From: David van der Spoel Date: Wed, 17 Sep 2014 14:43:01 +0000 (+0200) Subject: Merge release-5-0 into master X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=18306d714b31a011860d27ea03a8d45db64476a0;hp=dfc8e355534ae3c2743ded2162d8fe57d4b503d7;p=alexxy%2Fgromacs.git Merge release-5-0 into master Change-Id: I862e73932dea368b5bac883eb1bf5725314efd2d --- diff --git a/cmake/gmxCFlags.cmake b/cmake/gmxCFlags.cmake index c0eff548ba..f6056c376c 100644 --- 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 dc89367834..082fcc14ae 100644 --- 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 423c928bbe..29bb1a5cc9 100644 --- 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 8c34b3d2c5..f0fa212a60 100644 --- 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!
  • electrostatics (coulombtype, coulomb-modifier, rcoulomb-switch, rcoulomb, epsilon-r, epsilon-rf)
  • VdW (vdwtype, vdw-modifier, rvdw-switch, rvdw, DispCorr)
  • tables (table-extension, energygrp-table) -
  • Ewald (fourierspacing, fourier-nx, fourier-ny, fourier-nz, pme-order, ewald-rtol, ewald-geometry, epsilon-surface, optimize-fft) +
  • Ewald (fourierspacing, fourier-nx, fourier-ny, fourier-nz, pme-order, ewald-rtol, ewald-geometry, epsilon-surface)
  • Temperature coupling (tcoupl, nsttcouple, tc-grps, tau-t, ref-t)
  • Pressure coupling (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. - -
    optimize-fft:
    -
    -
    no
    -
    Don't calculate the optimal FFT plan for the grid at startup.
    -
    yes
    -
    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.
    -
    -
    @@ -2137,7 +2126,6 @@ reals to your subroutine. Check the inputrec definition in     nst-transition-matrix
    ns-type
    nwall
    -optimize-fft
    orire
    orire-fc
    orire-tau
    diff --git a/src/external/boost/boost/exception/exception.hpp b/src/external/boost/boost/exception/exception.hpp index 31d43178df..98b6083120 100644 --- 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 7cdd8baffa..c1f94697ba 100644 --- 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 56b73ecedf..a1d2755bf4 100644 --- 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 cbfc91cd2a..cdeabbb77d 100644 --- 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 e0ead05854..6d85dd6b05 100644 --- 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 491568b49f..f210b4b7ad 100644 --- 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 7364b1c7d5..1549d2a89a 100644 --- 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