Merging branches with master, adding model-net sampling

CONTRIBUTORS.md

+TODO: add contributors here

codes/codes-callback.h

@@ -7,6 +7,10 @@
 #ifndef CODES_CALLBACK_H
 #define CODES_CALLBACK_H
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 #include <assert.h>
 #include "codes/lp-msg.h"
 
@@ -83,6 +87,10 @@ struct codes_cb_params {
         assert(_esize >= (_cb_info_ptr)->cb_ret_offset + sizeof(_ret_type)); \
     } while (0)
 
+#ifdef __cplusplus
+}
+#endif
+
 #endif /* end of include guard: CODES_CALLBACK_H */
 
 /*

codes/codes-jobmap.h

@@ -20,6 +20,10 @@
 #ifndef CODES_JOBMAP_H
 #define CODES_JOBMAP_H
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 /** type markers and parameter defs for jobmaps **/
 
 enum codes_jobmap_type {
@@ -80,6 +84,10 @@ int codes_jobmap_get_num_jobs(struct codes_jobmap_ctx const * c);
 
 int codes_jobmap_get_num_ranks(int job_id, struct codes_jobmap_ctx const * c);
 
+#ifdef __cplusplus
+}
+#endif
+
 #endif
 
 /*

codes/codes-mapping-context.h

@@ -13,6 +13,10 @@
 #ifndef CODES_MAPPING_CONTEXT_H
 #define CODES_MAPPING_CONTEXT_H
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 #include <stdbool.h>
 #include <ross.h>
 
@@ -101,6 +105,10 @@ char const * codes_mctx_get_annotation(
         char const * dest_lp_name,
         tw_lpid sender_id);
 
+#ifdef __cplusplus
+}
+#endif
+
 #endif /* end of include guard: CODES_MAPPING_CONTEXT_H */
 
 /*

codes/codes-workload.h

@@ -12,6 +12,10 @@
 #ifndef CODES_WORKLOAD_H
 #define CODES_WORKLOAD_H
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 #include <ross.h>
 #include "configuration.h"
 
@@ -326,6 +330,10 @@ void codes_workload_add_method(struct codes_workload_method const * method);
  * will shut down automatically once they have issued their last event.
  */
 
+#ifdef __cplusplus
+}
+#endif
+
 #endif /* CODES_WORKLOAD_H */
 
 /*

codes/codes.h

@@ -8,6 +8,10 @@
 #ifndef CODES_H
 #define CODES_H
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 #include <ross.h>
 #include <assert.h>
 
@@ -90,6 +94,10 @@ static inline void codes_local_latency_reverse(tw_lp *lp)
     return;
 }
 
+#ifdef __cplusplus
+}
+#endif
+
 #endif /* CODES_H */
 
 /*

codes/codes_mapping.h

@@ -7,6 +7,14 @@
 /* SUMMARY:
  * CODES custom mapping file for ROSS
  */
+
+#ifndef CODES_MAPPING_H
+#define CODES_MAPPING_H
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 #include "configuration.h"
 #include "codes.h"
 #include "lp-type-lookup.h"
@@ -220,6 +228,12 @@ int codes_mapping_get_anno_cid_by_name(char const * annotation);
 int codes_mapping_get_anno_cid_by_lpid(tw_lpid id);
 char const * codes_mapping_get_anno_name_by_cid(int cid);
 
+#ifdef __cplusplus
+}
+#endif
+
+#endif
+
 /*
  * Local variables:
  *  c-indent-level: 4

codes/configuration.h

@@ -7,6 +7,10 @@
 #ifndef __CONFIGURATION_H__
 #define __CONFIGURATION_H__
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 #include <stddef.h>
 #include <inttypes.h>
 #include <mpi.h>
@@ -249,6 +253,10 @@ extern ConfigHandle config;
 
 extern config_lpgroups_t lpconf;
 
+#ifdef __cplusplus
+}
+#endif
+
 #endif
 
 /*

codes/jenkins-hash.h

@@ -7,6 +7,10 @@
 #ifndef __JENKINS_HASH__
 #define __JENKINS_HASH__
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 #include <sys/types.h>
 #include <stdint.h>
 
@@ -39,6 +43,10 @@ void bj_hashlittle2(
  */
 #define bj_hashmask(n) (bj_hashsize(n)-1)
 
+#ifdef __cplusplus
+}
+#endif
+
 #endif
 
 /*

codes/local-storage-model.h

@@ -7,6 +7,10 @@
 #ifndef __LS_MODEL__
 #define __LS_MODEL__
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 #include <ross.h>
 
 #include "codes-callback.h"
@@ -110,6 +114,10 @@ void lsm_configure(void);
 
 #define LSM_DEBUG 0
 
+#ifdef __cplusplus
+}
+#endif
+
 #endif
 
 /*

codes/lp-io.h

@@ -7,6 +7,10 @@
 #ifndef LP_IO_H
 #define LP_IO_H
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 #include <ross.h>
 
 typedef char* lp_io_handle;
@@ -33,6 +37,10 @@ static inline char* lp_io_handle_to_dir(lp_io_handle handle)
     return(strdup(handle));
 }
 
+#ifdef __cplusplus
+}
+#endif
+
 #endif /* LP_IO_H */
 
 /*

codes/lp-msg.h

@@ -7,6 +7,10 @@
 #ifndef LP_MSG_H
 #define LP_MSG_H
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 #include "ross.h"
 
 /* It is good practice to always include the src LPID, a unique message
@@ -24,6 +28,10 @@ typedef struct msg_header_s {
 /* data structure utilities */
 void msg_set_header(int magic, int event_type, tw_lpid src, msg_header *h);
 
+#ifdef __cplusplus
+}
+#endif
+
 #endif /* end of include guard: LP_MSG_H */
 
 /*

codes/lp-type-lookup.h

@@ -8,6 +8,10 @@
 #ifndef LP_TYPE_LOOKUP_H
 #define LP_TYPE_LOOKUP_H
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 #include "ross.h"
 
 /* look up the lp type registered through lp_type_register. Mostly used
@@ -17,6 +21,10 @@ const tw_lptype* lp_type_lookup(const char* name);
 /* register an LP with CODES/ROSS */
 void lp_type_register(const char* name, const tw_lptype* type);
 
+#ifdef __cplusplus
+}
+#endif
+
 #endif /* LP_TYPE_LOOKUP_H */
 
 /*

codes/model-net-inspect.h

@@ -10,6 +10,10 @@
 #ifndef MODEL_NET_INSPECT_H
 #define MODEL_NET_INSPECT_H
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 /* ALL FUNCTIONS
  * anno is the annotation specified in the configuration (NULL -> no
  * annotation), while ignore_annotations is a flag controlling whether
@@ -37,6 +41,10 @@ int model_net_torus_get_flat_id(
         const int * dim_lens,
         const int * dim_ids);
 
+#ifdef __cplusplus
+}
+#endif
+
 #endif /* end of include guard: MODEL_NET_INSPECT_H */
 
 /*

codes/model-net-lp.h

@@ -13,6 +13,10 @@
 #ifndef MODEL_NET_LP_H  
 #define MODEL_NET_LP_H
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 #include <ross.h>
 #include "codes/lp-msg.h"
 #include "model-net.h"
@@ -126,6 +130,10 @@ typedef struct model_net_wrap_msg {
     } msg;
 } model_net_wrap_msg;
 
+#ifdef __cplusplus
+}
+#endif
+
 #endif /* end of include guard: MODEL_NET_LP_H */
 
 /*

codes/model-net-method.h

@@ -7,6 +7,10 @@
 #ifndef MODELNET_METHOD_H
 #define MODELNET_METHOD_H
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 #include <ross.h>
 
 // forward decl of model_net_method since we currently have a circular include
@@ -63,6 +67,10 @@ struct model_net_method
 
 extern struct model_net_method * method_array[];
 
+#ifdef __cplusplus
+}
+#endif
+
 #endif /* MODELNET_METHOD_H */
 
 /*

codes/model-net-sched.h

@@ -9,6 +9,10 @@
 #ifndef MODEL_NET_SCHED_H
 #define MODEL_NET_SCHED_H
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 #include <ross.h>
 #include "model-net.h"
 
@@ -195,6 +199,10 @@ void model_net_sched_set_default_params(mn_sched_params *sched_params);
 
 extern char * sched_names[];
 
+#ifdef __cplusplus
+}
+#endif
+
 #endif /* end of include guard: MODEL_NET_SCHED_H */
 
 /*

codes/model-net.h

@@ -7,6 +7,10 @@
 #ifndef MODELNET_H
 #define MODELNET_H
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 #include <ross.h>
 #include <codes/lp-type-lookup.h>
 #include <codes/configuration.h>
@@ -397,6 +401,11 @@ void model_net_print_stats(tw_lpid lpid, mn_stats mn_stats_array[]);
 
 /* find model-net statistics */
 mn_stats* model_net_find_stats(char const * category, mn_stats mn_stats_array[]);
+
+#ifdef __cplusplus
+}
+#endif
+
 #endif /* MODELNET_H */
 
 /*

codes/net/dragonfly.h

@@ -7,6 +7,10 @@
 #ifndef DRAGONFLY_H
 #define DRAGONFLY_H
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 #include <ross.h>
 
 typedef struct terminal_message terminal_message;
@@ -92,6 +96,10 @@ struct terminal_message
    tw_lpid next_stop;
 };
 
+#ifdef __cplusplus
+}
+#endif
+
 #endif /* end of include guard: DRAGONFLY_H */
 
 /*

codes/net/loggp.h

@@ -7,6 +7,10 @@
 #ifndef LOGGP_H
 #define LOGGP_H
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 #include "../model-net-sched.h"
 
 /* types of events that will constitute triton requests */
@@ -45,6 +49,10 @@ struct loggp_message
     tw_stime recv_time_saved;
 };
 
+#ifdef __cplusplus
+}
+#endif
+
 #endif /* end of include guard: LOGGP_H */
 
 /*

codes/net/simplenet-upd.h

@@ -7,6 +7,10 @@
 #ifndef SIMPLENET_UPD_H
 #define SIMPLENET_UPD_H
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 typedef struct sn_message sn_message;
 
 /* types of events that will constitute triton requests */
@@ -39,6 +43,10 @@ struct sn_message
     tw_stime recv_time_saved;
 };
 
+#ifdef __cplusplus
+}
+#endif
+
 #endif /* end of include guard: SIMPLENET_UPD_H */
 /*
  * Local variables:

codes/net/simplep2p.h

@@ -7,6 +7,10 @@
 #ifndef SIMPLEP2P_H
 #define SIMPLEP2P_H
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 typedef struct sp_message sp_message;
 
 enum sp_event_type 
@@ -47,6 +51,10 @@ struct sp_message
     tw_stime recv_prev_idle_all_saved;
 };
 
+#ifdef __cplusplus
+}
+#endif
+
 #endif /* end of include guard: SIMPLEP2P_H */
 
 /*

codes/net/torus.h

@@ -7,6 +7,10 @@
 #ifndef TORUS_H
 #define TORUS_H
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 typedef enum nodes_event_t nodes_event_t;
 typedef struct nodes_message nodes_message;
 
@@ -90,6 +94,10 @@ struct nodes_message
   int remote_event_size_bytes;
 };
 
+#ifdef __cplusplus
+}
+#endif
+
 #endif /* end of include guard: TORUS_H */
 
 /*

codes/quickhash.h

@@ -14,6 +14,10 @@
 #ifndef SRC_COMMON_UTIL_QUICKHASH_H
 #define SRC_COMMON_UTIL_QUICKHASH_H
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 #include <stdlib.h>
 #include <stdint.h>
 #include "codes/quicklist.h"
@@ -336,6 +340,10 @@ static inline int quickhash_null32_hash(void *k, int table_size)
     return(int)(*tmp & (table_size - 1));
 }
 
+#ifdef __cplusplus
+}
+#endif
+
 #endif /* SRC_COMMON_UTIL_QUICKHASH_H */
 
 /*

codes/quicklist.h

@@ -25,6 +25,10 @@
 #ifndef QUICKLIST_H
 #define QUICKLIST_H
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 #include <stdlib.h>
 
 struct qlist_head {
@@ -289,4 +293,8 @@ static inline struct qlist_head * qlist_find(
  * vim: ts=8 sts=4 sw=4 expandtab
  */
 
+#ifdef __cplusplus
+}
+#endif
+
 #endif /* QUICKLIST_H */

codes/rc-stack.h

@@ -7,6 +7,10 @@
 #ifndef RC_STACK_H
 #define RC_STACK_H
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 #include <ross.h>
 
 /* A simple stack data structure that is GVT-aware for cleanup purposes. It's
@@ -49,6 +53,10 @@ int rc_stack_count(struct rc_stack const *s);
  * a NULL lp causes a delete-all */
 void rc_stack_gc(tw_lp const *lp, struct rc_stack *s);
 
+#ifdef __cplusplus
+}
+#endif
+
 #endif /* end of include guard: RC-STACK_H */
 
 /*

codes/resource-lp.h

@@ -11,6 +11,10 @@
 #ifndef RESOURCE_LP_H
 #define RESOURCE_LP_H
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 #include <ross.h>
 #include <stdint.h>
 
@@ -89,6 +93,10 @@ void resource_lp_reserve_rc(tw_lp *sender);
 void resource_lp_get_reserved_rc(tw_lp *sender);
 void resource_lp_free_reserved_rc(tw_lp *sender);
 
+#ifdef __cplusplus
+}
+#endif
+
 #endif /* end of include guard: RESOURCE_LP_H */
 
 /*

codes/resource.h

@@ -14,6 +14,10 @@
 #ifndef RESOURCE_H
 #define RESOURCE_H
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 #include <stdint.h>
 
 
@@ -69,6 +73,9 @@ struct resource_s {
     unsigned int num_tokens;
 };
 
+#ifdef __cplusplus
+}
+#endif
 
 #endif /* end of include guard: RESOURCE_H */
 

doc/BUILD_STEPS

@@ -27,17 +27,21 @@ working from the CODES master branches, use the ROSS master branch.
     If using ccmake to configure, don't forget to set CMAKE_C_COMPILER and
     CMAKE_CXX_COMPILER to mpicc/mpicxx
 
-1 - If you are building codes directly from the repository, run
+1 - If you are building CODES directly from the repository, run
 
     ./prepare.sh
 
-2 - Configure codes. This can be done in the source directory or in a
+2 - CODES requires pkg-config and non-ancient versions of flex/bison (i.e.
+    there have been problems with the Mac version). Use your favorite
+    package manager to obtain them.
+
+3 - Configure CODES. This can be done in the source directory or in a
     dedicated build directory if you prefer out-of-tree builds.  The CC
     environment variable must refer to an MPI compiler.
 
     mkdir build
     cd build
-    ../configure --prefix=/path/to/codes-base/install CC=mpicc PKG_CONFIG_PATH=/path/to/ross/install/lib/pkgconfig
+    ../configure --prefix=/path/to/codes/install CC=mpicc PKG_CONFIG_PATH=/path/to/ross/install/lib/pkgconfig
 
     To enable network tracing with dumpi
     (http://sst.sandia.gov/about_dumpi.html), use the option
@@ -57,15 +61,15 @@ working from the CODES master branches, use the ROSS master branch.
     <DARSHAN_PREFIX>/lib/pkgconfig to your PKG_CONFIG_PATH environment
     variable before calling configure.
    
-3 - Build and install codes-base
+4 - Build and install CODES
 
     make && make install
 
-4 - (optional) run test programs
+5 - (optional) run test programs
 
     make tests && make check
 
-5 - codes-base uses flex and bison (or lex and yacc) to generate several
+6 - codes uses flex and bison (or lex and yacc) to generate several
     parsers. These tools auto-generate C source files. To get around versioning
     issues, we've distributed the auto-generated sources directly. To remove
     all of the autogenerated files for these parsers, execute

doc/GETTING_STARTED

@@ -153,6 +153,38 @@ The following restrictions currently apply to the IO language:
   Hence, getgroupid should be completely ignored and getgrouprank and
   getgroupsize ignore the group ID parameter passed in.
 
+===== Limitations
+
+The IO language is frozen and no future development will be happening with it,
+so keep the following limitations in mind when using it.
+
+* There is currently no way to specify a "create" flag to open.
+* Variables are expected to be a single lowercase character.
+
+==== "Mock" IO workload
+
+The mock IO workload generator creates a sequential workload of N requests of
+size M. The generated file ID is either an optional input or 0 - there's also
+an option to add a (simulated) processes rank to the file IDs, giving in effect
+a unique file per rank. Relevant configuration parameters are:
+* mock_num_requests - the number of requests
+* mock_request_size - the size of each request
+* mock_request_type - the type of request ("read" or "write")
+* mock_file_id (optional) - the file ID to use, default 0
+* mock_use_unique_file_ids (optional) - if non-zero, add the workload
+  processor's rank to the file ID. Default is 0.
+* mock_rank_table_size (optional) - the hash table size to store the ranks in.
+  For minimal collisions, choose a value larger than the expected workload
+  number of ranks.
+
+==== Recorder IO workload
+
+TODO...
+
+==== Checkpoint IO workload
+
+TODO...
+
 === Network
 
 Our primary network workload generator is via the DUMPI tool

doc/codes-best-practices.tex

@@ -345,6 +345,9 @@ implement -- steps 2--4 are a few lines of code each. Also, LP-IO can be
 used upon encountering a suspend condition to give error specifics (the reverse
 write would occur in the reverse handler in step 3).
 
+Note that ROSS now has a self-suspend API -- the hand-implementation may still
+be used, but it is preferable to use the ROSS version.
+
 \subsection{Stash data needed for reverse computation within event structures}
 
 Writing discrete-event simulations will necessarily involve ``destructive''