add patches to allow offline build of Amber

easybuild/easyconfigs/a/Amber/Amber-24.3-foss-2023a-AmberTools-24.10.eb

@@ -2,9 +2,10 @@ name = 'Amber'
 local_amber_ver = 24
 local_ambertools_ver = 24
 # Patch levels from https://ambermd.org/AmberPatches.php and https://ambermd.org/ATPatches.php
-patchlevels = (10, 3)  # (AmberTools, Amber)
-version = '%s.%s' % (local_amber_ver, patchlevels[1])
-versionsuffix = '-AmberTools-%s.%s' % (local_ambertools_ver, patchlevels[0])
+patchlevels = None  # Do not use update_amber
+_ec_patchlevels = (10, 3)  # (AmberTools, Amber) patchlevels - corresponds to the first items in patches below
+version = '%s.%s' % (local_amber_ver, _ec_patchlevels[1])
+versionsuffix = '-AmberTools-%s.%s' % (local_ambertools_ver, _ec_patchlevels[0])
 
 homepage = 'https://ambermd.org/amber.html'
 description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing
@@ -18,6 +19,21 @@ sources = [
     {'filename': 'AmberTools%s.tar.bz2' % local_ambertools_ver, 'alt_location': 'AmberTools'},
 ]
 patches = [
+    # Amber/AmberTools patches
+    {'name': 'AmberTools-24_update.1.patch', 'alt_location': 'AmberTools', 'level': 0},
+    {'name': 'AmberTools-24_update.2.patch', 'alt_location': 'AmberTools', 'level': 0},
+    {'name': 'AmberTools-24_update.3.patch', 'alt_location': 'AmberTools', 'level': 0},
+    {'name': 'AmberTools-24_update.4.patch', 'alt_location': 'AmberTools', 'level': 0},
+    {'name': 'AmberTools-24_update.5.patch', 'alt_location': 'AmberTools', 'level': 0},
+    {'name': 'AmberTools-24_update.6.patch', 'alt_location': 'AmberTools', 'level': 0},
+    {'name': 'AmberTools-24_update.7.patch', 'alt_location': 'AmberTools', 'level': 0},
+    {'name': 'AmberTools-24_update.8.patch', 'alt_location': 'AmberTools', 'level': 0},
+    {'name': 'AmberTools-24_update.9.patch', 'alt_location': 'AmberTools', 'level': 0},
+    {'name': 'AmberTools-24_update.10.patch', 'alt_location': 'AmberTools', 'level': 0},
+    ('Amber-24_update.1.patch', 0),
+    ('Amber-24_update.2.patch', 0),
+    ('Amber-24_update.3.patch', 0),
+    # EasyBuild extra patches
     {'name': 'AmberTools-20_cmake-locate-netcdf.patch', 'alt_location': 'AmberTools'},
     {'name': 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', 'alt_location': 'AmberTools'},
     {'name': 'AmberTools-20_fix_xblas_missing_make_dependency.patch', 'alt_location': 'AmberTools'},
@@ -34,6 +50,19 @@ patches = [
 checksums = [
     {'Amber24.tar.bz2': '74a7dbc4530f6302ae1efe723ba54d0fcdb03bce2b7231663ce5afc2c5660076'},
     {'AmberTools24.tar.bz2': '52fb4fb3370a89b7ce738a2dc3e513c2fc1943fde4b4381846d9e75cc48d840f'},
+    {'AmberTools-24_update.1.patch': 'caa2c42c02bfee37e4e9c5c2bf4715928b3865ebabf07868b0303a1f56a4c9bc'},
+    {'AmberTools-24_update.2.patch': '1ffdf217c9b3c66cd3a1cae5a402c5765876c150d7d8ce706a47762409f120dd'},
+    {'AmberTools-24_update.3.patch': '1a22b44a73f250714406142253d66a9f1d8aba1a75af7f676f94dd6034dc4578'},
+    {'AmberTools-24_update.4.patch': 'e3b30f4d723fb395e70a943314b1f43cf92c4135392319992ad276c55461692a'},
+    {'AmberTools-24_update.5.patch': 'd93f1e135304aae15df7a24f348cc75cf37b42210d049ecd830023f292f0a286'},
+    {'AmberTools-24_update.6.patch': '37398e3e056d51514e6a715b336cc9436181568ea284114fec4e5ffffd979ef0'},
+    {'AmberTools-24_update.7.patch': 'c2f03657e125043342ec0b8fda0e25d8aec611312938e03e1d656679b66d8e57'},
+    {'AmberTools-24_update.8.patch': '59f6cb4f1e26d2f3c6cddbfdeed887af8890b9499e8654c428e88a8f4e2df959'},
+    {'AmberTools-24_update.9.patch': '09a41e8f1905e994e01c6e46aa3803881e753b8201d4912329c647aa3327f09f'},
+    {'AmberTools-24_update.10.patch': 'b358c26d9a9b999638a4b8b673110188b7d0f3913051b33d714f6612d430acf0'},
+    {'Amber-24_update.1.patch': '16b5b8fe992130857ca351c9a0001f2952db16490140d7c72fc299ad3765de7f'},
+    {'Amber-24_update.2.patch': '4944a61989bf4f907d32240f704aa1766926338d39c56992f40ab0d22602beb1'},
+    {'Amber-24_update.3.patch': '37c7e3040fe5867caf4e1ae95d7473cc97e7c9cfa4a797f3235cde77288a9bd7'},
     {'AmberTools-20_cmake-locate-netcdf.patch': '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0'},
     {'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch':
      '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc'},

easybuild/easyconfigs/a/Amber/Amber-24_update.1.patch

@@ -0,0 +1,34 @@
+*******> update.1:
+
+Author: Daniel R. Roe 
+
+Date: June 3, 2024
+
+Programs: pmemd
+
+Description: Fix H-REMD hanging for PMEMD
+--------------------------------------------------------------------------------
+ src/pmemd/src/remd_exchg.F90 | 10 +++++++++-
+ 1 file changed, 9 insertions(+), 1 deletion(-)
+
+diff --git src/pmemd/src/remd_exchg.F90 src/pmemd/src/remd_exchg.F90
+index 7f9f1a5..853be79 100644
+--- src/pmemd/src/remd_exchg.F90
++++ src/pmemd/src/remd_exchg.F90
+@@ -1000,7 +1000,15 @@ subroutine hamiltonian_exchange(atm_cnt, my_atm_lst, crd, vel, frc, &
+     end if
+
+     silent=(neighbor_rank .lt. 0)
+-    if (silent) i_do_exchg = .false.
++  endif ! master
++
++  ! Make sure non-master processes know about silent
++  call mpi_bcast(silent, 1, mpi_logical, 0, pmemd_comm, err_code_mpi)
++  if (silent) i_do_exchg = .false.
++  call mpi_bcast(i_do_exchg, 1, mpi_logical, 0, pmemd_comm, err_code_mpi)
++
++  ! Back to master-only stuff
++  if (master) then
+
+     ! Exchange coordinates with your neighbor. crd_temp must be a backup since
+     ! the reciprocal space sum needs the global array to be updated with the new