From 7143160cd3d13026c7b10ec635d501cbd78e6e23 Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Mon, 29 Aug 2022 13:16:52 +0200
Subject: [PATCH 1/2] fix top level Makefile for AmberTools 21

---
 .../easyconfigs/a/AmberTools/AmberTools-21-intel-2021b.eb | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21-intel-2021b.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-21-intel-2021b.eb
index 2ccde888920..f7489ace676 100644
--- a/easybuild/easyconfigs/a/AmberTools/AmberTools-21-intel-2021b.eb
+++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-21-intel-2021b.eb
@@ -13,7 +13,7 @@ toolchainopts = {'usempi': True}
 
 # download requires registration, see http://ambermd.org/AmberTools17-get.html
 local_download_credentials = '?Name=Easybuild&Institution=Easybuild&City=Internet&State=Other&Country=Belgium'
-source_urls = ['https://ambermd.org/cgi-bin/AmberTools21-get.pl']
+source_urls = ['https://ambermd.org/cgi-bin/AmberTools%s-get.pl' % version]
 sources = [{
     'download_filename': local_download_credentials,
     'filename': SOURCE_TAR_BZ2,
@@ -22,6 +22,7 @@ patches = [
     'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch',
     'AmberTools-20_cmake-locate-netcdf.patch',
     'AmberTools-20_fix_xblas_missing_make_dependency.patch',
+    'AmberTools-21_dont_include_config.h_in_top_Makefile.patch',
 ]
 checksums = [
     'f55fa930598d5a8e9749e8a22d1f25cab7fcf911d98570e35365dd7f262aaafd',  # AmberTools-21.tar.bz2
@@ -30,6 +31,8 @@ checksums = [
     '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0',  # AmberTools-20_cmake-locate-netcdf.patch
     # AmberTools-20_fix_xblas_missing_make_dependency.patch
     'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65',
+    # AmberTools-21_dont_include_config.h_in_top_Makefile.patch
+    'b5a20a63904344fc3d1469841f0ea7d5ddaaa01462742bab958c3bba4a9b7ad9',
 ]
 
 builddependencies = [
@@ -52,7 +55,6 @@ dependencies = [
 prebuildopts = """sed -i 's/import sys/import sys; os.environ["LDSHARED"] = "icc -shared "/g' """
 prebuildopts += "%(builddir)s/AmberTools/src/pysander/setup.py && "
 
-# Tests use pmemd which is not part of AmberTools
-runtest = False
+runtest = True
 
 moduleclass = 'chem'

From 223a52a32c1c2a1b6aae6fd6a1d007f330a8e4e8 Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Thu, 1 Sep 2022 11:32:29 +0200
Subject: [PATCH 2/2] Add patches from AT21.12

---
 .../a/AmberTools/AmberTools-21-intel-2021b.eb | 31 +++++++++++++++++--
 1 file changed, 28 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21-intel-2021b.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-21-intel-2021b.eb
index f7489ace676..b149c772a4a 100644
--- a/easybuild/easyconfigs/a/AmberTools/AmberTools-21-intel-2021b.eb
+++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-21-intel-2021b.eb
@@ -19,18 +19,43 @@ sources = [{
     'filename': SOURCE_TAR_BZ2,
 }]
 patches = [
-    'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch',
     'AmberTools-20_cmake-locate-netcdf.patch',
+    'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch',
     'AmberTools-20_fix_xblas_missing_make_dependency.patch',
+    'AmberTools-21_CMake-FlexiBLAS.patch',
+    'AmberTools-21_fix_DGESVD_workspace_query.patch',
+    'AmberTools-21_fix_incorrect_dvout_call.patch',
+    'AmberTools-21_fix_incorrect_mexit_calls.patch',
+    'AmberTools-21_fix_more_blas_argument_problems.patch',
+    'AmberTools-21_fix_multiple_definition.patch',
+    'AmberTools-21_fix_potential_use_before_init.patch',
+    'AmberTools-21_fix_rism_argument_mismatch.patch',
+    'AmberTools-21_fix_xray_fftpack_arg_mismatch.patch',
+    'AmberTools-22_fix_test_missing_cuda_dir.patch',
     'AmberTools-21_dont_include_config.h_in_top_Makefile.patch',
 ]
 checksums = [
-    'f55fa930598d5a8e9749e8a22d1f25cab7fcf911d98570e35365dd7f262aaafd',  # AmberTools-21.tar.bz2
+    'f55fa930598d5a8e9749e8a22d1f25cab7fcf911d98570e35365dd7f262aaafd',  # AmberTools21.tar.bz2
+    '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0',  # AmberTools-20_cmake-locate-netcdf.patch
     # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch
     '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc',
-    '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0',  # AmberTools-20_cmake-locate-netcdf.patch
     # AmberTools-20_fix_xblas_missing_make_dependency.patch
     'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65',
+    '9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36',  # AmberTools-21_CMake-FlexiBLAS.patch
+    # AmberTools-21_fix_DGESVD_workspace_query.patch
+    '560c73e9d8bd159c609098c63a0256cdee78f49e524d06ea94d16d3146f69bcd',
+    '1054d4007f5c79126a41582e1e80514267cf406416ed6c471574cd708b16319b',  # AmberTools-21_fix_incorrect_dvout_call.patch
+    'd1de8c596119dcedbb809515816f0c98762306c469e9caf2c0b878d9b0a1095f',  # AmberTools-21_fix_incorrect_mexit_calls.patch
+    # AmberTools-21_fix_more_blas_argument_problems.patch
+    'c6279b57752239184b942d37f760749494ae0eff95236f3368c76ac0d2726a7c',
+    'ce30eeaba9feea53aa115e4b0dcc5be943b8a55abe322480c807ca7ea963d83b',  # AmberTools-21_fix_multiple_definition.patch
+    # AmberTools-21_fix_potential_use_before_init.patch
+    '377e645b5bd2c91ebb4d0b6fbca0407a94289e5ddc5b1e7ed0cb0b0724ad2139',
+    # AmberTools-21_fix_rism_argument_mismatch.patch
+    '14255e5739cec39303df570f06820c7532f7395e1b73b1e4104377984e2c9fc1',
+    # AmberTools-21_fix_xray_fftpack_arg_mismatch.patch
+    '99c954e693659efc2a1d121f91510f56408006f0751d91595f45a34b03364e2f',
+    'fb1ab74314d7816169bb9f3f527b78085654aae2825c52cebf50a5760401b737',  # AmberTools-22_fix_test_missing_cuda_dir.patch
     # AmberTools-21_dont_include_config.h_in_top_Makefile.patch
     'b5a20a63904344fc3d1469841f0ea7d5ddaaa01462742bab958c3bba4a9b7ad9',
 ]