Sampling support + testing + omnitrace namespace (#19)

* omnitrace namespace

* Kokkos + Lulesh example/tests

* Sampling support + more

- OMNITRACE_BUILD_TESTING option
- sampling support
- pthread_gotcha
- fixes to labels for mpi_gotcha, fork_gotcha, omnitrace_component
- tasking::block_signals, tasking::unblock_signals
- instrumentation mode option in omnitrace exe
- argument option groups in omnitrace exe
- categories in omnitrace settings
- remove TIMEMORY_ prefixed options

* Release workflow updates

* Updated settings printing

* Fixed defaults in README

* Tweak setting defaults in README

* CMake fixes

* cmake-format

* clang-format

* LULESH_USE_MPI OFF

* LULESH_USE_MPI fix

* timemory add_secondary fix

* timemory ambiguous internal namespace fix

* Update timemory submodule

* Handle output path/prefix in omnitrace

- updated timemory
- updated test environment

* sampling + papi fix

* Fix to sampling without PAPI

* Fix for using too many processors in CI

* formatting

* Updated CI

- minor cmake tweaks
- updated timemory submodule

* Updated CI

* Updated CI

* CI + timemory updates

- data race fixes

* CI updates + debug for sampling

* Sampling updates

- moved tasking::{block,unblock}_signals to sampling namespace
- improvements to sampling w.r.t. thread-locality

* Minimum OMNITRACE_THREAD_COUNT of 128

* Handle multiple dims in sampler data

* Configure libunwind support for timemory

* Improved safeguards for sampling

- updated CI
- lulesh runtime-instrument test tweak

* formatting

* CI updates + sampler updates + misc

- fixed stack-buffer-overflow in omnitrace (get_*file_line_info)
- test labels
- steady_clock instead of system_clock in sampler
- update dyninst submodule with upgradePlaceholder fix
- disable OMNITRACE_BUILD_TESTING by default

* Updated timemory submodule

- hidden visibility for timemory
- storage finalizers do not capture this

* Update timemory submodule

- component visibility updates

* Reworked header includes

- use <...> for timemory headers
- always include <library/defines.hpp>

* Rename some config options

* Update PTL submodule

* Update kokkos submodule

* Updated sampling

* Updated CI

* Reworked instrumentation exe

- lowered min-address-range threshold to 256
- extended whole function exclude

* CI fix + timemory submodule update

- TIMEMORY_VISIBLE on component base
- RelWithDebugInfo -> RelWithDebInfo
- Info output for parallel-overhead

* Sampling flags + transpose update + CI update

- disable critical trace for parallel-overhead in CI
- SA_RESTART only in sampler
- reworked transpose example to use fewer threads

* CI update

- removed ubuntu-focal-external-debug
- reduced data artifacts upload

* CI timeouts

- updated timemory submodule
- minor tweaks to omnitrace exe logging

* LICENSE updates (partial)

* CI Test stage timeout extension

* Docker and Packaging updates

* Miscellaneous fixes/tweaks

- gpu.hpp / gpu.cpp
- disable roctracer component if no devices
- re-enable InstrStackFrames by default
- disable sampling by default
- pthread_gotcha::m_enable_sampling is false by default
- timemory submodule update w/ sampler and pop(tid) updates
- fix minor bug in sampler logic
- CMake: OMNITRACE_USE_HIP option
- roctracer + timemory fix

* Replaced OMNITRACE_USE_ROCTRACER with OMNITRACE_USE_HIP where appropriate

* cmake format

* Sampler deadlock fixes

* Removed debug messages from sampler

* Fix for MPI detection + test tweaks + misc

* Sampler deadlock fixes + misc

- removed papi_tot_ins
- pthread_gotcha blocks signals globally until sampler is setup
- metadata specialization for sampling components
- OMNITRACE_INSTRUMENTATION_MODE -> OMNITRACE_MODE
- default sampling delay increased to 0.05 from 1.0e-6
- removed {block,unblock}_signals from critical_trace and ptl
    - no longer necessary to use
- sampling delay minimum is 1.0e-3
- OMNITRACE_BUILD_HIDDEN_VISIBILITY

* omnitrace-avail + libunwind update + restructure

- restructured omnitrace components
- build custom omnitrace-avail executable
- updated libunwind to avoid malloc in get_unw_backtrace

* Fix remaining reorganization issues

- removed some duplicate code
- fixed some trait specializations after implicit instatiation
- formatting

* ensure_storage fix + avail improvements

- fix ensure_storage when component not avail
- suppress irrelevant info in omnitrace-avail

* Delay settings initialization

- slight tweak to tests w/ MPI

* Disable OpenMPI testing w/ ubuntu-bionic

- MPI testing is hanging bc of network interface issue on system:

> [[20462,1],0]: A high-performance Open MPI point-to-point messaging module
> was unable to find any relevant network interfaces:
> Module: OpenFabrics (openib)
>   Host: fv-az19-371
> Another transport will be used instead, although this may result in
> lower performance.
> NOTE: You can disable this warning by setting the MCA parameter
> btl_base_warn_component_unused to 0.

src/library/sampling.cpp

@@ -0,0 +1,219 @@
+// Copyright (c) 2018 Advanced Micro Devices, Inc. All Rights Reserved.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// with the Software without restriction, including without limitation the
+// rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
+// sell copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// * Redistributions of source code must retain the above copyright notice,
+// this list of conditions and the following disclaimers.
+//
+// * Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimers in the
+// documentation and/or other materials provided with the distribution.
+//
+// * Neither the names of Advanced Micro Devices, Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this Software without specific prior written permission.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH
+// THE SOFTWARE.
+
+#include "library/sampling.hpp"
+#include "library/config.hpp"
+#include "library/debug.hpp"
+#include "library/ptl.hpp"
+
+#include <timemory/backends/papi.hpp>
+#include <timemory/backends/threading.hpp>
+#include <timemory/components/data_tracker/components.hpp>
+#include <timemory/components/macros.hpp>
+#include <timemory/components/papi/extern.hpp>
+#include <timemory/components/papi/papi_array.hpp>
+#include <timemory/components/papi/papi_vector.hpp>
+#include <timemory/components/timing/backends.hpp>
+#include <timemory/components/trip_count/extern.hpp>
+#include <timemory/macros.hpp>
+#include <timemory/math.hpp>
+#include <timemory/mpl.hpp>
+#include <timemory/mpl/quirks.hpp>
+#include <timemory/mpl/type_traits.hpp>
+#include <timemory/operations.hpp>
+#include <timemory/sampling/allocator.hpp>
+#include <timemory/sampling/sampler.hpp>
+#include <timemory/storage.hpp>
+#include <timemory/utility/backtrace.hpp>
+#include <timemory/utility/demangle.hpp>
+#include <timemory/utility/types.hpp>
+#include <timemory/variadic.hpp>
+
+#include <array>
+#include <cstring>
+#include <ctime>
+#include <initializer_list>
+#include <mutex>
+#include <regex>
+#include <sstream>
+#include <string>
+#include <type_traits>
+
+#include <pthread.h>
+#include <signal.h>
+
+namespace omnitrace
+{
+namespace sampling
+{
+using bundle_t  = tim::lightweight_tuple<backtrace>;
+using sampler_t = tim::sampling::sampler<bundle_t, tim::sampling::dynamic>;
+}  // namespace sampling
+}  // namespace omnitrace
+
+TIMEMORY_DEFINE_CONCRETE_TRAIT(check_signals, omnitrace::sampling::sampler_t,
+                               std::false_type)
+
+TIMEMORY_DEFINE_CONCRETE_TRAIT(buffer_size, omnitrace::sampling::sampler_t,
+                               TIMEMORY_ESC(std::integral_constant<size_t, 256>))
+
+namespace omnitrace
+{
+namespace sampling
+{
+using signal_type_instances     = omnitrace_thread_data<std::set<int>, api::sampling>;
+using backtrace_init_instances  = omnitrace_thread_data<backtrace, api::sampling>;
+using sampler_running_instances = omnitrace_thread_data<bool, api::sampling>;
+using papi_vector_instances     = omnitrace_thread_data<comp::papi_vector, api::sampling>;
+
+namespace
+{
+std::unique_ptr<comp::papi_vector>&
+get_papi_vector(int64_t _tid)
+{
+    static auto& _v = papi_vector_instances::instances();
+    if(_tid == threading::get_id()) papi_vector_instances::construct();
+    return _v.at(_tid);
+}
+
+std::unique_ptr<backtrace>&
+get_backtrace_init(int64_t _tid)
+{
+    static auto& _v = backtrace_init_instances::instances();
+    return _v.at(_tid);
+}
+
+std::unique_ptr<bool>&
+get_sampler_running(int64_t _tid)
+{
+    static auto& _v = sampler_running_instances::instances();
+    return _v.at(_tid);
+}
+
+std::unique_ptr<std::set<int>>&
+get_signal_types(int64_t _tid)
+{
+    static auto& _v = signal_type_instances::instances();
+    // on the main thread, use both SIGALRM and SIGPROF.
+    // on secondary threads, only use SIGPROF.
+    signal_type_instances::construct((_tid == 0) ? std::set<int>{ SIGALRM, SIGPROF }
+                                                 : std::set<int>{ SIGPROF });
+    return _v.at(_tid);
+}
+
+template <typename... Args>
+void
+thread_sigmask(Args... _args)
+{
+    auto _err = pthread_sigmask(_args...);
+    if(_err != 0)
+    {
+        errno = _err;
+        perror("pthread_sigmask");
+        exit(EXIT_FAILURE);
+    }
+}
+
+template <typename Tp>
+sigset_t
+get_signal_set(Tp&& _v)
+{
+    sigset_t _sigset;
+    sigemptyset(&_sigset);
+    for(auto itr : _v)
+        sigaddset(&_sigset, itr);
+    return _sigset;
+}
+
+template <typename Tp>
+std::string
+get_signal_names(Tp&& _v)
+{
+    std::string _sig_names{};
+    for(auto&& itr : _v)
+        _sig_names += std::get<0>(tim::signal_settings::get_info(
+                          static_cast<tim::sys_signal>(itr))) +
+                      " ";
+    return _sig_names.substr(0, _sig_names.length() - 1);
+}
+}  // namespace
+
+std::set<int>
+setup()
+{
+    return backtrace::configure(true);
+}
+
+std::set<int>
+shutdown()
+{
+    return backtrace::configure(false);
+}
+
+void
+block_signals(std::set<int> _signals)
+{
+    if(_signals.empty()) _signals = *get_signal_types(threading::get_id());
+    if(_signals.empty())
+    {
+        OMNITRACE_PRINT("No signals to block...\n");
+        return;
+    }
+
+    OMNITRACE_DEBUG("Blocking signals [%s] on thread #%lu...\n",
+                    get_signal_names(_signals).c_str(), threading::get_id());
+
+    sigset_t _v = get_signal_set(_signals);
+    thread_sigmask(SIG_BLOCK, &_v, nullptr);
+}
+
+void
+unblock_signals(std::set<int> _signals)
+{
+    if(_signals.empty()) _signals = *get_signal_types(threading::get_id());
+    if(_signals.empty())
+    {
+        OMNITRACE_PRINT("No signals to unblock...\n");
+        return;
+    }
+
+    OMNITRACE_DEBUG("Unblocking signals [%s] on thread #%lu...\n",
+                    get_signal_names(_signals).c_str(), threading::get_id());
+
+    sigset_t _v = get_signal_set(_signals);
+    thread_sigmask(SIG_UNBLOCK, &_v, nullptr);
+}
+
+std::unique_ptr<sampler_t>&
+get_sampler(int64_t _tid)
+{
+    static auto& _v = sampler_instances::instances();
+    return _v.at(_tid);
+}
+}  // namespace sampling
+}  // namespace omnitrace