initial possion

ops/c/include/ops_checkpointing.h

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+/*
+* Open source copyright declaration based on BSD open source template:
+* http://www.opensource.org/licenses/bsd-license.php
+*
+* This file is part of the OPS distribution.
+*
+* Copyright (c) 2013, Mike Giles and others. Please see the AUTHORS file in
+* the main source directory for a full list of copyright holders.
+* All rights reserved.
+*
+* Redistribution and use in source and binary forms, with or without
+* modification, are permitted provided that the following conditions are met:
+* * Redistributions of source code must retain the above copyright
+* notice, this list of conditions and the following disclaimer.
+* * Redistributions in binary form must reproduce the above copyright
+* notice, this list of conditions and the following disclaimer in the
+* documentation and/or other materials provided with the distribution.
+* * The name of Mike Giles may not be used to endorse or promote products
+* derived from this software without specific prior written permission.
+*
+* THIS SOFTWARE IS PROVIDED BY Mike Giles ''AS IS'' AND ANY
+* EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+* DISCLAIMED. IN NO EVENT SHALL Mike Giles BE LIABLE FOR ANY
+* DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+/** @file
+  * @brief OPS checkpointing library function declarations
+  * @author Istvan Reguly
+  * @details function declarations for checkpointing
+  */
+
+#ifndef __OPS_CHECKPOINTING_H
+#define __OPS_CHECKPOINTING_H
+
+typedef enum {
+  OPS_BACKUP_GATHER,
+  OPS_BACKUP_LEADIN,
+  OPS_BACKUP_RESTORE,
+  OPS_BACKUP_BEGIN,
+  OPS_BACKUP_IN_PROCESS,
+  OPS_BACKUP_END,
+  OPS_NONE
+} ops_backup_state;
+typedef enum { OPS_NOT_SAVED, OPS_SAVED, OPS_UNDECIDED } ops_checkpoint_types;
+
+typedef enum {
+    /**
+     * Indicates that there are a number of parallel loops at the very beginning
+     * of the simulations which should be excluded from any checkpoint;
+     * mainly because they initialise datasets that do not change during the
+     * main body of the execution.
+     * During restore mode these loops are executed as usual.
+     * An example would be the computation of the mesh geometry, which can be
+     * excluded from the checkpoint if it is re-computed when recovering and
+     * restoring a checkpoint.
+     * The API call void ops_checkpointing_initphase_done() indicates the end
+     * of this initial phase.
+     */
+  OPS_CHECKPOINT_INITPHASE = 1,
+    /**
+     * Indicates that the user manually controls the location of the checkpoint,
+     * and explicitly specifies the list of ::ops_dat s to be saved.
+     */
+  OPS_CHECKPOINT_MANUAL_DATLIST = 2,
+    /**
+     * Indicates that the user manually controls the location of the checkpoint,
+     * and it also enables fast-forwarding, by skipping the execution of the
+     * application (even though none of the parallel loops would actually
+     * execute, there may be significant work outside of those) up to the
+     * checkpoint.
+     */
+  OPS_CHECKPOINT_FASTFW = 4,
+    /**
+     * Indicates that when the corresponding API function is called, the
+     * checkpoint should be created.
+     * Assumes the presence of the above two options as well.
+     */
+  OPS_CHECKPOINT_MANUAL = 8
+} ops_checkpoint_options;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/**
+ * Initialises the checkpointing system, has to be called after ops_partition().
+ *
+ * @param filename  name of the file for checkpointing.
+ *                In MPI, this will automatically be postfixed with the rank ID.
+ * @param interval  average time (seconds) between checkpoints
+ * @param options   a combinations of flags, defined by ::ops_checkpoint_options
+ * @return          `true` if the application launches in restore mode,
+ *                  `false` otherwise.
+ */
+bool ops_checkpointing_init(const char *filename, double interval, int options);
+void ops_checkpointing_initphase_done();
+bool ops_checkpointing_before(ops_arg *args, int nargs, int *range,
+                              int loop_id);
+bool ops_checkpointing_name_before(ops_arg *args, int nargs, int *range,
+                                   const char *s);
+void ops_checkpointing_exit();
+void ops_checkpointing_reduction(ops_reduction red);
+
+/**
+ * Call this routine at a point in the code to mark the location of a checkpoint.
+ *
+ * At this point, the list of datasets specified will be saved.
+ * The validity of what is saved is not checked by the checkpointing algorithm
+ * assuming that the user knows what data sets to be saved for full recovery.
+ * This routine should be called frequently (compared to check-pointing
+ * frequency) and it will trigger the creation of the checkpoint the first time
+ * it is called after the timeout occurs.
+ *
+ * @param ndats    number of datasets to be saved
+ * @param datlist  arrays of ::ops_dat handles to be saved
+ */
+void ops_checkpointing_manual_datlist(int ndats, ops_dat *datlist);
+
+/**
+ * Call this routine at a point in the code to mark the location of a checkpoint.
+ *
+ * At this point, the specified payload (e.g. iteration count, simulation time,
+ * etc.) along with the necessary datasets, as determined by the checkpointing
+ * algorithm will be saved.
+ * This routine should be called frequently (compared to checkpointing
+ * frequency), will trigger the creation of the checkpoint the first time it is
+ * called after the timeout occurs.
+ * In restore mode, will restore all datasets the first time it is called, and
+ * returns `true` indicating that the saved payload is returned in payload.
+ * Does not save reduction data.
+ *
+ * @param nbytes   size of the payload in bytes
+ * @param payload  pointer to memory into which the payload is packed
+ * @return
+ */
+bool ops_checkpointing_fastfw(int nbytes, char *payload);
+
+/**
+ * Combines the ops_checkpointing_manual_datlist() and
+ * ops_checkpointing_fastfw() calls.
+ *
+ * @param ndats    number of datasets to be saved
+ * @param datlist  arrays of ::ops_dat handles to be saved
+ * @param nbytes   size of the payload in bytes
+ * @param payload  pointer to memory into which the payload is packed
+ * @return
+ */
+bool ops_checkpointing_manual_datlist_fastfw(int ndats, ops_dat *datlist,
+                                             int nbytes, char *payload);
+
+/**
+ * With this routine it is possible to manually trigger checkpointing,
+ * instead of relying on the timeout process.
+ *
+ * It combines the ops_checkpointing_manual_datlist() and
+ * ops_checkpointing_fastfw() calls, and triggers the creation of a
+ * checkpoint when called.
+ *
+ * @param ndats    number of datasets to be saved
+ * @param datlist  arrays of ::ops_dat handles to be saved
+ * @param nbytes   size of the payload in bytes
+ * @param payload  pointer to memory into which the payload is packed
+ * @return
+ */
+bool ops_checkpointing_manual_datlist_fastfw_trigger(int ndats,
+                                                     ops_dat *datlist,
+                                                     int nbytes, char *payload);
+
+extern ops_backup_state backup_state;
+extern char *OPS_dat_ever_written;
+extern ops_checkpoint_types *OPS_dat_status;
+extern int OPS_ranks_per_node;
+extern int ops_checkpoint_inmemory;
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* __OPS_CHECKPOINTING_H */

ops/c/include/ops_hdf5.h

@@ -0,0 +1,177 @@
+/*
+* Open source copyright declaration based on BSD open source template:
+* http://www.opensource.org/licenses/bsd-license.php
+*
+* This file is part of the OPS distribution.
+*
+* Copyright (c) 2013, Mike Giles and others. Please see the AUTHORS file in
+* the main source directory for a full list of copyright holders.
+* All rights reserved.
+*
+* Redistribution and use in source and binary forms, with or without
+* modification, are permitted provided that the following conditions are met:
+* * Redistributions of source code must retain the above copyright
+* notice, this list of conditions and the following disclaimer.
+* * Redistributions in binary form must reproduce the above copyright
+* notice, this list of conditions and the following disclaimer in the
+* documentation and/or other materials provided with the distribution.
+* * The name of Mike Giles may not be used to endorse or promote products
+* derived from this software without specific prior written permission.
+*
+* THIS SOFTWARE IS PROVIDED BY Mike Giles ''AS IS'' AND ANY
+* EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+* DISCLAIMED. IN NO EVENT SHALL Mike Giles BE LIABLE FOR ANY
+* DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+/** @file
+  * @brief  Header file for the parallel I/O functions
+  * @author Gihan Mudalige (started 28-08-2015)
+  * @details
+  */
+
+#ifndef __OPS_HDF5_H
+#define __OPS_HDF5_H
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/**
+ * This routine defines a dataset to be read in from a named hdf5 file.
+ *
+ *
+ * @param block      structured block
+ * @param dat_size   dimension of dataset (number of items per grid element)
+ * @param type       the name of type used for output diagnostics
+ *                   (e.g. "double", "float")
+ * @param dat_name   name of the dat used for output diagnostics
+ * @param file_name  HDF5 file to read and obtain the data from
+ * @return
+ */
+ops_dat ops_decl_dat_hdf5(ops_block block, int dat_size, char const *type,
+                          char const *dat_name, char const *file_name);
+
+/**
+ * This routine reads the details of a structured grid block from a named
+ * HDF5 file.
+ *
+ * Although this routine does not read in any extra information about the block
+ * from the named HDF5 file than what is already specified in the arguments, it
+ * is included here for error checking(e.g. check if blocks defined in an HDF5
+ * file is matching with the declared arguments in an application) and
+ * completeness.
+ *
+ * @param dims        dimension of the block
+ * @param block_name  a name used for output diagnostics
+ * @param file_name   HDF5 file to read and obtain the block information from
+ * @return
+ */
+ops_block ops_decl_block_hdf5(int dims, const char *block_name,
+                              char const *file_name);
+
+/**
+ *
+ * @param dims          dimension of loop iteration
+ * @param points        number of points in the stencil
+ * @param stencil_name  string representing the name of the stencil
+ * @param file_name     HDF5 file to read from 
+ * @return
+ */
+ops_stencil ops_decl_stencil_hdf5(int dims, int points,
+                                  const char *stencil_name,
+                                  char const *file_name);
+
+/**
+ *
+ * @param dims          dimension of loop iteration
+ * @param points        number of points in the stencil
+ * @param stencil_name  string representing the name of the stencil
+ * @param file_name     HDF5 file to read from
+ * @return
+ */
+ops_stencil ops_decl_strided_stencil_hdf5(int dims, int points,
+                                          const char *stencil_name,
+                                          char const *file_name);
+
+/**
+ * This routine reads in a halo relationship between two datasets defined on
+ * two different blocks from a named HDF5 file.
+ *
+ * @param from       origin dataset
+ * @param to         destination dataset
+ * @param file_name  HDF5 file to read and obtain the data from
+ * @return
+ */
+ops_halo ops_decl_halo_hdf5(ops_dat from, ops_dat to, char const *file_name);
+
+/**
+ * Write the details of an ::ops_dat to a named HDF5 file.
+ *
+ * Can be used over MPI (puts the data in an ::ops_dat into an HDF5 file
+ * using MPI I/O)
+ * @param dat
+ * @param file_name
+ */
+void ops_fetch_dat_hdf5_file(ops_dat dat, char const *file_name);
+
+/**
+ * Write the details of an ::ops_block to a named HDF5 file.
+ *
+ * Can be used over MPI (puts the data in an ::ops_block into an HDF5 file
+ * using MPI I/O)
+ *
+ * @param block      ops block to be written
+ * @param file_name  HDF5 file to write to
+ */
+void ops_fetch_block_hdf5_file(ops_block block, char const *file_name);
+
+/**
+ * Write the details of an ::ops_stencil to a named HDF5 file.
+ *
+ * Can be used over MPI (puts the data in an ::ops_stencil into an HDF5 file
+ * using MPI I/O)
+ *
+ * @param stencil    ::ops_stencil to be written
+ * @param file_name  HDF5 file to write to
+ */
+void ops_fetch_stencil_hdf5_file(ops_stencil stencil, char const *file_name);
+
+/**
+ * Write the details of an ::ops_halo to a named HDF5 file.
+ *
+ * Can be used over MPI (puts the data in an ::ops_halo into an HDF5 file
+ * using MPI I/O)
+ *
+ * @param halo    ::ops_halo to be written
+ * @param file_name  HDF5 file to write to
+ */
+void ops_fetch_halo_hdf5_file(ops_halo halo, char const *file_name);
+
+#ifndef DOXYGEN_SHOULD_SKIP_THIS
+void ops_read_dat_hdf5(ops_dat dat);
+#endif /* DOXYGEN_SHOULD_SKIP_THIS*/
+
+/**
+ * Write all state (blocks, datasets, stencils) to a named HDF5 file.
+ *
+ * @param file_name  HDF5 file to write to
+ */
+void ops_dump_to_hdf5(char const *file_name);
+
+void ops_write_const_hdf5(char const *name, int dim, char const *type,
+                         char *const_data, char const *file_name);
+void ops_get_const_hdf5(char const *name, int dim, char const *type,
+                       char *const_data, char const *file_name);
+
+#ifdef __cplusplus
+}
+#endif
+#endif
+/* __OPS_HDF5_H */