allow mixed compilers if compatible

AUTHORS

@@ -19,11 +19,11 @@ Contributors:
 
 Acknowledgements:
 
-This work has been supported by EU H2020 ICT project LEGaTO, contract #780681, 
-the EU Horizon 2020 (H2020) funding framework under grant/award #824158;
-Energy oriented Centre of Excellence II (EoCoE-II) and the EU H2020 
+This work has been supported by EU H2020 ICT project LEGaTO contract #780681; 
+the EU Horizon 2020 (H2020) funding framework under grant/award #824158
+Energy oriented Centre of Excellence II (EoCoE-II); and the EU H2020 
 Mont-Blanc 2020 project under Grant Agreement #779877.
-This scientific/academic work is financed from financial resources for science
+This scientific/academic work is also financed from financial resources for science
 in the years 2016 - 2018 granted for the realization of the international
 project co-financed by Polish Ministry of Science and Higher Education.
 

CHANGELOG

@@ -1,3 +1,83 @@
+Version 1.6:
+ - Merge pull request #392 from leobago/develop
+ - Merge pull request #391 from leobago/O3
+ - only gcc again
+ - Merge pull request #390 from leobago/hotfix_warnings
+ - Merge pull request #389 from leobago/h5_async_buffer
+ - activate all compilers (reverse after pipeline run)
+ - compiles everything with build type release (adds O3 flag)
+ - removed O1
+ - removes compiler warnings
+ - free memory
+ - cleaned
+ - fixed vpr test
+ - itf checks vpr pass
+ - seems to work
+ - Merge pull request #388 from leobago/spack
+ - Merge remote-tracking branch 'origin/develop' into spack
+ - Merge pull request #387 from leobago/mpich_install
+ - pipeline only triggers PR-# branch checks and only triggers GCC for PR to develop. For PRs to master, the full pipeline is executed
+ - test pipeline
+ - test pipeline
+ - test pipeline
+ - test pipeline
+ - test pipeline
+ - test pipeline
+ - removed hdf5 check intel
+ - PGI without Fortran (GCC commented)
+ - PGI without Fortran
+ - escaped dollars
+ - added quotes to the cmd grep
+ - adjusted run wrapper
+ - tests intel mpich pgi and llvm
+ - prepared intel
+ - installed llvm compilers
+ - removes some artefacts and add a gitignore to include
+ - changes the install structure
+ - uncomment pgi stages
+ - installed pgi compilers
+ - fixes wrong type for blockMetaInfo_t
+ - added mpich
+ - quickfix
+ - source build script with a dot in shell env
+ - source build script with a dot in shell env
+ - source build script with a dot
+ - source build script
+ - uses another docker image
+ - added sionlib mpich
+ - installed hdf5 with mpich mpi
+ - export ld_library_path
+ - added mpich checks
+ - Merge pull request #386 from leobago/develop
+ - uncommented other checks
+ - corrected mount path
+ - update of PGI compilers to NVIDIA HPC SDK
+ - fixes Jenkinsfile for Clang and PGI CI
+ - Merge branch 'develop' of https://github.com/leobago/fti into develop
+ - Fix recover lL4 Warning, fast_forward bug and catch FTI_Init in heatDist
+ - Merge pull request #383 from leobago/bugfix/fix_osx_compile_error
+ - Update recover.c
+ - Renamed macros FREAD/FWRITE to FTI_EH_FREAD/FTI_EH_FWRITE/
+ - Merge pull request #382 from leobago/refactor-ci
+ - fixed linking issue for cpp app
+ - edited APIs for c++ string operability
+ - added test suite for c++ string operability
+ - Merge pull request #381 from leobago/refactor-ci
+ - fixed erroneous pointer assignment
+ - enhanced check for implicit var declaration in loop+fixed files formatting
+ - Merge pull request #378 from leobago/refactor-ci
+ - split standard/diffsizes into two suites each
+ - updated test stats in documentation
+ - updated docu + set fast_forward for tests
+ - Merge pull request #377 from leobago/refactor-ci
+ - fixed faulty step
+ - fixing compilerName missing variable
+ - moved compilation inside steps
+ - fixing nested steps
+ - moved compilation step inside stages
+ - restructured steps/stages of Jenkins
+ - Added fast_forward to convenient itf tests
+
 Version 1.5.1:
  - Merge branch 'master' of github.com:leobago/fti
  - Merge pull request #375 from leobago/develop

CMakeLists.txt

@@ -32,7 +32,7 @@ if(ENABLE_GPU)
   list(APPEND LANGUAGES "CUDA" "CXX")
 endif()
 
-project("FTI" VERSION 1.5.1 LANGUAGES ${LANGUAGES})
+project("FTI" VERSION 1.6 LANGUAGES ${LANGUAGES})
 
 # ----------------------- Global Properties and Set-up ------------------------
 
@@ -212,6 +212,14 @@ if(ENABLE_FORTRAN)
     set(F_CC_ID "${CMAKE_Fortran_COMPILER_ID}_${F_CC_MAJOR}")
     string(COMPARE NOTEQUAL ${C_CC_ID} ${F_CC_ID} COMPILER_VER_DIFFER)
     if(${COMPILER_VER_DIFFER})
+        message(WARNING
+                "Different compiler idetifications for Fortran and C!")
+    endif()
+
+    # 2.2.f) Check if c/c++ and fortran compilers are compatible
+    FortranCInterface_VERIFY()
+    FortranCInterface_VERIFY(CXX)
+    if((NOT ${FortranCInterface_VERIFIED_C}) AND (NOT ${FortranCInterface_VERIFIED_CXX}))
         message(FATAL_ERROR
                 "Different compiler idetifications for Fortran and C!")
     endif()

VERSION

@@ -1 +1 @@
-1.5.1
+1.6

docs/source/conf.py

@@ -31,7 +31,7 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['breathe', 'sphinx.ext.autosectionlabel']
+extensions = ['breathe', 'sphinx.ext.autosectionlabel', 'sphinx.ext.autodoc']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']

examples/heatd2.c

@@ -106,7 +106,7 @@ double doWork(int numprocs, int rank, int M, int nbLines, double *g,
 
 
 int main(int argc, char *argv[]) {
-    int rank, nbProcs, nbLines, i, j, N, M, res;
+    int rank, nbProcs, nbLines, i, N, M, res;
     double wtime, *h, *g, *grid, globalerror = 1;
     char fn[32];
 

examples/heatdis.c

@@ -119,7 +119,6 @@ int main(int argc, char *argv[]) {
 
     wtime = MPI_Wtime();
     for (i = 0; i < ITER_TIMES; i++) {
-        int checkpointed = FTI_Snapshot();
         localerror = doWork(nbProcs, rank, M, nbLines, g, h);
         if (((i%ITER_OUT) == 0) && (rank == 0)) {
             printf("Step : %d, error = %f\n", i, globalerror);

include/fti-intern.h

@@ -30,7 +30,7 @@
 #endif
 
 /** Malloc macro.                                                          */
-#define talloc(type, num) (type *)malloc(sizeof(type) * (num))
+#define talloc(type, num) (type *)malloc(sizeof(type) * ((size_t)num))
 
 #define LOCAL 0
 #define GLOBAL 1
@@ -127,26 +127,26 @@ extern "C" {
 #ifdef ENABLE_HDF5  // --> If HDF5 is installed
     typedef hsize_t FTIT_hsize_t;
 #else
-    typedef uint64_t FTIT_hsize_t;
+    typedef int64_t FTIT_hsize_t;
 #endif
 
     typedef struct FTIT_dimension {
         int ndims;
-        uint64_t count[32];
+        int64_t count[32];
     } FTIT_dimension;
 
     typedef uintptr_t           FTI_ADDRVAL;      /**< for ptr manipulation */
     typedef void*               FTI_ADDRPTR;      /**< void ptr type        */
 
     typedef struct FTIT_datasetInfo {
         int varID;
-        uint32_t varSize;
+        int64_t varSize;
     } FTIT_datasetInfo;
 
     typedef struct FTIT_dcpConfigurationPosix {
         unsigned int digestWidth;
         unsigned char* (*hashFunc)(const unsigned char *data,
-            uint64_t nBytes, unsigned char *hash);
+            unsigned long nBytes, unsigned char *hash);
         unsigned int StackSize;
         uint32_t BlockSize;
         unsigned int cachedCkpt;
@@ -156,23 +156,23 @@ extern "C" {
         int nbLayerReco;
         int nbVarReco;
         unsigned int Counter;
-        uint32_t FileSize;
-        uint32_t dataSize;
-        uint32_t dcpSize;
-        uint32_t LayerSize[MAX_STACK_SIZE];
+        int64_t FileSize;
+        int64_t dataSize;
+        int64_t dcpSize;
+        int64_t LayerSize[MAX_STACK_SIZE];
         FTIT_datasetInfo datasetInfo[MAX_STACK_SIZE][FTI_BUFS];
         char LayerHash[MAX_STACK_SIZE*MD5_DIGEST_STRING_LENGTH];
     } FTIT_dcpExecutionPosix;
 
     typedef struct FTIT_dcpDatasetPosix {
-        uint32_t hashDataSize;
+        int64_t hashDataSize;
         unsigned char* currentHashArray;
         unsigned char* oldHashArray;
     } FTIT_dcpDatasetPosix;
 
     typedef struct blockMetaInfo_t {
-        uint64_t varId : 18;
-        uint64_t blockId : 30;
+        int64_t varId : 18;
+        int64_t blockId : 30;
     } blockMetaInfo_t;
 
     /*-----------------------------------------------------------------------
@@ -229,15 +229,15 @@ extern "C" {
         char checksum[MD5_DIGEST_STRING_LENGTH]; /**< file hash without meta  */
         unsigned char myHash[MD5_DIGEST_LENGTH]; /**< hash of this struct     */
         int ckptId;           /**< Checkpoint ID                             */
-        size_t metaSize;      /**< size of ckpt data                         */
-        size_t ckptSize;      /**< also file size TODO remove                */
-        size_t dataSize;      /**< size of protected data without meta data  */
-        size_t pureDataSize;  /**< total data size (for printouts)           */
-        size_t fs;            /**< file size                                 */
-        size_t maxFs;         /**< maximum file size in group                */
-        size_t ptFs;          /**< partner copy file size                    */
-        uint64_t timestamp;   /**< time (ns) cp was created (CLOCK_REALTIME) */
-        size_t dcpSize;       /**< how much actually written by rank         */
+        int64_t metaSize;      /**< size of ckpt data                         */
+        int64_t ckptSize;      /**< also file size TODO remove                */
+        int64_t dataSize;      /**< size of protected data without meta data  */
+        int64_t pureDataSize;  /**< total data size (for printouts)           */
+        int64_t fs;            /**< file size                                 */
+        int64_t maxFs;         /**< maximum file size in group                */
+        int64_t ptFs;          /**< partner copy file size                    */
+        uint32_t timestamp;   /**< time (ns) cp was created (CLOCK_REALTIME) */
+        int64_t dcpSize;       /**< how much actually written by rank         */
     } FTIFF_metaInfo;
 
     /** @typedef    FTIT_DataDiffHash
@@ -253,7 +253,7 @@ extern "C" {
         uint32_t* bit32hash[2];      /**< CRC32 digest                        */
         uint16_t* blockSize;         /**< data block size                     */
         bool* isValid;               /**< indicates if data block is valid    */
-        int32_t nbHashes;            /**< number of hashes for the data chunk */
+        int64_t nbHashes;            /**< number of hashes for the data chunk */
         int currentId;
         int creationType;
         int lifetime;
@@ -275,8 +275,8 @@ extern "C" {
         bool hasCkpt;         /**< indicates if container is stored in ckpt   */
         uintptr_t dptr;       /**< data pointer offset                        */
         uintptr_t fptr;       /**< file pointer offset                        */
-        int32_t chunksize;    /**< chunk size of variable in this block       */
-        int32_t containersize;/**< cont size stored of variable in this block */
+        uint64_t chunksize;    /**< chunk size of variable in this block       */
+        uint64_t containersize;/**< cont size stored of variable in this block */
         unsigned char hash[MD5_DIGEST_LENGTH];  /**< hash of variable chunk   */
         unsigned char myhash[MD5_DIGEST_LENGTH];/**< hash of this structure   */
         bool update;    /**< TRUE if struct needs to be updated in ckpt file  */
@@ -293,7 +293,7 @@ extern "C" {
      */
     typedef struct FTIFF_db {
         int numvars;          /**< number of protected variables in datablock */
-        int32_t dbsize;       /**< size of metadata + data for block in bytes */
+        int64_t dbsize;       /**< size of metadata + data for block in bytes */
         unsigned char myhash[MD5_DIGEST_LENGTH]; /**< hash of variable chunk  */
         bool update;     /**< TRUE if struct needs to be updated in ckpt file */
         bool finalized;             /**< TRUE if block is stored in cp file   */
@@ -366,7 +366,7 @@ extern "C" {
      */
     typedef struct FTIT_Datatype {
         int id;                              /**< ID of the data type.        */
-        size_t size;                         /**< Size of the data type.      */
+        int64_t size;                         /**< Size of the data type.      */
         FTIT_complexType* structure;         /**< Logical structure for HDF5. */
         FTIT_H5Group* h5group;               /**< Group of this datatype.     */
 #ifdef ENABLE_HDF5
@@ -409,7 +409,7 @@ extern "C" {
     typedef struct FTIT_typeField {
         FTIT_Datatype *type;        /**< FTI type ID of the field.           */
         int id;                     /**< Order of the field in the structure */
-        size_t offset;              /**< Offset of the field in structure.   */
+        int64_t offset;              /**< Offset of the field in structure.   */
         int rank;                   /**< Field rank (max. 32)                */
         int dimLength[32];          /**< Lenght of each dimention            */
         char name[FTI_BUFS];        /**< Name of the field                   */
@@ -444,15 +444,15 @@ extern "C" {
      */
     typedef struct FTIT_dataset {
         int id;                            /**< ID to search/update dataset  */
-        int eleSize;                       /**< Element size for the dataset */
+        size_t eleSize;                       /**< Element size for the dataset */
         int rank;                          /**< Rank of dataset (for HDF5)   */
         int dimLength[32];                 /**< Lenght of each dimention     */
         bool recovered;                    /**< True if metadata restored    */
         bool isDevicePtr;                  /**< True if on device memory     */
-        int32_t count;                     /**< nb of elements in dataset    */
-        int32_t size;                      /**< size of the data             */
-        int32_t sizeStored;                /**< size of the data in last CP  */
-        size_t filePos;                    /**< offset of buffer in CP file  */
+        int64_t count;                     /**< nb of elements in dataset    */
+        int64_t size;                      /**< size of the data             */
+        int64_t sizeStored;                /**< size of the data in last CP  */
+        int64_t filePos;                    /**< offset of buffer in CP file  */
         FTIT_attribute attribute;
         FTIT_sharedData sharedData;        /**< Info if dataset is subset    */
         FTIT_dcpDatasetPosix dcpInfoPosix; /**< dCP info for posix I/O       */
@@ -473,9 +473,9 @@ extern "C" {
         int level;                            /**< checkpoint level           */
         int ckptId;                           /**< Current Ckpt ID            */
         int ckptIdL4;                         /**< Current L4 Ckpt ID         */
-        int32_t maxFs;                        /**< Maximum file size.         */
-        int32_t fs;                           /**< File size.                 */
-        int32_t pfs;                          /**< Partner file size.         */
+        int64_t maxFs;                        /**< Maximum file size.         */
+        int64_t fs;                           /**< File size.                 */
+        int64_t pfs;                          /**< Partner file size.         */
         char ckptFile[FTI_BUFS];              /**< Ckpt file name. [FTI_BUFS] */
     } FTIT_metadata;
 
@@ -522,7 +522,7 @@ extern "C" {
         char lTmpDir[FTI_BUFS];            /**< Local temporary directory.    */
         char gTmpDir[FTI_BUFS];            /**< Global temporary directory.   */
         char mTmpDir[FTI_BUFS];            /**< Metadata temporary directory. */
-        size_t cHostBufSize;               /**< Host buffer size for GPU data.*/
+        int64_t cHostBufSize;               /**< Host buffer size for GPU data.*/
         char suffix[4];                    /** Suffix of the checkpoint files */
         FTIT_dcpConfigurationPosix dcpInfoPosix; /**< dCP info for posix I/O  */
         // int fastForward;            /**< Fast forward rate for ckpt intervals */
@@ -618,7 +618,7 @@ extern "C" {
         int(*WriteData) (FTIT_dataset * ,
                 void *write_info);
         int(*finCKPT)   (void *fileDesc);
-        size_t(*getPos) (void *fileDesc);
+        int64_t(*getPos) (void *fileDesc);
         void(*finIntegrity) (unsigned char *, void*);
     }FTIT_IO;
 
@@ -678,7 +678,7 @@ extern "C" {
         unsigned int ckptId;                /**< Checkpoint ID.               */
         unsigned int ckptNext;              /**< Iteration for next CP.       */
         unsigned int ckptLast;              /**< Iteration for last CP.       */
-        int32_t ckptSize;                   /**< Checkpoint size.             */
+        int64_t ckptSize;                   /**< Checkpoint size.             */
         unsigned int nbVar;                 /**< nb of protected variables    */
         unsigned int nbVarStored;           /**< nb prot. var. stored in CP   */
         int nbGroup;                        /**< Number of protected groups.  */

include/fti.h

@@ -87,7 +87,7 @@ extern "C" {
   int FTI_InitGroup(FTIT_H5Group* h5group, const char* name,
    FTIT_H5Group* parent);
   int FTI_RenameGroup(FTIT_H5Group* h5group, const char* name);
-  int FTI_Protect(int id, void* ptr, int32_t count, fti_id_t tid);
+  int FTI_Protect(int id, void* ptr, int64_t count, fti_id_t tid);
   int FTI_SetAttribute(int id, FTIT_attribute attribute,
           FTIT_attributeFlag flag);
   int FTI_DefineDataset(int id, int rank, int* dimLength, const char* name,
@@ -102,7 +102,7 @@ extern "C" {
   int FTI_UpdateGlobalDataset(int id, int rank, FTIT_hsize_t* dimLength);
   int FTI_UpdateSubset(int id, int rank, FTIT_hsize_t* offset,
    FTIT_hsize_t* count, int did);
-  int32_t FTI_GetStoredSize(int id);
+  int64_t FTI_GetStoredSize(int id);
   void* FTI_Realloc(int id, void* ptr);
   int FTI_BitFlip(int datasetID);
   int FTI_Checkpoint(int id, int level);
@@ -130,9 +130,9 @@ extern "C" {
   fti_id_t FTI_InitCompositeType(const char* name, size_t size,
    FTIT_H5Group* h5g);
   int FTI_AddScalarField(fti_id_t id, const char* name, fti_id_t fid,
-   size_t offset);
+   int64_t offset);
   int FTI_AddVectorField(fti_id_t id, const char* name, fti_id_t tid,
-   size_t offset, int ndims, int* dim_sizes);
+   int64_t offset, int ndims, int* dim_sizes);
 
 #ifdef __cplusplus
 }