Add Fortran bindings

ci_support/run_docker_build.sh

@@ -41,6 +41,14 @@ conda clean --lock
 conda install --yes --quiet conda-forge-build-setup
 source run_conda_forge_build_setup
 
+
+# Install the yum requirements defined canonically in the
+# "recipe/yum_requirements.txt" file. After updating that file,
+# run "conda smithy rerender" and this line be updated
+# automatically.
+yum install -y devtoolset-2-gcc-gfortran
+
+
 # Embarking on 1 case(s).
     conda build /recipe_root --quiet || exit 1
     /feedstock_root/ci_support/upload_or_check_non_existence.py /recipe_root conda-forge --channel=main || exit 1

recipe/README.md

@@ -0,0 +1,6 @@
+About
+=====
+
+The C, C++, and fortran files in this directory are used to test the
+installation, and are copied from the HDF5 library. The copyright and license
+for these files is contained in the TEST_FILES_LICENSE.md file.

recipe/TEST_FILES_LICENSE.md

@@ -0,0 +1,41 @@
+HDF5 (Hierarchical Data Format 5) Software Library and Utilities
+Copyright 2006-2016 by The HDF Group.
+
+NCSA HDF5 (Hierarchical Data Format 5) Software Library and Utilities
+Copyright 1998-2006 by the Board of Trustees of the University of Illinois.
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted for any purpose (including commercial purposes) 
+provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, 
+   this list of conditions, and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, 
+   this list of conditions, and the following disclaimer in the documentation 
+   and/or materials provided with the distribution.
+
+3. In addition, redistributions of modified forms of the source or binary 
+   code must carry prominent notices stating that the original code was 
+   changed and the date of the change.
+
+4. All publications or advertising materials mentioning features or use of 
+   this software are asked, but not required, to acknowledge that it was 
+   developed by The HDF Group and by the National Center for Supercomputing 
+   Applications at the University of Illinois at Urbana-Champaign and 
+   credit the contributors.
+
+5. Neither the name of The HDF Group, the name of the University, nor the 
+   name of any Contributor may be used to endorse or promote products derived 
+   from this software without specific prior written permission from 
+   The HDF Group, the University, or the Contributor, respectively.
+
+DISCLAIMER: 
+THIS SOFTWARE IS PROVIDED BY THE HDF GROUP AND THE CONTRIBUTORS 
+"AS IS" WITH NO WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED.  In no 
+event shall The HDF Group or the Contributors be liable for any damages 
+suffered by the users arising out of the use of this software, even if 
+advised of the possibility of such damage. 
+

recipe/build.sh

@@ -11,13 +11,18 @@ source activate "${CONDA_DEFAULT_ENV}"
 if [ "$(uname)" == "Darwin" ]
 then
     export CXX="${CXX} -stdlib=libc++"
+    export DYLD_FALLBACK_LIBRARY_PATH=$PREFIX/lib
 fi
 
+export LIBRARY_PATH="${PREFIX}/lib"
+
 ./configure --prefix="${PREFIX}" \
-    --enable-linux-lfs \
-    --with-zlib="${PREFIX}" \
-    --with-pthread=yes  --enable-cxx \
-    --with-default-plugindir="${PREFIX}/lib/hdf5/plugin"
+            --enable-linux-lfs \
+            --with-zlib="${PREFIX}" \
+            --with-pthread=yes  \
+            --enable-cxx \
+            --enable-fortran \
+            --with-default-plugindir="${PREFIX}/lib/hdf5/plugin"
 
 make
 make check

recipe/h5_cmprss.c

@@ -0,0 +1,125 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group.                                               *
+ * Copyright by the Board of Trustees of the University of Illinois.         *
+ * All rights reserved.                                                      *
+ *                                                                           *
+ * This file is part of HDF5.  The full HDF5 copyright notice, including     *
+ * terms governing use, modification, and redistribution, is contained in    *
+ * the files COPYING and Copyright.html.  COPYING can be found at the root   *
+ * of the source code distribution tree; Copyright.html can be found at the  *
+ * root level of an installed copy of the electronic HDF5 document set and   *
+ * is linked from the top-level documents page.  It can also be found at     *
+ * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
+ * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/* 
+ *  This example illustrates how to create a compressed dataset.
+ *  It is used in the HDF5 Tutorial.
+ */ 
+
+#include "hdf5.h"
+
+#define FILE    "cmprss.h5"
+#define RANK    2
+#define DIM0    100
+#define DIM1    20
+
+int main () {
+
+    hid_t    file_id, dataset_id, dataspace_id; /* identifiers */
+    hid_t    plist_id; 
+
+    size_t   nelmts;
+    unsigned flags, filter_info;
+    H5Z_filter_t filter_type;
+
+    herr_t   status;
+    hsize_t  dims[2];
+    hsize_t  cdims[2];
+
+    int      idx;
+    int      i,j, numfilt;
+    int      buf[DIM0][DIM1];
+    int      rbuf [DIM0][DIM1];
+
+    /* Uncomment these variables to use SZIP compression 
+    unsigned szip_options_mask;
+    unsigned szip_pixels_per_block;
+    */
+
+    /* Create a file.  */
+    file_id = H5Fcreate (FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+
+
+    /* Create dataset "Compressed Data" in the group using absolute name.  */
+    dims[0] = DIM0;
+    dims[1] = DIM1;
+    dataspace_id = H5Screate_simple (RANK, dims, NULL);
+
+    plist_id  = H5Pcreate (H5P_DATASET_CREATE);
+
+    /* Dataset must be chunked for compression */
+    cdims[0] = 20;
+    cdims[1] = 20;
+    status = H5Pset_chunk (plist_id, 2, cdims);
+
+    /* Set ZLIB / DEFLATE Compression using compression level 6.
+     * To use SZIP Compression comment out these lines. 
+    */ 
+    status = H5Pset_deflate (plist_id, 6); 
+
+    /* Uncomment these lines to set SZIP Compression 
+    szip_options_mask = H5_SZIP_NN_OPTION_MASK;
+    szip_pixels_per_block = 16;
+    status = H5Pset_szip (plist_id, szip_options_mask, szip_pixels_per_block);
+    */
+
+    dataset_id = H5Dcreate2 (file_id, "Compressed_Data", H5T_STD_I32BE, 
+                            dataspace_id, H5P_DEFAULT, plist_id, H5P_DEFAULT); 
+
+    for (i = 0; i< DIM0; i++) 
+        for (j=0; j<DIM1; j++) 
+           buf[i][j] = i+j;
+
+    status = H5Dwrite (dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
+
+    status = H5Sclose (dataspace_id);
+    status = H5Dclose (dataset_id);
+    status = H5Pclose (plist_id);
+    status = H5Fclose (file_id);
+
+    /* Now reopen the file and dataset in the file. */
+    file_id = H5Fopen (FILE, H5F_ACC_RDWR, H5P_DEFAULT);
+    dataset_id = H5Dopen2 (file_id, "Compressed_Data", H5P_DEFAULT);
+
+    /* Retrieve filter information. */
+    plist_id = H5Dget_create_plist (dataset_id);
+
+    numfilt = H5Pget_nfilters (plist_id);
+    printf ("Number of filters associated with dataset: %i\n", numfilt);
+
+    for (i=0; i<numfilt; i++) {
+       nelmts = 0;
+       filter_type = H5Pget_filter2 (plist_id, 0, &flags, &nelmts, NULL, 0, NULL,
+                     &filter_info);
+       printf ("Filter Type: ");
+       switch (filter_type) {
+         case H5Z_FILTER_DEFLATE:
+              printf ("H5Z_FILTER_DEFLATE\n");
+              break;
+         case H5Z_FILTER_SZIP:
+              printf ("H5Z_FILTER_SZIP\n");
+              break;
+         default:
+              printf ("Other filter type included.\n");
+         }
+    }
+
+    status = H5Dread (dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, 
+                      H5P_DEFAULT, rbuf); 
+
+    status = H5Dclose (dataset_id);
+    status = H5Pclose (plist_id);
+    status = H5Fclose (file_id);
+}

recipe/h5_cmprss.f90

@@ -0,0 +1,131 @@
+! * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+!   Copyright by The HDF Group.                                               *
+!   Copyright by the Board of Trustees of the University of Illinois.         *
+!   All rights reserved.                                                      *
+!                                                                             *
+!   This file is part of HDF5.  The full HDF5 copyright notice, including     *
+!   terms governing use, modification, and redistribution, is contained in    *
+!   the files COPYING and Copyright.html.  COPYING can be found at the root   *
+!   of the source code distribution tree; Copyright.html can be found at the  *
+!   root level of an installed copy of the electronic HDF5 document set and   *
+!   is linked from the top-level documents page.  It can also be found at     *
+!   http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
+!   access to either file, you may request a copy from help@hdfgroup.org.     *
+! * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+! 
+!  This example illustrates how to create a compressed dataset.
+!  It is used in the HDF5 Tutorial.
+! 
+PROGRAM h5_cmprss
+
+  USE HDF5 ! This module contains all necessary modules 
+
+  IMPLICIT NONE
+  !
+  ! The dataset is stored in file "h5_cmprss.h5" 
+  !
+  CHARACTER(LEN=12), PARAMETER :: filename = "h5_cmprss.h5"
+  INTEGER, PARAMETER  :: rank = 2   ! Rank of the data set
+  INTEGER, PARAMETER  :: dim0 = 100 ! Data set sizes
+  INTEGER, PARAMETER  :: dim1 = 20
+
+  INTEGER(hid_t) :: file_id, dataset_id, dataspace_id ! Identifiers
+  INTEGER(hid_t) :: plist_id ! Property list identifier
+
+  INTEGER :: error
+  INTEGER(hsize_t), DIMENSION(1:rank) :: dims ! dimensions of data
+  INTEGER(hsize_t), DIMENSION(1:rank) :: cdims ! sizes of chunked data
+
+  INTEGER :: i,j, numfilt
+  INTEGER, DIMENSION(1:dim0,1:dim1) :: buf ! write buffer
+  INTEGER, DIMENSION(1:dim0,1:dim1) :: rbuf ! read buffer
+  INTEGER(HSIZE_T), DIMENSION(1:rank) :: data_dims ! dimensions of data buffers
+
+  INTEGER, DIMENSION(1:1) :: cd_values ! Auxiliary data for the filter
+  INTEGER(size_t) :: nelmts            ! Number of elements in cd_values
+  INTEGER :: flags ! Bit vector specifying certain general properties of the filter
+  INTEGER(SIZE_T) :: namelen = 180 ! Anticipated number of characters in name
+  CHARACTER(LEN=180) :: name ! Name of the filter
+  INTEGER :: filter_id ! Filter identification number
+
+  ! Uncomment these variables to use SZIP compression
+  !INTEGER :: szip_options_mask
+  !INTEGER :: szip_pixels_per_block
+
+  !
+  !Initialize FORTRAN predifined datatypes
+  !
+  CALL h5open_f(error)
+  !
+  ! Create a file
+  CALL h5fcreate_f(filename, H5F_ACC_TRUNC_F, file_id, error)
+  !
+  ! Create dataset "Compressed Data" in the group using absolute name.
+  dims(1:2) = (/dim0, dim1/)
+  CALL h5screate_simple_f(rank, dims, dataspace_id, error)
+  CALL h5pcreate_f(H5P_DATASET_CREATE_F, plist_id, error)
+  !
+  ! Dataset must be chunked for compression 
+  cdims(1:2) = 20
+  CALL h5pset_chunk_f(plist_id, 2, cdims, error)
+
+  ! Set ZLIB / DEFLATE Compression using compression level 6.
+  ! To use SZIP Compression comment out these lines. 
+  CALL h5pset_deflate_f(plist_id, 6, error)
+
+  ! Uncomment these lines to set SZIP Compression 
+  !szip_options_mask = H5_SZIP_NN_OM_F
+  !szip_pixels_per_block = 16
+  !CALL H5Pset_szip_f(plist_id, szip_options_mask, szip_pixels_per_block, error)
+
+  ! Create data set
+  CALL h5dcreate_f(file_id, "Compressed_Data", H5T_NATIVE_INTEGER, dataspace_id, &
+       dataset_id, error, dcpl_id=plist_id)
+
+  DO j = 1, dim1
+     DO i = 1, dim0
+        buf(i,j) = i+j
+     ENDDO
+  ENDDO
+
+  data_dims(1:2) = (/dim0,dim1/) 
+  CALL h5dwrite_f(dataset_id, H5T_NATIVE_INTEGER, buf, data_dims, error)
+
+  ! Close resources
+  CALL h5sclose_f(dataspace_id, error)
+  CALL h5pclose_f(plist_id, error)
+  CALL h5dclose_f(dataset_id, error)
+  CALL h5fclose_f(file_id, error)
+
+  ! Now reopen the file and dataset in the file.
+  CALL h5fopen_f(filename, H5F_ACC_RDONLY_F, file_id, error)
+  CALL h5dopen_f(file_id, "Compressed_Data", dataset_id, error)
+
+  ! Retrieve filter information. 
+  CALL h5dget_create_plist_f(dataset_id, plist_id, error)
+
+  CALL h5pget_nfilters_f(plist_id, numfilt, error)
+  WRITE(*,'(A, I0)') "Number of filters associated with dataset: ", numfilt
+
+  DO i = 1, numfilt
+     nelmts = 1
+     CALL h5pget_filter_f(plist_id, 0, flags, nelmts, cd_values, &
+          namelen, name, filter_id, error)
+
+      WRITE(*,'(30X,A)', ADVANCE='NO')"Filter Type: "
+      IF(filter_id.EQ.H5Z_FILTER_DEFLATE_F)THEN
+         WRITE(*,'(A)') "H5Z_FILTER_DEFLATE"
+      ELSEIF (filter_id.EQ.H5Z_FILTER_SZIP_F)THEN
+         WRITE(*,'(A)') "H5Z_FILTER_SZIP"
+      ELSE
+         WRITE(*,'(A)') "Other filter type included"
+      ENDIF
+   ENDDO
+  data_dims(1:2) = (/dim0,dim1/)
+  CALL h5dread_f(dataset_id, H5T_NATIVE_INTEGER, rbuf, data_dims, error)
+
+  CALL h5dclose_f(dataset_id, error)
+  CALL h5pclose_f(plist_id, error)
+  CALL h5fclose_f(file_id, error)
+
+END PROGRAM h5_cmprss