Merge branch release-2018

Trivial clash in post-submit matrix, where a TODO resolved in 2018
release collided with a new TODO in master branch.

Change-Id: I07366ecb232c7341c8cf17674be3112f44fc9cdd

diff --git a/admin/builds/gromacs.py b/admin/builds/gromacs.py
index 598feb3113cd919497e3795301fc527fb67cc735..5cbb8f1cad3bc1aeabc0bdbb1daaa6c1b4f593df 100644 (file)
--- a/admin/builds/gromacs.py
+++ b/admin/builds/gromacs.py
@@ -44,6 +44,7 @@ extra_options = {
     'release-with-assert': Option.simple,
     'release-with-debug-info': Option.simple,
     'asan': Option.simple,
+    'tng' : Option.bool,
     'mkl': Option.simple,
     'fftpack': Option.simple,
     'double': Option.simple,
@@ -113,6 +114,8 @@ def do_build(context):
         cmake_opts['GMX_MPI'] = 'ON'
     if context.opts.openmp is False:
         cmake_opts['GMX_OPENMP'] = 'OFF'
+    if context.opts.tng is False:
+        cmake_opts['GMX_USE_TNG'] = 'OFF'
 
     if context.opts.mkl:
         cmake_opts['GMX_FFT_LIBRARY'] = 'mkl'

diff --git a/admin/builds/post-submit-matrix.txt b/admin/builds/post-submit-matrix.txt
index d7b36ecb6045094ef2b86d749fd063bc142daf2e..89ec64b31b41f05325251d18cfca4a15295940ef 100644 (file)
--- a/admin/builds/post-submit-matrix.txt
+++ b/admin/builds/post-submit-matrix.txt
@@ -28,7 +28,8 @@ gcc-7 mpi no-openmp fftpack mdrun-only
 icc-17 simd=avx_256 npme=1 nranks=2 no-openmp  double fftpack release
 
 # Test CUDA build on a slave with no CUDA devices
-gcc-4.9 gpu cuda-7.0 openmp release-with-assert
+# Test without TNG support
+gcc-4.9 gpu cuda-7.0 openmp no-tng release-with-assert
 
 # Test non-default GMX_PREFER_STATIC_LIBS behavior
 # TODO enable this
@@ -73,7 +74,7 @@ icc-18 msvc-2017 fftpack simd=avx2_256 release
 # Add SIMD + OpenMP + CUDA asan build
 # Add OpenMP + CUDA + device sharing TSAN build
 # Re-enable Phi build (FIXME: do we still care?)
-# Test without TNG support
+# Test without hwloc support
 # Test with NVML support
 # Test statically linked hwloc support (if/when it can work well)
 # Test 3D DD (2D is partially covered in regressiontests)

diff --git a/src/gromacs/fileio/tngio.cpp b/src/gromacs/fileio/tngio.cpp
index d9d67fa0a5f23a1f4fa3d6f01254cd9743123224..eb62e4c7563a8acf309309cf6bf9a3193301c2a3 100644 (file)
--- a/src/gromacs/fileio/tngio.cpp
+++ b/src/gromacs/fileio/tngio.cpp
@@ -65,6 +65,10 @@
 #include "gromacs/utility/sysinfo.h"
 #include "gromacs/utility/unique_cptr.h"
 
+#if !GMX_USE_TNG
+using tng_trajectory_t = void *;
+#endif
+
 /*! \brief Gromacs Wrapper around tng datatype
  *
  * This could in principle hold any GROMACS-specific requirements not yet
@@ -92,6 +96,7 @@ struct gmx_tng_trajectory
     int              lambdaOutputInterval; //!< Number of steps between the output of lambdas
 };
 
+#if GMX_USE_TNG
 static const char *modeToVerb(char mode)
 {
     const char *p;
@@ -111,6 +116,7 @@ static const char *modeToVerb(char mode)
     }
     return p;
 }
+#endif
 
 void gmx_tng_open(const char           *filename,
                   char                  mode,

diff --git a/src/gromacs/tools/dump.cpp b/src/gromacs/tools/dump.cpp
index 421b5da38a6b60f84bb4b2b1672008b5d4e761fa..8f92475880fb57d9b3ca14cdf2975d277af7c2b3 100644 (file)
--- a/src/gromacs/tools/dump.cpp
+++ b/src/gromacs/tools/dump.cpp
@@ -316,6 +316,8 @@ static void list_xtc(const char *fn)
     close_xtc(xd);
 }
 
+#if GMX_USE_TNG
+
 /*! \brief Callback used by list_tng_for_gmx_dump. */
 static void list_tng_inner(const char *fn,
                            gmx_bool    bFirstFrame,
@@ -348,9 +350,11 @@ static void list_tng_inner(const char *fn,
     pr_reals_of_dim(stdout, indent, block_name, values, n_atoms, n_values_per_frame);
 }
 
+#endif
+
 static void list_tng(const char gmx_unused *fn)
 {
-#ifdef GMX_USE_TNG
+#if GMX_USE_TNG
     gmx_tng_trajectory_t tng;
     int64_t              nframe = 0;
     int64_t              i, *block_ids = nullptr, step, ndatablocks;

diff --git a/src/gromacs/utility/binaryinformation.cpp b/src/gromacs/utility/binaryinformation.cpp
index ab64d393cf3af7728d958f69aff3fd432bbb659f..28c4f32e06cfb24318d26a0a6d030c03b7033e60 100644 (file)
--- a/src/gromacs/utility/binaryinformation.cpp
+++ b/src/gromacs/utility/binaryinformation.cpp
@@ -257,7 +257,7 @@ void gmx_print_version_info(gmx::TextWriter *writer)
     writer->writeLine(formatString("SIMD instructions:  %s", GMX_SIMD_STRING));
     writer->writeLine(formatString("FFT library:        %s", getFftDescriptionString()));
     writer->writeLine(formatString("RDTSCP usage:       %s", HAVE_RDTSCP ? "enabled" : "disabled"));
-#ifdef GMX_USE_TNG
+#if GMX_USE_TNG
     writer->writeLine("TNG support:        enabled");
 #else
     writer->writeLine("TNG support:        disabled");

diff --git a/src/programs/mdrun/tests/trajectory_writing.cpp b/src/programs/mdrun/tests/trajectory_writing.cpp
index 09666e4d7eba3a4e74d802daa492bfa7ac5650c4..9ca0526a6edba6b26277563c63fdcf3de2781bf2 100644 (file)
--- a/src/programs/mdrun/tests/trajectory_writing.cpp
+++ b/src/programs/mdrun/tests/trajectory_writing.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2018, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -55,7 +55,7 @@ namespace
 {
 
 // TODO configure these tests so they test all formats for mdrun trajectory writing
-#ifdef GMX_USE_TNG
+#if GMX_USE_TNG
 
 //! Test fixture for mdrun trajectory writing
 class TrajectoryWritingTest :