From e25ebfffdb0d654523f71235de6d50e1950c7ebe Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Max=20L=C3=BCbke?= <mluebke@uni-potsdam.de>
Date: Thu, 29 Aug 2024 08:35:11 +0200
Subject: [PATCH 1/2] fix: distribute species names across all processes

---
 src/poet.cpp | 47 ++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 46 insertions(+), 1 deletion(-)

diff --git a/src/poet.cpp b/src/poet.cpp
index 6a16b177a..4a0abc2c1 100644
--- a/src/poet.cpp
+++ b/src/poet.cpp
@@ -32,6 +32,7 @@
 #include <Rcpp/DataFrame.h>
 #include <Rcpp/Function.h>
 #include <Rcpp/vector/instantiation.h>
+#include <cstdint>
 #include <cstdlib>
 #include <memory>
 #include <mpi.h>
@@ -41,6 +42,7 @@
 #include "Base/argh.hpp"
 
 #include <poet.hpp>
+#include <vector>
 
 using namespace std;
 using namespace poet;
@@ -403,6 +405,49 @@ static Rcpp::List RunMasterLoop(RInsidePOET &R, const RuntimeParameters &params,
   return profiling;
 }
 
+std::vector<std::string> getSpeciesNames(const Field &&field, int root,
+                                         MPI_Comm comm) {
+  std::uint32_t n_elements;
+  std::uint32_t n_string_size;
+
+  int rank;
+  MPI_Comm_rank(comm, &rank);
+
+  const bool is_master = root == rank;
+
+  // first, the master sends all the species names iterative
+  if (is_master) {
+    n_elements = field.GetProps().size();
+    MPI_Bcast(&n_elements, 1, MPI_UINT32_T, root, MPI_COMM_WORLD);
+
+    for (std::uint32_t i = 0; i < n_elements; i++) {
+      n_string_size = field.GetProps()[i].size();
+      MPI_Bcast(&n_string_size, 1, MPI_UINT32_T, root, MPI_COMM_WORLD);
+      MPI_Bcast(const_cast<char *>(field.GetProps()[i].c_str()), n_string_size,
+                MPI_CHAR, root, MPI_COMM_WORLD);
+    }
+
+    return field.GetProps();
+  }
+
+  // now all the worker stuff
+  MPI_Bcast(&n_elements, 1, MPI_UINT32_T, root, comm);
+
+  std::vector<std::string> species_names_out(n_elements);
+
+  for (std::uint32_t i = 0; i < n_elements; i++) {
+    MPI_Bcast(&n_string_size, 1, MPI_UINT32_T, root, MPI_COMM_WORLD);
+
+    char recv_buf[n_string_size];
+
+    MPI_Bcast(recv_buf, n_string_size, MPI_CHAR, root, MPI_COMM_WORLD);
+
+    species_names_out[i] = std::string(recv_buf, n_string_size);
+  }
+
+  return species_names_out;
+}
+
 int main(int argc, char *argv[]) {
   int world_size;
 
@@ -442,7 +487,7 @@ int main(int argc, char *argv[]) {
                               init_list.getChemistryInit(), MPI_COMM_WORLD);
 
     const ChemistryModule::SurrogateSetup surr_setup = {
-        init_list.getInitialGrid().GetProps(),
+        getSpeciesNames(init_list.getInitialGrid(), 0, MPI_COMM_WORLD),
         run_params.use_dht,
         run_params.dht_size,
         run_params.use_interp,

From 1f9ffe999f9f18b5ff0b91a2a4e96a2ecf3d089e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Max=20L=C3=BCbke?= <mluebke@uni-potsdam.de>
Date: Thu, 29 Aug 2024 08:35:17 +0200
Subject: [PATCH 2/2] Update subproject commit reference

---
 ext/iphreeqc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ext/iphreeqc b/ext/iphreeqc
index e6e5e0d51..48e65d87a 160000
--- a/ext/iphreeqc
+++ b/ext/iphreeqc
@@ -1 +1 @@
-Subproject commit e6e5e0d5156c093241a53e6ce074ef346d64ae26
+Subproject commit 48e65d87ad70f84aec01c27d9560cd3094a8129c