Merge remote-tracking branch 'origin/develop' into feature/sunstepper

.github/workflows/check-clang-format.yml

@@ -15,6 +15,12 @@ jobs:
           apt update
           apt install -y git python3-pip
 
+      - name: Install black
+        run: pip install black
+
+      - name: Print black version
+        run: black --version
+
       - name: Install fprettify
         run: pip install fprettify
 

CHANGELOG.md

@@ -1,5 +1,22 @@
 # SUNDIALS Changelog
 
+## Changes to SUNDIALS in release X.Y.Z
+
+### Major Features
+
+### New Features and Enhancements
+
+### Bug Fixes
+
+### Deprecation Notices
+
+## Changes to SUNDIALS in release 7.1.1
+
+### Bug Fixes
+
+Fixed a [bug](https://github.com/LLNL/sundials/pull/523) in v7.1.0 with the SYCL
+N_Vector `N_VSpace` function.
+
 ## Changes to SUNDIALS in release 7.1.0
 
 ### Major Features

CITATIONS.md

@@ -69,7 +69,7 @@ they are using rather than the combined SUNDIALS online guide:
   author = {Daniel R. Reynolds and David J. Gardner and Carol S. Woodward and Cody J. Balos},
   title  = {User Documentation for ARKODE},
   year   = {2024},
-  note   = {v6.1.0}
+  note   = {v6.1.1}
 }
 ```
 
@@ -78,7 +78,7 @@ they are using rather than the combined SUNDIALS online guide:
   author = {Alan C. Hindmarsh and Radu Serban and Cody J. Balos and David J. Gardner and Daniel R. Reynolds and Carol S. Woodward},
   title  = {User Documentation for CVODE},
   year   = {2024},
-  note   = {v7.1.0}
+  note   = {v7.1.1}
 }
 ```
 
@@ -87,7 +87,7 @@ they are using rather than the combined SUNDIALS online guide:
   author = {Alan C. Hindmarsh and Radu Serban and Cody J. Balos and David J. Gardner and Daniel R. Reynolds and Carol S. Woodward},
   title  = {User Documentation for CVODES},
   year   = {2024},
-  note   = {v7.1.0}
+  note   = {v7.1.1}
 }
 ```
 
@@ -96,7 +96,7 @@ they are using rather than the combined SUNDIALS online guide:
   author = {Alan C. Hindmarsh and Radu Serban and Cody J. Balos and David J. Gardner and Daniel R. Reynolds and Carol S. Woodward},
   title  = {User Documentation for IDA},
   year   = {2024},
-  note   = {v7.1.0}
+  note   = {v7.1.1}
 }
 ```
 
@@ -105,7 +105,7 @@ they are using rather than the combined SUNDIALS online guide:
   author = {Radu Serban and Cosmin Petra and Alan C. Hindmarsh and Cody J. Balos and David J. Gardner and Daniel R. Reynolds and Carol S. Woodward},
   title  = {User Documentation for IDAS},
   year   = {2024},
-  note   = {v6.1.0}
+  note   = {v6.1.1}
 }
 ```
 
@@ -114,6 +114,6 @@ they are using rather than the combined SUNDIALS online guide:
   author = {Alan C. Hindmarsh and Radu Serban and Cody J. Balos and David J. Gardner and Daniel R. Reynolds and Carol S. Woodward},
   title  = {User Documentation for KINSOL},
   year   = {2024},
-  note   = {v7.1.0}
+  note   = {v7.1.1}
 }
 ```

CMakeLists.txt

@@ -48,7 +48,7 @@ include(FindPackageHandleStandardArgs)
 # Set some variables with info on the SUNDIALS project
 set(PACKAGE_BUGREPORT "[email protected]")
 set(PACKAGE_NAME "SUNDIALS")
-set(PACKAGE_STRING "SUNDIALS 7.1.0")
+set(PACKAGE_STRING "SUNDIALS 7.1.1")
 set(PACKAGE_TARNAME "sundials")
 
 # Set SUNDIALS version numbers
@@ -58,7 +58,7 @@ message(STATUS "SUNDIALS_GIT_VERSION: ${SUNDIALS_GIT_VERSION}")
 # (use "" for the version label if none is needed)
 set(PACKAGE_VERSION_MAJOR "7")
 set(PACKAGE_VERSION_MINOR "1")
-set(PACKAGE_VERSION_PATCH "0")
+set(PACKAGE_VERSION_PATCH "1")
 set(PACKAGE_VERSION_LABEL "")
 
 if(PACKAGE_VERSION_LABEL)
@@ -73,37 +73,37 @@ endif()
 
 # Specify the VERSION and SOVERSION for shared libraries
 
-set(arkodelib_VERSION "6.1.0")
+set(arkodelib_VERSION "6.1.1")
 set(arkodelib_SOVERSION "6")
 
-set(cvodelib_VERSION "7.1.0")
+set(cvodelib_VERSION "7.1.1")
 set(cvodelib_SOVERSION "7")
 
-set(cvodeslib_VERSION "7.1.0")
+set(cvodeslib_VERSION "7.1.1")
 set(cvodeslib_SOVERSION "7")
 
-set(idalib_VERSION "7.1.0")
+set(idalib_VERSION "7.1.1")
 set(idalib_SOVERSION "7")
 
-set(idaslib_VERSION "6.1.0")
+set(idaslib_VERSION "6.1.1")
 set(idaslib_SOVERSION "6")
 
-set(kinsollib_VERSION "7.1.0")
+set(kinsollib_VERSION "7.1.1")
 set(kinsollib_SOVERSION "7")
 
 set(cpodeslib_VERSION "0.0.0")
 set(cpodeslib_SOVERSION "0")
 
-set(nveclib_VERSION "7.1.0")
+set(nveclib_VERSION "7.1.1")
 set(nveclib_SOVERSION "7")
 
-set(sunmatrixlib_VERSION "5.1.0")
+set(sunmatrixlib_VERSION "5.1.1")
 set(sunmatrixlib_SOVERSION "5")
 
-set(sunlinsollib_VERSION "5.1.0")
+set(sunlinsollib_VERSION "5.1.1")
 set(sunlinsollib_SOVERSION "5")
 
-set(sunnonlinsollib_VERSION "4.1.0")
+set(sunnonlinsollib_VERSION "4.1.1")
 set(sunnonlinsollib_SOVERSION "4")
 
 set(sundialslib_VERSION
@@ -117,7 +117,7 @@ set(sundialslib_SOVERSION "${PACKAGE_VERSION_MAJOR}")
 
 # Prohibit in-source build
 if("${CMAKE_SOURCE_DIR}" STREQUAL "${CMAKE_BINARY_DIR}")
-  print_error("In-source build prohibited.")
+  message(FATAL_ERROR "In-source build prohibited.")
 endif()
 
 # Organize targets into folders when using an IDE

README.md

@@ -1,5 +1,5 @@
 # SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic equation Solvers #
-### Version 7.1.0 (Jun 2024) ###
+### Version 7.1.1 (Jun 2024) ###
 
 **Center for Applied Scientific Computing, Lawrence Livermore National Laboratory**
 

benchmarks/advection_reaction_3D/scripts/compare_error.py

@@ -15,7 +15,8 @@
 import glob
 import sys
 import matplotlib
-matplotlib.use('Agg')
+
+matplotlib.use("Agg")
 from mpl_toolkits.mplot3d import Axes3D
 import matplotlib.pyplot as plt
 import pandas as pd
@@ -25,75 +26,75 @@
 # load pickled data
 def load_data(file):
     data = np.load(file)
-    m = data['mesh']
-    t = data['t']
-    u = data['u']
-    v = data['v']
-    w = data['w']
+    m = data["mesh"]
+    t = data["t"]
+    u = data["u"]
+    v = data["v"]
+    w = data["w"]
 
-    hx = m[0,1] - m[0,0]
-    hy = m[1,1] - m[1,0]
-    hz = m[2,1] - m[2,0]
+    hx = m[0, 1] - m[0, 0]
+    hy = m[1, 1] - m[1, 0]
+    hz = m[2, 1] - m[2, 0]
 
-    return { 'm': m, 'h': (hx,hy,hz), 't': t, 'u': u, 'v': v, 'w': w }
+    return {"m": m, "h": (hx, hy, hz), "t": t, "u": u, "v": v, "w": w}
 
 
 # grid function norm
 def norm_3Dgrid(h, x, q=1):
-    hx,hy,hz = h
+    hx, hy, hz = h
     s = np.shape(x)
-    return (hx*hy*hz*np.sum(np.abs(x)**q, axis=(1,2,3)))**(1./q)
+    return (hx * hy * hz * np.sum(np.abs(x) ** q, axis=(1, 2, 3))) ** (1.0 / q)
 
 
 # load data files
-np111 = load_data('np-111/output-with-h-8.33e-02.npz')
-np211 = load_data('np-211/output-with-h-8.33e-02.npz')
-np311 = load_data('np-311/output-with-h-8.33e-02.npz')
-np131 = load_data('np-131/output-with-h-8.33e-02.npz')
-np113 = load_data('np-113/output-with-h-8.33e-02.npz')
-np911 = load_data('np-911/output-with-h-8.33e-02.npz')
+np111 = load_data("np-111/output-with-h-8.33e-02.npz")
+np211 = load_data("np-211/output-with-h-8.33e-02.npz")
+np311 = load_data("np-311/output-with-h-8.33e-02.npz")
+np131 = load_data("np-131/output-with-h-8.33e-02.npz")
+np113 = load_data("np-113/output-with-h-8.33e-02.npz")
+np911 = load_data("np-911/output-with-h-8.33e-02.npz")
 # np133 = load_data('np-133/output-with-h-8.33e-02.npz')
-np313 = load_data('np-313/output-with-h-8.33e-02.npz')
-np331 = load_data('np-331/output-with-h-8.33e-02.npz')
-np333 = load_data('np-333/output-with-h-8.33e-02.npz')
+np313 = load_data("np-313/output-with-h-8.33e-02.npz")
+np331 = load_data("np-331/output-with-h-8.33e-02.npz")
+np333 = load_data("np-333/output-with-h-8.33e-02.npz")
 # np666 = load_data('np-666/output-with-h-8.33e-02.npz')
 
-for component in ['u', 'v', 'w']:
+for component in ["u", "v", "w"]:
     # Reference solution
     ref = np111[component]
 
     # Now compute E(h) = ||U(h) - \bar{U}(h)|| using the grid-function norm
-    E_np211 = norm_3Dgrid(np211['h'], np211[component] - ref)
-    E_np311 = norm_3Dgrid(np311['h'], np311[component] - ref)
-    E_np131 = norm_3Dgrid(np131['h'], np131[component] - ref)
-    E_np113 = norm_3Dgrid(np113['h'], np113[component] - ref)
-    E_np911 = norm_3Dgrid(np911['h'], np911[component] - ref)
+    E_np211 = norm_3Dgrid(np211["h"], np211[component] - ref)
+    E_np311 = norm_3Dgrid(np311["h"], np311[component] - ref)
+    E_np131 = norm_3Dgrid(np131["h"], np131[component] - ref)
+    E_np113 = norm_3Dgrid(np113["h"], np113[component] - ref)
+    E_np911 = norm_3Dgrid(np911["h"], np911[component] - ref)
     # E_np133 = norm_3Dgrid(np133['h'], np133[component] - ref)
-    E_np313 = norm_3Dgrid(np313['h'], np313[component] - ref)
-    E_np331 = norm_3Dgrid(np331['h'], np331[component] - ref)
-    E_np333 = norm_3Dgrid(np333['h'], np333[component] - ref)
+    E_np313 = norm_3Dgrid(np313["h"], np313[component] - ref)
+    E_np331 = norm_3Dgrid(np331["h"], np331[component] - ref)
+    E_np333 = norm_3Dgrid(np333["h"], np333[component] - ref)
     # E_np666 = norm_3Dgrid(np666['h'], np666[component] - ref)
 
     # Plot error across time
-    X, Y = np.meshgrid(np111['m'][0,:], np111['t'])
+    X, Y = np.meshgrid(np111["m"][0, :], np111["t"])
     # fig = plt.figure()
     # ax = plt.subplot(311, projection='3d')
     # ax.plot_surface(X, Y, np.abs(np911[component][:,:,0,0] - ref[:,:,0,0]))
     # ax = plt.subplot(312, projection='3d')
     # ax.plot_surface(X, Y, np.abs(np911[component][:,0,:,0] - ref[:,0,:,0]))
     # ax = plt.subplot(313, projection='3d')
     # ax.plot_surface(X, Y, np.abs(np911[component][:,0,0,:] - ref[:,0,0,:]))
-    plt.plot(np111['t'], E_np211)
-    plt.plot(np111['t'], E_np131)
-    plt.plot(np111['t'], E_np113)
-    plt.plot(np111['t'], E_np911)
+    plt.plot(np111["t"], E_np211)
+    plt.plot(np111["t"], E_np131)
+    plt.plot(np111["t"], E_np113)
+    plt.plot(np111["t"], E_np911)
     # plt.plot(np111['t'], E_np133)
-    plt.plot(np111['t'], E_np313)
-    plt.plot(np111['t'], E_np331)
-    plt.plot(np111['t'], E_np333)
+    plt.plot(np111["t"], E_np313)
+    plt.plot(np111["t"], E_np331)
+    plt.plot(np111["t"], E_np333)
     # plt.plot(np111['t'], E_np666)
     # plt.legend(['2 1 1', '3 1 1', '1 3 3', '3 1 3', '3 3 1', '3 3 3', '6 6 6'])
     # plt.legend(['3 1 1', '1 3 1', '1 1 3', '9 1 1', '1 3 3', '3 1 3', '3 3 1'])
-    plt.ylabel('||E(hx,hy,hz)||')
-    plt.xlabel('time')
-    plt.savefig('compare-error-plot-%s.png' % component)
+    plt.ylabel("||E(hx,hy,hz)||")
+    plt.xlabel("time")
+    plt.savefig("compare-error-plot-%s.png" % component)