HiCMA v0.1.3

Author: kadircs

.gitmodules

@@ -6,5 +6,7 @@
 	url = https://github.com/ecrc/stars-h.git
 [submodule "chameleon"]
 	path = chameleon
-        url = https://gitlab.inria.fr/solverstack/chameleon.git
-	#url = [email protected]:ecrc/chameleon.git
+    url = https://gitlab.inria.fr/solverstack/chameleon.git
+[submodule "hcore"]
+	path = hcore
+	url = https://github.com/ecrc/hcore

CMakeLists.txt

@@ -1,3 +1,22 @@
+# Installation on ECRC servers
+
+1.  Go to home directory
+
+2.  Get HiCMA from git repository
+
+        git clone [email protected]:ecrc/hicma-dev
+
+3.  Run the following command: (This command will also setup PKG_CONFIG_PATH for STARS-H)
+
+        . hicma-dev/scripts/build-nompi.sh
+
+4.  Run the following command for seeing which experimental cases will be executed:
+    
+        cd ./hicma-dev
+        ./exp/distruns.sh exp/cases/statistics.sh dry
+
+5.  Remove the keyword "dry" to really run the cases.
+
 # Installation
 
 Installation requires `CMake` of version 3.2.3 at least. To build HiCMA,
@@ -46,6 +65,15 @@ Now you can use `pkg-config` executable to collect compiler and linker flags for
 
 There are `scripts/build.sh` and `scripts/build-nompi.sh` scripts in the repository to build the whole software stack.
 
+# CTests
+
+You can run CTests in the build folder via the following command:
+
+        ctest
+
+A specific test can be run in verbose mode as follows:
+
+        ctest -R time_zgemm_tile-mpi-edsin -V
 
 # CMake Configuration
 

INSTALL INSTALL.md

@@ -43,7 +43,7 @@ module load hwloc/1.11.8-gcc-5.5.0
 module load openmpi/3.0.0-gcc-5.5.0
 module load ecrc-extras
 module load starpu/1.2.4-gcc-5.5.0-mkl-openmpi-3.0.0
-module load gsl/2.4-gcc-5.5.0
+#module load gsl/2.4-gcc-5.5.0
 
 
 module list
@@ -54,31 +54,43 @@ set -x
 
 HICMADEVDIR=$PWD
 
-# Update submodules
-#git submodule update --init --recursive
+INSTALLDIR=$PWD/dependencies-prefix
+mkdir -p $INSTALLDIR
+rm -rf $INSTALLDIR/*
+export PKG_CONFIG_PATH=$INSTALLDIR/lib/pkgconfig:$PKG_CONFIG_PATH
 
 # STARS-H
+cd $HICMADEVDIR
 cd stars-h
 rm -rf build
-mkdir -p build/installdir
+mkdir -p build
 cd build
-cmake .. -DCMAKE_INSTALL_PREFIX=$PWD/installdir -DMPI=OFF -DOPENMP=OFF -DSTARPU=OFF
+cmake .. -DCMAKE_INSTALL_PREFIX=$INSTALLDIR -DMPI=OFF -DOPENMP=OFF -DSTARPU=OFF -DGSL=OFF
 make clean
-make -j
+make -j 4
 make install
-export PKG_CONFIG_PATH=$PWD/installdir/lib/pkgconfig:$PKG_CONFIG_PATH
 
 # CHAMELEON
 cd $HICMADEVDIR
 cd chameleon
 rm -rf build
-mkdir -p build/installdir
+mkdir -p build
 cd build
-cmake .. -DCMAKE_BUILD_TYPE=Debug -DCHAMELEON_USE_MPI=ON  -DCMAKE_INSTALL_PREFIX=$PWD/installdir
+cmake .. -DCMAKE_BUILD_TYPE=Debug -DCHAMELEON_USE_MPI=ON  -DCMAKE_INSTALL_PREFIX=$INSTALLDIR
 make clean
-make -j
+make -j 4
+make install
+
+# HCORE
+cd $HICMADEVDIR
+cd hcore
+rm -rf build
+mkdir -p build
+cd build
+cmake .. -DCMAKE_INSTALL_PREFIX=$INSTALLDIR
+make clean
+make -j 4
 make install
-export PKG_CONFIG_PATH=$PWD/installdir/lib/pkgconfig:$PKG_CONFIG_PATH
 
 # HICMA
 cd $HICMADEVDIR
@@ -87,7 +99,7 @@ mkdir -p build/installdir
 cd build
 cmake .. -DCMAKE_INSTALL_PREFIX=$PWD/installdir -DHICMA_USE_MPI=ON
 make clean
-make -j
+make -j 4
 make install
 export PKG_CONFIG_PATH=$PWD/installdir/lib/pkgconfig:$PKG_CONFIG_PATH
 
@@ -110,7 +122,7 @@ module load cmake/3.9.6
 module load hwloc/1.11.8-gcc-5.5.0
 module load ecrc-extras
 module load starpu/1.2.4-gcc-5.5.0-mkl-openmpi-3.0.0
-module load gsl/2.4-gcc-5.5.0
+#module load gsl/2.4-gcc-5.5.0
 
 module list
 
@@ -120,31 +132,42 @@ set -x
 
 HICMADEVDIR=$PWD
 
-# Update submodules
-#git submodule update --init --recursive
+INSTALLDIR=$PWD/dependencies-prefix
+mkdir -p $INSTALLDIR
+rm -rf $INSTALLDIR/*
+export PKG_CONFIG_PATH=$INSTALLDIR/lib/pkgconfig:$PKG_CONFIG_PATH
 
 # STARS-H
 cd stars-h
 rm -rf build
-mkdir -p build/installdir
+mkdir -p build
 cd build
-cmake .. -DCMAKE_INSTALL_PREFIX=$PWD/installdir -DMPI=OFF -DOPENMP=OFF -DSTARPU=OFF
+cmake .. -DCMAKE_INSTALL_PREFIX=$INSTALLDIR -DMPI=OFF -DOPENMP=OFF -DSTARPU=OFF -DGSL=OFF
 make clean
-make -j
+make -j 4
 make install
-export PKG_CONFIG_PATH=$PWD/installdir/lib/pkgconfig:$PKG_CONFIG_PATH
 
 # CHAMELEON
 cd $HICMADEVDIR
 cd chameleon
 rm -rf build
-mkdir -p build/installdir
+mkdir -p build
 cd build
-cmake .. -DCMAKE_BUILD_TYPE=Release -DCHAMELEON_USE_MPI=OFF  -DCMAKE_INSTALL_PREFIX=$PWD/installdir
+cmake .. -DCMAKE_BUILD_TYPE=Release -DCHAMELEON_USE_MPI=OFF  -DCMAKE_INSTALL_PREFIX=$INSTALLDIR
 make clean
-make -j
+make -j 4
+make install
+
+# HCORE
+cd $HICMADEVDIR
+cd hcore
+rm -rf build
+mkdir -p build
+cd build
+cmake .. -DCMAKE_INSTALL_PREFIX=$INSTALLDIR
+make clean
+make -j 4
 make install
-export PKG_CONFIG_PATH=$PWD/installdir/lib/pkgconfig:$PKG_CONFIG_PATH
 
 # HICMA
 cd $HICMADEVDIR
@@ -153,7 +176,7 @@ mkdir -p build/installdir
 cd build
 cmake .. -DCMAKE_INSTALL_PREFIX=$PWD/installdir -DHICMA_USE_MPI=OFF
 make clean
-make -j
+make -j 4
 make install
 export PKG_CONFIG_PATH=$PWD/installdir/lib/pkgconfig:$PKG_CONFIG_PATH
 
@@ -179,7 +202,7 @@ module load hwloc/1.11.8-gcc-5.5.0
 module load openmpi/3.0.0-gcc-5.5.0
 module load ecrc-extras
 module load starpu/1.2.4-gcc-5.5.0-mkl-openmpi-3.0.0
-module load gsl/2.4-gcc-5.5.0
+#module load gsl/2.4-gcc-5.5.0
 
 module list
 
@@ -189,7 +212,7 @@ ctest -T Test --no-compress-output -V
 if [ "$BRANCH_NAME" != "master" ]
 then
     # valgring for timing takes too long. Test the rest
-    #ctest -T memcheck -LE timing 
+    #ctest -T memcheck -LE timing
     :
 fi
 
@@ -215,7 +238,7 @@ module load cmake/3.9.6
 module load hwloc/1.11.8-gcc-5.5.0
 module load ecrc-extras
 module load starpu/1.2.4-gcc-5.5.0-mkl-openmpi-3.0.0
-module load gsl/2.4-gcc-5.5.0
+#module load gsl/2.4-gcc-5.5.0
 
 module list
 
@@ -225,7 +248,7 @@ ctest -T Test --no-compress-output -V
 if [ "$BRANCH_NAME" != "master" ]
 then
     # valgring for timing takes too long. Test the rest
-    #ctest -T memcheck -LE timing 
+    #ctest -T memcheck -LE timing
     :
 fi
 
@@ -253,7 +276,7 @@ module load hwloc/1.11.8-gcc-5.5.0
 module load openmpi/3.0.0-gcc-5.5.0
 module load ecrc-extras
 module load starpu/1.2.4-gcc-5.5.0-mkl-openmpi-3.0.0
-module load gsl/2.4-gcc-5.5.0
+#module load gsl/2.4-gcc-5.5.0
 module list
 cd $WORKSPACE/build
 make docs
@@ -282,10 +305,10 @@ cppcheck-htmlreport --source-encoding="iso8859-1" --title="HiCMA" --source-dir=.
         //failure {
         //}
          unstable {
-             emailext body: "${env.JOB_NAME} - Please go to ${env.BUILD_URL}", subject: "Jenkins Pipeline build is UNSTABLE", recipientProviders: [[$class: 'CulpritsRecipientProvider'], [$class: 'RequesterRecipientProvider']]
+             emailext body: "${env.JOB_NAME} - Please go to ${env.BUILD_URL}", subject: "Jenkins Pipeline build is UNSTABLE", recipientProviders: [culprits(),requestor()]
          }
          failure {
-             emailext body: "${env.JOB_NAME} - Please go to ${env.BUILD_URL}", subject: "Jenkins Pipeline build FAILED", recipientProviders: [[$class: 'CulpritsRecipientProvider'], [$class: 'RequesterRecipientProvider']]
+             emailext body: "${env.JOB_NAME} - Please go to ${env.BUILD_URL}", subject: "Jenkins Pipeline build FAILED", recipientProviders: [culprits(),requestor()]
          }
      }
 }

Jenkinsfile

@@ -10,7 +10,7 @@ computations operating on the underlying tile low-rank data format, while satisf
 numerical accuracy and leveraging performance from massively parallel hardware architectures. 
 
 
-Features of HiCMA 0.1.1
+Features of HiCMA 0.1.3
 -----------------------------
 * Matrix-Matrix Multiplication
 * Cholesky Factorization/Solve
@@ -43,12 +43,27 @@ HiCMA depends on the following libraries:
 * StarPU
 * MPI
 
+Installation
+------------
+
+Please see INSTALL.md for information about installing and testing.
+
 
 References
 -----------
 1. K. Akbudak, H. Ltaief, A. Mikhalev, and D. E. Keyes, *Tile Low Rank Cholesky Factorization for 
 Climate/Weather Modeling Applications on Manycore Architectures*, **International Supercomputing 
 Conference (ISC17)**, June 18-22, 2017, Frankfurt, Germany.
 
+2. K. Akbudak, H. Ltaief, A. Mikhalev, A. Charara, and D. E. Keyes, *Exploiting Data Sparsity for Large-Scale Matrix Computations*, **Euro-Par 2018**, August 27-31, 2018, Turin, Italy.
+
+3. Q. Cao, Y. Pei, T. Herauldt, K. Akbudak, A. Mikhalev, G. Bosilca, H. Ltaief, D. E. Keyes, and J. Dongarra, *Performance Analysis of Tile Low-Rank Cholesky Factorization Using PaRSEC Instrumentation Tools*, **2019 IEEE/ACM International Workshop on Programming and Performance Visualization Tools (ProTools)**, Denver, CO, USA, 2019, pp. 25-32.
+
+4. Q. Cao, Y. Pei, K. Akbudak, A. Mikhalev, G. Bosilca, H. Ltaief, D. E. Keyes, and J. Dongarra, *Extreme-Scale Task-Based Cholesky Factorization Toward Climate and Weather Prediction Applications*, **The Platform for Advanced Scientific Computing (PASC 2020)**.
+
+5. N. Al-Harthi, R. Alomairy, K. Akbudak, R. Chen, H. Ltaief, H. Bagci, and D. E. Keyes, *Solving Acoustic Boundary Integral Equations Using High Performance Tile Low-Rank LU Factorization*, **International Supercomputing Conference (ISC 2020)**.
+
+
+
 
 ![Handout](docs/HiCMA-handout-SC17.png)

README.md

@@ -0,0 +1,37 @@
+# Release 0.1.3
+
+## Features
+* Support for a new application that simulates the 3D unstructured mesh deformation of a population of the novel coronaviruses (i.e.,  SARS-CoV-2). This relies on the virus geometry extracted from the Protein Data Bank (PDB) codenamed PDBID 6VXX available at (https://www.rcsb.org/structure/6VXX). The corresponding basis function and data geometry are available at STARS-H (https://github.com/ecrc/stars-h).
+
+# Release 0.1.2
+
+## Features
+* New matrix kernel (3D exponential) for statistics application from STARS-H (https://github.com/ecrc/stars-h) is supported.
+* Sequential operations on low-rank tiles are moved into a standalone library called HCORE (https://github.com/ecrc/hcore).
+* Number of flops is reported. See the driver routines under timing folder. 
+* Multiplication order of tiles in each inner product performed by HiCMA_GEMM can be changed via adding --reorderinnerproducts flag while calling timing/time_zgemm_tile. This flag enables sorting tiles according to increasing sum of ranks of tile pairs that which will be multiplied.
+* More tests in timing/CMakeLists.txt 
+
+## Bug Fixes and Other Changes
+* Set minimum number of singular vectors in HCORE_GEMM to 1 instead of 2 
+
+# Release 0.1.1
+
+## Features
+* Triangular solve (left) for low rank A and B/X
+* Triangular solve (left, lower) for low rank A and full rank B/X  
+* Testing routine for POSV and TRSM
+* HCORE routine for C=C+AB where A is low rank and B and C are full rank 
+* Separate routines for dense and low rank matrix generation 
+
+# Release 0.1.0
+
+## Features
+* Matrix-Matrix Multiplication
+* Cholesky Factorization
+* Double Precision
+* Task-based Programming Models
+* Shared and Distributed-Memory Environments
+* Support for StarPU Dynamic Runtime Systems
+* Testing Suite and Examples
+

RELEASE.md

@@ -23,7 +23,7 @@
 #  @author Emmanuel Agullo
 #  @author Mathieu Faverge
 #  @author Florent Pruvost
-#  @date 2018-11-08
+#  @date 2020-01-07
 #
 ###
 
@@ -40,10 +40,10 @@ MACRO(CONVERT_LIBSTYLE_TO_PKGCONFIG _liblist)
 	if (${_dep} MATCHES "^/")
 	  get_filename_component(dep_libname ${_dep} NAME)
 	  get_filename_component(dep_libdir  ${_dep} DIRECTORY)
+	  STRING(REPLACE ".dylib" "" dep_libname "${dep_libname}")
 	  STRING(REPLACE "lib"    "" dep_libname "${dep_libname}")
 	  STRING(REPLACE ".so"    "" dep_libname "${dep_libname}")
 	  STRING(REPLACE ".a"     "" dep_libname "${dep_libname}")
-	  STRING(REPLACE ".dylib" "" dep_libname "${dep_libname}")
 	  STRING(REPLACE ".dll"   "" dep_libname "${dep_libname}")
 	  list(APPEND ${_liblist} -L${dep_libdir} -l${dep_libname})
 	elseif(NOT ${_dep} MATCHES "^-")
@@ -81,11 +81,11 @@ ENDMACRO(CLEAN_LIB_LIST)
 MACRO(GENERATE_PKGCONFIG_FILE)
   # The link flags specific to this package and any required libraries
   # that don't support PkgConfig
-  set(HICMA_PKGCONFIG_LIBS "-lhicma")
+  set(HICMA_PKGCONFIG_LIBS "-lhicma -lhcore")
 
   # The link flags for private libraries required by this package but not
   # exposed to applications
-  set(HICMA_PKGCONFIG_LIBS_PRIVATE "")
+  set(HICMA_PKGCONFIG_LIBS_PRIVATE "-lhcore")
 
   # A list of packages required by this package
   set(HICMA_PKGCONFIG_REQUIRED "")

chameleon

@@ -21,7 +21,7 @@
 #
 #  @author Florent Pruvost
 #  @author Eduardo Gonzalez
-#  @date 22-08-2017
+#  @date 2019-11-25
 #
 ###
 set(dep_message "\nConfiguration of HiCMA:\n"
@@ -57,6 +57,7 @@ set(dep_message "${dep_message}"
 "\n"
 "       Chameleon ...........: ${CHAMELEON_DIR_FOUND}\n"
 "       STARS-H .............: ${STARSH_DIR_FOUND}\n"
+"       HCORE . .............: ${HCORE_DIR_FOUND}\n"
 "\n"
 "       Trace ...............: ${HICMA_ENABLE_TRACING}\n"
 "       Simulation mode .....: ${HICMA_SIMULATION}\n"