Merge pull request #252 from leobago/release1.3

Release1.3

AUTHORS

@@ -3,6 +3,7 @@ Creator:
     Leonardo A. Bautista Gomez
 
 Contributors:
+    Konstantinos Parasyris
     Karol Sierociński
     Kai Keller
     Tomasz Paluszkiewicz

CMakeLists.txt

@@ -228,9 +228,13 @@ set_target_properties(fti.static fti.shared PROPERTIES POSITION_INDEPENDENT_CODE
 append_property(SOURCE ${SRC_FTI}
     PROPERTY COMPILE_FLAGS "${MPI_C_COMPILE_FLAGS}" "${SIONLIB_CFLAGS}" "${ADD_CFLAGS}")
 
+if( NOT ZLIB_FOUND )
+append_property(SOURCE ${SRC_CUDA_FTI}
+    PROPERTY COMPILE_FLAGS "-DFTI_NOZLIB")
+else()
 append_property(SOURCE ${SRC_CUDA_FTI}
     PROPERTY COMPILE_FLAGS )
-
+endif()
 
 append_property(TARGET fti.static fti.shared
 	PROPERTY LINK_FLAGS "${MPI_C_LINK_FLAGS}")

include/fti.h

@@ -74,7 +74,7 @@ extern "C" {
     FTI public functions
     ---------------------------------------------------------------------------*/
 
-  int FTI_Init(char *configFile, MPI_Comm globalComm);
+  int FTI_Init(const char *configFile, MPI_Comm globalComm);
   int FTI_Status();
   int FTI_InitType(FTIT_type* type, int size);
   int FTI_InitComplexType(FTIT_type* newType, FTIT_complexType* typeDefinition, int length,
@@ -87,7 +87,7 @@ extern "C" {
   int FTI_RenameGroup(FTIT_H5Group* h5group, char* name);
   int FTI_Protect(int id, void* ptr, long count, FTIT_type type);
   int FTI_DefineDataset(int id, int rank, int* dimLength, char* name, FTIT_H5Group* h5group);
-  int FTI_DefineGlobalDataset(int id, int rank, hsize_t* dimLength, char* name, FTIT_H5Group* h5group, FTIT_type type);
+  int FTI_DefineGlobalDataset(int id, int rank, hsize_t* dimLength, const char* name, FTIT_H5Group* h5group, FTIT_type type);
   int FTI_AddSubset( int id, int rank, hsize_t* offset, hsize_t* count, int did );
   int FTI_RecoverDatasetDimension( int did ); 
   hsize_t* FTI_GetDatasetSpan( int did, int rank );

src/IO/cuda-md5/md5Opt.c

@@ -1,3 +1,43 @@
+/**
+ *  Copyright (c) 2017 Leonardo A. Bautista-Gomez
+ *  All rights reserved
+ *
+ *  FTI - A multi-level checkpointing library for C/C++/Fortran applications
+ *
+ *  Revision 1.0 : Fault Tolerance Interface (FTI)
+ *
+ *  Redistribution and use in source and binary forms, with or without
+ *  modification, are permitted 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 other materials provided with the distribution.
+ *
+ *  3. Neither the name of the copyright holder nor the names of its contributors
+ *  may be used to endorse or promote products derived from this software without
+ *  specific prior written permission.
+ *
+ *  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "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 THE COPYRIGHT HOLDER OR CONTRIBUTORS 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.
+ *
+ *  @author Konstantinos Parasyris ([email protected])
+ *  @file   diff-checkpoint.c
+ *  @date   February, 2018
+ *  @brief  Routines to compute the MD5 checksum  
+ */
+
+
 #include <stdlib.h>
 #include <stdio.h>
 #include <string.h>
@@ -20,14 +60,21 @@ long totalWork= 0;
 long worker_exit = 0;
 int deviceId;
 unsigned char* (*cpuHash)( const unsigned char *data, unsigned long nBytes, unsigned char *hash );
-
-
-
-
-
 long tempBufferSize;
 long md5ChunkSize;
 
+
+/*-------------------------------------------------------------------------*/
+/**
+  @brief     This function initializes the MD5 checksum functions  for DCP
+  @param     cSize Size of the chunk  
+  @param     tempSize Size of intermediate buffers (Not used in this file) 
+  @param     FTI_Conf Pointer to the configuration options 
+  @return     integer         FTI_SCES if successfu.
+
+  This function initializes parameters for the computation of DCP MD5 checksums
+ **/
+/*-------------------------------------------------------------------------*/
 int FTI_initMD5(long cSize, long tempSize, FTIT_configuration *FTI_Conf){
     if ( FTI_Conf->dcpInfoPosix.cachedCkpt)
         usesAsync = 1;
@@ -40,6 +87,15 @@ int FTI_initMD5(long cSize, long tempSize, FTIT_configuration *FTI_Conf){
     return FTI_SCES;
 }
 
+/*-------------------------------------------------------------------------*/
+/**
+  @brief     This function computes the checksums of an Protected Variable 
+  @param     FTI_DataVar Variable We need to compute the checksums
+  @return     integer         FTI_SCES if successfu.
+
+  This function computes the checksums of a specific variable 
+ **/
+/*-------------------------------------------------------------------------*/
 int MD5CPU(FTIT_dataset *FTI_DataVar){
     unsigned long dataSize = FTI_DataVar->size;
     unsigned char block[md5ChunkSize];
@@ -60,28 +116,86 @@ int MD5CPU(FTIT_dataset *FTI_DataVar){
     return FTI_SCES;
 }
 
+/*-------------------------------------------------------------------------*/
+/**
+  @brief     This function computes the checksums of a Protected Variable 
+  @param     FTI_DataVar Variable We need to compute the checksums
+  @return     integer         FTI_SCES if successfu.
 
+  This function performs the computation of DCP MD5 checksums
+  it is actually an interface between the FTI and the async methods
+ **/
+/*-------------------------------------------------------------------------*/
 int FTI_MD5CPU(FTIT_dataset *FTI_DataVar){
-    MD5CPU(FTI_DataVar);
-    return 1;
+    return MD5CPU(FTI_DataVar);
 }
 
+
+/*-------------------------------------------------------------------------*/
+/**
+  @brief     This function computes the checksums of a Protected Variable (GPU) 
+  @param     FTI_DataVar Variable We need to compute the checksums
+  @return     integer         FTI_SCES if successfu.
+
+  This function initializes parameters for the computation of DCP MD5 checksums
+  it is actually an interface between the FTI and the async methods
+ **/
+/*-------------------------------------------------------------------------*/
 int FTI_MD5GPU(FTIT_dataset *FTI_DataVar){
     return 1;
 }
 
+/*-------------------------------------------------------------------------*/
+/**
+  @brief     This function synchronizes the file writes with the stable storages 
+  @param     f pointer to the file to be synchronized 
+  @return     integer         FTI_SCES if successfull.
+
+    This function is an interface, atm not implemented for NON-GPU optimized 
+    checkpoints.
+ **/
+/*-------------------------------------------------------------------------*/
 int FTI_CLOSE_ASYNC(FILE *f){
     return 1;
 }
 
+
+/*-------------------------------------------------------------------------*/
+/**
+  @brief     This function synchronizes the computation of the checksum with 
+             the current thread
+  @return     integer         FTI_SCES if successfu.
+
+
+  This function should not be called when compiling without GPU optimizations
+   **/
+/*-------------------------------------------------------------------------*/
 int FTI_SyncMD5(){
     return FTI_SCES;
 }
 
+
+/*-------------------------------------------------------------------------*/
+/**
+  @brief     This function fires the async thread to start computing work 
+  @return     integer         FTI_SCES if successfull.
+
+  This function should not be called when compiling without GPU optimizations
+ **/
+/*-------------------------------------------------------------------------*/
 int FTI_startMD5(){
     return FTI_SCES;
 }
 
+
+/*-------------------------------------------------------------------------*/
+/**
+  @brief     This function destroys the internal MD5 data structures 
+  @return     integer         FTI_SCES if successfull.
+
+  This function should not be called when compiling without GPU optimizations
+ **/
+/*-------------------------------------------------------------------------*/
 int FTI_destroyMD5(){
     return FTI_SCES;
 }