Bug fixes

res/TemplateBatchFiles/SM-2019.bf

@@ -53,8 +53,9 @@ utility.ForEachPair (sm.partitions , "_key_", "_value_", '
 ');
 
 
-sm.bootstrap = trees.BootstrapSupport (sm.tree);
+sm.replicates = io.PromptUser(">How many bootstrap replicates", 100, 1, 1000000, TRUE);
 
+sm.bootstrap = trees.BootstrapSupport (sm.tree);
 sm.bootstrap_weighting = {"default" : 0.2};
 
 if (utility.Array1D (sm.bootstrap )) {
@@ -68,16 +69,8 @@ if (utility.Array1D (sm.bootstrap )) {
 
 }
 
-/*
-sm.method = io.SelectAnOption ({"Standard" : "Permute leaf labels freely (unconstrained)", 
-                                "Restricted"  : "Permute leaf labels in subtrees defined by randomly chosen internal branches (rate 1/4)"},
-                                "Resampling method"
-                                );
-*/
 
 
-sm.replicates = io.PromptUser(">How many bootstrap replicates", 100, 1, 1000000, TRUE);
-
 sm.tree.string = sm.tree[terms.trees.newick_with_lengths];
 sm.node_labels = {};
 
@@ -95,13 +88,8 @@ utility.ForEachPair (sm.partitions, "_regexp_", "_leaves_",
 );
 
 
-//console.log (T);
-//console.log (sm.node_labels);
-
-sm.mp = //trees.ParsimonyLabel ("T", sm.node_labels);
-Max (T, {"labels": sm.node_labels});
-//console.log (sm.mp);
 
+sm.mp = Max (T, {"labels": sm.node_labels});
 sm.score = sm.mp ["score"];
 
 io.ReportProgressMessageMD('SM',  'result', 'Inferred **' +  sm.score + '** migration events');
@@ -148,7 +136,6 @@ sm.dist.structured.cutoff = sm.dist.structured [sm.replicates * 90 $ 100];
 
 sm.structured.p = +sm.dist.shuffled["_MATRIX_ELEMENT_VALUE_<= sm.dist.structured.cutoff"];
 
-
 sm.sampled_stats = math.GatherDescriptiveStats (sm.resampled_distribution[-1][0]);
 sm.sampled_stuctured_stats = math.GatherDescriptiveStats (sm.resampled_distribution[-1][1]);
 
@@ -167,6 +154,9 @@ io.ReportProgressMessageMD('SM',  'reshuffled', 'Based on **' + sm.replicates +
          + Format ( sm.structured.p /(sm.replicates+1), 6, 3));
 io.ReportProgressMessageMD('SM',  'reshuffled', '\n> This p-value is derived by comparing the distribution of migration events from the panmictic reshuffle to the 90% percentile of the simulated distribution of expected migrations if leaf labels are permuted partially respecting subtree structure (block permutations), which results in **' + sm.dist.structured.cutoff + '** expected migrations');
 
+sm.json_path = sm.tree[terms.data.file] + ".json";
+io.ReportProgressMessageMD('SM',  'file', 'Saving detailed report as a JSON file to \`' + sm.json_path + '\`');
+
 sm.json = {
     'replicates' : sm.replicates,
     'compartments' : sm.group_count, 
@@ -178,7 +168,9 @@ sm.json = {
     'simulations' : {
         'panmictic' : sm.dist.shuffled,
         'structured' : sm.dist.structured   
-    }
+    },
+    "events" : sm.mp["substitutions"]
 };
 
+io.SpoolJSON (sm.json, sm.json_path);
 return sm.json;

res/TemplateBatchFiles/libv3/tasks/trees.bf

@@ -141,6 +141,8 @@ lfunction trees.GetTreeString(look_for_newick_tree) {
             SetDialogPrompt("Please select a tree file for the data:");
             fscanf(PROMPT_FOR_FILE, REWIND, "Raw", treeString);
             fprintf(stdout, "\n");
+
+            look_for_newick_tree = utility.getGlobalValue ("LAST_FILE_PATH");
 
             if (regexp.Find(treeString, "^#NEXUS")) {
                 ExecuteCommands(treeString);
@@ -196,7 +198,11 @@ lfunction trees.GetTreeString(look_for_newick_tree) {
         }
     }
 
-    return treeString;
+    return 
+    {
+        utility.getGlobalValue("terms.data.file"): look_for_newick_tree,
+        utility.getGlobalValue("terms.data.tree"): treeString
+    };
 }
 
 
@@ -379,6 +385,13 @@ lfunction trees.RootTree(tree_info, root_on) {
  */
 lfunction trees.ExtractTreeInfo(tree_string) {
 
+    if (Type (tree_string) == "AssociativeList") {
+        file_name   = tree_string[^"terms.data.file"];
+        tree_string = tree_string[^"terms.data.tree"];
+    } else {
+        file_name = None;
+    }
+
     Topology T = tree_string;
 
     branch_lengths = BranchLength(T, -1);
@@ -418,6 +431,8 @@ lfunction trees.ExtractTreeInfo(tree_string) {
         ^"terms.trees.model_list": Columns(modelMap),
         ^"terms.trees.rooted" : rooted,
         ^"terms.trees.meta" : T.__meta,
+        ^"terms.data.file" : file_name
+
     };
 }
 

src/core/batchlan.cpp

@@ -263,15 +263,15 @@ void    MPISendString       (_String const& theMessage, long destID, bool isErro
 {
 
     long    messageLength = theMessage.length(),
-            transferCount = 0;
+            transferCount = 0L;
 
     if (isError) {
         messageLength = -messageLength;
     }
 
     ReportMPIError(MPI_Send(&messageLength, 1, MPI_LONG, destID, HYPHY_MPI_SIZE_TAG, MPI_COMM_WORLD),true);
 
-    if (messageLength == 0) {
+    if (messageLength == 0L) {
         return;
     }
 
@@ -300,8 +300,8 @@ void    MPISendString       (_String const& theMessage, long destID, bool isErro
 //____________________________________________________________________________________
 _String*    MPIRecvString       (long senderT, long& senderID) {
     _String*    theMessage = nil;
-    long        messageLength = 0,
-                transferCount = 0;
+    long        messageLength = 0L,
+                transferCount = 0L;
 
     int         actualReceived = 0;
     bool        isError       = false;
@@ -329,6 +329,8 @@ _String*    MPIRecvString       (long senderT, long& senderID) {
         isError = true;
         messageLength = -messageLength;
     }
+
+    //printf ("MPIRecvString size tag %ld (size chunk %ld) \n",messageLength, MPI_SEND_CHUNK);
 
     if (!isError) {
         //MPI_Get_count (&status,MPI_CHAR,&actualReceived);
@@ -352,6 +354,7 @@ _String*    MPIRecvString       (long senderT, long& senderID) {
         }
 
         if (messageLength-transferCount) {
+            //printf ("Clause 2 %d %d\n", messageLength-transferCount, theMessage->length());
             ReportMPIError(MPI_Recv((void*)(theMessage->get_str()+transferCount), messageLength-transferCount, MPI_CHAR, senderT, HYPHY_MPI_STRING_TAG, MPI_COMM_WORLD,&status),false);
             MPI_Get_count (&status,MPI_CHAR,&actualReceived);
             if (actualReceived!=messageLength-transferCount) {

src/core/batchlanruntime.cpp

@@ -1969,21 +1969,17 @@ bool      _ElementaryCommand::HandleMPIReceive (_ExecutionList& current_program)
 
 #ifdef __HYPHYMPI__
 
-
-
-
     receptacle = _ValidateStorageVariable (current_program, 1UL);
     _Variable* node_index_storage = _ValidateStorageVariable (current_program, 2UL);
 
     long target_node = _ProcessNumericArgumentWithExceptions(*GetIthParameter(0UL), current_program.nameSpacePrefix),
-    node_count  = hy_env::EnvVariableGetDefaultNumber(hy_env::mpi_node_count);
+    node_count  = hy_env::EnvVariableGetNumber(hy_env::mpi_node_count);
 
     if (target_node < -1L || target_node >= node_count) {
-      throw (GetIthParameter(1UL)->Enquote () & " (=" & node_count & ") is not a valid MPI node index (or -1 to accept from any node");
+      throw (GetIthParameter(1UL)->Enquote () & " (=" & node_count & ") must be a valid MPI node index (or -1 to accept from any node");
     }
 
     long received_from;
-
     receptacle->SetValue(new _FString (MPIRecvString (target_node,received_from)), false);
     node_index_storage->SetValue (new _Constant (received_from), false);
 
@@ -2009,10 +2005,10 @@ bool      _ElementaryCommand::HandleMPISend (_ExecutionList& current_program){
 
 #ifdef __HYPHYMPI__
    long target_node = _ProcessNumericArgumentWithExceptions(*GetIthParameter(0UL), current_program.nameSpacePrefix),
-         node_count  = hy_env::EnvVariableGetDefaultNumber(hy_env::mpi_node_count);
+         node_count  = hy_env::EnvVariableGetNumber(hy_env::mpi_node_count);
 
     if (target_node < 0L || target_node >= node_count) {
-      throw (GetIthParameter(1UL)->Enquote () & " (=" & node_count & ") is not a valid MPI node index");
+        throw (GetIthParameter(1UL)->Enquote () & " (=" & node_count & ") is not a valid MPI node index; valud range is " & target_node & " to " & (node_count-1));
     }
 
     _StringBuffer message_to_send (1024UL);
@@ -2039,7 +2035,7 @@ bool      _ElementaryCommand::HandleMPISend (_ExecutionList& current_program){
     if (message_to_send.nonempty()) {
       MPISendString(message_to_send, target_node);
     } else {
-      throw ("An ivalid (empty) MPI message");
+      throw (_String ("An invalid (empty) MPI message"));
     }
 #else
     throw ("Command not supported for non-MPI versions of HyPhy. HBL scripts need to check for MPI before calling MPI features");

src/core/global_things.cpp

@@ -57,6 +57,8 @@
 
 using     namespace hy_env;
 
+#define __HYPHY_MPI_MESSAGE_LOGGING__
+
 extern _SimpleList freeSlots;
 
 
@@ -356,6 +358,13 @@ namespace hy_global {
         has_terminal_stdout = isatty (STDOUT_FILENO);
         has_terminal_stderr = isatty (STDERR_FILENO);
 
+
+
+#ifdef __HYPHYMPI__
+        hy_env :: EnvVariableSet (hy_env::mpi_node_id, new _Constant (hy_mpi_node_rank), false);
+        hy_env :: EnvVariableSet (hy_env::mpi_node_count, new _Constant (hy_mpi_node_count), false);
+#endif
+
 #if not defined (__HYPHY_MPI_MESSAGE_LOGGING__) && defined (__HYPHYMPI__)
         if (hy_mpi_node_rank == 0L) {
 #endif

src/core/matrix.cpp

@@ -6067,7 +6067,7 @@ HBLObjectRef _Matrix::Random (HBLObjectRef kind) {
             _String             pdfkey      ("PDF"),
                                 * arg0      = (_String *)keys->GetItem(0L);
             DeleteObject (keys);
-            if (arg0->Equal(&pdfkey)) {
+            if (arg0->Equal(pdfkey)) {
                 _String     pdf ((_String *) (pdfArgs->GetByKey(pdfkey,STRING))->toStr()),
                             arg ("ARG0");
 

src/mains/unix.cpp

@@ -600,23 +600,16 @@ int main (int argc, char* argv[])
 #endif
 
 #ifdef  __HYPHYMPI__
-    int            rank,
-                   size;
-
     MPI_Init       (&argc, &argv);
+    int            rank,
+    size;
+
     MPI_Comm_rank(MPI_COMM_WORLD, &rank);
     MPI_Comm_size(MPI_COMM_WORLD, &size);
-
-    hy_env :: EnvVariableSet (hy_env::mpi_node_id, new _Constant (rank), false);
-    hy_env :: EnvVariableSet (hy_env::mpi_node_count, new _Constant (size), false);
-
     hy_mpi_node_rank  = rank;
     hy_mpi_node_count = size;
-
-    if (rank == 0) {
-        mpiNodesThatCantSwitch.Populate (size,1,0);
-    }
-
+
+
     /*
     int i = 0;
     char hostname[256];

src/utils/hyphyunixutils.cpp

@@ -61,7 +61,6 @@ void            mpiNormalLoop    (int, int, _String &);
 void            mpiOptimizerLoop (int, int);
 
 void            mpiBgmLoop (int, int);
-_SimpleList     mpiNodesThatCantSwitch;
 #endif
 
 extern _List batchLanguageFunctionNames;
@@ -242,7 +241,7 @@ void mpiNormalLoop    (int rank, int size, _String & baseDir)
             ReportWarning           ("[MPI] Returned from mpiOptimizer loop");
             hyphyMPIOptimizerMode   = _hyphyLFMPIModeNone;
             PushFilePath(baseDir, false, false);
-        } else if ( theMessage->Equal (&mpiLoopSwitchToBGM) ) {
+        } else if ( *theMessage == mpiLoopSwitchToBGM) {
             ReportWarning       ("[MPI] Received signal to switch to mpiBgmLoop");
             MPISendString       (mpiLoopSwitchToBGM, senderID); // feedback to source to confirm receipt of message
             mpiBgmLoop          (rank, size);
@@ -291,8 +290,7 @@ void mpiNormalLoop    (int rank, int size, _String & baseDir)
             }
 
             MPISendString(*resStr,senderID);
-
-
+
             if (hy_env::EnvVariableTrue (preserveSlaveNodeState) == false) {
                 PurgeAll (true);
                 InitializeGlobals ();

tests/hbltests/UnitTests/HBLCommands/Random.bf

@@ -57,11 +57,11 @@ function runTest () {
   // *** set a breakpoint in malloc_error_break to debug
 
   // The code below returns the errors
-  //mean1 = {{1,1,1}};
-  //cov1 = {{1,0}{0,1}};
-  //a1 = {"PDF":"Gaussian","ARG0":cov1};
-  //z = Random(mean1,a1);
-  //fprintf (stdout, 'z: ', z, '\n');
+  mean1 = {{1,1,1}};
+  cov1 = {{1,0}{0,1}};
+  a1 = {"PDF":"Gaussian","ARG0":cov1};
+  z = Random(mean1,a1);
+  fprintf (stdout, 'z: ', z, '\n');
 
   //mean2 = {{1,1,1}};
   //cov2 = {{1,0}{0,1}};

tests/hbltests/libv3/BUSTED.wbf

@@ -2,5 +2,5 @@ LoadFunctionLibrary("SelectionAnalyses/BUSTED.bf", {
     "0": "Universal",
     "1": PATH_TO_CURRENT_BF + "data/CD2.nex",
     "2": "GROUP3",
-    "3": "All"
+    "3": "No"
 });