Merge branch 'develop' of https://github.com/QMCPACK/qmcpack into gpa…

…w_converter

.github/workflows/ci-github-actions-self-hosted.yaml

@@ -5,13 +5,110 @@ on:
     types: [created]
 
 jobs:
+  cpu-intel64:
+    if: |
+      github.repository_owner == 'QMCPACK' &&
+      github.event.issue.pull_request &&
+      ( startsWith(github.event.comment.body, 'Test this please') || 
+        startsWith(github.event.comment.body, 'Start testing in-house') )
+
+    runs-on: [self-hosted, Linux, X64, gpu, cuda]
+
+    env:
+      GH_JOBNAME: ${{matrix.jobname}}
+      GH_OS: Linux
+    strategy:
+      fail-fast: false
+      matrix:
+        jobname: [
+            GCC8-NoMPI-MKL-Real-Mixed, # mixed precision
+            GCC8-NoMPI-MKL-Complex-Mixed,
+            GCC8-NoMPI-MKL-Real, # full precision
+            GCC8-NoMPI-MKL-Complex,
+          ]
+
+    steps:
+      - name: Verify actor
+        # Only trigger for certain "actors" (those commenting the PR, not the PR originator)
+        # this is in-line with the current workflow
+        env:
+          ACTOR_TOKEN: ${{secrets.TOKENIZER}}${{github.actor}}${{secrets.TOKENIZER}}
+          SECRET_ACTORS: ${{secrets.CI_GPU_ACTORS}}
+        if: contains(env.SECRET_ACTORS, env.ACTOR_TOKEN)
+        id: check
+        run: |
+          echo "::set-output name=triggered::true"
+
+      # Request repo info, required since issue_comment doesn't point at PR commit, but develop
+      - name: GitHub API Request
+        if: steps.check.outputs.triggered == 'true'
+        id: request
+        uses: octokit/request-action@v2.0.0
+        with:
+          route: ${{github.event.issue.pull_request.url}}
+        env:
+          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+
+      # Create a separate PR status pointing at GitHub Actions tab URL
+      # just like any other third-party service
+      - name: Create PR status
+        if: steps.check.outputs.triggered == 'true'
+        uses: Sibz/github-status-action@v1
+        with:
+          authToken: ${{secrets.GITHUB_TOKEN}}
+          context: "GitHub Actions self-hosted CI ${{ matrix.jobname }}"
+          state: "pending"
+          sha: ${{fromJson(steps.request.outputs.data).head.sha}}
+          target_url: https://github.com/${{github.repository}}/actions/runs/${{github.run_id}}
+
+      - name: Get PR information
+        if: steps.check.outputs.triggered == 'true'
+        id: pr_data
+        run: |
+          echo "::set-output name=branch::${{ fromJson(steps.request.outputs.data).head.ref }}"
+          echo "::set-output name=repo_name::${{ fromJson(steps.request.outputs.data).head.repo.full_name }}"
+          echo "::set-output name=repo_clone_url::${{ fromJson(steps.request.outputs.data).head.repo.clone_url }}"
+          echo "::set-output name=repo_ssh_url::${{ fromJson(steps.request.outputs.data).head.repo.ssh_url }}"
+
+      - name: Checkout PR branch
+        if: steps.check.outputs.triggered == 'true'
+        uses: actions/checkout@v2
+        with:
+          token: ${{secrets.GITHUB_TOKEN}}
+          repository: ${{fromJson(steps.request.outputs.data).head.repo.full_name}}
+          ref: ${{steps.pr_data.outputs.branch}}
+
+      - name: Configure
+        if: steps.check.outputs.triggered == 'true'
+        run: tests/test_automation/github-actions/ci/run_step.sh configure
+
+      - name: Build
+        if: steps.check.outputs.triggered == 'true'
+        run: tests/test_automation/github-actions/ci/run_step.sh build
+
+      - name: Test
+        if: steps.check.outputs.triggered == 'true'
+        run: tests/test_automation/github-actions/ci/run_step.sh test
+
+      - name: Report PR status
+        if: always() && steps.check.outputs.triggered == 'true'
+        uses: Sibz/github-status-action@v1
+        with:
+          authToken: ${{secrets.GITHUB_TOKEN}}
+          context: "GitHub Actions self-hosted CI ${{matrix.jobname}}"
+          state: ${{job.status}}
+          sha: ${{fromJson(steps.request.outputs.data).head.sha}}
+          target_url: https://github.com/${{github.repository}}/actions/runs/${{github.run_id}}
+
   gpu-cuda:
     if: |
       github.repository_owner == 'QMCPACK' &&
       github.event.issue.pull_request &&
       ( startsWith(github.event.comment.body, 'Test this please') || 
         startsWith(github.event.comment.body, 'Start testing in-house') )
 
+    needs: cpu-intel64
+
     runs-on: [self-hosted, Linux, X64, gpu, cuda]
 
     env:
@@ -31,6 +128,9 @@ jobs:
             GCC8-MPI-CUDA-AFQMC-Complex,
             Clang14Dev-MPI-CUDA-AFQMC-Offload-Real-Mixed, # auxiliary field, offload requires development llvm14
             Clang14Dev-MPI-CUDA-AFQMC-Offload-Real,
+            Intel19-MPI-CUDA-AFQMC-Real-Mixed, # auxiliary field, requires MPI
+            Intel19-MPI-CUDA-AFQMC-Complex-Mixed,
+            Intel19-MPI-CUDA-AFQMC-Real,
           ]
 
     steps:

.github/workflows/ci-github-actions.yaml

@@ -84,14 +84,14 @@ jobs:
         run: tests/test_automation/github-actions/ci/run_step.sh test
 
       - name: Coverage
-        if: contains(matrix.jobname, 'coverage')
+        if: contains(matrix.jobname, 'Gcov')
         run: tests/test_automation/github-actions/ci/run_step.sh coverage
 
       - name: Upload Coverage
-        if: contains(matrix.jobname, 'coverage') && github.repository_owner == 'QMCPACK'
-        uses: codecov/codecov-action@v1
+        if: contains(matrix.jobname, 'Gcov') && github.repository_owner == 'QMCPACK'
+        uses: codecov/codecov-action@v2
         with:
-          file: ../qmcpack-build/coverage.xml
+          files: ../qmcpack-build/coverage.xml
           flags: tests-deterministic # optional
           name: codecov-QMCPACK # optional
           fail_ci_if_error: true # optional (default = false)

CHANGELOG.md

@@ -2,11 +2,71 @@
 
 Notable changes to QMCPACK are documented in this file.
 
-## [Unreleased]
+## [3.12.0] - 2021-12-08
+
+### Notes
+
+This release incorporates several hundred changes to QMCPACK and the supporting
+ecosystem. It is a recommended release for all users. Note that compilers
+supporting C++17 and CMake version 3.15 or newer are now required. Changes
+include newly added support for the DIRAC quantum chemistry code, the RMG-DFT
+code, and updates for the latest version of Quantum ESPRESSO. Through DIRAC it
+is now possible to perform highly accurate molecular calculations incorporating
+spin-orbit with multideterminant trial wavefunctions. Behind the scenes updates
+include increased checking of inputs, fixes to many edge case bugs, and removal
+of memory leaks in both QMCPACK and the various converters. In readiness for
+transition to the new batched drivers that support both CPU and GPU execution,
+more features are supported and performance improved. Test coverage and
+robustness is improved in all areas. For developers, tests, sanitizers, and code
+coverage are now run on Pull Requests using GitHub Actions. 
 
-* C++17 is required [\#3348](https://github.com/QMCPACK/qmcpack/pull/3348).
-* Quantum ESPRESSO (QE) v6.8 support. [\#3301](https://github.com/QMCPACK/qmcpack/pull/3301).
 * To aid coexistence of real and complex builds, the qmcpack executable is now named qmcpack_complex for builds with QMC_COMPLEX=1
+* Added DIRAC converter and support for MSD wave functions [\#3510](https://github.com/QMCPACK/qmcpack/pull/3510)
+* Spin-Orbit implementation completed [\#1770](https://github.com/QMCPACK/qmcpack/issues/1770)
+* Quantum ESPRESSO (QE) v6.8 support [\#3301](https://github.com/QMCPACK/qmcpack/pull/3301)
+* Support for RMG DFT code [\#3351](https://github.com/QMCPACK/qmcpack/pull/3351)
+* CMake 3.15 minimum required [\#3492](https://github.com/QMCPACK/qmcpack/pull/3492)
+* C++17 is required [\#3348](https://github.com/QMCPACK/qmcpack/pull/3348)
+* CMake CUDA support uses modern FindCUDAToolkit [\#3460](https://github.com/QMCPACK/qmcpack/issues/3460)
+* Support latest Sphinx-contrib BibTeX 2.x [\#3176](https://github.com/QMCPACK/qmcpack/issues/3176)
+* One Body Density Matrices supported in batched drivers [\#3622](https://github.com/QMCPACK/qmcpack/pull/3622)
+* Batched performant Slater matrix inverses [\#3470](https://github.com/QMCPACK/qmcpack/pull/3470)
+* Safeguards for requesting more orbitals than the input h5 provide [\#2341](https://github.com/QMCPACK/qmcpack/issues/2341)
+* Implemented One-body spin-dependent Jastrow [\#3257](https://github.com/QMCPACK/qmcpack/pull/3257)
+* Fixes for low particle counts, such as using a two body Jastrow with more than 2 particle types but only one particle of each type [\#3137](https://github.com/QMCPACK/qmcpack/issues/3137)
+* ppconvert is built by default [\#3143](https://github.com/QMCPACK/qmcpack/pull/3143)
+* Documentation on revised input format where SPO sets are created outside the determinant [\#3456](https://github.com/QMCPACK/qmcpack/issues/3456)
+
+### NEXUS
+
+*  Add Density functionality to qdens tool [\#3541](https://github.com/QMCPACK/qmcpack/pull/3541)
+*  Add new qdens-radial tool for radial analysis of densities [\#3587](https://github.com/QMCPACK/qmcpack/pull/3587)
+*  Radial density of requested species only [\#3099](https://github.com/QMCPACK/qmcpack/pull/3099)
+*  Extend structure plotting capabilities for 2D materials [\#3220](https://github.com/QMCPACK/qmcpack/pull/3220)
+*  Support grand-canonical twist averaging [\#3153](https://github.com/QMCPACK/qmcpack/pull/3153) 
+*  Extend excitations to allow 'lowest' gap [\#3628](https://github.com/QMCPACK/qmcpack/pull/3628)
+*  Allow singlet/triplet excitation types [\#2290](https://github.com/QMCPACK/qmcpack/pull/2290)
+*  Allow bandstructure plotting with custom k-path [\#3293](https://github.com/QMCPACK/qmcpack/pull/3293)
+*  Generate PySCF inputs without a template [\#3550](https://github.com/QMCPACK/qmcpack/pull/3550)
+*  Add punch extension for GAMESS analysis [\#3433](https://github.com/QMCPACK/qmcpack/pull/3433)
+*  Read pseduopotentials in numhf format (Eric Shirley's numerical HF code) [\#3097](https://github.com/QMCPACK/qmcpack/pull/3097)
+*  Add L2 generation functionality [\#3079](https://github.com/QMCPACK/qmcpack/pull/3079)
+*  Support QMCPACK batched drivers [\#2901](https://github.com/QMCPACK/qmcpack/pull/2901)
+*  Make qdens test more informative [\#3593](https://github.com/QMCPACK/qmcpack/pull/3593) 
+*  Resource lock Nexus examples for reliable parallel execution [\#3585](https://github.com/QMCPACK/qmcpack/pull/3585)
+*  Support running tests without mpirun available [\#3584](https://github.com/QMCPACK/qmcpack/pull/3584)
+*  Small fix for custom band plotting [\#3566](https://github.com/QMCPACK/qmcpack/pull/3566)
+*  Improve error handling for bad Jastrow requests [\#3554](https://github.com/QMCPACK/qmcpack/pull/3554)
+*  Fix sizing problem in some single atom workflows [\#3553](https://github.com/QMCPACK/qmcpack/pull/3553)
+*  Fix syntax warnings [\#3497](https://github.com/QMCPACK/qmcpack/pull/3497)
+*  Fix convert4qmc usage [\#3495](https://github.com/QMCPACK/qmcpack/pull/3495)
+*  Verify cif2cell is available before running ntest\_nexus\_structure [\#3511](https://github.com/QMCPACK/qmcpack/pull/3511)
+*  Fix to add\_L2 function in pseudopotential.py [\#3386](https://github.com/QMCPACK/qmcpack/pull/3386)
+*  Expand eshdf features [\#3334](https://github.com/QMCPACK/qmcpack/pull/3334)
+*  Add delay\_rank input [\#3218](https://github.com/QMCPACK/qmcpack/pull/3218)
+*  Add max\_seconds input [\#3159](https://github.com/QMCPACK/qmcpack/pull/3159)
+*  Add Tref \(initial tilematrix\) argument to optimal\_tilematrix [\#3141](https://github.com/QMCPACK/qmcpack/pull/3141)
+*  Use OS environment by default [\#3108](https://github.com/QMCPACK/qmcpack/pull/3108)
 
 ## [3.11.0] - 2021-04-09
 

CMake/ClangCompilers.cmake

@@ -13,7 +13,7 @@ endif()
 # Enable OpenMP
 if(QMC_OMP)
   set(ENABLE_OPENMP 1)
-  if(ENABLE_OFFLOAD AND NOT CMAKE_SYSTEM_NAME STREQUAL "CrayLinuxEnvironment")
+  if(ENABLE_OFFLOAD)
     if (QMC_CUDA2HIP)
       set(OFFLOAD_TARGET_DEFAULT "amdgcn-amd-amdhsa")
     else()

CMake/GNUCompilers.cmake

@@ -8,7 +8,7 @@ if(QMC_OMP)
   set(ENABLE_OPENMP 1)
   set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fopenmp")
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp")
-  if(ENABLE_OFFLOAD AND NOT CMAKE_SYSTEM_NAME STREQUAL "CrayLinuxEnvironment")
+  if(ENABLE_OFFLOAD)
     set(OFFLOAD_TARGET
         "nvptx-none"
         CACHE STRING "Offload target architecture")

CMake/NVHPCCompilers.cmake

@@ -5,7 +5,7 @@
 if(QMC_OMP)
   set(ENABLE_OPENMP 1)
   set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -mp=allcores")
-  if(ENABLE_OFFLOAD AND NOT CMAKE_SYSTEM_NAME STREQUAL "CrayLinuxEnvironment")
+  if(ENABLE_OFFLOAD)
     message(WARNING "QMCPACK OpenMP offload is not ready for NVIDIA HPC compiler.")
     if(NOT DEFINED OFFLOAD_ARCH AND DEFINED CMAKE_CUDA_ARCHITECTURES)
       list(LENGTH CMAKE_CUDA_ARCHITECTURES NUMBER_CUDA_ARCHITECTURES)

CMake/python.cmake

@@ -6,7 +6,7 @@
 function(TEST_PYTHON_MODULE MODULE_NAME MODULE_PRESENT)
   message(VERBOSE "Checking import python module ${MODULE_NAME}")
   execute_process(
-    COMMAND ${qmcpack_SOURCE_DIR}/tests/scripts/test_import.py ${MODULE_NAME}
+    COMMAND ${Python3_EXECUTABLE} ${qmcpack_SOURCE_DIR}/tests/scripts/test_import.py ${MODULE_NAME}
     OUTPUT_VARIABLE TMP_OUTPUT_VAR
     OUTPUT_STRIP_TRAILING_WHITESPACE)
   set(${MODULE_PRESENT}

CMake/test_labels.cmake

@@ -1,18 +1,20 @@
 function(ADD_TEST_LABELS TEST_NAME TEST_LABELS)
-  set(SUCCESS FALSE)
   set(TEST_LABELS_TEMP "")
-  execute_process(
-    COMMAND ${qmcpack_SOURCE_DIR}/tests/scripts/test_labels.py ${TEST_NAME} ${QMC_CUDA} ${QMC_COMPLEX}
-            ${QMC_MIXED_PRECISION}
-    OUTPUT_VARIABLE TEST_LABELS_TEMP
-    RESULT_VARIABLE SUCCESS)
-  #MESSAGE("  Label script return value: ${SUCCESS}")
-  if(NOT ${SUCCESS} STREQUAL "0")
-    message("Warning: test labeling failed.  Test labeling error output:\n${TEST_LABELS_TEMP}")
-    set(TEST_LABELS_TEMP "")
-    #ELSE()
-    #  MESSAGE("  Test: ${TEST_NAME}")
-    #  MESSAGE("    ${TEST_LABELS_TEMP}")
+  if (DEFINED TEST_LABELS_${TEST_NAME}_${QMC_CUDA}_${QMC_COMPLEX}_${QMC_MIXED_PRECISION})
+    set(TEST_LABELS_TEMP TEST_LABELS_${${TEST_NAME}_${QMC_CUDA}_${QMC_COMPLEX}_${QMC_MIXED_PRECISION}})
+  else()
+    set(SUCCESS FALSE)
+    execute_process(
+      COMMAND ${qmcpack_SOURCE_DIR}/tests/scripts/test_labels.py ${TEST_NAME} ${QMC_CUDA} ${QMC_COMPLEX}
+              ${QMC_MIXED_PRECISION}
+      OUTPUT_VARIABLE TEST_LABELS_TEMP
+      RESULT_VARIABLE SUCCESS)
+    if(${SUCCESS} STREQUAL "0")
+      set(TEST_LABELS_${TEST_NAME}_${QMC_CUDA}_${QMC_COMPLEX}_${QMC_MIXED_PRECISION} ${TEST_LABELS_TEMP} CACHE INTERNAL "for internal use only; do not modify")
+    else()
+      message("Warning: test labeling failed.  Test labeling error output:\n${TEST_LABELS_TEMP}")
+      set(TEST_LABELS_TEMP "")
+    endif()
   endif()
   # Remove unstable label from direct execution.
   # It will still be added to statistical child tests.

CMakeLists.txt

@@ -16,7 +16,7 @@ cmake_policy(SET CMP0075 NEW)
 ######################################################################
 project(
   qmcpack
-  VERSION 3.11.9
+  VERSION 3.12.9
   LANGUAGES C CXX)
 
 #--------------------------------------------------------------------
@@ -730,6 +730,11 @@ if(QMC_CUDA OR ENABLE_CUDA)
     set(CMAKE_CUDA_EXTENSIONS OFF)
     enable_language(CUDA)
     find_package(CUDAToolkit REQUIRED)
+    if(NOT TARGET CUDA::cublas)
+      message(FATAL_ERROR "Found an incomplete CUDA toolkit installation. "
+                          "This often happens when CMake failed in recognizing the NVHPC internal CUDA toolkit. "
+                          "Set CMAKE_CUDA_COMPILER to the full path of nvcc from a complete CUDA toolkit installation.")
+    endif()
     # Automatically set the default NVCC flags
     set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -Drestrict=__restrict__ -DNO_CUDA_MAIN")
     if(QMC_COMPLEX)

README.md

@@ -41,13 +41,13 @@ encouraged for highest performance and easiest configuration.
 Nightly testing currently includes the following software versions on x86:
 
 * Compilers
-  * GCC 11.2.0, 9.1.0
-  * Clang/LLVM 12.0.1
+  * GCC 11.2.0, 9.2.0
+  * Clang/LLVM 13.0.0
   * Intel 19.1.1.217 configured to use C++ library from GCC 9.1.0 
   * NVIDIA HPC SDK 21.5 configured to use C++ library from GCC 9.1.0
 * Boost 1.77.0, 1.68.0
-* HDF5 1.12.1, 1.8.19
-* FFTW 3.3.9, 3.3.4
+* HDF5 1.12.1
+* FFTW 3.3.10, 3.3.8
 * CMake 3.21.1, 3.15.0
 * MPI
   * OpenMPI 4.1.1, 3.1.6

docs/additional_tools.rst

@@ -671,7 +671,7 @@ Periodic boundary conditions with Gaussian orbitals from PySCF is fully supporte
 
     convert4qmc -gamess Myrun.out -hdf5
 
-  This option is only used/usefull with the gamess code as it is the onlycode not providing an HDF5 output
+  This option is only used/useful with the gamess code as it is the only code not providing an HDF5 output
   The result will create QMCPACK input files but will also store all key data in the HDF5 format.
 
 - **Mixing orbitals and multideterminants**

docs/developing.rst

@@ -149,7 +149,7 @@ Naming
 The balance between description and ease of implementation should be balanced such that the code remains self-documenting within a
 single terminal window.  If an extremely short variable name is used, its scope must be shorter than :math:`\sim 40` lines. An
 exception is made for template parameters, which must be in all CAPS. Legacy code contains a great variety of hard to read code
-style, read this section and do not immitate existing code that violates it.
+style, read this section and do not imitate existing code that violates it.
 
 Namespace names
 ~~~~~~~~~~~~~~~
@@ -1696,7 +1696,7 @@ zeroed at the beginning of each step and accumulated upon call to
   unload, and collect. In the evaluate stage,
   ``QMCHamiltonian::Observables`` is populated by a list of
   ``OperatorBase``. In the load stage, ``QMCHamiltonian::Observables``
-  is transfered to ``Properties`` by ``QMCDriver``. In the unload stage,
+  is transferred to ``Properties`` by ``QMCDriver``. In the unload stage,
   ``Properties`` is copied to ``LocalEnergyEstimator::scalars``. In the
   collect stage, ``LocalEnergyEstimator::scalars`` is block-averaged to
   ``EstimatorManagerBase``