Merge pull request #1759 from QMCPACK/rc_380

Rc 380

Author: mdewing

CHANGELOG.md

@@ -2,6 +2,59 @@
 
 Notable changes to QMCPACK are documented in this file.
 
+## [3.8.0] - 2019-07-23
+
+### Notes
+
+This release includes Quantum Espresso v6.4.1 support, new examples
+for adding wavefunctions and Jastrow functions, and many updates to the
+AFQMC code functionality. Additionally, all the updated scripts and
+functionality utilized during the [2019 QMCPACK
+workshop](https://github.com/QMCPACK/qmcpack_workshop_2019) are
+provided; this link also includes several new tutorials. A large
+number of feature refinements, bugfixes, testing improvements and
+source code cleanup have also been performed.
+
+* Quantum Espresso v6.4.1 support [\#1732](https://github.com/QMCPACK/qmcpack/pull/1732).
+* New tutorial for adding a simple wavefunction (He) [\#1621](https://github.com/QMCPACK/qmcpack/pull/1621).
+* New tutorial and capability for adding Jastrow functors from symbolic expressions written in Python [\#1557](https://github.com/QMCPACK/qmcpack/pull/1557).
+* [Updated compiler and library support policy](https://github.com/QMCPACK/qmcpack#prerequisites), and matching testing. We aim to support open source compilers and
+  libraries within two years of release. Use of older software is discouraged and untested. Support for closed source compilers over the same period may require use of an exact version.
+* Many updates to AFQMC code to support more compilers and libraries.
+* Newly expanded deterministic test set should now pass on all platforms and be usable as an.
+  installation check. Recommend to run "ctest -L deterministic" after building QMCPACK.
+* AFQMC code now only reads HDF5 format data to improve I/O performance and storage utilization.
+* K-point AFQMC code usable in production (e.g. bug fix [\#1524](https://github.com/QMCPACK/qmcpack/pull/1524)).
+* Updated AFQMC workflow scripts for interfacing with PySCF.
+* Faster initial cusp correction calculation for all-electron calculations, e.g. [\#1643](https://github.com/QMCPACK/qmcpack/pull/1643).
+* Improved stability of cusp correction calculation [\#1594](https://github.com/QMCPACK/qmcpack/pull/1594).
+* New short-ranged e-n Jastrow [\#1680](https://github.com/QMCPACK/qmcpack/pull/1680).
+* Substantially faster 1-body reduced density matrix (1DRDM) estimator [\#1672](https://github.com/QMCPACK/qmcpack/pull/1672).
+* Performance tests added for LCAO code and Gaussian basis sets [\#1639](https://github.com/QMCPACK/qmcpack/pull/1639).
+* Reduced configuration output by default. Use -DQMC_VERBOSE_CONFIGURATION=1 on CMake line for greater detail.
+* Partial support for forces in LCAO basis e.g. [\#1559](https://github.com/QMCPACK/qmcpack/pull/1559). See details given at
+  2019 QMCPACK Workshop and in manual.
+* Improved human-readable Jastrow output [\#1525](https://github.com/QMCPACK/qmcpack/pull/1525).
+* Improved MPI implementation. QMCPACK is now compatible with OpenMPI v4.
+* Majority of the manual has been professionally edited.
+
+### Known bugs
+
+See [list of open bugs](https://github.com/QMCPACK/qmcpack/issues?q=is%3Aissue+is%3Aopen+label%3Abug).
+
+* There is a general problem with MVAPICH2 involving aligned memory allocations that will cause
+  QMCPACK to crash if MVAPICH is compiled using defaults. See  [\#1703](https://github.com/QMCPACK/qmcpack/issues/1703) for details and workaround.
+
+### NEXUS
+
+* Examples added of PySCF molecular and solid-state workflows [\#1552](https://github.com/QMCPACK/qmcpack/pull/1552).
+* Update support for Quantum Package 2.0 [\#1538](https://github.com/QMCPACK/qmcpack/pull/1538).
+* Support for additional machines including SuperMUC-NG [\#1665](https://github.com/QMCPACK/qmcpack/pull/1665).
+* Support for ghost atoms [\#1653](https://github.com/QMCPACK/qmcpack/pull/1653).
+* Update outdated cubic specifier to alat for QE [\#1642](https://github.com/QMCPACK/qmcpack/pull/1642).
+* K-point grids are symmetrized with spglib [\#1544](https://github.com/QMCPACK/qmcpack/pull/1544).
+* Bundling of jobs at NERSC [\#1748](https://github.com/QMCPACK/qmcpack/pull/1748).
+
 ## [3.7.0] - 2019-03-29
 
 ### Notes

CMake/ClangCompilers.cmake

@@ -63,7 +63,7 @@ ELSEIF(CMAKE_SYSTEM_PROCESSOR MATCHES "x86_64")
     endif() #(CMAKE_CXX_FLAGS MATCHES "-march=" AND CMAKE_C_FLAGS MATCHES "-march=")
   else() #(CMAKE_CXX_FLAGS MATCHES "-march=" OR CMAKE_C_FLAGS MATCHES "-march=")
     # use -march=native
-    SET(CMAKE_C_FLAGS   "${CMAKE_C_FLAGS}   -march=native")
+    SET(CMAKE_C_FLAGS     "${CMAKE_C_FLAGS} -march=native")
     SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=native")
   endif()  #(CMAKE_CXX_FLAGS MATCHES "-march=" OR CMAKE_C_FLAGS MATCHES "-march=")
 ELSEIF(CMAKE_SYSTEM_PROCESSOR MATCHES "ppc64" OR CMAKE_SYSTEM_PROCESSOR MATCHES "aarch64")
@@ -77,7 +77,7 @@ ELSEIF(CMAKE_SYSTEM_PROCESSOR MATCHES "ppc64" OR CMAKE_SYSTEM_PROCESSOR MATCHES
     endif() #(CMAKE_CXX_FLAGS MATCHES "-mcpu=" AND CMAKE_C_FLAGS MATCHES "-mcpu=")
   else() #(CMAKE_CXX_FLAGS MATCHES "-mcpu=" OR CMAKE_C_FLAGS MATCHES "-mcpu=")
     # use -mcpu=native
-    SET(CMAKE_C_FLAGS   "${CMAKE_C_FLAGS}   -mcpu=native")
+    SET(CMAKE_C_FLAGS     "${CMAKE_C_FLAGS} -mcpu=native")
     SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mcpu=native")
   endif() #(CMAKE_CXX_FLAGS MATCHES "-mcpu=" OR CMAKE_C_FLAGS MATCHES "-mcpu=")
 ENDIF()
@@ -97,7 +97,7 @@ IF (ENABLE_GCOV)
 ENDIF(ENABLE_GCOV)
 
 SET(XRAY_PROFILE FALSE CACHE BOOL "Use llvm xray profiling")
-SET(XRAY_INSTRUCTION_THRESHOLD 200 CACHE INT "Instruction threshold for xray instrumentation")
+SET(XRAY_INSTRUCTION_THRESHOLD 200 CACHE STRING "Instruction threshold for xray instrumentation")
 
 IF(XRAY_PROFILE)
   set(XRAY_FLAGS "-fxray-instrument -fxray-instruction-threshold=${XRAY_INSTRUCTION_THRESHOLD}")

CMake/FindLibxml2QMC.cmake

@@ -34,18 +34,6 @@ ELSE()
   ENDIF()
 ENDIF()
 
-IF ( NOT HAVE_MKL_VML )
-  FILE( WRITE "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeTmp/src_glibc.cxx"
-      "#include <iostream>\n#if __GLIBC__ == 2 && ( __GLIBC_MINOR__ == 22 || __GLIBC_MINOR__ == 23 )\n#error buggy glibc version\n#endif\n int main() { return 0; }\n" )
-  try_compile(PASS_GLIBC ${CMAKE_BINARY_DIR}
-        ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeTmp/src_glibc.cxx
-        CMAKE_FLAGS "${CMAKE_CXX_FLAGS}" )
-
-  IF ( NOT PASS_GLIBC )
-    MESSAGE(WARNING "Using glibc 2.22 or 2.23 which contains a buggy libmvec crashing QMCPACK. Workaround needed for this issue.")
-  ENDIF()
-ENDIF()
-
 IF ( NOT HAVE_VECTOR_MATH )
   MESSAGE(STATUS "No usable vector math library detected.")
 ENDIF()

CMake/FindVectorMath.cmake

@@ -23,6 +23,10 @@ SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fomit-frame-pointer -finline-limit=1000
 SET(CMAKE_C_FLAGS     "${CMAKE_C_FLAGS} -Wno-deprecated")
 SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-deprecated")
 
+# treat VLA as error
+SET(CMAKE_C_FLAGS     "${CMAKE_C_FLAGS} -Werror=vla")
+SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wvla")
+
 # Set extra optimization specific flags
 SET( CMAKE_C_FLAGS_RELEASE     "${CMAKE_C_FLAGS_RELEASE} -ffast-math" )
 SET( CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -ffast-math" )
@@ -50,7 +54,7 @@ ELSEIF(CMAKE_SYSTEM_PROCESSOR MATCHES "x86_64")
     endif() #(CMAKE_CXX_FLAGS MATCHES "-march=" AND CMAKE_C_FLAGS MATCHES "-march=")
   else() #(CMAKE_CXX_FLAGS MATCHES "-march=" OR CMAKE_C_FLAGS MATCHES "-march=")
     # use -march=native
-    SET(CMAKE_C_FLAGS   "${CMAKE_C_FLAGS}   -march=native")
+    SET(CMAKE_C_FLAGS     "${CMAKE_C_FLAGS} -march=native")
     SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=native")
   endif()  #(CMAKE_CXX_FLAGS MATCHES "-march=" OR CMAKE_C_FLAGS MATCHES "-march=")
 ELSEIF(CMAKE_SYSTEM_PROCESSOR MATCHES "ppc64" OR CMAKE_SYSTEM_PROCESSOR MATCHES "aarch64")
@@ -64,11 +68,21 @@ ELSEIF(CMAKE_SYSTEM_PROCESSOR MATCHES "ppc64" OR CMAKE_SYSTEM_PROCESSOR MATCHES
     endif() #(CMAKE_CXX_FLAGS MATCHES "-mcpu=" AND CMAKE_C_FLAGS MATCHES "-mcpu=")
   else() #(CMAKE_CXX_FLAGS MATCHES "-mcpu=" OR CMAKE_C_FLAGS MATCHES "-mcpu=")
     # use -mcpu=native
-    SET(CMAKE_C_FLAGS   "${CMAKE_C_FLAGS}   -mcpu=native")
+    SET(CMAKE_C_FLAGS     "${CMAKE_C_FLAGS} -mcpu=native")
     SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mcpu=native")
   endif() #(CMAKE_CXX_FLAGS MATCHES "-mcpu=" OR CMAKE_C_FLAGS MATCHES "-mcpu=")
 ENDIF()
 
+# protect buggy libmvec
+FILE( WRITE "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeTmp/src_glibc.cxx"
+    "#include <iostream>\n#if __GLIBC__ == 2 && ( __GLIBC_MINOR__ == 22 || __GLIBC_MINOR__ == 23 )\n#error buggy glibc version\n#endif\n int main() { return 0; }\n" )
+try_compile(PASS_GLIBC ${CMAKE_BINARY_DIR}
+      ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeTmp/src_glibc.cxx
+      CMAKE_FLAGS "${CMAKE_CXX_FLAGS}" )
+IF ( NOT PASS_GLIBC )
+  MESSAGE(FATAL_ERROR "Your system and GNU compiler are using glibc 2.22 or 2.23 which contains a buggy libmvec. This results in crashes. Workaround needed. Alternatively upgrade or use another compiler.")
+ENDIF()
+
 # Add static flags if necessary
 IF(QMC_BUILD_STATIC)
 SET(CMAKE_CXX_LINK_FLAGS " -static")

CMake/GNUCompilers.cmake

@@ -31,21 +31,11 @@ SET( CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -restrict -unroll -ip"
 SET( CMAKE_C_FLAGS_RELWITHDEBINFO     "${CMAKE_C_FLAGS_RELWITHDEBINFO} -restrict -unroll -ip" )
 SET( CMAKE_CXX_FLAGS_RELWITHDEBINFO "${CMAKE_CXX_FLAGS_RELWITHDEBINFO} -restrict -unroll -ip" )
 
-# Use deprecated options prior to 11.1
-SET(ICC_DEPRECATED_OPTS FALSE)
-IF ( CMAKE_CXX_COMPILER_VERSION VERSION_LESS 11.1 )
-SET(CMAKE_C_FLAGS     "${CMAKE_C_FLAGS} -prefetch ")
-SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -prefetch" )
-ELSEIF(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16 )  
-SET(CMAKE_C_FLAGS     "${CMAKE_C_FLAGS} -opt-prefetch" )
-SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -opt-prefetch" )
-ELSE()
-SET(CMAKE_C_FLAGS     "${CMAKE_C_FLAGS} -qopt-prefetch" )
+# Set prefetch flag
 SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -qopt-prefetch" )
-ENDIF()
 
 #check if -ftz is accepted
-CHECK_C_COMPILER_FLAG( "${CMAKE_CXX_FLAGS} -ftz" INTEL_FTZ )
+CHECK_CXX_COMPILER_FLAG( "${CMAKE_CXX_FLAGS} -ftz" INTEL_FTZ )
 IF( INTEL_FTZ)
 SET(CMAKE_C_FLAGS     "${CMAKE_C_FLAGS} -ftz" )
 SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -ftz" )

CMake/IntelCompilers.cmake

@@ -102,7 +102,7 @@ FUNCTION( RUN_QMC_APP_NO_COPY TESTNAME WORKDIR PROCS THREADS TEST_ADDED TEST_LAB
     SET( TEST_ADDED_TEMP FALSE )
     IF ( USE_MPI )
         IF ( ${TOT_PROCS} GREATER ${TEST_MAX_PROCS} )
-            MESSAGE("Disabling test ${TESTNAME} (exceeds maximum number of processors ${TEST_MAX_PROCS})")
+            MESSAGE_VERBOSE("Disabling test ${TESTNAME} (exceeds maximum number of processors ${TEST_MAX_PROCS})")   
         ELSEIF ( USE_MPI )
             ADD_TEST( ${TESTNAME} ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${PROCS} ${QMC_APP} ${ARGN} )
             SET_TESTS_PROPERTIES( ${TESTNAME} PROPERTIES FAIL_REGULAR_EXPRESSION "${TEST_FAIL_REGULAR_EXPRESSION}" 
@@ -118,7 +118,7 @@ FUNCTION( RUN_QMC_APP_NO_COPY TESTNAME WORKDIR PROCS THREADS TEST_ADDED TEST_LAB
                 ENVIRONMENT OMP_NUM_THREADS=${THREADS} )
             SET( TEST_ADDED_TEMP TRUE )
         ELSE()
-            MESSAGE("Disabling test ${TESTNAME} (building without MPI)")
+            MESSAGE_VERBOSE("Disabling test ${TESTNAME} (building without MPI)")
         ENDIF()
     ENDIF()
     SET(TEST_LABELS_TEMP "")
@@ -170,7 +170,7 @@ FUNCTION(QMC_RUN_AND_CHECK BASE_NAME BASE_DIR PREFIX INPUT_FILE PROCS THREADS SH
     SET( TEST_ADDED FALSE )
     SET( TEST_LABELS "")
     SET( FULL_NAME "${BASE_NAME}-${PROCS}-${THREADS}" )
-    MESSAGE("Adding test ${FULL_NAME}")
+    MESSAGE_VERBOSE("Adding test ${FULL_NAME}")
     RUN_QMC_APP(${FULL_NAME} ${BASE_DIR} ${PROCS} ${THREADS} TEST_ADDED TEST_LABELS ${INPUT_FILE})
     IF ( TEST_ADDED )
         SET_PROPERTY(TEST ${FULL_NAME} APPEND PROPERTY LABELS "QMCPACK")
@@ -244,7 +244,7 @@ function(SIMPLE_RUN_AND_CHECK base_name base_dir input_file procs threads check_
 
   # build test name
   set(full_name "${base_name}-${procs}-${threads}")
-  message("Adding test ${full_name}")
+  MESSAGE_VERBOSE("Adding test ${full_name}")
 
   # add run (task 1)
   set (test_added false)
@@ -303,3 +303,10 @@ FUNCTION( CPU_LIMIT_RUN TESTNAME SRC_DIR PROCS THREADS TIME ${ARGN} )
       SET_PROPERTY(TEST ${FULLNAME} APPEND PROPERTY PASS_REGULAR_EXPRESSION "Time limit reached for")
     ENDIF()
 ENDFUNCTION()
+
+# Print THE_MESSAGE if verbose configuration is enabled
+FUNCTION ( MESSAGE_VERBOSE THE_MESSAGE )
+    IF ( QMC_VERBOSE_CONFIGURATION )
+      MESSAGE( ${THE_MESSAGE} )
+    ENDIF()
+ENDFUNCTION()

CMake/macros.cmake

@@ -16,7 +16,7 @@ FUNCTION( RUN_QE_TEST BASE_NAME SRC_DIR PROCS1 PROCS2 PROCS3 NPOOL1 NPOOL2 NPOOL
     SET( FULL_NAME ${BASE_NAME}-np-${PROCS1}-${PROCS2}-${PROCS3}-nk-${NPOOL1}-${NPOOL2}-${NPOOL3} )
     SET( ${TEST_NAME} ${FULL_NAME} PARENT_SCOPE)
     SET( MY_WORKDIR ${CMAKE_CURRENT_BINARY_DIR}/${FULL_NAME} )
-    MESSAGE("Adding test ${FULL_NAME}")
+    MESSAGE_VERBOSE("Adding test ${FULL_NAME}")
     COPY_DIRECTORY( "${SRC_DIR}" "${MY_WORKDIR}" )
     ADD_QE_TEST(${FULL_NAME}-scf  ${PROCS1} ${QE_BIN}/pw.x         ${NPOOL1} ${MY_WORKDIR} ${TEST_INPUT_PREFIX}-scf.in )
     IF(PROCS2 EQUAL 0)
@@ -36,3 +36,18 @@ FUNCTION( SOFTLINK_H5 SOURCE TARGET PREFIX FILENAME TEST_NAME)
     SET_TESTS_PROPERTIES(LINK_${SOURCE}_TO_${TARGET} PROPERTIES DEPENDS ${SOURCE}-pw2x)
     SET_PROPERTY( TEST LINK_${SOURCE}_TO_${TARGET} APPEND PROPERTY LABELS "converter" )
 ENDFUNCTION()
+
+FUNCTION( VERIFY_QE_PRESENT QE_BIN )
+ IF ( EXISTS "${QE_BIN}/pw.x" )
+  MESSAGE( STATUS "Found pw.x at ${QE_BIN}/pw.x")
+ ELSE()
+  MESSAGE( "QE_BIN was specified but could not find ${QE_BIN}/pw.x" )
+  MESSAGE( FATAL_ERROR "QE should be built ahead of QMCPACK. See qmcpack/external_codes/quantum_espresso/README for details on building patched version." ) 
+ ENDIF()
+ IF ( EXISTS "${QE_BIN}/pw2qmcpack.x" )
+  MESSAGE( STATUS "Found pw2qmcpack.x at ${QE_BIN}/pw.x")
+ ELSE()
+  MESSAGE( "QE_BIN was specified but could not find ${QE_BIN}/pw2qmcpack.x" )
+  MESSAGE( FATAL_ERROR "See qmcpack/external_codes/quantum_espresso/README for details on building patched version" ) 
+ ENDIF()
+ENDFUNCTION()

CMake/run_qe.cmake

@@ -3,7 +3,7 @@ INCLUDE("${PROJECT_SOURCE_DIR}/CMake/test_labels.cmake")
 
 # Runs unit tests
 FUNCTION( ADD_UNIT_TEST TESTNAME TEST_BINARY )
-    MESSAGE("Adding test ${TESTNAME}")
+    MESSAGE_VERBOSE("Adding test ${TESTNAME}")
     IF ( USE_MPI )
         ADD_TEST(NAME ${TESTNAME} COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} 1 ${TEST_BINARY} ${ARGN})
         #SET_TESTS_PROPERTIES( ${TESTNAME} PROPERTIES ENVIRONMENT OMP_NUM_THREADS=1 )