Re: [netcdf-hdf] errors building netcdf4 for parallel I/O

NOTE: The netcdf-hdf mailing list is no longer active. The list archives are made available for historical reasons.

On Wed, Sep 12, 2007 at 02:55:42PM -0500, Quincey Koziol wrote:
>       This should probably be "H5Pget_fapl_mpio" instead.

Indeed it should.  A little search and replace on configure got us
past that issue.  Now USE_PARALLEL_MPIO gets defined, but that's not
the true cause of the build errors I was seeing.

On Wed, Sep 12, 2007 at 01:55:54PM -0600, Ed Hartnett wrote:
> Try commenting out the two lines that redefine MPI_Comm and
> MPI_Info...

Ed is the winner!

It turns out libsrc4/netcdf.h has some incorrect checks with regards
to MPI: the '#ifndef MPI_Comm' and '#ifndef MPI_Info' checks just
won't work with MPICH2.  

I've bludgeoned the code into compiling, and attached the patch. Some
things to note:

- conditionally include mpi.h in libsrc4/netcdf.h

- include config.h in libsrc4/netcdf.h, so as to correctly
  conditionally redefine MPI_Comm and MPI_Info.  Leave Comm and Info
  alone if USE_PARALLEL_MPIO defined.

- rearrange header files to work around brokenness in MPI-2 C++
  standard.  The standard wants SEEK_SET SEEK_CUR and SEEK_END in
  MPI's namespace, but those values collide with those in stdio.h and
  iostream.  Yeah, it's gross.  I had nothing to do with MPI's C++
  interface!

I'm not suggesting you apply the attached patch. Just wanted to
document what I had to do to get things building.  There might be a
more "netcdf4" way to accomplish the same things and if so, fantastic.

Thanks much for all your help.  In the end, I don't think I really
need h5pcc as long as I use mpicc, and --enable-parallel happens
automatically as long as --with-hdf5 and --enable-netcdf4 are given.

==rob

-- 
Rob Latham
Mathematics and Computer Science Division    A215 0178 EA2D B059 8CDF
Argonne National Lab, IL USA                 B29D F333 664A 4280 315B

diff -burpN -x build -x autom4te.cache -x 'cscope*' -x '*~' 
netcdf-4.0-beta1.dist/configure netcdf-4.0-beta1/configure
--- netcdf-4.0-beta1.dist/configure     2007-04-23 07:37:00.000000000 -0500
+++ netcdf-4.0-beta1/configure  2007-09-12 15:06:22.000000000 -0500
@@ -29104,9 +29104,9 @@ _ACEOF
    fi
 
    # The user may have parallel HDF5 based on MPI mumble mumble.
-   { echo "$as_me:$LINENO: checking for H5Pget_fapl_mpipo in -lhdf5" >&5
-echo $ECHO_N "checking for H5Pget_fapl_mpipo in -lhdf5... $ECHO_C" >&6; }
-if test "${ac_cv_lib_hdf5_H5Pget_fapl_mpipo+set}" = set; then
+   { echo "$as_me:$LINENO: checking for H5Pget_fapl_mpio in -lhdf5" >&5
+echo $ECHO_N "checking for H5Pget_fapl_mpio in -lhdf5... $ECHO_C" >&6; }
+if test "${ac_cv_lib_hdf5_H5Pget_fapl_mpio+set}" = set; then
   echo $ECHO_N "(cached) $ECHO_C" >&6
 else
   ac_check_lib_save_LIBS=$LIBS
@@ -29124,11 +29124,11 @@ cat >>conftest.$ac_ext <<_ACEOF
 #ifdef __cplusplus
 extern "C"
 #endif
-char H5Pget_fapl_mpipo ();
+char H5Pget_fapl_mpio ();
 int
 main ()
 {
-return H5Pget_fapl_mpipo ();
+return H5Pget_fapl_mpio ();
   ;
   return 0;
 }
@@ -29151,21 +29151,21 @@ eval "echo \"\$as_me:$LINENO: $ac_try_ec
         test ! -s conftest.err
        } && test -s conftest$ac_exeext &&
        $as_test_x conftest$ac_exeext; then
-  ac_cv_lib_hdf5_H5Pget_fapl_mpipo=yes
+  ac_cv_lib_hdf5_H5Pget_fapl_mpio=yes
 else
   echo "$as_me: failed program was:" >&5
 sed 's/^/| /' conftest.$ac_ext >&5
 
-       ac_cv_lib_hdf5_H5Pget_fapl_mpipo=no
+       ac_cv_lib_hdf5_H5Pget_fapl_mpio=no
 fi
 
 rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
       conftest$ac_exeext conftest.$ac_ext
 LIBS=$ac_check_lib_save_LIBS
 fi
-{ echo "$as_me:$LINENO: result: $ac_cv_lib_hdf5_H5Pget_fapl_mpipo" >&5
-echo "${ECHO_T}$ac_cv_lib_hdf5_H5Pget_fapl_mpipo" >&6; }
-if test $ac_cv_lib_hdf5_H5Pget_fapl_mpipo = yes; then
+{ echo "$as_me:$LINENO: result: $ac_cv_lib_hdf5_H5Pget_fapl_mpio" >&5
+echo "${ECHO_T}$ac_cv_lib_hdf5_H5Pget_fapl_mpio" >&6; }
+if test $ac_cv_lib_hdf5_H5Pget_fapl_mpio = yes; then
   enable_parallel_mpio=yes
 fi
 
diff -burpN -x build -x autom4te.cache -x 'cscope*' -x '*~' 
netcdf-4.0-beta1.dist/configure.ac netcdf-4.0-beta1/configure.ac
--- netcdf-4.0-beta1.dist/configure.ac  2007-04-23 07:36:04.000000000 -0500
+++ netcdf-4.0-beta1/configure.ac       2007-09-12 16:00:49.000000000 -0500
@@ -859,7 +859,7 @@ if test "x$enable_netcdf_4" = xyes; then
    fi
 
    # The user may have parallel HDF5 based on MPI mumble mumble.
-   AC_CHECK_LIB([hdf5], [H5Pget_fapl_mpipo], [enable_parallel_mpio=yes], [])
+   AC_CHECK_LIB([hdf5], [H5Pget_fapl_mpio], [enable_parallel_mpio=yes], [])
    if test "x$enable_parallel_mpio" = xyes; then
       AC_DEFINE([USE_PARALLEL_MPIO], [1], [if true, compile in parallel 
netCDF-4 based on MPI/IO])
    fi
diff -burpN -x build -x autom4te.cache -x 'cscope*' -x '*~' 
netcdf-4.0-beta1.dist/cxx/ncvalues.cpp netcdf-4.0-beta1/cxx/ncvalues.cpp
--- netcdf-4.0-beta1.dist/cxx/ncvalues.cpp      2006-12-29 10:38:56.000000000 
-0600
+++ netcdf-4.0-beta1/cxx/ncvalues.cpp   2007-09-12 15:55:03.000000000 -0500
@@ -8,10 +8,10 @@
  *********************************************************************/
 
 #include <config.h>
+#include "ncvalues.h"
 #include <iostream>
 #include <string>
 
-#include "ncvalues.h"
 
 NcValues::NcValues( void ) : the_type(ncNoType), the_number(0)
 {}
diff -burpN -x build -x autom4te.cache -x 'cscope*' -x '*~' 
netcdf-4.0-beta1.dist/cxx/ncvalues.h netcdf-4.0-beta1/cxx/ncvalues.h
--- netcdf-4.0-beta1.dist/cxx/ncvalues.h        2006-07-26 16:12:06.000000000 
-0500
+++ netcdf-4.0-beta1/cxx/ncvalues.h     2007-09-12 15:54:17.000000000 -0500
@@ -10,10 +10,10 @@
 #ifndef Ncvalues_def
 #define Ncvalues_def
 
+#include "netcdf.h"
 #include <iostream>
 #include <sstream>
 #include <limits.h>
-#include "netcdf.h"
 
 // Documentation warned this might change and now it has, for
 // consistency with C interface 
diff -burpN -x build -x autom4te.cache -x 'cscope*' -x '*~' 
netcdf-4.0-beta1.dist/cxx/netcdf.cpp netcdf-4.0-beta1/cxx/netcdf.cpp
--- netcdf-4.0-beta1.dist/cxx/netcdf.cpp        2007-04-02 15:55:02.000000000 
-0500
+++ netcdf-4.0-beta1/cxx/netcdf.cpp     2007-09-12 15:50:51.000000000 -0500
@@ -10,8 +10,8 @@
 #include <config.h>
 #include <string.h>
 #include <stdlib.h>
-#include <iostream>
 #include "netcdfcpp.h"
+#include <iostream> /* SEEK_SET/SEEK_CUR/SEEK_END namespace collisions */
 
 #ifndef TRUE
 #define TRUE 1
diff -burpN -x build -x autom4te.cache -x 'cscope*' -x '*~' 
netcdf-4.0-beta1.dist/libsrc4/netcdf.h netcdf-4.0-beta1/libsrc4/netcdf.h
--- netcdf-4.0-beta1.dist/libsrc4/netcdf.h      2007-04-10 15:17:10.000000000 
-0500
+++ netcdf-4.0-beta1/libsrc4/netcdf.h   2007-09-12 15:48:00.000000000 -0500
@@ -37,6 +37,10 @@
 
 #include <stddef.h> /* size_t, ptrdiff_t */
 #include <errno.h>  /* netcdf functions sometimes return system errors */
+#include <config.h>
+#ifdef USE_PARALLEL_MPIO
+#include <mpi.h>
+#endif
 
 typedef int nc_type;
 
@@ -343,12 +347,14 @@ nc_open(const char *path, int mode, int 
 
 /* If these aren't defined, then define them as ints, because we must
  * be building without parallel. */
+#ifndef USE_PARALLEL_MPIO
 #ifndef MPI_Comm
 #define MPI_Comm int
 #endif
 #ifndef MPI_Info
 #define MPI_Info int
 #endif
+#endif
 
 EXTERNL int
 nc_create_par(const char *path, int cmode, MPI_Comm comm, MPI_Info info,
  • 2007 messages navigation, sorted by:
    1. Thread
    2. Subject
    3. Author
    4. Date
    5. ↑ Table Of Contents
  • Search the netcdf-hdf archives: