From cea41d09cc86c5011da06017905a344e2db6d5a0 Mon Sep 17 00:00:00 2001
From: Sam Yates <halfflat@gmail.com>
Date: Mon, 5 Sep 2016 15:31:31 +0200
Subject: [PATCH] Finalize fvm_multicell
* Fix bug in 'close' event delivery for multicell.
* Fix displacement scaling bug in gather_all_with_partition.
* Command line parameter io, reporting for new miniapp options.
* Only master rank performs command line parameter writing.
* Add test for mpi::gather_all and mpi::gather_all_with_partition.
* Extend utility of `util::assign`, `util::append`.
---
miniapp/io.cpp | 8 +-
miniapp/io.hpp | 2 +-
miniapp/miniapp.cpp | 2 +-
src/cell_group.hpp | 3 +-
src/communication/mpi.hpp | 7 +-
src/fvm_multicell.hpp | 1 +
src/util/range.hpp | 9 +-
tests/global_communication/CMakeLists.txt | 1 +
.../test_mpi_gather_all.cpp | 100 ++++++++++++++++++
9 files changed, 124 insertions(+), 9 deletions(-)
create mode 100644 tests/global_communication/test_mpi_gather_all.cpp
diff --git a/miniapp/io.cpp b/miniapp/io.cpp
index c1d4f6fc..348489ac 100644
--- a/miniapp/io.cpp
+++ b/miniapp/io.cpp
@@ -110,7 +110,7 @@ static void update_option(util::optional<T>& opt, const nlohmann::json& j, const
}
// Read options from (optional) json file and command line arguments.
-cl_options read_options(int argc, char** argv) {
+cl_options read_options(int argc, char** argv, bool allow_write) {
// Default options:
const cl_options defopts{
@@ -271,7 +271,7 @@ cl_options read_options(int argc, char** argv) {
}
// Save option values if requested.
- if (save_file != "") {
+ if (save_file != "" && allow_write) {
std::ofstream fid(save_file);
if (fid) {
try {
@@ -284,6 +284,8 @@ cl_options read_options(int argc, char** argv) {
fopts["dt"] = options.dt;
fopts["tfinal"] = options.tfinal;
fopts["all_to_all"] = options.all_to_all;
+ fopts["ring"] = options.ring;
+ fopts["group_size"] = options.group_size;
fopts["probe_ratio"] = options.probe_ratio;
fopts["probe_soma_only"] = options.probe_soma_only;
fopts["trace_prefix"] = options.trace_prefix;
@@ -316,6 +318,8 @@ std::ostream& operator<<(std::ostream& o, const cl_options& options) {
o << " simulation time : " << options.tfinal << "\n";
o << " dt : " << options.dt << "\n";
o << " all to all network : " << (options.all_to_all ? "yes" : "no") << "\n";
+ o << " ring network : " << (options.ring ? "yes" : "no") << "\n";
+ o << " group size : " << options.group_size << "\n";
o << " probe ratio : " << options.probe_ratio << "\n";
o << " probe soma only : " << (options.probe_soma_only ? "yes" : "no") << "\n";
o << " trace prefix : " << options.trace_prefix << "\n";
diff --git a/miniapp/io.hpp b/miniapp/io.hpp
index 1c5bba81..ac769d43 100644
--- a/miniapp/io.hpp
+++ b/miniapp/io.hpp
@@ -51,7 +51,7 @@ public:
std::ostream& operator<<(std::ostream& o, const cl_options& opt);
-cl_options read_options(int argc, char** argv);
+cl_options read_options(int argc, char** argv, bool allow_write = true);
} // namespace io
diff --git a/miniapp/miniapp.cpp b/miniapp/miniapp.cpp
index 9ad224ef..2b5df5d9 100644
--- a/miniapp/miniapp.cpp
+++ b/miniapp/miniapp.cpp
@@ -51,7 +51,7 @@ int main(int argc, char** argv) {
banner();
// read parameters
- io::cl_options options = io::read_options(argc, argv);
+ io::cl_options options = io::read_options(argc, argv, global_policy::id()==0);
std::cout << options << "\n";
std::cout << "\n";
std::cout << ":: simulation to " << options.tfinal << " ms in "
diff --git a/src/cell_group.hpp b/src/cell_group.hpp
index d8fd2f2a..30bdd99d 100644
--- a/src/cell_group.hpp
+++ b/src/cell_group.hpp
@@ -11,6 +11,7 @@
#include <event_queue.hpp>
#include <spike.hpp>
#include <spike_source.hpp>
+#include <util/debug.hpp>
#include <util/partition.hpp>
#include <util/range.hpp>
@@ -130,7 +131,7 @@ public:
// time step. This should be a parameter. e.g. with for variable
// order time stepping, use the minimum possible time step size.
while(auto e = events_.pop_if_before(cell_.time()+dt/10.)) {
- auto handle = get_target_handle(next->target);
+ auto handle = get_target_handle(e->target);
cell_.deliver_event(handle, e->weight);
}
}
diff --git a/src/communication/mpi.hpp b/src/communication/mpi.hpp
index 9ebb0ca4..472c6403 100644
--- a/src/communication/mpi.hpp
+++ b/src/communication/mpi.hpp
@@ -11,6 +11,7 @@
#include <algorithms.hpp>
#include <communication/gathered_vector.hpp>
+#include <util/debug.hpp>
namespace nest {
namespace mc {
@@ -97,7 +98,7 @@ namespace mpi {
}
template <typename T>
- std::vector<T> gather_all(const std::vector<T> &values) {
+ std::vector<T> gather_all(const std::vector<T>& values) {
static_assert(
true,//std::is_trivially_copyable<T>::value,
"gather_all can only be performed on trivally copyable types");
@@ -149,6 +150,10 @@ namespace mpi {
MPI_COMM_WORLD
);
+ for (auto& d : displs) {
+ d /= traits::count();
+ }
+
return gathered_type(
std::move(buffer),
std::vector<count_type>(displs.begin(), displs.end())
diff --git a/src/fvm_multicell.hpp b/src/fvm_multicell.hpp
index f885906f..1c9c799a 100644
--- a/src/fvm_multicell.hpp
+++ b/src/fvm_multicell.hpp
@@ -19,6 +19,7 @@
#include <segment.hpp>
#include <stimulus.hpp>
#include <util.hpp>
+#include <util/debug.hpp>
#include <util/meta.hpp>
#include <util/partition.hpp>
#include <util/span.hpp>
diff --git a/src/util/range.hpp b/src/util/range.hpp
index 89fcaddb..3addca60 100644
--- a/src/util/range.hpp
+++ b/src/util/range.hpp
@@ -332,13 +332,16 @@ range<const T*> singleton_view(const T& item) {
*/
template <typename Container, typename Seq>
-void append(Container &c, const Seq& seq) {
- c.insert(c.end(), seq.begin(), seq.end());
+Container& append(Container &c, const Seq& seq) {
+ auto canon = canonical_view(seq);
+ c.insert(c.end(), std::begin(canon), std::end(canon));
+ return c;
}
template <typename AssignableContainer, typename Seq>
AssignableContainer& assign(AssignableContainer& c, const Seq& seq) {
- c.assign(seq.begin(), seq.end());
+ auto canon = canonical_view(seq);
+ c.assign(std::begin(canon), std::end(canon));
return c;
}
diff --git a/tests/global_communication/CMakeLists.txt b/tests/global_communication/CMakeLists.txt
index cc1e1af8..800e7d19 100644
--- a/tests/global_communication/CMakeLists.txt
+++ b/tests/global_communication/CMakeLists.txt
@@ -4,6 +4,7 @@ set(HEADERS
set(COMMUNICATION_SOURCES
test_exporter_spike_file.cpp
test_communicator.cpp
+ test_mpi_gather_all.cpp
# unit test driver
test.cpp
diff --git a/tests/global_communication/test_mpi_gather_all.cpp b/tests/global_communication/test_mpi_gather_all.cpp
new file mode 100644
index 00000000..ed99089f
--- /dev/null
+++ b/tests/global_communication/test_mpi_gather_all.cpp
@@ -0,0 +1,100 @@
+#include "gtest.h"
+
+#ifdef WITH_MPI
+
+#include <cstring>
+#include <vector>
+
+#include <communication/mpi_global_policy.hpp>
+#include <communication/mpi.hpp>
+#include <util/range.hpp>
+
+using namespace nest::mc;
+using namespace nest::mc::communication;
+
+struct big_thing {
+ big_thing() {}
+ big_thing(int i): value_(i) {}
+
+ bool operator==(const big_thing& other) const {
+ return value_==other.value_ && !memcmp(salt_, other.salt_, sizeof(salt_));
+ }
+
+ bool operator!=(const big_thing& other) const {
+ return !(*this==other);
+ }
+
+private:
+ int value_;
+ char salt_[32] = "it's a lovely day for a picnic";
+};
+
+TEST(mpi, gather_all) {
+ using policy = mpi_global_policy;
+
+ int id = policy::id();
+
+ std::vector<big_thing> data;
+ // odd ranks: three items; even ranks: one item.
+ if (id%2) {
+ data = { id, id+7, id+8 };
+ }
+ else {
+ data = { id };
+ }
+
+ std::vector<big_thing> expected;
+ for (int i = 0; i<policy::size(); ++i) {
+ if (i%2) {
+ int rank_data[] = { i, i+7, i+8 };
+ util::append(expected, rank_data);
+ }
+ else {
+ int rank_data[] = { i };
+ util::append(expected, rank_data);
+ }
+ }
+
+ auto gathered = mpi::gather_all(data);
+
+ EXPECT_EQ(expected, gathered);
+}
+
+TEST(mpi, gather_all_with_partition) {
+ using policy = mpi_global_policy;
+
+ int id = policy::id();
+
+ std::vector<big_thing> data;
+ // odd ranks: three items; even ranks: one item.
+ if (id%2) {
+ data = { id, id+7, id+8 };
+ }
+ else {
+ data = { id };
+ }
+
+ std::vector<big_thing> expected_values;
+ std::vector<unsigned> expected_divisions;
+
+ expected_divisions.push_back(0);
+ for (int i = 0; i<policy::size(); ++i) {
+ if (i%2) {
+ int rank_data[] = { i, i+7, i+8 };
+ util::append(expected_values, rank_data);
+ expected_divisions.push_back(expected_divisions.back()+util::size(rank_data));
+ }
+ else {
+ int rank_data[] = { i };
+ util::append(expected_values, rank_data);
+ expected_divisions.push_back(expected_divisions.back()+util::size(rank_data));
+ }
+ }
+
+ auto gathered = mpi::gather_all_with_partition(data);
+
+ EXPECT_EQ(expected_values, gathered.values());
+ EXPECT_EQ(expected_divisions, gathered.partition());
+}
+
+#endif // WITH_MPI
--
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