Merge release-5-0 into master

Change-Id: I862e73932dea368b5bac883eb1bf5725314efd2d

diff --git a/cmake/gmxCFlags.cmake b/cmake/gmxCFlags.cmake
index c0eff548ba523da0122f679e4cfc7c064d125d58..f6056c376cab071f0e9c3f900b59fa4111e4f16e 100644 (file)
--- a/cmake/gmxCFlags.cmake
+++ b/cmake/gmxCFlags.cmake
@@ -140,14 +140,49 @@ MACRO(gmx_c_flags)
     if (CMAKE_C_COMPILER_ID MATCHES "Intel")
         if (NOT WIN32) 
             if(NOT GMX_OPENMP)
-                GMX_TEST_CFLAG(CFLAGS_PRAGMA "-wd161" GMXC_CFLAGS)
+                if(CMAKE_C_COMPILER_VERSION VERSION_GREATER 13.99.99)
+# 3180: unrecognized OpenMP #pragma
+                    GMX_TEST_CFLAG(CFLAGS_PRAGMA "-wd3180" GMXC_CFLAGS)
+                else()
+# 161: unrecognized #pragma
+                    GMX_TEST_CFLAG(CFLAGS_PRAGMA "-wd161" GMXC_CFLAGS)
+                endif()
             endif()
+# 111: statement is unreachable
+# 177: function ".." was declared but never referenced
+# 181: argument of type ".." is incompatible with format "..", expecting argument of type ".."
+# 193: zero used for undefined preprocessing identifier ".."
+# 271: trailing comma is nonstandard
+# 304: access control not specified ("public" by default)
+# 383: value copied to temporary, reference to temporary used
+# 424: extra ";" ignored
+# 444: destructor for base class ".." is not virtual
+# 522: function ".." redeclared "inline" after being called
+# 593: variable ".." was set but never used
+# 869: parameter ".." was never referenced
+# 981: operands are evaluated in unspecified order
+#1418: external function definition with no prior declaration
+#1419: external declaration in primary source file
+#1572: floating-point equality and inequality comparisons are unreliable
+#1599: declaration hides variable ".."
+#2259: non-pointer conversion from ".." to ".." may lose significant bits
+#2415: variable ".." of static storage duration was declared but never referenced
+#2547: ".." was specified as both a system and non-system include directory
+#2557: comparison between signed and unsigned operands
+#3280: declaration hides member ".."
+#3346: dynamic exception specifications are deprecated
             GMX_TEST_CFLAG(CFLAGS_WARN "-w3 -wd111 -wd177 -wd181 -wd193 -wd271 -wd304 -wd383 -wd424 -wd444 -wd522 -wd593 -wd869 -wd981 -wd1418 -wd1419 -wd1572 -wd1599 -wd2259 -wd2415 -wd2547 -wd2557 -wd3280 -wd3346" GMXC_CFLAGS)
             GMX_TEST_CFLAG(CFLAGS_STDGNU "-std=gnu99" GMXC_CFLAGS)
             GMX_TEST_CFLAG(CFLAGS_OPT "-ip -funroll-all-loops -alias-const -ansi-alias" GMXC_CFLAGS_RELEASE)
+            #documented to be default but not set for ICC15. Gives remarks that inlining is not possible because of max-size setting
+            GMX_TEST_CFLAG(CFLAGS_INLINE "-no-inline-max-size -no-inline-max-total-size" GMXC_CFLAGS)
         else()
             if(NOT GMX_OPENMP)
-                GMX_TEST_CFLAG(CFLAGS_PRAGMA "/wd161" GMXC_CFLAGS)
+                if(CMAKE_C_COMPILER_VERSION VERSION_GREATER 13.99.99)
+                    GMX_TEST_CFLAG(CFLAGS_PRAGMA "/wd3180" GMXC_CFLAGS)
+                else()
+                    GMX_TEST_CFLAG(CFLAGS_PRAGMA "/wd161" GMXC_CFLAGS)
+                endif()
             endif()
             GMX_TEST_CFLAG(CFLAGS_WARN "/W3 /wd111 /wd177 /wd181 /wd193 /wd271 /wd304 /wd383 /wd424 /wd444 /wd522 /wd593 /wd869 /wd981 /wd1418 /wd1419 /wd1572 /wd1599 /wd2259 /wd2415 /wd2547 /wd2557 /wd3280 /wd3346" GMXC_CFLAGS)
             GMX_TEST_CFLAG(CFLAGS_OPT "/Qip" GMXC_CFLAGS_RELEASE)
@@ -157,15 +192,27 @@ MACRO(gmx_c_flags)
     if (CMAKE_CXX_COMPILER_ID MATCHES "Intel")
         if (NOT WIN32) 
             if(NOT GMX_OPENMP)
-                GMX_TEST_CXXFLAG(CXXFLAGS_PRAGMA "-wd161" GMXC_CXXFLAGS)
+                if(CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 13.99.99)
+                    GMX_TEST_CXXFLAG(CXXFLAGS_PRAGMA "-wd3180" GMXC_CXXFLAGS)
+                else()
+                    GMX_TEST_CXXFLAG(CXXFLAGS_PRAGMA "-wd161" GMXC_CXXFLAGS)
+                endif()
             endif()
-            GMX_TEST_CXXFLAG(CXXFLAGS_WARN "-w3 -wd111 -wd177 -wd181 -wd193 -wd271 -wd304 -wd383 -wd424 -wd444 -wd522 -wd593 -wd869 -wd981 -wd1418 -wd1419 -wd1572 -wd1599 -wd2259 -wd2415 -wd2547 -wd2557 -wd3280 -wd3346 -wd1782" GMXC_CXXFLAGS)
+#All but the following warnings are identical for the C-compiler (see above)
+#1782: #pragma once is obsolete
+#2282: unrecognized GCC pragma
+            GMX_TEST_CXXFLAG(CXXFLAGS_WARN "-w3 -wd111 -wd177 -wd181 -wd193 -wd271 -wd304 -wd383 -wd424 -wd444 -wd522 -wd593 -wd869 -wd981 -wd1418 -wd1419 -wd1572 -wd1599 -wd2259 -wd2415 -wd2547 -wd2557 -wd3280 -wd3346 -wd1782 -wd2282" GMXC_CXXFLAGS)
             GMX_TEST_CXXFLAG(CXXFLAGS_OPT "-ip -funroll-all-loops -alias-const -ansi-alias" GMXC_CXXFLAGS_RELEASE)
+            GMX_TEST_CXXFLAG(CXXFLAGS_INLINE "-no-inline-max-size -no-inline-max-total-size" GMXC_CXXFLAGS)
         else()
             if(NOT GMX_OPENMP)
-                GMX_TEST_CXXFLAG(CXXFLAGS_PRAGMA "/wd161" GMXC_CXXFLAGS)
+                if(CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 13.99.99)
+                    GMX_TEST_CXXFLAG(CXXFLAGS_PRAGMA "/wd3180" GMXC_CFLAGS)
+                else()
+                    GMX_TEST_CXXFLAG(CXXFLAGS_PRAGMA "/wd161" GMXC_CXXFLAGS)
+                endif()
             endif()
-            GMX_TEST_CXXFLAG(CXXFLAGS_WARN "/W3 /wd111 /wd177 /wd181 /wd193 /wd271 /wd304 /wd383 /wd424 /wd444 /wd522 /wd593 /wd869 /wd981 /wd1418 /wd1419 /wd1572 /wd1599 /wd2259 /wd2415 /wd2547 /wd2557 /wd3280 /wd3346 /wd1782" GMXC_CXXFLAGS)
+            GMX_TEST_CXXFLAG(CXXFLAGS_WARN "/W3 /wd111 /wd177 /wd181 /wd193 /wd271 /wd304 /wd383 /wd424 /wd444 /wd522 /wd593 /wd869 /wd981 /wd1418 /wd1419 /wd1572 /wd1599 /wd2259 /wd2415 /wd2547 /wd2557 /wd3280 /wd3346 /wd1782 /wd2282" GMXC_CXXFLAGS)
             GMX_TEST_CXXFLAG(CXXFLAGS_OPT "/Qip" GMXC_CXXFLAGS_RELEASE)
         endif()
     endif()

diff --git a/cmake/legacy_and_external.supp b/cmake/legacy_and_external.supp
index dc893678343103c1b20e5cbd683f2a115cbe299e..082fcc14ae51c18e905299c884f0b73a6880a677 100644 (file)
--- a/cmake/legacy_and_external.supp
+++ b/cmake/legacy_and_external.supp
@@ -162,6 +162,14 @@
    fun:__vfprintf
 }
 
+{
+   printf
+   Memcheck:Leak
+   fun:malloc
+   ...
+   fun:vfprintf_l
+}
+
 {
    strtof
    Memcheck:Leak

diff --git a/docs/old-html/online/mdp.html b/docs/old-html/online/mdp.html
index 423c928bbed7f4357b5a1a6d38dcf7623b58e7a4..29bb1a5cc9965e7027a15897cb792b038b055fbc 100644 (file)
--- a/docs/old-html/online/mdp.html
+++ b/docs/old-html/online/mdp.html
@@ -136,7 +136,6 @@ fourier-nz               = 0
 pme-order                = 4
 ewald-rtol               = 1e-05
 epsilon-surface          = 0
-optimize-fft             = no
 
 ; OPTIONS FOR WEAK COUPLING ALGORITHMS = 
 ; Temperature coupling   = 

diff --git a/docs/old-html/online/mdp_opt.html b/docs/old-html/online/mdp_opt.html
index 8c34b3d2c5717dd8e6f20e8d51767ecb3b3b4c72..f0fa212a606c3e4f5963e0171440304271ac2aa9 100644 (file)
--- a/docs/old-html/online/mdp_opt.html
+++ b/docs/old-html/online/mdp_opt.html
@@ -25,7 +25,7 @@ IF YOU'RE NOT SURE ABOUT WHAT YOU'RE DOING, DON'T DO IT!
 <li><A HREF="#el"><b>electrostatics</b></A> (coulombtype, coulomb-modifier, rcoulomb-switch, rcoulomb, epsilon-r, epsilon-rf)
 <li><A HREF="#vdw"><b>VdW</b></A> (vdwtype, vdw-modifier, rvdw-switch, rvdw, DispCorr)
 <li><A HREF="#table"><b>tables</b></A> (table-extension, energygrp-table)
-<li><A HREF="#ewald"><b>Ewald</b></A> (fourierspacing, fourier-nx, fourier-ny, fourier-nz, pme-order, ewald-rtol, ewald-geometry, epsilon-surface, optimize-fft)
+<li><A HREF="#ewald"><b>Ewald</b></A> (fourierspacing, fourier-nx, fourier-ny, fourier-nz, pme-order, ewald-rtol, ewald-geometry, epsilon-surface)
 <li><A HREF="#tc"><b>Temperature coupling</b></A> (tcoupl, nsttcouple, tc-grps, tau-t, ref-t)
 <li><A HREF="#pc"><b>Pressure coupling</b></A> (pcoupl, pcoupltype,
   nstpcouple, tau-p, compressibility, ref-p, refcoord-scaling)
@@ -906,17 +906,6 @@ of the relative permittivity of the imaginary surface around your infinite syste
 careful - you shouldn't use this if you have free mobile charges in your system. 
 This value does not affect the slab 3DC variant of the long range corrections.</dd>
 
-
-<dt><b>optimize-fft:</b></dt>
-<dd><dl compact>
-<dt><b>no</b></dt>
-<dd>Don't calculate the optimal FFT plan for the grid at startup.</dd>
-<dt><b>yes</b></dt>
-<dd>Calculate the optimal FFT plan for the grid at startup. This saves a
-few percent for long simulations, but takes a couple of minutes
-at start.</dd>
-</dl></dd>
-
 </dl>
 
 <A NAME="tc"><br>
@@ -2137,7 +2126,6 @@ reals to your subroutine. Check the inputrec definition in
 <A HREF="#expanded">nst-transition-matrix</A><br>
 <A HREF="#nl">ns-type</A><br>
 <A HREF="#wall">nwall</A><br>
-<A HREF="#ewald">optimize-fft</A><br>
 <A HREF="#nmr2">orire</A><br>
 <A HREF="#nmr2">orire-fc</A><br>
 <A HREF="#nmr2">orire-tau</A><br>

diff --git a/src/external/boost/boost/exception/exception.hpp b/src/external/boost/boost/exception/exception.hpp
index 31d43178df6c32f44920674c567509833d01c5d6..98b6083120a08fa31817c717bb41b69f0667b0b5 100644 (file)
--- a/src/external/boost/boost/exception/exception.hpp
+++ b/src/external/boost/boost/exception/exception.hpp
@@ -5,6 +5,9 @@
 
 #ifndef UUID_274DA366004E11DCB1DDFE2E56D89593
 #define UUID_274DA366004E11DCB1DDFE2E56D89593
+#if defined(__ICC) && !defined(BOOST_EXCEPTION_ENABLE_WARNINGS)
+#pragma warning(disable:367) //GMX: For ICC15 "disable duplicate friend declaration" warning
+#endif
 #if (__GNUC__*100+__GNUC_MINOR__>301) && !defined(BOOST_EXCEPTION_ENABLE_WARNINGS)
 #pragma GCC system_header
 #endif

diff --git a/src/gromacs/analysisdata/tests/analysisdata.cpp b/src/gromacs/analysisdata/tests/analysisdata.cpp
index 7cdd8baffa67df33e607a06d0a96e06c14e94cd3..c1f94697bac778e339a42512283d33c70c010963 100644 (file)
--- a/src/gromacs/analysisdata/tests/analysisdata.cpp
+++ b/src/gromacs/analysisdata/tests/analysisdata.cpp
@@ -154,7 +154,7 @@ class SimpleInputData
     public:
         static const AnalysisDataTestInput &get()
         {
-#ifndef INTEL_STATIC_ANON_NAMESPACE_BUG
+#ifndef STATIC_ANON_NAMESPACE_BUG
             static SimpleInputData singleton;
             return singleton.data_;
 #else
@@ -181,7 +181,7 @@ class DataSetsInputData
     public:
         static const AnalysisDataTestInput &get()
         {
-#ifndef INTEL_STATIC_ANON_NAMESPACE_BUG
+#ifndef STATIC_ANON_NAMESPACE_BUG
             static DataSetsInputData singleton;
             return singleton.data_;
 #else
@@ -216,7 +216,7 @@ class MultipointInputData
     public:
         static const AnalysisDataTestInput &get()
         {
-#ifndef INTEL_STATIC_ANON_NAMESPACE_BUG
+#ifndef STATIC_ANON_NAMESPACE_BUG
             static MultipointInputData singleton;
             return singleton.data_;
 #else
@@ -253,7 +253,7 @@ class MultipointDataSetsInputData
     public:
         static const AnalysisDataTestInput &get()
         {
-#ifndef INTEL_STATIC_ANON_NAMESPACE_BUG
+#ifndef STATIC_ANON_NAMESPACE_BUG
             static MultipointDataSetsInputData singleton;
             return singleton.data_;
 #else

diff --git a/src/gromacs/analysisdata/tests/arraydata.cpp b/src/gromacs/analysisdata/tests/arraydata.cpp
index 56b73ecedfd6c48c7578e9c09e4beacdce48f22a..a1d2755bf48e0f57de17e8d7411f7d498f253d62 100644 (file)
--- a/src/gromacs/analysisdata/tests/arraydata.cpp
+++ b/src/gromacs/analysisdata/tests/arraydata.cpp
@@ -71,7 +71,7 @@ class SimpleInputData
     public:
         static const AnalysisDataTestInput &get()
         {
-#ifndef INTEL_STATIC_ANON_NAMESPACE_BUG
+#ifndef STATIC_ANON_NAMESPACE_BUG
             static SimpleInputData singleton;
             return singleton.data_;
 #else

diff --git a/src/gromacs/analysisdata/tests/average.cpp b/src/gromacs/analysisdata/tests/average.cpp
index cbfc91cd2aa5e8523104ade246b20d579889b1dd..cdeabbb77d0fa160f0761b1df16d4ba0e9b563b6 100644 (file)
--- a/src/gromacs/analysisdata/tests/average.cpp
+++ b/src/gromacs/analysisdata/tests/average.cpp
@@ -68,7 +68,7 @@ class SimpleInputData
     public:
         static const AnalysisDataTestInput &get()
         {
-#ifndef INTEL_STATIC_ANON_NAMESPACE_BUG
+#ifndef STATIC_ANON_NAMESPACE_BUG
             static SimpleInputData singleton;
             return singleton.data_;
 #else
@@ -95,7 +95,7 @@ class MultipointInputData
     public:
         static const AnalysisDataTestInput &get()
         {
-#ifndef INTEL_STATIC_ANON_NAMESPACE_BUG
+#ifndef STATIC_ANON_NAMESPACE_BUG
             static MultipointInputData singleton;
             return singleton.data_;
 #else
@@ -129,7 +129,7 @@ class MultiDataSetInputData
     public:
         static const AnalysisDataTestInput &get()
         {
-#ifndef INTEL_STATIC_ANON_NAMESPACE_BUG
+#ifndef STATIC_ANON_NAMESPACE_BUG
             static MultiDataSetInputData singleton;
             return singleton.data_;
 #else

diff --git a/src/gromacs/analysisdata/tests/datatest.h b/src/gromacs/analysisdata/tests/datatest.h
index e0ead05854fefac7035d5e10b518682a72ab6ec1..6d85dd6b05c080827daef2ca26cb912b77ab9b2b 100644 (file)
--- a/src/gromacs/analysisdata/tests/datatest.h
+++ b/src/gromacs/analysisdata/tests/datatest.h
@@ -54,8 +54,8 @@
 #include "testutils/refdata.h"
 
 // currently the bug manifests itself only in AbstractAnalysisData testing
-#if (defined __ICL && __ICL >= 1400) || (defined __ICC & __ICC >= 1400)
-#define INTEL_STATIC_ANON_NAMESPACE_BUG //see #1558 for details
+#if (defined __ICL && __ICL >= 1400) || (defined __ICC && __ICC >= 1400) || (defined __PATHSCALE__)
+#define STATIC_ANON_NAMESPACE_BUG //see #1558 for details
 #endif
 
 namespace gmx

diff --git a/src/gromacs/analysisdata/tests/histogram.cpp b/src/gromacs/analysisdata/tests/histogram.cpp
index 491568b49f84ef21bc5ce8924de779e728ef9272..f210b4b7adba43a839c4afec591959ef1063674f 100644 (file)
--- a/src/gromacs/analysisdata/tests/histogram.cpp
+++ b/src/gromacs/analysisdata/tests/histogram.cpp
@@ -160,7 +160,7 @@ class SimpleInputData
     public:
         static const AnalysisDataTestInput &get()
         {
-#ifndef INTEL_STATIC_ANON_NAMESPACE_BUG
+#ifndef STATIC_ANON_NAMESPACE_BUG
             static SimpleInputData singleton;
             return singleton.data_;
 #else
@@ -246,7 +246,7 @@ class WeightedSimpleInputData
     public:
         static const AnalysisDataTestInput &get()
         {
-#ifndef INTEL_STATIC_ANON_NAMESPACE_BUG
+#ifndef STATIC_ANON_NAMESPACE_BUG
             static WeightedSimpleInputData singleton;
             return singleton.data_;
 #else
@@ -283,7 +283,7 @@ class WeightedDataSetInputData
     public:
         static const AnalysisDataTestInput &get()
         {
-#ifndef INTEL_STATIC_ANON_NAMESPACE_BUG
+#ifndef STATIC_ANON_NAMESPACE_BUG
             static WeightedDataSetInputData singleton;
             return singleton.data_;
 #else
@@ -455,7 +455,7 @@ class AverageInputData
     public:
         static const AnalysisDataTestInput &get()
         {
-#ifndef INTEL_STATIC_ANON_NAMESPACE_BUG
+#ifndef STATIC_ANON_NAMESPACE_BUG
             static AverageInputData singleton;
             return singleton.data_;
 #else

diff --git a/src/gromacs/analysisdata/tests/lifetime.cpp b/src/gromacs/analysisdata/tests/lifetime.cpp
index 7364b1c7d587211a193a180d36b6429923a6cfb8..1549d2a89ad54ce65cfa3018c0e23ec2faaa9412 100644 (file)
--- a/src/gromacs/analysisdata/tests/lifetime.cpp
+++ b/src/gromacs/analysisdata/tests/lifetime.cpp
@@ -67,7 +67,7 @@ class SimpleInputData
     public:
         static const AnalysisDataTestInput &get()
         {
-#ifndef INTEL_STATIC_ANON_NAMESPACE_BUG
+#ifndef STATIC_ANON_NAMESPACE_BUG
             static SimpleInputData singleton;
             return singleton.data_;
 #else
@@ -94,7 +94,7 @@ class MultiDataSetInputData
     public:
         static const AnalysisDataTestInput &get()
         {
-#ifndef INTEL_STATIC_ANON_NAMESPACE_BUG
+#ifndef STATIC_ANON_NAMESPACE_BUG
             static MultiDataSetInputData singleton;
             return singleton.data_;
 #else