pybamm-team#633 modified install to use the libsuitesparse-dev apt pa…

…ckage

CMakeLists.txt

@@ -23,25 +23,28 @@ TARGET_LINK_LIBRARIES(klu PRIVATE ${RT})
 
 ## KLU ------
 ## Add the includes
-set(KLU_INCLUDE_DIR "SuiteSparse/KLU/Include")
-set(AMD_INCLUDE_DIR "SuiteSparse/AMD/Include")
-set(COLAMD_INCLUDE_DIR "SuiteSparse/COLAMD/Include")
-set(BTF_INCLUDE_DIR "SuiteSparse/BTF/Include")
-set(SUITESPARSECONFIG_INCLUDE_DIR "SuiteSparse/SuiteSparse_config")
-TARGET_INCLUDE_DIRECTORIES(klu PRIVATE 
-    ${AMD_INCLUDE_DIR} 
-    ${COLAMD_INCLUDE_DIR} 
-    ${BTF_INCLUDE_DIR} 
-    ${SUITESPARSECONFIG_INCLUDE_DIR} 
-    ${KLU_INCLUDE_DIR}
-    )
+# set(KLU_INCLUDE_DIR "SuiteSparse/KLU/Include")
+# set(AMD_INCLUDE_DIR "SuiteSparse/AMD/Include")
+# set(COLAMD_INCLUDE_DIR "SuiteSparse/COLAMD/Include")
+# set(BTF_INCLUDE_DIR "SuiteSparse/BTF/Include")
+# set(SUITESPARSECONFIG_INCLUDE_DIR "SuiteSparse/SuiteSparse_config")
+# TARGET_INCLUDE_DIRECTORIES(klu PRIVATE 
+#     ${AMD_INCLUDE_DIR} 
+#     ${COLAMD_INCLUDE_DIR} 
+#     ${BTF_INCLUDE_DIR} 
+#     ${SUITESPARSECONFIG_INCLUDE_DIR} 
+#     ${KLU_INCLUDE_DIR}
+#     )
+
+# set(SUITESPARSE_INCLUDE_DIR "/usr/include/suitesparse")
+INCLUDE_DIRECTORIES(${SUITESPARSE_INCLUDE_DIR})
 
 ## Link Libraries
-find_library(KLU klu PATHS "SuiteSparse/KLU/Lib" NO_DEFAULT_PATH)
-find_library(AMD amd PATHS "SuiteSparse/AMD/Lib" NO_DEFAULT_PATH)
-find_library(COLAMD colamd PATHS "SuiteSparse/COLAMD/Lib" NO_DEFAULT_PATH)
-find_library(BTF btf PATHS "SuiteSparse/BTF/Lib" NO_DEFAULT_PATH)
-find_library(SUITESPARSE_CONFIG suitesparseconfig PATHS "SuiteSparse/SuiteSparse_config" NO_DEFAULT_PATH)
+find_library(KLU klu)
+find_library(AMD amd)
+find_library(COLAMD colamd)
+find_library(BTF btf)
+find_library(SUITESPARSE_CONFIG suitesparseconfig)
 TARGET_LINK_LIBRARIES(klu PRIVATE 
     ${KLU} 
     ${AMD} 

INSTALL-LINUX.md

@@ -158,33 +158,13 @@ To install KLU, from within the main PyBaMM directory type
 Note that this script has only been tested on Ubuntu 18.04.3 LTS. If this script does not work for you, you can try following the step-by-step instructions below:
 
 #### Download and Build SuiteSparse (KLU)
-The sparse linear solver, KLU, is contained within SuiteSparse. For more information on the installation process please refer to the README.txt contained in the SuiteSparse download.
-
-In PyBaMM home directory, i.e.
-```
-cd PyBaMM
-```
-download SuiteSparse using:
-```bash
-wget http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-5.4.0.tar.gz -O SuiteSparse-5.4.0.tar.gz
-```
-Unpack the compressed SuiteSparse files using:
+The sparse linear solver, KLU, is contained within SuiteSparse. Suitesparse is available on the apt store on Debian based systems (e.g. Ubuntu). Therefore, it can be installed by simply typing
 ```bash
-tar -xvf SuiteSparse-5.4.0.tar.gz
-```
-and remove the .tar.gz file to keep your directory clean using:
-```bash
-rm SuiteSparse-5.4.0.tar.gz
-```
-Now build SuiteSparse using:
-```bash
-cd SuiteSparse
-make
-cd ..
+    sudo apt install suitesparse-dev
 ```
-and set the path of the SuiteSparse directory for reference later:
+We will need to know the location of the include directories for suitesparse. In ubuntu, this can be set with the following
 ```bash
-SUITESPARSE_DIR=`pwd`/SuiteSparse
+    SUITESPARSE_INCLUDE_DIR="/usr/include/suitesparse"
 ```
 
 #### Download and build Sundials 4.1.0
@@ -219,7 +199,7 @@ cmake -DBLAS_ENABLE=ON\
       -DEXAMPLES_ENABLE:BOOL=OFF\
       -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR ../sundials-4.1.0/\
       -DKLU_ENABLE=ON\
-      -DSUITESPARSE_DIR=$SUITESPARSE_DIR\
+      -DSUITESPARSE_INCLUDE_DIR=$SUITESPARSE_INCLUDE_DIR\
       ../sundials-4.1.0
 make install
 ```
@@ -246,9 +226,9 @@ pip install pybind11
 #### Build the KLU wrapper
 We now have all the tools to build a shared library to interface to the KLU solver. Within your PyBaMM home directory build the required Makefile using
 ```
-cmake .
+cmake -DSUITESPARSE_INCLUDE_DIR=$SUITESPARSE_INCLUDE_DIR.
 ```
-This will automatically find the latest version of python installed on your machine. If you are using an older version (e.g python3.6) within your virtual environment, then you instead can use `cmake -DPYBIND11_PYTHON_VERSION=3.6 .`.
+This will automatically find the headers for the latest version of python installed on your machine. If you are using an older version (e.g python3.6) within your virtual environment, then you instead can use `cmake -DPYBIND11_PYTHON_VERSION=3.6 .`.
 
 You can now simply run make to build the library (you can just run this command if you make some changes to klu.cpp)
 ```

scripts/install_sundials_4.1.0.sh

@@ -1,18 +1,6 @@
 #!/bin/bash
 CURRENT_DIR=`pwd`
 
-# build SparseSuite to use KLU sparse linear solver
-SUITESPARSE_URL=http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-5.4.0.tar.gz
-SUITESPARSE_NAME=SuiteSparse-5.4.0.tar.gz
-wget $SUITESPARSE_URL -O $SUITESPARSE_NAME
-tar -xvf $SUITESPARSE_NAME
-SUITESPARSE_DIR=$CURRENT_DIR/SuiteSparse
-cd $SUITESPARSE_DIR
-make clean
-make
-cd $CURRENT_DIR
-rm $SUITESPARSE_NAME
-
 # install sundials-4.1.0
 SUNDIALS_URL=https://computing.llnl.gov/projects/sundials/download/sundials-4.1.0.tar.gz
 SUNDIALS_NAME=sundials-4.1.0.tar.gz
@@ -44,7 +32,7 @@ cmake -DBLAS_ENABLE=ON\
       -DEXAMPLES_ENABLE:BOOL=OFF\
       -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR ../sundials-4.1.0/\
       -DKLU_ENABLE=ON\
-      -DSUITESPARSE_DIR=$SUITESPARSE_DIR\
+      -DSUITESPARSE_INCLUDE_DIR="/usr/include/suitesparse"\
       ../sundials-4.1.0
 
 

scripts/replace-cmake/CMakeLists.txt

@@ -995,27 +995,37 @@ IF(KLU_ENABLE)
 
   # setting the paths for KLU directly without testing - scott marquis
   # INCLUDE(SundialsKLU) 
-  set(KLU_LIBRARY ${SUITESPARSE_DIR}/KLU/Lib/libklu.a)
-  set(AMD_LIBRARY ${SUITESPARSE_DIR}/AMD/Lib/libamd.a)
-  set(COLAMD_LIBRARY ${SUITESPARSE_DIR}/COLAMD/Lib/libcolamd.a)
-  set(BTF_LIBRARY ${SUITESPARSE_DIR}/BTF/Lib/libbtf.a)
-  set(SUITESPARSECONFIG_LIBRARY ${SUITESPARSE_DIR}/SuiteSparse_config/libsuitesparseconfig.a)
+  # set(KLU_LIBRARY ${SUITESPARSE_DIR}/KLU/Lib/libklu.a)
+  # set(AMD_LIBRARY ${SUITESPARSE_DIR}/AMD/Lib/libamd.a)
+  # set(COLAMD_LIBRARY ${SUITESPARSE_DIR}/COLAMD/Lib/libcolamd.a)
+  # set(BTF_LIBRARY ${SUITESPARSE_DIR}/BTF/Lib/libbtf.a)
+  # set(SUITESPARSECONFIG_LIBRARY ${SUITESPARSE_DIR}/SuiteSparse_config/libsuitesparseconfig.a)
+  # set(KLU_LIBRARIES ${KLU_LIBRARY} ${AMD_LIBRARY} ${COLAMD_LIBRARY} ${BTF_LIBRARY} ${SUITESPARSECONFIG_LIBRARY})
+
+  find_library(KLU_LIBRARY klu)
+  find_library(AMD_LIBRARY amd)
+  find_library(COLAMD_LIBRARY colamd)
+  find_library(BTF_LIBRARY btf)
+  find_library(SUITESPARSECONFIG_LIBRARY suitesparseconfig)
   set(KLU_LIBRARIES ${KLU_LIBRARY} ${AMD_LIBRARY} ${COLAMD_LIBRARY} ${BTF_LIBRARY} ${SUITESPARSECONFIG_LIBRARY})
 
 
   set(KLU_FOUND TRUE)
 
-  IF(KLU_FOUND)
+  # include is now simply /usr/include
+  # IF(KLU_FOUND)
     # sundials_config.h symbol
-    SET(SUNDIALS_KLU TRUE)
-    set(KLU_INCLUDE_DIR ${SUITESPARSE_DIR}/KLU/Include)
-    set(AMD_INCLUDE_DIR ${SUITESPARSE_DIR}/AMD/Include)
-    set(COLAMD_INCLUDE_DIR ${SUITESPARSE_DIR}/COLAMD/Include)
-    set(BTF_INCLUDE_DIR ${SUITESPARSE_DIR}/BTF/Include)
-    set(SUITESPARSECONFIG_INCLUDE_DIR ${SUITESPARSE_DIR}/SuiteSparse_config)
-
-    INCLUDE_DIRECTORIES(${AMD_INCLUDE_DIR} ${COLAMD_INCLUDE_DIR} ${BTF_INCLUDE_DIR} ${SUITESPARSECONFIG_INCLUDE_DIR} ${KLU_INCLUDE_DIR})
-  ENDIF(KLU_FOUND)
+    # SET(SUNDIALS_KLU TRUE)
+    # set(KLU_INCLUDE_DIR ${SUITESPARSE_DIR}/KLU/Include)
+    # set(AMD_INCLUDE_DIR ${SUITESPARSE_DIR}/AMD/Include)
+    # set(COLAMD_INCLUDE_DIR ${SUITESPARSE_DIR}/COLAMD/Include)
+    # set(BTF_INCLUDE_DIR ${SUITESPARSE_DIR}/BTF/Include)
+    # set(SUITESPARSECONFIG_INCLUDE_DIR ${SUITESPARSE_DIR}/SuiteSparse_config)
+
+    # INCLUDE_DIRECTORIES(${AMD_INCLUDE_DIR} ${COLAMD_INCLUDE_DIR} ${BTF_INCLUDE_DIR} ${SUITESPARSECONFIG_INCLUDE_DIR} ${KLU_INCLUDE_DIR})
+  # ENDIF(KLU_FOUND)
+  # set(SUITESPARSE_INCLUDE_DIR "/usr/include/suitesparse") # leave for user to set
+  INCLUDE_DIRECTORIES(${SUITESPARSE_INCLUDE_DIR})
 
   IF(KLU_LIBRARIES AND NOT KLU_FOUND)
     PRINT_WARNING("KLU not functional - support will not be provided"