v0.8 changes (#48)

* Multiple bug fixes in parCon and parRSB
* Added CI tests for parCon and parRSB
* Refactor examples
* Added I/O routines for `.re2`, `.co2` and `.ma2` files

.github/workflows/ci.yml

@@ -0,0 +1,63 @@
+name: parRSB CI Tests
+on: [push, pull_request]
+env:
+  GITHUB.TOKEN: ${{ secrets.token }}
+jobs:
+  main:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        test: [box_2x2x2, pyramid, tgv, e3q, solid, ethier, vortex, expansion]
+        np: [1, 2, 3, 4]
+      fail-fast: false
+    name: "${{ matrix.test }}"
+    env:
+      GSVER: 1.0.7
+      CC: mpicc
+    steps:
+      - uses: actions/checkout@v2
+      - name: Install apt dependencies
+        shell: bash
+        run: |
+          sudo apt -y update
+          sudo apt install -y mpich libmpich-dev python3-pytest
+          sudo apt install -y libblas-dev liblapack-dev
+      - name: Build gslib
+        shell: bash
+        run: |
+          wget --no-check-certificate -O v$GSVER.tar.gz http://github.com/gslib/gslib/archive/v$GSVER.tar.gz
+          mkdir gslib
+          tar -zxvf v$GSVER.tar.gz -C ./gslib --strip-components=1
+          cd gslib
+          make -j4
+      - name: Build parRSB
+        shell: bash
+        run: |
+          export GSLIBPATH=`pwd`/gslib/build/
+          make -j1
+      - name: Clone tests
+        shell: bash
+        run: |
+          git clone https://github.com/thilinarmtb/parRSB-tests.git
+      - name: gencon
+        shell: bash
+        run: |
+          export EXAMPLEDIR=`pwd`/build/examples
+
+          cd parRSB-tests/${{ matrix.test }}
+          tol=(`cat test.txt | grep tol`); tol=${tol[2]}
+
+          echo "localhost:4" > hostfile
+          mpirun -np ${{ matrix.np }} --hostfile hostfile ${EXAMPLEDIR}/gencon --mesh ${{ matrix.test }} --tol=${tol} --no-dump --test
+      - name: genmap
+        shell: bash
+        run: |
+          export EXAMPLEDIR=`pwd`/build/examples
+          export PARRSB_RSB_PRE=0
+          export PARRSB_RSB_ALGO=0
+
+          cd parRSB-tests/${{ matrix.test }}
+          tol=(`cat test.txt | grep tol`); tol=${tol[2]}
+
+          echo "localhost:4" > hostfile
+          mpirun -np ${{ matrix.np }} --hostfile hostfile ${EXAMPLEDIR}/genmap --mesh ${{ matrix.test }} --tol=${tol} --no-dump --test

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2019, UCHICAGO ARGONNE, LLC. 
+Copyright (c) 2019 - 2021, UCHICAGO ARGONNE, LLC.
 
 The UChicago Argonne, LLC as Operator of Argonne National
 Laboratory holds copyright in the Software. The copyright holder

Makefile

@@ -3,8 +3,11 @@ DEBUG ?= 0
 MPI ?= 1
 CC ?= mpicc
 CFLAGS ?= -g -O0
-BLAS ?= 1
 UNDERSCORE ?= 1
+SYNC_BY_REDUCTION ?= 1
+BLAS ?= 0
+BLASDIR ?=
+BLASFLAGS ?= -lblas -llapack
 
 ## Don't touch what follows ##
 MKFILEPATH = $(abspath $(lastword $(MAKEFILE_LIST)))
@@ -29,10 +32,6 @@ GENCONDIR = $(SRCROOT)/src/gencon
 GENCONSRCS = $(wildcard $(GENCONDIR)/*.c)
 SRCOBJS += $(patsubst $(SRCROOT)/%.c,$(BUILDDIR)/%.o,$(GENCONSRCS))
 
-TESTDIR = $(SRCROOT)/tests
-TESTSRCS = $(wildcard $(TESTDIR)/*.c)
-TESTOBJS = $(patsubst $(SRCROOT)/%.c,$(BUILDDIR)/%,$(TESTSRCS))
-
 EXAMPLEDIR = $(SRCROOT)/examples
 EXAMPLESRCS = $(wildcard $(EXAMPLEDIR)/*.c)
 EXAMPLEOBJS = $(patsubst $(SRCROOT)/%.c,$(BUILDDIR)/%,$(EXAMPLESRCS))
@@ -55,32 +54,27 @@ endif
 
 ifneq ($(BLAS),0)
   PP += -DGENMAP_BLAS
-  LDFLAGS += -L$(BLASLIBPATH) -lblasLapack -lgfortran
-endif
-
-ifneq ($(UNDERSCORE),0)
-  PP += -DGENMAP_UNDERSCORE
-endif
-
-ifneq ($(BLAS),0)
-  PP += -DGENMAP_BLAS
-  LDFLAGS += -L$(BLASLIBPATH) -lblasLapack
+  ifneq ($(BLASDIR),)
+    LDFLAGS+= -L$(BLASDIR)
+  endif
+  LDFLAGS += $(BLASFLAGS)
 endif
 
 ifneq ($(MPI),0)
   PP += -DMPI
 endif
 
+ifneq ($(SYNC_BY_REDUCTION),0)
+  PP += -DGENMAP_SYNC_BY_REDUCTION
+endif
+
 INSTALLDIR=
 ifneq (,$(strip $(DESTDIR)))
   INSTALLDIR = $(realpath $(DESTDIR))
 endif
 
-.PHONY: default
-default: check lib examples install
-
 .PHONY: all
-all: check lib tests examples install
+all: check lib examples install
 
 .PHONY: check
 check:
@@ -132,5 +126,4 @@ print-%:
 $(shell mkdir -p $(BUILDDIR)/src/sort)
 $(shell mkdir -p $(BUILDDIR)/src/precond)
 $(shell mkdir -p $(BUILDDIR)/src/gencon)
-$(shell mkdir -p $(BUILDDIR)/tests)
 $(shell mkdir -p $(BUILDDIR)/examples)

README.md

@@ -14,20 +14,31 @@ instructions there to build it.
 
 ### Run Example
 
+You can run both `genmap` and `gencon` examples in `build/examples` directory after
+building parRSB. Examples invoked with all available options are shown below.
+
 ```sh
 
-cd example
-mpirun -np 4 ./partition 2 case01.co2
+cd build/examples
+mpirun -np 4 ./genmap --mesh ethier --nactive=2 --tol=0.2 --test --no-dump
+mpirun -np 4 ./gencon --mesh ethier --tol=0.2 --test --no-dump
 ```
 
+`--mesh` is the name of the input mesh (.re2 file) and is required. `--tol` is the
+tolerance used for finding connectivity. `--test` will run a check to see if `genmap`
+or `gencon` examples passed the builtin tests. If `--no-dump` is not specified, the
+examples will write a `.re2` or a `.ma2` file by default. `--nactive` parameter specify
+how many MPI ranks are active in the examples. Please note that `--tol` and `--nactive`
+requires a `=` sign (since they are optional) while `--mesh` does not need one.
+
 ### C Interface
 
 ```C
-int parRSB_partMesh(int *part, int *seq, long long *vtx, double *coord, int nel,
-                    int nv, parRSB_options *options, MPI_Comm comm);
+int parrsb_part_mesh(int *part, int *seq, long long *vtx, double *coord, int nel,
+                    int nv, parrsb_options options, MPI_Comm comm);
 ```
 
-See `example/partition.c` for an example.
+See `example/genmap.c` for an example.
 
 #### Parameters
 
@@ -42,23 +53,37 @@ options (in)    ... Additional configuration options (See below for a detailed e
 comm    (in)    ... MPI Communicator (size determines number of partitions).
 ```
 
-`options` is a `struct` of type `parRSB_options` declared in `parRSB.h`.
+`options` is a `struct` of type `parrsb_options` declared in `parRSB.h`.
 ```C
 typedef struct {
   /* General options */
-  int global_partitioner; // -1 - None, 0 - RSB, 1 - RCB, 2 - RIB (Default: 0)
-  int local_partitioner;  // -1 - None, 0 - RSB, 1 - RCB, 2 - RIB (Default: -1)
-  int debug_level;        // 0, 1, 2, .. etc (Default: 0)
-  int print_timing_info;  // 0 or 1 (Default: 0)
+  int partitioner;   // 0 - RSB, 1 - RCB, 2 - RIB (Default: 0)
+  int debug_level;   // 0, 1, 2, .. etc (Default: 0)
+  int profile_level; // 0, 1, 2, .. etc (Default: 0)
 
   /* RSB specific */
-  int rsb_algo;         // 0 - Lanczos, 1 - MG (Default: 0)
-  int rsb_prepartition; // 0 - None, 1 - RCB , 2 - RIB (Default: 1)
-  int rsb_grammian;     // 0 or 1 (Default: 1)
-} parRSB_options;
+  int rsb_algo;     // 0 - Lanczos, 1 - RQI (Default: 0)
+  int rsb_pre;      // 0 - None, 1 - RCB , 2 - RIB (Default: 1)
+  int rsb_grammian; // 0 or 1 (Default: 0)
+
+  /* Other */
+  int repair; // 0 - No, 1 - Yes (Default: 1)
+} parrsb_options;
 ```
 
 You can use `parrsb_default_options` struct instance to pass default options
-to `parRSB_partMesh` routine.
+to `parrsb_part_mesh` routine. All of these options can be controlled at runtime
+setting up the relevant env. variable to the corresponding value as well. Below
+is the list of env. variables:
+
+```
+PARRSB_PARTITIONER
+PARRSB_DEBUG_LEVEL
+PARRSB_PROFILE_LEVEL
+PARRSB_RSB_ALGO
+PARRSB_RSB_PRE
+PARRSB_RSB_GRAMMIAN
+PARRSB_REPAIR
+```
 
 Note, any initial distribution of mesh elements is valid.