Toolchain: Updates of COSMA and HDF5 (#4910)

src/hdf5_wrapper.F

@@ -16,17 +16,19 @@ MODULE hdf5_wrapper
 #ifdef __HDF5
    USE hdf5, ONLY: &
       h5aclose_f, h5acreate_f, h5aopen_f, h5aread_f, h5awrite_f, h5close_f, h5dclose_f, &
-      h5dcreate_f, h5dget_space_f, h5dopen_f, h5dread_f, h5dwrite_f, h5f_acc_rdonly_f, &
+      h5dcreate_f, h5dget_space_f, h5dopen_f, h5dread_f, h5dwrite_f, h5f_acc_rdonly_f, h5f_acc_rdwr_f, &
       h5f_acc_trunc_f, h5fclose_f, h5fcreate_f, h5fopen_f, h5gclose_f, h5gcreate_f, h5gopen_f, &
       h5open_f, h5s_scalar_f, h5sclose_f, h5screate_f, h5screate_simple_f, &
       h5sget_simple_extent_npoints_f, h5t_c_s1, h5t_cset_utf8_f, h5t_enum_f, h5t_native_double, &
       h5t_native_integer, h5t_str_nullpad_f, h5t_string, h5tclose_f, h5tcopy_f, h5tcreate_f, &
+      h5pcreate_f, h5pclose_f, h5pset_fapl_mpio_f, h5p_file_access_f, h5p_default_f, &
       h5tenum_insert_f, h5tset_cset_f, h5tset_size_f, h5tset_strpad_f, hid_t, hsize_t, size_t
 #endif
    USE iso_c_binding, ONLY: C_LOC, &
                             c_ptr
    USE cp_log_handling, ONLY: cp_logger_get_default_io_unit
    USE kinds, ONLY: dp
+   USE message_passing, ONLY: mp_comm_world, mp_info_null
 #include "./base/base_uses.f90"
 
    IMPLICIT NONE
@@ -71,8 +73,12 @@ CONTAINS
       INTEGER(KIND=hid_t), INTENT(OUT)                   :: file_id
 
       INTEGER                                            :: error
+      INTEGER(KIND=hid_t)                                :: plist_id
 
-      CALL h5fcreate_f(filename, h5f_acc_trunc_f, file_id, error)
+      CALL h5pcreate_f(h5p_file_access_f, plist_id, error)
+      CALL h5pset_fapl_mpio_f(plist_id, mp_comm_world%get_handle(), mp_info_null%get_handle(), error)
+      CALL h5fcreate_f(filename, h5f_acc_trunc_f, file_id, error, access_prp=plist_id)
+      CALL h5pclose_f(plist_id, error)
       IF (error < 0) CPABORT('ERROR: failed to create HDF5 file')
 
    END SUBROUTINE h5fcreate
@@ -87,8 +93,12 @@ CONTAINS
       INTEGER(KIND=hid_t), INTENT(OUT)                   :: file_id
 
       INTEGER                                            :: error
+      INTEGER(KIND=hid_t)                                :: plist_id
 
-      CALL h5fopen_f(TRIM(filename), h5f_acc_rdonly_f, file_id, error)
+      CALL h5pcreate_f(h5p_file_access_f, plist_id, error)
+      CALL h5pset_fapl_mpio_f(plist_id, mp_comm_world%get_handle(), mp_info_null%get_handle(), error)
+      CALL h5fopen_f(filename, h5f_acc_rdwr_f, file_id, error, access_prp=plist_id)
+      CALL h5pclose_f(plist_id, error)
       IF (error < 0) CPABORT('ERROR: failed to open HDF5 file')
 
    END SUBROUTINE h5fopen

tests/QS/regtest-as-qcschema/TEST_FILES.toml

@@ -0,0 +1,9 @@
+# runs are executed in the same order as in this file
+# the second field tells which test should be run in order to compare with the last available output
+# e.g. 0 means do not compare anything, running is enough
+#      1 compares the last total energy in the file
+#      for details see cp2k/tools/do_regtest
+#
+"h2o.inp"                               = [{matcher="E_total", tol=1e-12, ref=-17.12434837130648}]
+"be.inp"                                = [{matcher="E_total", tol=1e-12, ref=-14.49107600944466}]
+#EOF

tests/QS/regtest-as-qcschema/be.inp

@@ -0,0 +1,69 @@
+&GLOBAL
+  PRINT_LEVEL LOW
+  RUN_TYPE ENERGY
+&END GLOBAL
+
+&FORCE_EVAL
+  METHOD Quickstep
+  &DFT
+    &ACTIVE_SPACE
+      ACTIVE_ELECTRONS 4
+      ACTIVE_ORBITALS 3
+      ORBITAL_SELECTION CANONICAL
+      QCSCHEMA be.h5
+      &ERI
+        METHOD FULL_GPW
+        OPERATOR COULOMB
+      &END ERI
+      &ERI_GPW
+        PRINT_LEVEL LOW
+      &END ERI_GPW
+      &FCIDUMP
+      &END FCIDUMP
+    &END ACTIVE_SPACE
+    &MGRID
+      CUTOFF 300
+    &END MGRID
+    &POISSON
+      PERIODIC NONE
+      POISSON_SOLVER ANALYTIC
+    &END POISSON
+    &QS
+      EPS_DEFAULT 1.0E-10
+    &END QS
+    &SCF
+      ADDED_MOS 2
+      EPS_SCF 1.0E-5
+      SCF_GUESS ATOMIC
+      &OT OFF
+        MINIMIZER DIIS
+        PRECONDITIONER FULL_ALL
+      &END OT
+    &END SCF
+    &XC
+      &HF
+        &MEMORY
+          MAX_MEMORY 10
+        &END MEMORY
+        &SCREENING
+          EPS_SCHWARZ 1.0E-10
+        &END SCREENING
+      &END HF
+      &XC_FUNCTIONAL NONE
+      &END XC_FUNCTIONAL
+    &END XC
+  &END DFT
+  &SUBSYS
+    &CELL
+      ABC 10.0 10.0 10.0
+      PERIODIC NONE
+    &END CELL
+    &COORD
+      Be   0.000000   0.000000    0.000000
+    &END COORD
+    &KIND Be
+      BASIS_SET ORB DZV-GTH-PADE
+      POTENTIAL GTH-PBE
+    &END KIND
+  &END SUBSYS
+&END FORCE_EVAL

tests/QS/regtest-as-qcschema/h2o.inp

@@ -0,0 +1,66 @@
+&GLOBAL
+  PRINT_LEVEL LOW
+  PROJECT h2o
+  RUN_TYPE ENERGY
+&END GLOBAL
+
+&FORCE_EVAL
+  METHOD Quickstep
+  &DFT
+    &ACTIVE_SPACE
+      ACTIVE_ELECTRONS 4
+      ACTIVE_ORBITALS 6
+      ORBITAL_SELECTION CANONICAL
+      QCSCHEMA h2o.h5
+      &ERI
+        METHOD FULL_GPW
+        OPERATOR COULOMB
+      &END ERI
+      &ERI_GPW
+        PRINT_LEVEL MEDIUM
+      &END ERI_GPW
+      &FCIDUMP
+      &END FCIDUMP
+      &PRINT_ORBITAL_CUBES
+        ALIST 3 4 1
+        BLIST
+        FILENAME Active_orbital
+        STRIDE 3
+      &END PRINT_ORBITAL_CUBES
+    &END ACTIVE_SPACE
+    &MGRID
+      CUTOFF 200
+    &END MGRID
+    &QS
+      EPS_DEFAULT 1.0E-8
+    &END QS
+    &SCF
+      ADDED_MOS 4
+      IGNORE_CONVERGENCE_FAILURE
+      MAX_SCF 4
+      SCF_GUESS ATOMIC
+    &END SCF
+    &XC
+      &XC_FUNCTIONAL Pade
+      &END XC_FUNCTIONAL
+    &END XC
+  &END DFT
+  &SUBSYS
+    &CELL
+      ABC 6.0 6.0 6.0
+    &END CELL
+    &COORD
+      H   0.000000   -0.757136    0.520545
+      O   0.000000    0.000000   -0.065587
+      H   0.000000    0.757136    0.520545
+    &END COORD
+    &KIND H
+      BASIS_SET ORB DZV-GTH-PADE
+      POTENTIAL GTH-PADE-q1
+    &END KIND
+    &KIND O
+      BASIS_SET ORB DZVP-GTH-PADE
+      POTENTIAL GTH-PADE-q6
+    &END KIND
+  &END SUBSYS
+&END FORCE_EVAL

tests/TEST_DIRS

@@ -361,6 +361,7 @@ QS/regtest-tddfpt-prop
 QS/regtest-pao-3
 QS/regtest-double-hybrid-stress-numer-laplace               libxc !ifx
 QS/regtest-as                                               libint !ifx
+QS/regtest-as-qcschema                                      hdf5 libint !ifx
 QS/regtest-double-hybrid-2                                  libint !ifx
 QS/regtest-sccs-2
 FE/regtest-3

tools/toolchain/scripts/stage4/install_cosma.sh

@@ -6,12 +6,12 @@
 [ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
 SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
 
-cosma_ver="2.7.0"
-cosma_sha256="f4775d18379539d7bb5053bff8acb4e13d6ed31a9677f498d9099a7500488789"
-costa_ver="2.2.2"
-costa_sha256="e87bc37aad14ac0c5922237be5d5390145c9ac6aef0350ed17d86cb2d994e67c"
-tiled_mm_ver="2.3.1"
-tiled_mm_sha256="68914a483e62f796b790ea428210b1d5ef5943d6289e53d1aa62f56a20fbccc8"
+cosma_ver="2.8.1"
+cosma_sha256="563bb0785dca32ede780a05ad424db9b6d7f473a909ca423931b96204e2b5d9c"
+costa_ver="2.3.0"
+costa_sha256="0413311a2821d4cd1f3f026672a75a5b5a2956f61305c07d7fc14565a126b517"
+tiled_mm_ver="2.3.2"
+tiled_mm_sha256="1f91ca02f6ee8e400835fa90630618baf86a7b425b4bbbb4151068f72658b858"
 
 source "${SCRIPT_DIR}"/common_vars.sh
 source "${SCRIPT_DIR}"/tool_kit.sh

tools/toolchain/scripts/stage7/install_hdf5.sh

@@ -6,8 +6,8 @@
 [ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
 SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
 
-hdf5_ver="1.14.6"
-hdf5_sha256="e4defbac30f50d64e1556374aa49e574417c9e72c6b1de7a4ff88c4b1bea6e9b"
+hdf5_ver="2.1.0"
+hdf5_sha256="ce7f5515a95d588b8606c3fb50643f8b88ac52ffbbde9c63bb1edca6a256e964"
 
 source "${SCRIPT_DIR}"/common_vars.sh
 source "${SCRIPT_DIR}"/tool_kit.sh
@@ -39,15 +39,19 @@ case "$with_hdf5" in
       cd hdf5-${hdf5_ver}
       mkdir build
       cd build
-      cmake \
+      # Add "-DHDF5_ENABLE_ZLIB_SUPPORT=ON" because HDF5 2.x doesn't enable ZLIB support by default
+      CMAKE_OPTIONS="-DBUILD_TESTING=OFF -DHDF5_BUILD_FORTRAN=ON -DHDF5_ENABLE_ZLIB_SUPPORT=ON"
+      if [ "$(find_in_paths "libsz.*" $LIB_PATHS)" != "__FALSE__" ]; then
+        CMAKE_OPTIONS="${CMAKE_OPTIONS} -DHDF5_ENABLE_SZIP_SUPPORT=ON"
+      fi
+      if [ "${MPI_MODE}" != "no" ]; then
+        CMAKE_OPTIONS="${CMAKE_OPTIONS} -DHDF5_ENABLE_PARALLEL=ON"
+      fi
+      cmake .. \
         -DCMAKE_INSTALL_PREFIX="${pkg_install_dir}" \
-        -DCMAKE_BUILD_TYPE="RelWithDebInfo" \
         -DCMAKE_VERBOSE_MAKEFILE=ON \
-        -DHDF5_BUILD_FORTRAN=ON \
-        -DHDF5_ENABLE_Z_LIB_SUPPORT=ON \
-        .. > configure.log 2>&1 || tail_excerpt configure.log
-      make -j $(get_nprocs) > make.log 2>&1 || tail_excerpt make.log
-      make install > install.log 2>&1 || tail_excerpt install.log
+        ${CMAKE_OPTIONS} > configure.log 2>&1 || tail_excerpt configure.log
+      make install -j $(get_nprocs) > make.log 2>&1 || tail_excerpt make.log
       cd ..
       write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage7/$(basename ${SCRIPT_NAME})"
     fi
@@ -91,10 +95,8 @@ if [ "${with_hdf5}" != "__DONTUSE__" ]; then
     else
       HDF5_LIBS="-lhdf5_fortran -lhdf5_f90cstub -lhdf5 -lz"
     fi
-    if [ -f "${pkg_install_dir}/lib/pkgconfig/hdf5.pc" ]; then
-      if [ -n "$(grep libsz ${pkg_install_dir}/lib/pkgconfig/hdf5.pc)" ]; then
-        HDF5_LIBS="${HDF5_LIBS} -lsz"
-      fi
+    if [ -n "$(grep "lsz" ${pkg_install_dir}/lib/pkgconfig/hdf5.pc)" ]; then
+      HDF5_LIBS="${HDF5_LIBS} -lsz"
     fi
     cat << EOF > "${BUILDDIR}/setup_hdf5"
 prepend_path LD_LIBRARY_PATH "${pkg_install_dir}/lib"
@@ -110,11 +112,8 @@ EOF
     else
       HDF5_LIBS="-lhdf5_fortran -lhdf5_hl -lhdf5 -lz"
     fi
-    if [ -f "${pkg_install_dir}/lib/pkgconfig/hdf5.pc" ]; then
-      if [ -n "$(grep libsz ${pkg_install_dir}/lib/pkgconfig/hdf5.pc)" ]; then
-        HDF5_LIBS="${HDF5_LIBS} -lsz"
-      fi
-    elif [ -n "$(grep -- "-lsz" ${pkg_install_dir}/lib/libhdf5.settings)" ]; then
+    if [ -n "$(grep "lsz" ${pkg_install_dir}/lib/pkgconfig/hdf5.pc)" ] ||
+      [ -n "$(grep "lsz" ${pkg_install_dir}/lib/libhdf5.settings)" ]; then
       HDF5_LIBS="${HDF5_LIBS} -lsz"
     fi
   fi