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<title>[121070] trunk/dports/science/netcdf</title>
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<dt>Revision</dt> <dd><a href="https://trac.macports.org/changeset/121070">121070</a></dd>
<dt>Author</dt> <dd>sean@macports.org</dd>
<dt>Date</dt> <dd>2014-06-16 14:17:38 -0700 (Mon, 16 Jun 2014)</dd>
</dl>
<h3>Log Message</h3>
<pre>netcdf: add patch for mpi variants; fixes #43867</pre>
<h3>Modified Paths</h3>
<ul>
<li><a href="#trunkdportssciencenetcdfPortfile">trunk/dports/science/netcdf/Portfile</a></li>
</ul>
<h3>Added Paths</h3>
<ul>
<li><a href="#trunkdportssciencenetcdffilespatchmpiposixdiff">trunk/dports/science/netcdf/files/patch-mpiposix.diff</a></li>
</ul>
</div>
<div id="patch">
<h3>Diff</h3>
<a id="trunkdportssciencenetcdfPortfile"></a>
<div class="modfile"><h4>Modified: trunk/dports/science/netcdf/Portfile (121069 => 121070)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/netcdf/Portfile 2014-06-16 21:08:37 UTC (rev 121069)
+++ trunk/dports/science/netcdf/Portfile 2014-06-16 21:17:38 UTC (rev 121070)
</span><span class="lines">@@ -46,6 +46,12 @@
</span><span class="cx"> destroot.destdir prefix=${destroot}${prefix} \
</span><span class="cx"> MANDIR=\\\${prefix}/share/man
</span><span class="cx">
</span><ins>+pre-patch {
+ if {[mpi_variant_isset]} {
+ patchfiles-append patch-mpiposix.diff
+ }
+}
+
</ins><span class="cx"> post-destroot {
</span><span class="cx"> file delete -force ${destroot}${prefix}/share/man/whatis.db
</span><span class="cx"> }
</span></span></pre></div>
<a id="trunkdportssciencenetcdffilespatchmpiposixdiff"></a>
<div class="addfile"><h4>Added: trunk/dports/science/netcdf/files/patch-mpiposix.diff (0 => 121070)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/netcdf/files/patch-mpiposix.diff (rev 0)
+++ trunk/dports/science/netcdf/files/patch-mpiposix.diff 2014-06-16 21:17:38 UTC (rev 121070)
</span><span class="lines">@@ -0,0 +1,121 @@
</span><ins>+--- RELEASE_NOTES.md
++++ RELEASE_NOTES.md
+@@ -9,6 +9,8 @@ This file contains a high-level description of this package's evolution. Release
+
+ ### 4.3.3-rc1 Released TBD
+
++* When the NC_MPIPOSIX flag is given for parallel I/O access and the HDF5 library does not have the MPI-POSIX VFD configured in, the NC_MPIPOSIX flag is transparently aliased to the NC_MPIIO flag within the netCDF-4 library.
++
+ ## 4.3.2 Released 2014-04-23
+
+ * As part of an ongoing project, the Doxygen-generated netcdf documentation has been reorganized. The goal is to make the documentation easier to parse, and to eliminate redundant material. This project is ongoing.
+--- libsrc4/nc4file.c
++++ libsrc4/nc4file.c
+@@ -308,12 +308,21 @@ nc4_create_file(const char *path, int cmode, MPI_Comm comm, MPI_Info info,
+ if (H5Pset_fapl_mpio(fapl_id, comm, info) < 0)
+ BAIL(NC_EPARINIT);
+ }
++#ifdef USE_PARALLEL_POSIX
+ else /* MPI/POSIX */
+ {
+ LOG((4, "creating parallel file with MPI/posix"));
+ if (H5Pset_fapl_mpiposix(fapl_id, comm, 0) < 0)
+ BAIL(NC_EPARINIT);
+ }
++#else /* USE_PARALLEL_POSIX */
++ /* Should not happen! Code in NC4_create/NC4_open should alias the
++ * NC_MPIPOSIX flag to NC_MPIIO, if the MPI-POSIX VFD is not
++ * available in HDF5. -QAK
++ */
++ else /* MPI/POSIX */
++ BAIL(NC_EPARINIT);
++#endif /* USE_PARALLEL_POSIX */
+
+ /* Keep copies of the MPI Comm & Info objects */
+ if (MPI_SUCCESS != MPI_Comm_dup(comm, &nc4_info->comm))
+@@ -465,6 +474,17 @@ NC4_create(const char* path, int cmode, size_t initialsz, int basepe,
+ )
+ return NC_EINVAL;
+
++#ifndef USE_PARALLEL_POSIX
++/* If the HDF5 library has been compiled without the MPI-POSIX VFD, alias
++ * the NC_MPIPOSIX flag to NC_MPIIO. -QAK
++ */
++ if(cmode & NC_MPIPOSIX)
++ {
++ cmode &= ~NC_MPIPOSIX;
++ cmode |= NC_MPIIO;
++ }
++#endif /* USE_PARALLEL_POSIX */
++
+ cmode |= NC_NETCDF4;
+
+ /* Apply default create format. */
+@@ -2168,12 +2188,21 @@ nc4_open_file(const char *path, int mode, MPI_Comm comm,
+ if (H5Pset_fapl_mpio(fapl_id, comm, info) < 0)
+ BAIL(NC_EPARINIT);
+ }
++#ifdef USE_PARALLEL_POSIX
+ else /* MPI/POSIX */
+ {
+ LOG((4, "opening parallel file with MPI/posix"));
+ if (H5Pset_fapl_mpiposix(fapl_id, comm, 0) < 0)
+ BAIL(NC_EPARINIT);
+ }
++#else /* USE_PARALLEL_POSIX */
++ /* Should not happen! Code in NC4_create/NC4_open should alias the
++ * NC_MPIPOSIX flag to NC_MPIIO, if the MPI-POSIX VFD is not
++ * available in HDF5. -QAK
++ */
++ else /* MPI/POSIX */
++ BAIL(NC_EPARINIT);
++#endif /* USE_PARALLEL_POSIX */
+
+ /* Keep copies of the MPI Comm & Info objects */
+ if (MPI_SUCCESS != MPI_Comm_dup(comm, &nc4_info->comm))
+@@ -2640,6 +2669,17 @@ NC4_open(const char *path, int mode, int basepe, size_t *chunksizehintp,
+ (mode & NC_MPIIO && mode & NC_MPIPOSIX))
+ return NC_EINVAL;
+
++#ifndef USE_PARALLEL_POSIX
++/* If the HDF5 library has been compiled without the MPI-POSIX VFD, alias
++ * the NC_MPIPOSIX flag to NC_MPIIO. -QAK
++ */
++ if(mode & NC_MPIPOSIX)
++ {
++ mode &= ~NC_MPIPOSIX;
++ mode |= NC_MPIIO;
++ }
++#endif /* USE_PARALLEL_POSIX */
++
+
+ /* Depending on the type of file, open it. */
+
+--- nc_test4/tst_nc4perf.c
++++ nc_test4/tst_nc4perf.c
+@@ -244,6 +244,11 @@ int test_pio_4d(size_t cache_size, int facc_type, int access_flag, MPI_Comm comm
+ return 0;
+ }
+
++/* Note: When the MPI-POSIX VFD is not compiled in to HDF5, the NC_MPIPOSIX
++ * flag will be aliased to the NC_MPIIO flag within the library, and
++ * therefore this test will exercise the aliasing, with the MPI-IO VFD,
++ * under that configuration. -QAK
++ */
+ #define NUM_MODES 2
+ #define NUM_FACC 2
+ #define NUM_CHUNK_COMBOS_2D 3
+--- nc_test4/tst_parallel3.c
++++ nc_test4/tst_parallel3.c
+@@ -129,6 +129,11 @@ int main(int argc, char **argv)
+ if (mpi_rank == 0)
+ SUMMARIZE_ERR;
+
++/* Note: When the MPI-POSIX VFD is not compiled in to HDF5, the NC_MPIPOSIX
++ * flag will be aliased to the NC_MPIIO flag within the library, and
++ * therefore this test will exercise the aliasing, with the MPI-IO VFD,
++ * under that configuration. -QAK
++ */
+ if (mpi_rank == 0)
+ printf("*** Testing parallel IO for raw-data with MPIPOSIX-IO (driver)...");
+ facc_type = NC_NETCDF4|NC_MPIPOSIX;
</ins></span></pre>
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