From 29b6c6be3a5697d41e5b30fcbfdf1033ff4269cd Mon Sep 17 00:00:00 2001
From: Harun Mustafa <hmusta@users.noreply.github.com>
Date: Thu, 20 Jun 2024 14:19:46 +0200
Subject: [PATCH] Fix warnings and multi-threading issues

---
 external/pthash        | 2 +-
 include/minimizers.hpp | 8 ++++++--
 include/util.hpp       | 5 ++++-
 3 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/external/pthash b/external/pthash
index 28aedcb..09b9bec 160000
--- a/external/pthash
+++ b/external/pthash
@@ -1 +1 @@
-Subproject commit 28aedcb03af096c0e9988b1ad240da7b4cf010d7
+Subproject commit 09b9bec3a9027b47c131061ec6a485454a698bcc
diff --git a/include/minimizers.hpp b/include/minimizers.hpp
index f58cb90..937c4db 100644
--- a/include/minimizers.hpp
+++ b/include/minimizers.hpp
@@ -13,7 +13,7 @@ struct minimizers {
         mphf_config.seed = util::get_seed_for_hash_function(build_config);
         mphf_config.minimal_output = true;
         mphf_config.verbose_output = false;
-        mphf_config.num_threads = std::thread::hardware_concurrency();
+        mphf_config.num_threads = build_config.num_threads;
         mphf_config.num_partitions = 4 * mphf_config.num_threads;
 
         if (size / mphf_config.num_partitions < pthash::constants::min_partition_size) {
@@ -29,6 +29,10 @@ struct minimizers {
 
         mphf_config.ram = 4 * essentials::GB;
         mphf_config.tmp_dir = build_config.tmp_dirname;
+        if (size <= 1) {
+            throw std::runtime_error(
+                "each partition must contain more than one key: use less partitions");
+        }
         m_mphf.build_in_external_memory(begin, size, mphf_config);
     }
 
@@ -49,4 +53,4 @@ struct minimizers {
     minimizers_pthash_type m_mphf;
 };
 
-}  // namespace sshash
\ No newline at end of file
+}  // namespace sshash
diff --git a/include/util.hpp b/include/util.hpp
index 0667fda..3cc1218 100644
--- a/include/util.hpp
+++ b/include/util.hpp
@@ -3,6 +3,7 @@
 #include <array>
 #include <cassert>
 #include <fstream>
+#include <thread>
 #include <cmath>  // for std::ceil on linux
 
 #include "hash_util.hpp"
@@ -74,6 +75,7 @@ struct build_configuration {
         : k(31)
         , m(17)
         , seed(constants::seed)
+        , num_threads(std::thread::hardware_concurrency())
 
         , l(constants::min_l)
         , c(constants::c)
@@ -87,6 +89,7 @@ struct build_configuration {
     uint64_t k;  // kmer size
     uint64_t m;  // minimizer size
     uint64_t seed;
+    uint64_t num_threads;
 
     uint64_t l;  // drive dictionary trade-off
     double c;    // drive PTHash trade-off
@@ -302,4 +305,4 @@ struct buffered_lines_iterator {
     uint64_t m_read_chars;
 };
 
-}  // namespace sshash
\ No newline at end of file
+}  // namespace sshash