google-research / agent-based-epidemic-sim

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This repository contains code released by Google Research.

All datasets in this repository are released under the CC BY 4.0 International license, which can be found here: https://creativecommons.org/licenses/by/4.0/legalcode. All source files in this repository are released under the Apache 2.0 license, the text of which can be found in the LICENSE file.

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Updated in 2023.

agent-based-epidemic-sim's Issues

optimization : use "--no-install-recommends" flag in apt-get to reduce download and install space

pull is open at #22

Output agent-level information

Hi,

would it be possible to output agent-level adjacency matrices (capturing contacts between agents) and SEIR status per time point?
This would be super useful to check advanced testing schemes that have appeared in the literature.

Thanks a lot!
Ingmar

Compilation error

Hi team,

I wanted to try our this simulator (and figure out how to integrate https://github.com/zalandoresearch/CRISP for COVID-19 infection risk score estimation) but I am getting the following error when running bazel build -c opt agent_based_epidemic_sim/applications/home_work:main

ERROR: /Users/rherbrich/src/agent-based-epidemic-sim/agent_based_epidemic_sim/port/BUILD:81:11: C++ compilation of rule '//agent_based_epidemic_sim/port:executor' failed (Exit 1) cc_wrapper.sh failed: error executing command external/local_config_cc/cc_wrapper.sh -U_FORTIFY_SOURCE -fstack-protector -Wall -Wthread-safety -Wself-assign -fcolor-diagnostics -fno-omit-frame-pointer -g0 -O2 '-D_FORTIFY_SOURCE=1' -DNDEBUG ... (remaining 26 argument(s) skipped)

Use --sandbox_debug to see verbose messages from the sandbox
agent_based_epidemic_sim/port/executor.cc:38:28: error: implicit instantiation of undefined template 'std::__1::vector<std::__1::thread, std::__1::allocator<std::__1::thread> >'
  std::vector<std::thread> threads_;
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/iosfwd:217:28: note: template is declared here
class _LIBCPP_TEMPLATE_VIS vector;
                           ^
agent_based_epidemic_sim/port/executor.cc:40:39: error: implicit instantiation of undefined template 'std::__1::vector<std::__1::function<void ()>, std::__1::allocator<std::__1::function<void ()> > >'
  std::vector<std::function<void()> > work_ GUARDED_BY(mu_);
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/iosfwd:217:28: note: template is declared here
class _LIBCPP_TEMPLATE_VIS vector;
                           ^
agent_based_epidemic_sim/port/executor.cc:40:45: warning: attribute guarded_by ignored, because it is not attached to a declaration [-Wignored-attributes]
  std::vector<std::function<void()> > work_ GUARDED_BY(mu_);
                                            ^
external/com_google_absl/absl/base/internal/thread_annotations.h:64:63: note: expanded from macro 'GUARDED_BY'
#define GUARDED_BY(x) THREAD_ANNOTATION_ATTRIBUTE__(guarded_by(x))
                                                              ^
agent_based_epidemic_sim/port/executor.cc:117:10: error: no viable conversion from returned value of type 'unique_ptr<pandemic::(anonymous namespace)::StdThreadExecutor>' to function return type 'unique_ptr<pandemic::Executor>'
  return absl::make_unique<StdThreadExecutor>(max_parallelism);
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2401:28: note: candidate constructor (the implicit copy constructor) not viable: no known conversion from 'typename __unique_if<StdThreadExecutor>::__unique_single' (aka 'unique_ptr<pandemic::(anonymous namespace)::StdThreadExecutor>') to 'const std::__1::unique_ptr<pandemic::Executor, std::__1::default_delete<pandemic::Executor> > &' for 1st argument
class _LIBCPP_TEMPLATE_VIS unique_ptr {
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2466:13: note: candidate constructor template not viable: no known conversion from 'typename __unique_if<StdThreadExecutor>::__unique_single' (aka 'unique_ptr<pandemic::(anonymous namespace)::StdThreadExecutor>') to 'std::nullptr_t' (aka 'nullptr_t') for 1st argument
  constexpr unique_ptr(nullptr_t) noexcept : __ptr_(pointer()) {}
            ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2494:3: note: candidate constructor not viable: no known conversion from 'typename __unique_if<StdThreadExecutor>::__unique_single' (aka 'unique_ptr<pandemic::(anonymous namespace)::StdThreadExecutor>') to 'std::__1::unique_ptr<pandemic::Executor, std::__1::default_delete<pandemic::Executor> > &&' for 1st argument
  unique_ptr(unique_ptr&& __u) noexcept
  ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2503:3: note: candidate template ignored: requirement 'is_convertible<pandemic::(anonymous namespace)::StdThreadExecutor *, pandemic::Executor *>::value' was not satisfied [with _Up = pandemic::(anonymous namespace)::StdThreadExecutor, _Ep = std::__1::default_delete<pandemic::(anonymous namespace)::StdThreadExecutor>]
  unique_ptr(unique_ptr<_Up, _Ep>&& __u) _NOEXCEPT
  ^
1 warning and 3 errors generated.