@:>@;
+  int cmdnum = atoi(numarg);
+  int procnum = 1;
+  xmpi(MPI_Allreduce(MPI_IN_PLACE, &procnum, 1, MPI_INT, MPI_SUM,
+                     MPI_COMM_WORLD));
+  xmpi(MPI_Finalize());
+  return (procnum == cmdnum)?EXIT_SUCCESS:EXIT_FAILURE;
+}
+])],
+        [AS_IF([$MPI_LAUNCH -n m4_ifval([$1],[$1],[4]) ./conftest$EXEEXT m4_ifval([$1],[$1],[4])],
+           [AC_MSG_RESULT([yes])],
+           [AC_MSG_RESULT([no])
+            MPI_LAUNCH=true])],
+        [MPI_LAUNCH=true
+         m4_ifval([$3],[$3],[AC_MSG_FAILURE([Cannot compile simple MPI program])])])
+      AC_LANG_POP([C])])
+   AS_IF([test x"$MPI_LAUNCH" = xtrue],
+     [m4_ifval([$3],[$3],[AC_MSG_FAILURE([failed to run MPI programs])])],
+     [$2])
+])
+dnl
+dnl Local Variables:
+dnl mode: autoconf
+dnl license-project-url: "https://www.dkrz.de/redmine/projects/show/scales-ppm"
+dnl license-default: "bsd"
+dnl End: