Bump to 2.13

1 files changed, 47 insertions, 72 deletions

diff --git a/namd.patch b/namd.patch
index 24ba5cb62fb3..6f45c68008a9 100644
--- a/namd.patch
+++ b/namd.patch
@@ -1,81 +1,38 @@
---- config	2016-10-20 23:50:56.000000000 +0300
-+++ config	2018-03-20 19:01:59.899252611 +0300
-@@ -400,43 +400,6 @@
-     goto syntax
-   endif
+--- Makefile	2018-11-09 23:14:44.000000000 +0300
++++ Makefile	2019-01-23 14:31:17.359911095 +0300
+@@ -671,7 +671,7 @@
+ 	# prevent gmake from deleting intermediate files
  
--  if ( $use_cuda || $use_mic ) then
+ $(INCDIR)/%.decl.h $(INCDIR)/%.def.h: $(MKINCDIR) $(SRCDIR)/%.ci
+-	cpp -E -P $(CIPPFLAGS) $(SRCDIR)/$*.ci > $(INCDIR)/$*.ci
++	cpp-7 -E -P $(CIPPFLAGS) $(SRCDIR)/$*.ci > $(INCDIR)/$*.ci
+ 	$(CHARMXI) $(INCDIR)/$*.ci
+ 	$(RM) $(INCDIR)/$*.ci
+ 	$(MOVE) $*.def.h $(INCDIR)
+--- Make.charm	2018-08-30 19:07:32.050220504 +0300
++++ Make.charm	2018-08-30 19:14:51.040637131 +0300
+@@ -1,6 +1,2 @@
+-# Set CHARMBASE to the top level charm directory.
+-# The config script will override this setting if there is a directory
+-# called charm-6.8.2 or charm in the NAMD base directory.
 -
--    if ( $?CHARM_ARCH ) then
--      set CHARM_ARCH_TEST = $CHARM_ARCH
--    else
--      set CHARM_ARCH_TEST = `awk '/^CHARMARCH =/ {print $3}' arch/$ARCH.arch`
--    endif
--
--    if ( $CHARM_ARCH_TEST =~ mpi-* ) then
--      set charm_arch_mpi = 1
--      if ( $CHARM_ARCH_TEST =~ *-win32* || $CHARM_ARCH_TEST =~ *-win64* ) then
--        set charm_arch_mpi = 0
--      endif
--    else
--      set charm_arch_mpi = 0
--    endif
--
--    if ( $CHARM_ARCH_TEST =~ *-smp* || $CHARM_ARCH_TEST =~ multicore-* ) then
--      set charm_arch_smp = 1
--    else
--      set charm_arch_smp = 0
--    endif
--
--    if ( $use_cuda ) set ERRTYPE = "CUDA"
--    if ( $use_mic ) set ERRTYPE = "MIC"
--
--    if ( $charm_arch_mpi || ! $charm_arch_smp ) then
--      echo ''
--      echo "ERROR: $ERRTYPE builds require non-MPI SMP or multicore Charm++ arch for reasonable performance."
--      echo ''
--      echo "Consider ibverbs-smp or verbs-smp (InfiniBand), gni-smp (Cray), or multicore (single node)."
--      echo ''
--      exit 1
--    endif
--
--  endif
--
-   if ( $use_python ) then
-     if ( ! $use_tcl ) then
-       echo ''
---- arch/Linux-x86_64-g++.arch	2015-09-18 23:58:43.000000000 +0300
-+++ arch/Linux-x86_64-g++.arch	2018-03-20 16:41:08.896644617 +0300
-@@ -1,8 +1,8 @@
- NAMD_ARCH = Linux-x86_64
--CHARMARCH = multicore-linux64
-+CHARMARCH = mpi-linux-x86_64
+-CHARMBASE = /Projects/namd2/charm-6.8.2
++CHARMBASE = ./charm-6.8.2
+
+--- arch/Linux-x86_64-g++.arch	2018-08-30 19:07:32.056887076 +0300
++++ arch/Linux-x86_64-g++.arch	2018-08-30 19:17:08.078690680 +0300
+@@ -2,7 +2,7 @@
+ CHARMARCH = multicore-linux64
  
- CXX = g++ -m64 -std=c++0x -O3
+-CXX = g++ -m64 -std=c++0x -O3
++CXX = g++-7 -m64 -std=c++0x -O3
 -CXXOPTS = -fexpensive-optimizations -ffast-math 
-+CXXOPTS = -fexpensive-optimizations -ffast-math -fPIC
- CC = gcc -m64 -O3
++CXXOPTS = -fexpensive-optimizations -ffast-math -fPIC 
+-CC = gcc -m64 -O3
++CC = gcc-7 -m64 -O3
 -COPTS = -fexpensive-optimizations -ffast-math
 +COPTS = -fexpensive-optimizations -ffast-math -fPIC
- 
---- arch/Linux-x86_64.cuda	2016-11-11 01:18:30.000000000 +0300
-+++ arch/Linux-x86_64.cuda	2018-03-20 18:16:33.861159104 +0300
-@@ -1,5 +1,5 @@
- 
--CUDADIR=/usr/local/encap/cuda-6.5
-+CUDADIR=/opt/cuda
- CUDAINCL=-I$(CUDADIR)/include
- CUBDIR=.rootdir/cub
- CUBINCL=-I$(CUBDIR)
-@@ -9,6 +9,5 @@
- CUDAFLAGS=-DNAMD_CUDA
- CUDAOBJS=$(CUDAOBJSRAWSTATIC)
- CUDA=$(CUDAFLAGS) -I. $(CUDAINCL) $(CUBINCL)
--CUDACC=$(CUDADIR)/bin/nvcc -O3 --maxrregcount 48 $(CUDAGENCODE) -Xcompiler "-m64" $(CUDA)
--CUDAGENCODE=-gencode arch=compute_30,code=sm_30 -gencode arch=compute_30,code=compute_30 -gencode arch=compute_35,code=sm_35 -gencode arch=compute_35,code=compute_35 -gencode arch=compute_50,code=sm_50 -gencode arch=compute_50,code=compute_50
--
-+CUDACC=$(CUDADIR)/bin/nvcc -O3 --maxrregcount 48 $(CUDAGENCODE) -Xcompiler "-m64" $(CUDA) --compiler-options -fPIC
-+CUDAGENCODE=-gencode arch=compute_30,code=sm_30 -gencode arch=compute_35,code=sm_35 -gencode arch=compute_37,code=sm_37 -gencode arch=compute_50,code=sm_50 -gencode arch=compute_52,code=sm_52 -gencode arch=compute_60,code=sm_60 -gencode arch=compute_61,code=sm_61 -gencode arch=compute_61,code=compute_61
+
 --- arch/Linux-x86_64.fftw3	2011-07-12 22:23:09.000000000 +0400
 +++ arch/Linux-x86_64.fftw3	2018-03-20 16:41:30.256474225 +0300
 @@ -1,5 +1,5 @@
@@ -97,3 +54,21 @@
  TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl -lpthread
  TCLFLAGS=-DNAMD_TCL
  TCL=$(TCLINCL) $(TCLFLAGS)
+--- charm-6.8.2/src/arch/common/cc-gcc.sh	2017-10-25 22:54:51.000000000 +0300
++++ charm-6.8.2/src/arch/common/cc-gcc.sh	2019-01-23 14:12:39.450351575 +0300
+@@ -1,9 +1,9 @@
+-CMK_CPP_CHARM='cpp -P'
+-CMK_CPP_C='gcc -E'
+-CMK_CC='gcc'
+-CMK_CXX='g++'
+-CMK_LD='gcc'
+-CMK_LDXX='g++'
++CMK_CPP_CHARM='cpp-7 -P'
++CMK_CPP_C='gcc-7 -E'
++CMK_CC='gcc-7'
++CMK_CXX='g++-7'
++CMK_LD='gcc-7'
++CMK_LDXX='g++-7'
+
+ CMK_LD_SHARED='-shared'
+ CMK_LD_LIBRARY_PATH="-Wl,-rpath,$CHARMLIBSO/"