Merge pull request #1 from ccsb-scripps/boost_upgrade

Remove deprecated Boost features and improve compiling for newer Boost versions

.gitignore

@@ -0,0 +1 @@
+*.o

build/linux/debug/Makefile

@@ -1,8 +1,8 @@
-BASE=/usr/local
-BOOST_VERSION=1_41
+BASE=/usr
+BOOST_VERSION=
 BOOST_INCLUDE = $(BASE)/include
 C_PLATFORM=-static -pthread
-GPP=/usr/local/bin/g++
+GPP=/usr/bin/g++
 C_OPTIONS= -g
 BOOST_LIB_VERSION=
 

build/linux/release/Makefile

@@ -1,8 +1,8 @@
-BASE=/usr/local
-BOOST_VERSION=1_41
+BASE=/usr
+BOOST_VERSION=
 BOOST_INCLUDE = $(BASE)/include
 C_PLATFORM=-static -pthread
-GPP=/usr/local/bin/g++
+GPP=/usr/bin/g++
 C_OPTIONS= -O3 -DNDEBUG
 BOOST_LIB_VERSION=
 

build/mac/debug/Makefile

@@ -1,8 +1,8 @@
 BASE=/usr/local
-BOOST_VERSION=1_41
+BOOST_VERSION=1_71
 BOOST_INCLUDE = $(BASE)/include
-C_PLATFORM=-arch i386 -arch ppc -isysroot /Developer/SDKs/MacOSX10.5.sdk -mmacosx-version-min=10.4
-GPP=/usr/bin/g++
+C_PLATFORM=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
+GPP=clang++
 C_OPTIONS= -g
 BOOST_LIB_VERSION=
 

build/mac/release/Makefile

@@ -1,9 +1,9 @@
 BASE=/usr/local
-BOOST_VERSION=1_41
+BOOST_VERSION=1_71
 BOOST_INCLUDE = $(BASE)/include
-C_PLATFORM=-arch i386 -arch ppc -isysroot /Developer/SDKs/MacOSX10.5.sdk -mmacosx-version-min=10.4
-GPP=/usr/bin/g++
-C_OPTIONS= -O3 -DNDEBUG
+C_PLATFORM=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
+GPP=clang++
+C_OPTIONS= -O2 -DNDEBUG
 BOOST_LIB_VERSION=
 
 include ../../makefile_common

build/makefile_common

@@ -10,7 +10,16 @@ CC = ${GPP} ${C_PLATFORM} -ansi -Wno-long-long ${C_OPTIONS} $(INCFLAGS)
 
 LDFLAGS = -L$(BASE)/lib -L.
 
-LIBS = -l boost_system${BOOST_LIB_VERSION} -l boost_thread${BOOST_LIB_VERSION} -l boost_serialization${BOOST_LIB_VERSION} -l boost_filesystem${BOOST_LIB_VERSION} -l boost_program_options${BOOST_LIB_VERSION}#-l pthread
+# test if boost_thread-mt exists, this is
+# necessary as some versions of boost only
+# install libboost_thread-mt, but not
+# libboost_thread (e.g. macOS)
+$(shell echo "int main(){ return 0; }" > linktest.cpp)
+$(shell $(GPP) $(LDFLAGS) -l boost_thread-mt linktest.cpp -o linktest >/dev/null 2>&1)
+threadmt:=$(shell if [ -f ./linktest ]; then echo "-mt"; rm ./linktest; fi;)
+$(shell rm ./linktest.cpp)
+
+LIBS = -l boost_system${BOOST_LIB_VERSION} -l boost_thread${threadmt}${BOOST_LIB_VERSION} -l boost_serialization${BOOST_LIB_VERSION} -l boost_filesystem${BOOST_LIB_VERSION} -l boost_program_options${BOOST_LIB_VERSION}#-l pthread
 
 .SUFFIXES: .cpp .o
 

src/lib/array3d.h

@@ -1,77 +1,77 @@
-/*
-
- Copyright (c) 2006-2010, The Scripps Research Institute
-
- Licensed under the Apache License, Version 2.0 (the "License");
- you may not use this file except in compliance with the License.
- You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing, software
- distributed under the License is distributed on an "AS IS" BASIS,
- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- See the License for the specific language governing permissions and
- limitations under the License.
-
- Author: Dr. Oleg Trott <ot14@columbia.edu>, 
- The Olson Lab, 
- The Scripps Research Institute
-
-*/
-
-#ifndef VINA_ARRAY3D_H
-#define VINA_ARRAY3D_H
-
-#include <exception> // std::bad_alloc
-#include "common.h"
-
-inline sz checked_multiply(sz i, sz j) {
- if(i == 0 || j == 0) return 0;
- const sz tmp = i * j;
- if(tmp < i || tmp < j || tmp / i != j)
- throw std::bad_alloc(); // can't alloc if the size makes sz wrap around
- return tmp;
-}
-
-inline sz checked_multiply(sz i, sz j, sz k) {
- return checked_multiply(checked_multiply(i, j), k);
-}
-
-template<typename T>
-class array3d {
- sz m_i, m_j, m_k;
- std::vector<T> m_data;
- friend class boost::serialization::access;
- template<typename Archive>
- void serialize(Archive& ar, const unsigned version) {
- ar & m_i;
- ar & m_j;
- ar & m_k;
- ar & m_data;
- }
-public:
- array3d() : m_i(0), m_j(0), m_k(0) {}
- array3d(sz i, sz j, sz k) : m_i(i), m_j(j), m_k(k), m_data(checked_multiply(i, j, k)) {}
- sz dim0() const { return m_i; }
- sz dim1() const { return m_j; }
- sz dim2() const { return m_k; }
- sz dim(sz i) const {
- switch(i) {
- case 0: return m_i;
- case 1: return m_j;
- case 2: return m_k;
- default: assert(false); return 0; // to get rid of the warning
- }
- }
- void resize(sz i, sz j, sz k) { // data is essentially garbled
- m_i = i;
- m_j = j;
- m_k = k;
- m_data.resize(checked_multiply(i, j, k));
- }
- T& operator()(sz i, sz j, sz k) { return m_data[i + m_i*(j + m_j*k)]; }
- const T& operator()(sz i, sz j, sz k) const { return m_data[i + m_i*(j + m_j*k)]; }
-};
-
-#endif
+/*
+
+ Copyright (c) 2006-2010, The Scripps Research Institute
+
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+
+ Author: Dr. Oleg Trott <ot14@columbia.edu>, 
+ The Olson Lab, 
+ The Scripps Research Institute
+
+*/
+
+#ifndef VINA_ARRAY3D_H
+#define VINA_ARRAY3D_H
+
+#include <exception> // std::bad_alloc
+#include "common.h"
+
+inline sz checked_multiply(sz i, sz j) {
+ if(i == 0 || j == 0) return 0;
+ const sz tmp = i * j;
+ if(tmp < i || tmp < j || tmp / i != j)
+ throw std::bad_alloc(); // can't alloc if the size makes sz wrap around
+ return tmp;
+}
+
+inline sz checked_multiply(sz i, sz j, sz k) {
+ return checked_multiply(checked_multiply(i, j), k);
+}
+
+template<typename T>
+class array3d {
+ sz m_i, m_j, m_k;
+ std::vector<T> m_data;
+ friend class boost::serialization::access;
+ template<typename Archive>
+ void serialize(Archive& ar, const unsigned version) {
+ ar & m_i;
+ ar & m_j;
+ ar & m_k;
+ ar & m_data;
+ }
+public:
+ array3d() : m_i(0), m_j(0), m_k(0) {}
+ array3d(sz i, sz j, sz k) : m_i(i), m_j(j), m_k(k), m_data(checked_multiply(i, j, k)) {}
+ sz dim0() const { return m_i; }
+ sz dim1() const { return m_j; }
+ sz dim2() const { return m_k; }
+ sz dim(sz i) const {
+ switch(i) {
+ case 0: return m_i;
+ case 1: return m_j;
+ case 2: return m_k;
+ default: assert(false); return 0; // to get rid of the warning
+ }
+ }
+ void resize(sz i, sz j, sz k) { // data is essentially garbled
+ m_i = i;
+ m_j = j;
+ m_k = k;
+ m_data.resize(checked_multiply(i, j, k));
+ }
+ T& operator()(sz i, sz j, sz k) { return m_data[i + m_i*(j + m_j*k)]; }
+ const T& operator()(sz i, sz j, sz k) const { return m_data[i + m_i*(j + m_j*k)]; }
+};
+
+#endif

src/lib/atom.h

@@ -1,78 +1,78 @@
-/*
-
- Copyright (c) 2006-2010, The Scripps Research Institute
-
- Licensed under the Apache License, Version 2.0 (the "License");
- you may not use this file except in compliance with the License.
- You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing, software
- distributed under the License is distributed on an "AS IS" BASIS,
- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- See the License for the specific language governing permissions and
- limitations under the License.
-
- Author: Dr. Oleg Trott <ot14@columbia.edu>, 
- The Olson Lab, 
- The Scripps Research Institute
-
-*/
-
-#ifndef VINA_ATOM_H
-#define VINA_ATOM_H
-
-#include "atom_base.h"
-
-struct atom_index {
- sz i;
- bool in_grid;
- atom_index() : i(max_sz), in_grid(false) {}
- atom_index(sz i_, bool in_grid_) : i(i_), in_grid(in_grid_) {}
-private:
- friend class boost::serialization::access;
- template<class Archive> 
- void serialize(Archive& ar, const unsigned version) {
- ar & i;
- ar & in_grid;
- }
-};
-
-inline bool operator==(const atom_index& i, const atom_index& j) {
- return i.i == j.i && i.in_grid == j.in_grid;
-}
-
-struct bond {
- atom_index connected_atom_index;
- fl length;
- bool rotatable;
- bond() : length(0), rotatable(false) {}
- bond(const atom_index& connected_atom_index_, fl length_, bool rotatable_) : connected_atom_index(connected_atom_index_), length(length_), rotatable(rotatable_) {}
-private:
- friend class boost::serialization::access;
- template<class Archive> 
- void serialize(Archive& ar, const unsigned version) {
- ar & connected_atom_index;
- ar & length;
- ar & rotatable;
- }
-};
-
-struct atom : public atom_base {
- vec coords;
- std::vector<bond> bonds;
- atom() : coords(max_vec) {}
-private:
- friend class boost::serialization::access;
- template<class Archive> 
- void serialize(Archive& ar, const unsigned version) {
- ar & boost::serialization::base_object<atom_base>(*this);
- ar & coords;
- ar & bonds;
- }
-};
-
-typedef std::vector<atom> atomv;
-
-#endif
+/*
+
+ Copyright (c) 2006-2010, The Scripps Research Institute
+
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+
+ Author: Dr. Oleg Trott <ot14@columbia.edu>, 
+ The Olson Lab, 
+ The Scripps Research Institute
+
+*/
+
+#ifndef VINA_ATOM_H
+#define VINA_ATOM_H
+
+#include "atom_base.h"
+
+struct atom_index {
+ sz i;
+ bool in_grid;
+ atom_index() : i(max_sz), in_grid(false) {}
+ atom_index(sz i_, bool in_grid_) : i(i_), in_grid(in_grid_) {}
+private:
+ friend class boost::serialization::access;
+ template<class Archive> 
+ void serialize(Archive& ar, const unsigned version) {
+ ar & i;
+ ar & in_grid;
+ }
+};
+
+inline bool operator==(const atom_index& i, const atom_index& j) {
+ return i.i == j.i && i.in_grid == j.in_grid;
+}
+
+struct bond {
+ atom_index connected_atom_index;
+ fl length;
+ bool rotatable;
+ bond() : length(0), rotatable(false) {}
+ bond(const atom_index& connected_atom_index_, fl length_, bool rotatable_) : connected_atom_index(connected_atom_index_), length(length_), rotatable(rotatable_) {}
+private:
+ friend class boost::serialization::access;
+ template<class Archive> 
+ void serialize(Archive& ar, const unsigned version) {
+ ar & connected_atom_index;
+ ar & length;
+ ar & rotatable;
+ }
+};
+
+struct atom : public atom_base {
+ vec coords;
+ std::vector<bond> bonds;
+ atom() : coords(max_vec) {}
+private:
+ friend class boost::serialization::access;
+ template<class Archive> 
+ void serialize(Archive& ar, const unsigned version) {
+ ar & boost::serialization::base_object<atom_base>(*this);
+ ar & coords;
+ ar & bonds;
+ }
+};
+
+typedef std::vector<atom> atomv;
+
+#endif