Merge pull request #141 from matsim-vsp/library-updates

Library updates
matsim-vsp · Nov 28, 2024 · 919fa2b · 919fa2b
2 parents a48dc40 + b68e29d
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diff --git a/Cargo.lock b/Cargo.lock
diff --git a/Cargo.toml b/Cargo.toml
@@ -8,42 +8,43 @@ edition = "2021"
 [dependencies]
 serde = { version = "1.0.137", features = ["derive"] }
 serde_json = "1.0.93"
+# sticking with quick-xml 0.23.0 because the serialization API changed: https://github.com/tafia/quick-xml/issues/499
+# since the new API would need an adapter from std::fmt::Write to std::io::Write, we stick with the old API
 quick-xml = { version = "0.23.0", features = ["serialize"] }
 flate2 = { version = "1.0.24" }
 rand = "0.8.5"
-metis = "0.1.2"
-flexi_logger = { version = "0.22", features = ["async"] }
+metis = "0.2.2"
+flexi_logger = { version = "0.29.6", features = ["async"] }
 clap = { version = "4.0.29", features = ["derive"] }
-# point to the github repo directly because we need a more recent version of bindgen. Otherwise the build fails
-# due to some incompatibility starting with macOs 13.6
-mpi = { git = "https://github.com/rsmpi/rsmpi", rev = "1622101c9fc3a78620e9649f7f895616289d3558" }
+mpi = "0.8.0"
 # dependencies for serialization with protobuf
-prost = "0.11.5"
+prost = "0.13.3"
 # bytes replaces the signature of std::io::Cursor to implemnt Buf somehow...
 bytes = "1.3.0"
-serial_test = "2.0.0"
+serial_test = "3.2.0"
 wait-timeout = "0.2.0"
 tracing = "0.1"
 tracing-subscriber = { version = "0.3.0", features = ["json", "fmt", "std", "registry"] }
 tracing-appender = "0.2"
-itertools = "0.10.5"
+itertools = "0.13.0"
 assert_approx_eq = "1.1.0"
 nohash-hasher = "0.2.0"
 rand_distr = "0.4.3"
 serde_path_to_error = "0.1.14"
-geo = "0.26.0"
+geo = "0.29.1"
 ahash = "0.8.6"
 keyed_priority_queue = "0.4.1"
 xml = "0.8.10"
 lz4_flex = "0.11.1"
-typetag = "0.2.13"
+typetag = "0.2.18"
 serde_yaml = "0.9.27"
 
 [build-dependencies]
 # generates types based on .proto files
 prost-build = "0.11"
 # provides the protoc compiler - this makes the build slow but one doesn't need to
 # install the protoc compiler as prerequisite.
+# updating to 2.1.0 causes huge compile times (https://github.com/MaterializeInc/rust-protobuf-native/issues/24). Maybe we should switch to another crate.
 protobuf-src = "1.1.0"
 
 [profile.bench]

diff --git a/README.md b/README.md
@@ -8,6 +8,7 @@ The most recent release can be cited with the following reference
 [![DOI](https://zenodo.org/badge/498376436.svg)](https://zenodo.org/doi/10.5281/zenodo.13928119)
 
 The project is described in two conference papers, which were presented at ISPDC 24 in Chur, Switzerland, July 2024:
+
 - [High-Performance Simulations for Urban Planning: Implementing Parallel Distributed Multi-Agent Systems in MATSim](https://doi.org/10.1109/ISPDC62236.2024.10705395)
 - [Real-Time Routing in Traffic Simulations: A Distributed Event Processing Approach](https://doi.org/10.1109/ISPDC62236.2024.10705399)
 
@@ -16,8 +17,8 @@ The project is described in two conference papers, which were presented at ISPDC
 Install Rust for your operating system as described [here](https://www.rust-lang.org/tools/install). For WSL this would
 be
 
-```
-$ curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
+```shell
+curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
 ```
 
 ## Set Up Prerequisites
@@ -28,8 +29,8 @@ compiled with the project, but need to be present on the operating system.
 ### METIS
 
 The project uses the [metis](https://crates.io/crates/metis) crate as a dependency which
-is a wrapper for the [METIS C Library](https://github.com/KarypisLab/METIS). The C-Library is 
-expected to be present on the machine. Also, the `metis` crate requires `libclang` on the machine 
+is a wrapper for the [METIS C Library](https://github.com/KarypisLab/METIS). The C-Library is
+expected to be present on the machine. Also, the `metis` crate requires `libclang` on the machine
 this project is built on.
 
 ### MPI
@@ -51,61 +52,105 @@ The dependencies named above need to be installed before the project can be buit
 
 Install dev versions of required packages because dev stuff is required during compilation
 
-```
-$ sudo apt -y install libclang-dev llvm-dev libmetis-dev libopenmpi-dev
+```shell
+sudo apt -y install libclang-dev llvm-dev libmetis-dev libopenmpi-dev
 ```
 
 #### MacOs
 
 The dependencies are available via [homebrew](https://brew.sh/) on macOS.
 
-```
-$ brew install metis open-mpi
+```shell
+brew install metis open-mpi
 ```
 
 The project contains a `config.toml` which tries to set the `CPATH` and the `RUSTFLAGS` environment variable. In case
 this doesn't work, they need to be set like the following:
-```
-$ export CPATH=$HOMEBREW_PREFIX/include
-$ export RUSTFLAGS="-L$HOMEBREW_PREFIX/lib"
+
+```shell
+export CPATH=$HOMEBREW_PREFIX/include
+export RUSTFLAGS="-L$HOMEBREW_PREFIX/lib"
 ```
 
 Both variables are necessary to compile the METIS and MPI wrapper libraries.
 
 #### Math Cluster
 
 The math cluster has all dependencies installed. They need to be enabled via the module system:
+
+```shell
+module load metis-5.1 ompi/gcc/4.1.2
 ```
-$ module load metis-5.1 ompi/gcc/4.1.2
-```
+
 #### HLRN
 
-The HLRN cluster has all dependencies installed. They need to be enabled via the module system:
+##### Setup conda
+
+Unfortunately, there is no `libclang` dependency installed. You need to install it yourself via `conda`. If you use it
+for the first time, load the conda module and initialize it, such that it is available in your shell whenever you login:
+
+```shell
+module load anaconda3/2023.09
+conda init bash
+```
+
+Then create your own environment and install `libclang`:
+
+```shell
+conda create -n your_env_name
+conda activate your_env_name
+conda install libclang 
+```
+
+##### Load dependencies
+
+The HLRN cluster has **some** dependencies installed. They need to be enabled via the module system:
+
+```shell
+module load intel/2024.2 openmpi/gcc/5.0.3
 ```
-$ module load gcc/9.3.0 llvm/9.0.0 openmpi/gcc.9/4.1.4 metis/5.1.0
+
+So, before you run the project, you need to activate the environment:
+
+```shell
+conda activate your_env_name
 ```
 
+The activation automatically updates the environment variables such that `libclang` files can be found by the compiler.
+
+Source: https://nhr-zib.atlassian.net/wiki/spaces/PUB/pages/430343/Anaconda+conda+and+Mamba
+
 ## Run the project
 
 The project is built using cargo.
 
-```
-$ cargo build --release
+```shell
+cargo build --release
 ```
 
 Then a simulation can be started like the following:
-```
-$ mpirun -np 2 ./target/release/mpi_qsim --config-path /path/to/config.yml
+
+```shell
+mpirun -np 2 ./target/release/mpi_qsim --config-path /path/to/config.yml
 ```
 
 It is also possible to execute a build before running by executing the following. This is way, one doesn't
 forget to re-compile before running.
-```
-$  cargo mpirun --np 2 --release --bin mpi_qsim -- --config-path /path/to/config.yaml
+
+```shell
+cargo mpirun --np 2 --release --bin mpi_qsim -- --config-path /path/to/config.yaml
 ```
 
 We also have a
 
 ### Test
 
 Run `$ cargo test` to execute all tests. To have immediate output use `$ cargo test -- --nocapture`
+
+## Create input files
+
+You need to create protobuf files from the xml files. This can be done with the following command:
+
+```shell
+cargo run --bin convert_to_binary --release -- --network network.xml --population population.xml --vehicles vehicles.xml --output-dir output --run-id run
+```
diff --git a/assets/adhoc_routing/with_updates/network.xml b/assets/adhoc_routing/with_updates/network.xml
@@ -2,23 +2,86 @@
 <!DOCTYPE network SYSTEM "http://www.matsim.org/files/dtd/network_v2.dtd">
 <network>
     <nodes>
-        <node id="node0" x="-100.0" y="0.0"/>
-        <node id="node1" x="0.0" y="0.0"/>
-        <node id="node2" x="100.0" y="0.0"/>
-        <node id="node3" x="1100.0" y="0.0"/>
-        <node id="node4" x="1200.0" y="0.0" />
-        <node id="node5" x="1300.0" y="0.0" />
-        <node id="node6" x="600.0" y="300.0" />
+        <node id="node0" x="-100.0" y="0.0">
+            <attributes>
+                <attribute name="partition" class="java.lang.Integer">1</attribute>
+            </attributes>
+        </node>
+        <node id="node1" x="0.0" y="0.0">
+            <attributes>
+                <attribute name="partition" class="java.lang.Integer">1</attribute>
+            </attributes>
+        </node>
+        <node id="node2" x="100.0" y="0.0">
+            <attributes>
+                <attribute name="partition" class="java.lang.Integer">1</attribute>
+            </attributes>
+        </node>
+        <node id="node3" x="1100.0" y="0.0">
+            <attributes>
+                <attribute name="partition" class="java.lang.Integer">0</attribute>
+            </attributes>
+        </node>
+        <node id="node4" x="1200.0" y="0.0">
+            <attributes>
+                <attribute name="partition" class="java.lang.Integer">0</attribute>
+            </attributes>
+        </node>
+        <node id="node5" x="1300.0" y="0.0">
+            <attributes>
+                <attribute name="partition" class="java.lang.Integer">0</attribute>
+            </attributes>
+        </node>
+        <node id="node6" x="600.0" y="300.0">
+            <attributes>
+                <attribute name="partition" class="java.lang.Integer">1</attribute>
+            </attributes>
+        </node>
     </nodes>
     <links capperiod="01:00:00" effectivecellsize="7.5" effectivelanewidth="3.75">
-        <link id="0" from="node0" to="node1" length="100" freespeed="10" capacity="100.0" permlanes="1.0" oneway="1" modes="bike,car" />
-        <link id="1" from="node1" to="node2" length="100" freespeed="10" capacity="100.0" permlanes="1.0" oneway="1" modes="bike,car" />
-        <link id="2" from="node2" to="node3" length="1000" freespeed="10" capacity="3.0" permlanes="1.0" oneway="1" modes="bike,car" />
-        <link id="3" from="node3" to="node4" length="100" freespeed="10" capacity="100.0" permlanes="1.0" oneway="1" modes="bike,car" />
-        <link id="4" from="node4" to="node5" length="100" freespeed="10" capacity="100.0" permlanes="1.0" oneway="1" modes="bike,car"/>
+        <link id="0" from="node0" to="node1" length="100" freespeed="10" capacity="100.0" permlanes="1.0" oneway="1"
+              modes="bike,car">
+            <attributes>
+                <attribute name="partition" class="java.lang.Integer">1</attribute>
+            </attributes>
+        </link>
+        <link id="1" from="node1" to="node2" length="100" freespeed="10" capacity="100.0" permlanes="1.0" oneway="1"
+              modes="bike,car">
+            <attributes>
+                <attribute name="partition" class="java.lang.Integer">1</attribute>
+            </attributes>
+        </link>
+        <link id="2" from="node2" to="node3" length="1000" freespeed="10" capacity="3.0" permlanes="1.0" oneway="1"
+              modes="bike,car">
+            <attributes>
+                <attribute name="partition" class="java.lang.Integer">0</attribute>
+            </attributes>
+        </link>
+        <link id="3" from="node3" to="node4" length="100" freespeed="10" capacity="100.0" permlanes="1.0" oneway="1"
+              modes="bike,car">
+            <attributes>
+                <attribute name="partition" class="java.lang.Integer">0</attribute>
+            </attributes>
+        </link>
+        <link id="4" from="node4" to="node5" length="100" freespeed="10" capacity="100.0" permlanes="1.0" oneway="1"
+              modes="bike,car">
+            <attributes>
+                <attribute name="partition" class="java.lang.Integer">0</attribute>
+            </attributes>
+        </link>
 
-        <link id="5" from="node2" to="node6" length="1000" freespeed="10" capacity="100.0" permlanes="1.0" oneway="1" modes="bike,car"/>
-        <link id="6" from="node6" to="node3" length="1000" freespeed="10" capacity="100.0" permlanes="1.0" oneway="1" modes="bike,car"/>
+        <link id="5" from="node2" to="node6" length="1000" freespeed="10" capacity="100.0" permlanes="1.0" oneway="1"
+              modes="bike,car">
+            <attributes>
+                <attribute name="partition" class="java.lang.Integer">1</attribute>
+            </attributes>
+        </link>
+        <link id="6" from="node6" to="node3" length="1000" freespeed="10" capacity="100.0" permlanes="1.0" oneway="1"
+              modes="bike,car">
+            <attributes>
+                <attribute name="partition" class="java.lang.Integer">0</attribute>
+            </attributes>
+        </link>
 
     </links>
 </network>
diff --git a/assets/rvr-1pct.config.yml b/assets/rvr-1pct.config.yml
@@ -0,0 +1,27 @@
+modules:
+  protofiles:
+    type: ProtoFiles
+    network: /Users/paulheinrich/Nextcloud/Shared/RustQSim/scenarios/rvr/input/rvr-1pct/rvr-1pct.network.binpb
+    population: /Users/paulheinrich/Nextcloud/Shared/RustQSim/scenarios/rvr/input/rvr-1pct/rvr-1pct.plans.binpb
+    vehicles: /Users/paulheinrich/Nextcloud/Shared/RustQSim/scenarios/rvr/input/rvr-1pct/rvr-1pct.vehicles.binpb
+    ids: /Users/paulheinrich/Nextcloud/Shared/RustQSim/scenarios/rvr/input/rvr-1pct/rvr-1pct.ids.binpb
+  partitioning:
+    type: Partitioning
+    num_parts: 0
+    method: !Metis
+      vertex_weight:
+        - PreComputed
+  output:
+    type: Output
+    output_dir: ./assets/rvr-1pct/size
+    profiling: !CSV
+      level: INFO
+  routing:
+    type: Routing
+    mode: UsePlans
+  simulation:
+    type: Simulation
+    start_time: 0
+    end_time: 129600
+    sample_size: 0.01
+    stuck_threshold: 30
diff --git a/rust-toolchain.toml b/rust-toolchain.toml
@@ -1,5 +1,2 @@
-# use nighly build because rust road router need experimental features.
 [toolchain]
-# due to https://github.com/intellij-rust/intellij-rust/issues/10427
-#channel = "nightly-2023-05-01"
 channel = "stable"
diff --git a/src/simulation/controller.rs b/src/simulation/controller.rs
@@ -60,13 +60,16 @@ pub fn run_channel() {
 pub fn run_mpi() {
     let universe = mpi::initialize().unwrap();
     let world = universe.world();
+    let size = world.size();
+    let rank = world.rank();
+
     let comm = MpiSimCommunicator {
         mpi_communicator: world,
     };
 
     let mut args = CommandLineArgs::parse();
     // override the num part argument, with the number of processes mpi has started.
-    args.num_parts = Some(world.size() as u32);
+    args.num_parts = Some(size as u32);
     let config = Config::from_file(&args);
 
     let _guards = logging::init_logging(&config, &args.config_path, comm.rank());
@@ -77,9 +80,9 @@ pub fn run_mpi() {
     );
     execute_partition(comm, &args);
 
-    info!("#{} at barrier.", world.rank());
+    info!("#{} at barrier.", rank);
     universe.world().barrier();
-    info!("Process #{} finishing.", world.rank());
+    info!("Process #{} finishing.", rank);
 }
 
 fn execute_partition<C: SimCommunicator + 'static>(comm: C, args: &CommandLineArgs) {
@@ -230,7 +233,7 @@ pub fn get_numbered_output_filename(output_dir: &Path, input_file: &Path, part:
     insert_number_in_proto_filename(&out, part)
 }
 
-fn create_output_filename(output_dir: &Path, input_file: &Path) -> PathBuf {
+pub fn create_output_filename(output_dir: &Path, input_file: &Path) -> PathBuf {
     let filename = input_file.file_name().unwrap();
     output_dir.join(filename)
 }