merged master

CONTRIBUTORS.md

@@ -3,8 +3,10 @@ Nikhil Jain, Abhinav Bhatele (LLNL)
     - Addition of direct scheme for setting up dragonfly network topology.
     - Network configuration setup for custom dragonfly model.
     - Topology generations scripts for custom dragonfly model.
+    - Bug fix for virtual channel deadlocks in custom dragonfly model.
     - Bug reporter for CODES network models.
     - Fat tree network setup and adaptive routing.
+    - Pending: Merging Express mesh model to master.
 
 Jens Domke (U. of Dresden)
     - Static routing in fat tree network model.

codes/codes-workload.h

@@ -72,6 +72,7 @@ struct dumpi_trace_params {
 #ifdef ENABLE_CORTEX_PYTHON
    char cortex_script[MAX_NAME_LENGTH_WKLD];
    char cortex_class[MAX_NAME_LENGTH_WKLD];
+   char cortex_gen[MAX_NAME_LENGTH_WKLD];
 #endif
 };
 

codes/model-net-lp.h

@@ -22,6 +22,7 @@ extern "C" {
 #include "model-net.h"
 #include "model-net-sched.h"
 #include "net/dragonfly.h"
+#include "net/dragonfly-custom.h"
 #include "net/slimfly.h"
 #include "net/fattree.h"
 #include "net/loggp.h"
@@ -124,6 +125,7 @@ typedef struct model_net_wrap_msg {
     union {
         model_net_base_msg      m_base;  // base lp
         terminal_message        m_dfly;  // dragonfly
+        terminal_custom_message        m_custom_dfly;  // dragonfly-custom
         slim_terminal_message   m_slim;  // slimfly
 	fattree_message		m_fat;   // fattree
         loggp_message           m_loggp; // loggp

configure.ac

@@ -140,7 +140,7 @@ AC_ARG_WITH([boost],[AS_HELP_STRING([--with-boost@<:@=DIR@:>@],
 			[location of Boost Python installation])])
 
 if [ test "x${with_python}" != "x" -a "x${with_boost}" != "x"] ; then
-        AC_CHECK_FILES([${with_python}/lib/libpython2.7.a ${with_boost}/lib/libboost_python.a],
+        AC_CHECK_FILES([${with_python}/lib/libpython2.7.so ${with_boost}/lib/libboost_python.a],
                 AM_CONDITIONAL(USE_PYTHON, true),
                 AC_MSG_ERROR(Could not find Python and/or Boost-Python libraries))
         PYTHON_CFLAGS="-I${with_python}/include -I${with_boost}/include"

scripts/allocation_gen/config_alloc.conf

 rand
-792
-200
+8316
+2048 2048
 

scripts/gen-cray-topo/connections_general.c

@@ -29,12 +29,15 @@ int main(int argc, char **argv) {
   int r = atoi(argv[2]);
   int c = atoi(argv[3]);
 
+  int total_routers = g * r * c; 
+
   FILE *intra = fopen(argv[4], "wb");
   FILE *inter = fopen(argv[5], "wb");
 
   int router = 0;
   int green = 0, black = 1;
   int groups = 0;
+  printf("\n Rows %d Cols %d Groups %d ", r, c, g);
   for(int rows = 0; rows < r; rows++) {
     for(int cols = 0; cols < c; cols++) {
       for(int cols1 = 0; cols1 < c; cols1++) {
@@ -71,7 +74,7 @@ int main(int argc, char **argv) {
         } else {
           ndstg--;
         }
-        int gsize = 2, gs = 16;
+        int gsize = 2, gs = c;
         for(int row = 0; row < r; row++) {
           int srcrB = srcg * r * c + row * c, srcr;
           int dstrB = dstg * r * c + row * c, dstr;
@@ -79,15 +82,19 @@ int main(int argc, char **argv) {
           int dstB = (nsrcg % (gs/2)) * 2;
           srcr = srcrB + srcB;
           dstr = dstrB + dstB;
-          for(int r = 0; r < 2; r++) {
-            for(int block = 0; block < gsize; block++) {
-              fwrite(&srcr, sizeof(int), 1, inter);
-              fwrite(&dstr, sizeof(int), 1, inter);
-              printf("INTER %d %d\n", srcr, dstr);
+
+          if(srcr >= total_routers || dstr >= total_routers)
+              printf("\n connection between invalid routers src %d and dest %d ", srcr, dstr);
+
+            for(int r = 0; r < 2; r++) {
+                for(int block = 0; block < gsize; block++) {
+                fwrite(&srcr, sizeof(int), 1, inter);
+                fwrite(&dstr, sizeof(int), 1, inter);
+                printf("INTER %d %d srcg %d destg %d srcrb %d dstrB %d \n", srcr, dstr, srcg, dstg, srcrB, dstrB);
             }
             srcr++;
             dstr++;
-          }
+            }
         }
       }
     }

scripts/gen-cray-topo/connections_general_patched.c

+//////////////////////////////////////////////////////////////////////////////
+// Copyright (c) 2014, Lawrence Livermore National Security, LLC.
+// Produced at the Lawrence Livermore National Laboratory.
+//
+// Written by:
+//     Nikhil Jain <nikhil.jain@acm.org>
+//     Abhinav Bhatele <bhatele@llnl.gov>
+//     Peer-Timo Bremer <ptbremer@llnl.gov>
+//
+// LLNL-CODE-678961. All rights reserved.
+//
+// This file is part of Damselfly. For details, see:
+// https://github.com/scalability-llnl/damselfly
+// Please also read the LICENSE file for our notice and the LGPL.
+//////////////////////////////////////////////////////////////////////////////
+
+#include "stdio.h"
+#include "stdlib.h"
+
+//Usage ./binary num_groups num_rows num_columns intra_file inter_file
+
+int main(int argc, char **argv) {
+  if(argc < 3) {
+    printf("Correct usage: %s <num_group> <num_rows> <num_cols> <cons_across_groups> <cons_in_row> <cons_in_col> <intra_file> <inter_file>", argv[0]);
+    exit(0);
+  }
+
+  int g = atoi(argv[1]);
+  int r = atoi(argv[2]);
+  int c = atoi(argv[3]);
+  int g_p = atoi(argv[4]);
+  int r_p = atoi(argv[5]);
+  int c_p = atoi(argv[6]);
+
+  int total_routers = g * r * c; 
+  int routers_per_g = r * c; 
+
+  FILE *intra = fopen(argv[7], "wb");
+  FILE *inter = fopen(argv[8], "wb");
+
+  int router = 0;
+  int green = 0, black = 1;
+  int groups = 0;
+  for(int rows = 0; rows < r; rows++) {
+    for(int cols = 0; cols < c; cols++) {
+      for(int cols1 = 0; cols1 < c; cols1++) {
+        if(cols1 != cols) {
+          int dest = (rows * c) + cols1;
+          for(int link = 0; link < c_p; link++) {
+            fwrite(&router, sizeof(int), 1, intra);
+            fwrite(&dest, sizeof(int), 1, intra);
+            fwrite(&green, sizeof(int), 1, intra);
+            printf("INTRA %d %d %d\n", router, dest, green);
+          }
+        }
+      }
+      for(int rows1 = 0; rows1 < r; rows1++) {
+        if(rows1 != rows) {
+          int dest = (rows1 * c) + cols;
+          for(int link = 0; link < r_p; link++) {
+            fwrite(&router, sizeof(int), 1, intra);
+            fwrite(&dest, sizeof(int), 1, intra);
+            fwrite(&black, sizeof(int), 1, intra);
+            printf("INTRA %d %d %d\n", router, dest, black);
+          }
+        }
+      }
+      router++;
+    }
+  }
+
+  for(int srcg = 0; srcg < g; srcg++) {
+    for(int dstg = 0; dstg < g; dstg++) {
+      if(srcg != dstg) {
+        int nsrcg = srcg;
+        int ndstg = dstg;
+        if(srcg > dstg) {
+          nsrcg--;
+        } else {
+          ndstg--;
+        }
+        int startSrc = ndstg * g_p;
+        int startDst = nsrcg * g_p;
+        for(int link = 0; link < g_p; link++) {
+          int srcrB = srcg * routers_per_g, srcr;
+          int dstrB = dstg * routers_per_g, dstr;
+          srcr = srcrB + (startSrc + link) % routers_per_g;
+          dstr = dstrB + (startDst + link) % routers_per_g;
+
+          if(srcr >= total_routers || dstr >= total_routers)
+            printf("\n connection between invalid routers src %d and dest %d ", srcr, dstr);
+
+          fwrite(&srcr, sizeof(int), 1, inter);
+          fwrite(&dstr, sizeof(int), 1, inter);
+          printf("INTER %d %d srcg %d destg %d\n", srcr, dstr, srcg, dstg);
+        }
+      }
+    }
+  }
+
+  fclose(intra);
+  fclose(inter);
+}

src/network-workloads/conf/dragonfly-custom/modelnet-test-dragonfly-custom-768-nodes.conf.in

@@ -49,9 +49,9 @@ PARAMS
 # number of global channels per router 
    num_global_channels="10";
 # network config file for intra-group connections 
-   intra-group-connections="@abs_srcdir@/intra-custom-small";
+   intra-group-connections="@abs_srcdir@/intra-theta";
 # network config file for inter-group connections
-   inter-group-connections="@abs_srcdir@/inter-custom-small";
+   inter-group-connections="@abs_srcdir@/inter-theta";
 # routing protocol to be used 
    routing="prog-adaptive";
 }

src/network-workloads/conf/dragonfly-custom/modelnet-test-dragonfly-custom.conf

@@ -2,11 +2,11 @@ LPGROUPS
 {
    MODELNET_GRP
    {
-      repetitions="1600";
+      repetitions="1520";
 # name of this lp changes according to the model
-      nw-lp="4";
+      nw-lp="8";
 # these lp names will be the same for dragonfly-custom model
-      modelnet_dragonfly_custom="4";
+      modelnet_dragonfly_custom="8";
       modelnet_dragonfly_custom_router="1";
    }
 }
@@ -24,11 +24,11 @@ PARAMS
    # number of routers within each group
    # this is dictated by the dragonfly configuration files
    # intra-group rows for routers
-   num_router_rows="4";
+   num_router_rows="1";
    # intra-group columns for routers
-   num_router_cols="20";
+   num_router_cols="40";
    # number of groups in the network
-   num_groups="20";
+   num_groups="38";
 # buffer size in bytes for local virtual channels 
    local_vc_size="8192";
 #buffer size in bytes for global virtual channels 
@@ -38,20 +38,24 @@ PARAMS
 #bandwidth in GiB/s for local channels 
    local_bandwidth="5.25";
 # bandwidth in GiB/s for global channels 
-   global_bandwidth="18.75";
+   global_bandwidth="4.69";
 # bandwidth in GiB/s for compute node-router channels 
    cn_bandwidth="8.0";
+# Number of row channels
+   num_row_chans="2";
+# Number of column channels
+   num_col_chans="1";
 # ROSS message size 
    message_size="592";
 # number of compute nodes connected to router, dictated by dragonfly config
 # file
-   num_cns_per_router="4";
+   num_cns_per_router="8";
 # number of global channels per router 
-   num_global_channels="10";
+   num_global_channels="4";
 # network config file for intra-group connections 
-   intra-group-connections="../src/network-workloads/conf/dragonfly-custom/intra-custom";
+   intra-group-connections="/Users/mmubarak/Documents/software_development/codes/scripts/gen-cray-topo/intratest";
 # network config file for inter-group connections
-   inter-group-connections="../src/network-workloads/conf/dragonfly-custom/inter-custom";
+   inter-group-connections="/Users/mmubarak/Documents/software_development/codes/scripts/gen-cray-topo/intertest";
 # routing protocol to be used 
    routing="prog-adaptive";
 }

src/network-workloads/conf/dragonfly-custom/modelnet-test-dragonfly-theta.conf

@@ -37,7 +37,7 @@ PARAMS
 #bandwidth in GiB/s for local channels 
    local_bandwidth="5.25";
 # bandwidth in GiB/s for global channels 
-   global_bandwidth="18.75";
+   global_bandwidth="4.69";
 # bandwidth in GiB/s for compute node-router channels 
    cn_bandwidth="16.0";
 # ROSS message size 
@@ -46,7 +46,7 @@ PARAMS
 # file
    num_cns_per_router="4";
 # number of global channels per router 
-   num_global_channels="10";
+   num_global_channels="4";
 # network config file for intra-group connections 
    intra-group-connections="../src/network-workloads/conf/dragonfly-custom/intra-theta";
 # network config file for inter-group connections

src/network-workloads/model-net-mpi-replay.c

@@ -13,26 +13,42 @@
 #include "codes/model-net.h"
 #include "codes/rc-stack.h"
 #include "codes/quicklist.h"
+#include "codes/quickhash.h"
 #include "codes/codes-jobmap.h"
 
 /* turning on track lp will generate a lot of output messages */
 #define MN_LP_NM "modelnet_dragonfly_custom"
 
+#define CONTROL_MSG_SZ 64
 #define TRACK_LP -1
 #define TRACE -1
 #define MAX_WAIT_REQS 512
 #define CS_LP_DBG 0
+#define EAGER_THRESHOLD 81920000
+#define RANK_HASH_TABLE_SZ 2000
+#define NOISE 3.0
+#define NW_LP_NM "nw-lp"
 #define lprintf(_fmt, ...) \
         do {if (CS_LP_DBG) printf(_fmt, __VA_ARGS__);} while (0)
 #define MAX_STATS 65536
+#define PAYLOAD_SZ 1024
 
+static int msg_size_hash_compare(
+            void *key, struct qhash_head *link);
+
+int enable_msg_tracking = 0;
+
+int unmatched = 0;
 char workload_type[128];
 char workload_file[8192];
 char offset_file[8192];
 static int wrkld_id;
 static int num_net_traces = 0;
+static int num_dumpi_traces = 0;
+
 static int alloc_spec = 0;
-static double self_overhead = 10.0;
+static tw_stime self_overhead = 10.0;
+static tw_stime mean_interval = 100000;
 
 /* Doing LP IO*/
 static char lp_io_dir[256] = {'\0'};
@@ -41,21 +57,23 @@ static unsigned int lp_io_use_suffix = 0;
 static int do_lp_io = 0;
 
 /* variables for loading multiple applications */
-/* Xu's additions start */
 char workloads_conf_file[8192];
 char alloc_file[8192];
 int num_traces_of_job[5];
+tw_stime soft_delay_mpi = 2500;
+tw_stime nic_delay = 1000;
+tw_stime copy_per_byte_eager = 0.55;
 char file_name_of_job[5][8192];
 
 struct codes_jobmap_ctx *jobmap_ctx;
 struct codes_jobmap_params_list jobmap_p;
-/* Xu's additions end */
 
 /* Variables for Cortex Support */
 /* Matthieu's additions start */
 #ifdef ENABLE_CORTEX_PYTHON
-static char cortex_file[512];
-static char cortex_class[512];
+static char cortex_file[512] = "\0";
+static char cortex_class[512] = "\0";
+static char cortex_gen[512] = "\0";
 #endif
 /* Matthieu's additions end */
 
@@ -65,9 +83,12 @@ typedef int32_t dumpi_req_id;
 
 static int net_id = 0;
 static float noise = 5.0;
-static int num_net_lps = 0, num_mpi_lps = 0;
+static int num_nw_lps = 0, num_mpi_lps = 0;
+
+static int num_syn_clients;
 
 FILE * workload_log = NULL;
+FILE * msg_size_log = NULL;
 FILE * workload_agg_log = NULL;
 FILE * workload_meta_log = NULL;
 
@@ -76,6 +97,9 @@ static uint64_t sample_bytes_written = 0;
 long long num_bytes_sent=0;
 long long num_bytes_recvd=0;
 
+long long num_syn_bytes_sent = 0;
+long long num_syn_bytes_recvd = 0;
+
 double max_time = 0,  max_comm_time = 0, max_wait_time = 0, max_send_time = 0, max_recv_time = 0;
 double avg_time = 0, avg_comm_time = 0, avg_wait_time = 0, avg_send_time = 0, avg_recv_time = 0;
 
@@ -102,6 +126,12 @@ enum MPI_NW_EVENTS
 	MPI_SEND_ARRIVED,
     MPI_SEND_ARRIVED_CB, // for tracking message times on sender
 	MPI_SEND_POSTED,
+    MPI_REND_ARRIVED,
+    MPI_REND_ACK_ARRIVED,
+    CLI_BCKGND_FIN,
+    CLI_BCKGND_ARRIVE,
+    CLI_BCKGND_GEN,
+    CLI_NBR_FINISH,
 };
 
 struct mpi_workload_sample
@@ -145,6 +175,15 @@ struct pending_waits
     struct qlist_head ql;
 };
 
+struct msg_size_info
+{
+    int64_t msg_size;
+    int num_msgs;
+    tw_stime agg_latency;
+    tw_stime avg_latency;
+    struct qhash_head * hash_link;
+    struct qlist_head ql; 
+};
 typedef struct mpi_msgs_queue mpi_msgs_queue;
 typedef struct completed_requests completed_requests;
 typedef struct pending_waits pending_waits;
@@ -158,6 +197,9 @@ struct nw_state
     int app_id;
     int local_rank;
 
+    int is_finished;
+    int neighbor_completed;
+
     struct rc_stack * processed_ops;
     struct rc_stack * matched_reqs;
 
@@ -194,9 +236,18 @@ struct nw_state
     /* Pending wait operation */
     struct pending_waits * wait_op;
 
+    /* Message size latency information */
+    struct qhash_table * msg_sz_table;
+    struct qlist_head msg_sz_list;
+
+    /* quick hash for maintaining message latencies */
+
     unsigned long num_bytes_sent;
     unsigned long num_bytes_recvd;
 
+    unsigned long syn_data;
+    unsigned long gen_data;
+    
     /* For sampling data */
     int sampling_indx;
     int max_arr_size;
@@ -242,9 +293,12 @@ struct nw_message
    } rc;
 };
 
+static void send_ack_back(nw_state* s, tw_bf * bf, nw_message * m, tw_lp * lp, mpi_msgs_queue * mpi_op);
+
+static void send_ack_back_rc(nw_state* s, tw_bf * bf, nw_message * m, tw_lp * lp);
 /* executes MPI isend and send operations */
 static void codes_exec_mpi_send(
-        nw_state* s, tw_bf * bf, nw_message * m, tw_lp* lp, struct codes_workload_op * mpi_op);
+        nw_state* s, tw_bf * bf, nw_message * m, tw_lp* lp, struct codes_workload_op * mpi_op, int is_rend);
 /* execute MPI irecv operation */
 static void codes_exec_mpi_recv(
         nw_state* s, tw_bf * bf, nw_message * m, tw_lp * lp, struct codes_workload_op * mpi_op);
@@ -292,6 +346,286 @@ static void update_message_time_rc(
 /* conversion from seconds to eanaoseconds */
 static tw_stime s_to_ns(tw_stime ns);
 
+static void update_message_size_rc(
+        struct nw_state * ns,
+        tw_lp * lp,
+        tw_bf * bf,
+        struct nw_message * m)
+{
+
+}
+/* update the message size */
+static void update_message_size(
+        struct nw_state * ns,
+        tw_lp * lp,
+        tw_bf * bf,
+        struct nw_message * m,
+        mpi_msgs_queue * qitem,
+        int is_eager,
+        int is_send)
+{
+            struct qhash_head * hash_link = NULL;
+            tw_stime msg_init_time = qitem->req_init_time;
+        
+            if(!ns->msg_sz_table)
+                ns->msg_sz_table = qhash_init(msg_size_hash_compare, quickhash_64bit_hash, RANK_HASH_TABLE_SZ); 
+            
+            hash_link = qhash_search(ns->msg_sz_table, &(qitem->num_bytes));
+
+            if(is_send)
+                msg_init_time = m->fwd.sim_start_time;
+            
+            /* update hash table */
+            if(!hash_link)
+            {
+                struct msg_size_info * msg_info = malloc(sizeof(struct msg_size_info));
+                msg_info->msg_size = qitem->num_bytes;
+                msg_info->num_msgs = 1;
+                msg_info->agg_latency = tw_now(lp) - msg_init_time;
+                msg_info->avg_latency = msg_info->agg_latency;
+                qhash_add(ns->msg_sz_table, &(msg_info->msg_size), &(msg_info->hash_link));
+                qlist_add(&msg_info->ql, &ns->msg_sz_list);
+                //printf("\n Msg size %d aggregate latency %f num messages %d ", m->fwd.num_bytes, msg_info->agg_latency, msg_info->num_msgs);
+            }
+            else
+            {
+                struct msg_size_info * tmp = qhash_entry(hash_link, struct msg_size_info, hash_link);
+                tmp->num_msgs++;
+                tmp->agg_latency += tw_now(lp) - msg_init_time;  
+                tmp->avg_latency = (tmp->agg_latency / tmp->num_msgs);
+//                printf("\n Msg size %d aggregate latency %f num messages %d ", qitem->num_bytes, tmp->agg_latency, tmp->num_msgs);
+            }
+}
+static void notify_background_traffic_rc(
+	    struct nw_state * ns,
+        tw_lp * lp,
+        tw_bf * bf,
+        struct nw_message * m)
+{
+    tw_rand_reverse_unif(lp->rng); 
+}
+
+static void notify_background_traffic(
+	    struct nw_state * ns,
+        tw_lp * lp,
+        tw_bf * bf,
+        struct nw_message * m)
+{
+        struct codes_jobmap_id jid; 
+        jid = codes_jobmap_to_local_id(ns->nw_id, jobmap_ctx);
+        
+        int num_jobs = codes_jobmap_get_num_jobs(jobmap_ctx); 
+        
+        for(int other_id = 0; other_id < num_jobs; other_id++)
+        {
+            if(other_id == jid.job)
+                continue;
+
+            struct codes_jobmap_id other_jid;
+            other_jid.job = other_id;
+
+            int num_other_ranks = codes_jobmap_get_num_ranks(other_id, jobmap_ctx);
+
+            lprintf("\n Other ranks %ld ", num_other_ranks);
+            tw_stime ts = (1.1 * g_tw_lookahead) + tw_rand_exponential(lp->rng, mean_interval/10000);
+            tw_lpid global_dest_id;
+     
+            for(int k = 0; k < num_other_ranks; k++)    
+            {
+                other_jid.rank = k;
+                int intm_dest_id = codes_jobmap_to_global_id(other_jid, jobmap_ctx); 
+                global_dest_id = codes_mapping_get_lpid_from_relative(intm_dest_id, NULL, NW_LP_NM, NULL, 0);
+
+                tw_event * e;
+                struct nw_message * m_new;  
+                e = tw_event_new(global_dest_id, ts, lp);
+                m_new = tw_event_data(e);
+                m_new->msg_type = CLI_BCKGND_FIN;
+                tw_event_send(e);   
+            }
+        }
+        return;
+}
+static void notify_neighbor_rc(
+	    struct nw_state * ns,
+        tw_lp * lp,
+        tw_bf * bf,
+        struct nw_message * m)
+{
+       if(bf->c0)
+       {
+            notify_background_traffic_rc(ns, lp, bf, m);
+            return;
+       }
+   
+       if(bf->c1)
+       {
+          tw_rand_reverse_unif(lp->rng); 
+       }
+} 
+static void notify_neighbor(
+	    struct nw_state * ns,
+        tw_lp * lp,
+        tw_bf * bf,
+        struct nw_message * m)
+{
+    if(ns->local_rank == num_dumpi_traces - 1 
+            && ns->is_finished == 1
+            && ns->neighbor_completed == 1)
+    {
+        printf("\n All workloads completed, notifying background traffic ");
+        bf->c0 = 1;