AmberTools 21

author: Viktor Drobot 2021-05-04 22:40:09 +0300
committer: Viktor Drobot 2021-05-04 22:40:09 +0300
commit: 0c68d5874f871f3bb7478d448cea91dd98f31bed (patch)
tree: 7ff80eea7d4c1f7a59f96a749172701c5de26d3f
parent: 7afcb31a74743069432e3ccdd969dfa875b52738 (diff)
download: aur-0c68d5874f871f3bb7478d448cea91dd98f31bed.tar.gz
7 files changed, 33 insertions, 91 deletions
diff --git a/.SRCINFO b/.SRCINFO
index 04e70a98a9d2..1c0dc412d6d3 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,41 +1,39 @@
 pkgbase = pmemd
 	pkgdesc = PMEMD module of AMBER software package
 	pkgver = 20
-	pkgrel = 6
+	pkgrel = 7
 	url = http://ambermd.org/
 	arch = x86_64
 	license = custom
-	makedepends = cmake>=3.8.1
+	makedepends = cmake>=3.10
 	makedepends = make
-	makedepends = gcc9
+	makedepends = gcc
 	makedepends = flex
 	makedepends = bison
 	makedepends = patch
 	makedepends = tcsh
 	makedepends = imake
-	makedepends = openmpi-gcc9
-	makedepends = cuda>=10.1
+	makedepends = openmpi
+	makedepends = cuda>=11.1
 	depends = ambertools
-	optdepends = openmpi-gcc9: MPI support
+	optdepends = openmpi: MPI support
 	optdepends = cuda: GPU acceleration support
 	optdepends = plumed: metadynamics support
 	optdepends = plumed-mpi: metadynamics support with MPI
 	optdepends = vmd: visualize trajectories
 	options = !buildflags
-	source = local://AmberTools20.tar.bz2
+	source = local://AmberTools21.tar.bz2
 	source = local://Amber20.tar.bz2
 	source = pmemd
 	source = pmemd.MPI
 	source = pmemd.cuda
 	source = pmemd.cuda.MPI
-	source = cuda-11.1.patch
-	sha256sums = b1e1f8f277c54e88abc9f590e788bbb2f7a49bcff5e8d8a6eacfaf332a4890f9
+	sha256sums = f55fa930598d5a8e9749e8a22d1f25cab7fcf911d98570e35365dd7f262aaafd
 	sha256sums = a4c53639441c8cc85adee397933d07856cc4a723c82c6bea585cd76c197ead75
-	sha256sums = 8bd1f818e0b55e866b906ecd497831f674b9a7b995c85899f6c4adc77a908f51
-	sha256sums = d454d03f3c88efe231a2282758c0e6b655396d00af40fd4b3ecfb1d8641009b7
-	sha256sums = 2a4a139923fcecbe319ae6728a860e8e64835c1dd2d9e626eb5125116a0d790c
-	sha256sums = df8b260dc4782a0fd0935ba1fdec8eb013b17c1082cfecff60e933a38a38d5a0
-	sha256sums = b666b2f186c5fd40b0be71a52b854060deea690205dbca24606c13c97cbf07de
+	sha256sums = 2c954683c1176f49f29c4899208ef3ae7ec4b050dd1f891c71998f4f27b1cd5a
+	sha256sums = 41f59ec0c13cdda7584f351d83d2238060cf22b95fb53ea476152664116bfcae
+	sha256sums = 11f0225dd52ebfa214cc88ac34a2e037924551e2c1f715876b167e2782c187d8
+	sha256sums = 8cbdffefa5ac731283d10d9b1daa32d2e20ffe4c5aec34525042c36f664cf766
 
 pkgname = pmemd
 
diff --git a/PKGBUILD b/PKGBUILD
index ca9fc6a30fb9..fcef7f94bc72 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -2,16 +2,15 @@
 
 pkgname=pmemd
 pkgver=20
-_toolsver=20
-_gccver=9.3.0
-pkgrel=6
+_toolsver=21
+pkgrel=7
 pkgdesc="PMEMD module of AMBER software package"
 url="http://ambermd.org/"
 license=(custom)
 arch=(x86_64)
 depends=(ambertools)
-makedepends=('cmake>=3.8.1' make gcc9 flex bison patch tcsh imake openmpi-gcc9 'cuda>=10.1')
-optdepends=('openmpi-gcc9: MPI support'
+makedepends=('cmake>=3.10' make gcc flex bison patch tcsh imake openmpi 'cuda>=11.1')
+optdepends=('openmpi: MPI support'
             'cuda: GPU acceleration support'
             'plumed: metadynamics support'
             'plumed-mpi: metadynamics support with MPI'
@@ -25,22 +24,19 @@ source=("local://AmberTools${_toolsver}.tar.bz2"
         "pmemd"
         "pmemd.MPI"
         "pmemd.cuda"
-        "pmemd.cuda.MPI"
-        "cuda-11.1.patch")
-sha256sums=('b1e1f8f277c54e88abc9f590e788bbb2f7a49bcff5e8d8a6eacfaf332a4890f9'
+        "pmemd.cuda.MPI")
+sha256sums=('f55fa930598d5a8e9749e8a22d1f25cab7fcf911d98570e35365dd7f262aaafd'
             'a4c53639441c8cc85adee397933d07856cc4a723c82c6bea585cd76c197ead75'
-            '8bd1f818e0b55e866b906ecd497831f674b9a7b995c85899f6c4adc77a908f51'
-            'd454d03f3c88efe231a2282758c0e6b655396d00af40fd4b3ecfb1d8641009b7'
-            '2a4a139923fcecbe319ae6728a860e8e64835c1dd2d9e626eb5125116a0d790c'
-            'df8b260dc4782a0fd0935ba1fdec8eb013b17c1082cfecff60e933a38a38d5a0'
-            'b666b2f186c5fd40b0be71a52b854060deea690205dbca24606c13c97cbf07de')
+            '2c954683c1176f49f29c4899208ef3ae7ec4b050dd1f891c71998f4f27b1cd5a'
+            '41f59ec0c13cdda7584f351d83d2238060cf22b95fb53ea476152664116bfcae'
+            '11f0225dd52ebfa214cc88ac34a2e037924551e2c1f715876b167e2782c187d8'
+            '8cbdffefa5ac731283d10d9b1daa32d2e20ffe4c5aec34525042c36f664cf766')
 
 prepare() {
   cd ${srcdir}/amber${pkgver}_src
 
+  # apply updates manually
   ./update_amber --update
-
-  patch -Np0 -i "${srcdir}/cuda-11.1.patch"
 }
 
 build() {
@@ -48,10 +44,10 @@ build() {
 
   export AMBER_PREFIX="${srcdir}"
 
-  CC=gcc-9 CXX=g++-9 FC=gfortran-9 cmake $AMBER_PREFIX/amber${pkgver}_src \
+  cmake $AMBER_PREFIX/amber${pkgver}_src \
       -DCMAKE_INSTALL_PREFIX=/opt/amber \
       -DCHECK_UPDATES=FALSE \
-      -DCOMPILER=MANUAL  \
+      -DCOMPILER=GNU  \
       -DMPI=TRUE -DCUDA=TRUE \
       -DOPENMP=TRUE \
       -DINSTALL_TESTS=FALSE \
diff --git a/cuda-11.1.patch b/cuda-11.1.patch
deleted file mode 100644
index c5f68a5719ab..000000000000
--- a/cuda-11.1.patch
+++ /dev/null
@@ -1,52 +0,0 @@
---- cmake/CudaConfig.cmake	2020-10-16 14:43:24.152111622 +0300
-+++ cmake/CudaConfig.cmake	2020-10-16 14:56:02.361337230 +0300
-@@ -17,12 +17,12 @@
- 	
- 	if(CUDA)
- 	
- 		set(CUDA_HOST_COMPILER ${CMAKE_CXX_COMPILER})
- 
--		#Note at present we do not include SM3.5 or SM3.7 since they sometimes show performance
--		#regressions over just using SM3.0.
-+        #SM8.6  -- not currently used, but should be tested on Cuda 11.1
-+        set(SM86FLAGS -gencode arch=compute_86,code=sm_86)
-         #SM8.0 = A100
-         set(SM80FLAGS -gencode arch=compute_80,code=sm_80)
-         #SM7.5 = RTX20xx, RTX Titan, T4 and Quadro RTX
- 		set(SM75FLAGS -gencode arch=compute_60,code=sm_75)        
- 		#SM7.0 = V100 and Volta Geforce / GTX Ampere?
-@@ -37,11 +37,11 @@
- 		set(SM53FLAGS -gencode arch=compute_53,code=sm_53)
- 		#SM5.2 = GM200 = GTX-Titan-X, M6000 etc.
- 		set(SM52FLAGS -gencode arch=compute_52,code=sm_52)
- 		#SM5.0 = GM204 = GTX980, 970 etc
- 		set(SM50FLAGS -gencode arch=compute_50,code=sm_50)
--		#SM3.7 = GK210 = K80
-+		#SM3.7 = GK210 = K80  -- not currently used, since SM3.0 may be better
- 		set(SM37FLAGS -gencode arch=compute_37,code=sm_37)
- 		#SM3.5 = GK110 + 110B = K20, K20X, K40, GTX780, GTX-Titan, GTX-Titan-Black, GTX-Titan-Z
- 		set(SM35FLAGS -gencode arch=compute_35,code=sm_35)
- 		#SM3.0 = GK104 = K10, GTX680, 690 etc.
- 		set(SM30FLAGS -gencode arch=compute_30,code=sm_30)
-@@ -67,13 +67,19 @@
- 		elseif(${CUDA_VERSION} VERSION_EQUAL 11.0)
-                         # Implement the standard compilation rather than a warp-synchronous one, which is deprecated as of CUDA 11
- 		        set(SM70FLAGS -gencode arch=compute_70,code=sm_70)
- 			set(SM75FLAGS -gencode arch=compute_75,code=sm_75)
-             message(STATUS "Configuring for SM3.5, SM5.0, SM5.2, SM5.3, SM6.0, SM6.1, SM7.0, SM7.5 and SM8.0")
--            list(APPEND CUDA_NVCC_FLAGS ${SM35FLAGS} ${SM50FLAGS} ${SM52FLAGS} ${SM53FLAGS} ${SM60FLAGS} ${SM61FLAGS} ${SM70FLAGS} ${SM75FLAGS} ${SM80FLAGS} -Wno-deprecated-gpu-targets -Wno-deprecated-declarations)                                      
-+            list(APPEND CUDA_NVCC_FLAGS ${SM35FLAGS} ${SM50FLAGS} ${SM52FLAGS} ${SM53FLAGS} ${SM60FLAGS} ${SM61FLAGS} ${SM70FLAGS} ${SM75FLAGS} ${SM80FLAGS} -Wno-deprecated-gpu-targets -Wno-deprecated-declarations)
-+		elseif(${CUDA_VERSION} VERSION_EQUAL 11.1)
-+                        # Implement the standard compilation rather than a warp-synchronous one, which is deprecated as of CUDA 11
-+		        set(SM70FLAGS -gencode arch=compute_70,code=sm_70)
-+			set(SM75FLAGS -gencode arch=compute_75,code=sm_75)
-+            message(STATUS "Configuring for SM3.5, SM5.0, SM5.2, SM5.3, SM6.0, SM6.1, SM7.0, SM7.5 and SM8.6")
-+            list(APPEND CUDA_NVCC_FLAGS ${SM35FLAGS} ${SM50FLAGS} ${SM52FLAGS} ${SM53FLAGS} ${SM60FLAGS} ${SM61FLAGS} ${SM70FLAGS} ${SM75FLAGS} ${SM80FLAGS} -Wno-deprecated-gpu-targets -Wno-deprecated-declarations)
- 		else()
--			message(FATAL_ERROR "Error: Unsupported CUDA version. AMBER requires CUDA version >= 7.5 and <= 11.0.
-+			message(FATAL_ERROR "Error: Unsupported CUDA version. AMBER requires CUDA version >= 7.5 and <= 11.1.
- 				Please upgrade your CUDA installation or disable building with CUDA.")
- 		endif()
- 						
- 		set(CUDA_PROPAGATE_HOST_FLAGS FALSE)
- 				
diff --git a/pmemd b/pmemd
index 87c6cadbdc52..c56ae1316def 100755
--- a/pmemd
+++ b/pmemd
@@ -1,7 +1,7 @@
 #!/usr/bin/bash
 
-export _gccver=9.3.0
-export LD_LIBRARY_PATH="/usr/lib/gcc/x86_64-pc-linux-gnu/${_gccver}:$LD_LIBRARY_PATH"
+#export _gccver=10.2.0
+#export LD_LIBRARY_PATH="/usr/lib/gcc/x86_64-pc-linux-gnu/${_gccver}:$LD_LIBRARY_PATH"
 /opt/amber/bin/pmemd "$@"
 
 exit 0
diff --git a/pmemd.MPI b/pmemd.MPI
index 94a48c129988..7b4b8d3072c9 100755
--- a/pmemd.MPI
+++ b/pmemd.MPI
@@ -1,7 +1,7 @@
 #!/usr/bin/bash
 
-export _gccver=9.3.0
-export LD_LIBRARY_PATH="/usr/lib/gcc/x86_64-pc-linux-gnu/${_gccver}:$LD_LIBRARY_PATH"
+#export _gccver=10.2.0
+#export LD_LIBRARY_PATH="/usr/lib/gcc/x86_64-pc-linux-gnu/${_gccver}:$LD_LIBRARY_PATH"
 /opt/amber/bin/pmemd.MPI "$@"
 
 exit 0
diff --git a/pmemd.cuda b/pmemd.cuda
index 193bcb025277..2add47b64ba2 100755
--- a/pmemd.cuda
+++ b/pmemd.cuda
@@ -1,7 +1,7 @@
 #!/usr/bin/bash
 
-export _gccver=9.3.0
-export LD_LIBRARY_PATH="/usr/lib/gcc/x86_64-pc-linux-gnu/${_gccver}:$LD_LIBRARY_PATH"
+#export _gccver=10.2.0
+#export LD_LIBRARY_PATH="/usr/lib/gcc/x86_64-pc-linux-gnu/${_gccver}:$LD_LIBRARY_PATH"
 /opt/amber/bin/pmemd.cuda_SPFP "$@"
 
 exit 0
diff --git a/pmemd.cuda.MPI b/pmemd.cuda.MPI
index 042e7f27da7d..94721a91f55f 100755
--- a/pmemd.cuda.MPI
+++ b/pmemd.cuda.MPI
@@ -1,7 +1,7 @@
 #!/usr/bin/bash
 
-export _gccver=9.3.0
-export LD_LIBRARY_PATH="/usr/lib/gcc/x86_64-pc-linux-gnu/${_gccver}:$LD_LIBRARY_PATH"
+#export _gccver=10.2.0
+#export LD_LIBRARY_PATH="/usr/lib/gcc/x86_64-pc-linux-gnu/${_gccver}:$LD_LIBRARY_PATH"
 /opt/amber/bin/pmemd.cuda_SPFP.MPI "$@"
 
 exit 0
author	Viktor Drobot	2021-05-04 22:40:09 +0300
committer	Viktor Drobot	2021-05-04 22:40:09 +0300
commit	0c68d5874f871f3bb7478d448cea91dd98f31bed (patch)
tree	7ff80eea7d4c1f7a59f96a749172701c5de26d3f
parent	7afcb31a74743069432e3ccdd969dfa875b52738 (diff)
download	aur-0c68d5874f871f3bb7478d448cea91dd98f31bed.tar.gz