/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
- * inclusion in the official distribution, but derived work must not
- * be called official GROMACS. Details are found in the README & COPYING
- * files - if they are missing, get the official version at www.gromacs.org.
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
- * For more info, check our website at http://www.gromacs.org
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
*
- * And Hey:
- * GROningen Mixture of Alchemy and Childrens' Stories
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "copyrite.h"
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/copyrite.h"
-#ifdef HAVE_CONFIG_H
#include "config.h"
-#endif
#include <stdio.h>
#include <stdlib.h>
#ifdef HAVE_LIBMKL
#include <mkl.h>
#endif
+#ifdef HAVE_EXTRAE
+#include <extrae_user_events.h>
+#endif
+#include <boost/version.hpp>
/* This file is completely threadsafe - keep it that way! */
-#include "gromacs/fileio/futil.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/random.h"
-#include "gromacs/legacyheaders/smalloc.h"
-#include "gromacs/legacyheaders/statutil.h"
-#include "gromacs/legacyheaders/strdb.h"
-#include "gromacs/legacyheaders/string2.h"
-#include "gromacs/legacyheaders/vec.h"
-
+#include "buildinfo.h"
#include "gromacs/fft/fft.h"
+#include "gromacs/fileio/strdb.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/random/random.h"
+#include "gromacs/utility/baseversion.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxassert.h"
-#include "gromacs/utility/programinfo.h"
-
-#include "buildinfo.h"
+#include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/smalloc.h"
static gmx_bool be_cool(void)
{
static void pukeit(const char *db, const char *defstring, char *retstring,
int retsize, int *cqnum)
{
- FILE *fp;
- char **help;
- int i, nhlp;
- int seed;
+ FILE *fp;
+ char **help;
+ int i, nhlp;
+ gmx_rng_t rng;
if (be_cool() && ((fp = low_libopen(db, FALSE)) != NULL))
{
nhlp = fget_lines(fp, &help);
/* for libraries we can use the low-level close routines */
- ffclose(fp);
- seed = time(NULL);
- *cqnum = static_cast<int>(nhlp*rando(&seed));
+ gmx_ffclose(fp);
+ rng = gmx_rng_init(gmx_rng_make_seed());
+ *cqnum = static_cast<int>(nhlp*gmx_rng_uniform_real(rng));
+ gmx_rng_destroy(rng);
if (strlen(help[*cqnum]) >= STRLEN)
{
help[*cqnum][STRLEN-1] = '\0';
static void printCopyright(FILE *fp)
{
+ static const char * const Contributors[] = {
+ "Emile Apol",
+ "Rossen Apostolov",
+ "Herman J.C. Berendsen",
+ "Par Bjelkmar",
+ "Aldert van Buuren",
+ "Rudi van Drunen",
+ "Anton Feenstra",
+ "Sebastian Fritsch",
+ "Gerrit Groenhof",
+ "Christoph Junghans",
+ "Peter Kasson",
+ "Carsten Kutzner",
+ "Per Larsson",
+ "Justin A. Lemkul",
+ "Magnus Lundborg",
+ "Pieter Meulenhoff",
+ "Erik Marklund",
+ "Teemu Murtola",
+ "Szilard Pall",
+ "Sander Pronk",
+ "Roland Schulz",
+ "Alexey Shvetsov",
+ "Michael Shirts",
+ "Alfons Sijbers",
+ "Peter Tieleman",
+ "Christian Wennberg",
+ "Maarten Wolf"
+ };
static const char * const CopyrightText[] = {
- "GROMACS is written by:",
- "Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,",
- "Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,",
- "Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,",
- "Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,",
- "Michael Shirts, Alfons Sijbers, Peter Tieleman,\n",
- "Berk Hess, David van der Spoel, and Erik Lindahl.\n",
"Copyright (c) 1991-2000, University of Groningen, The Netherlands.",
- "Copyright (c) 2001-2013, The GROMACS development team at",
- "Uppsala University & The Royal Institute of Technology, Sweden.",
+ "Copyright (c) 2001-2014, The GROMACS development team at",
+ "Uppsala University, Stockholm University and",
+ "the Royal Institute of Technology, Sweden.",
"check out http://www.gromacs.org for more information."
};
-
static const char * const LicenseText[] = {
"GROMACS is free software; you can redistribute it and/or modify it",
"under the terms of the GNU Lesser General Public License",
"of the License, or (at your option) any later version."
};
+#define NCONTRIBUTORS (int)asize(Contributors)
#define NCR (int)asize(CopyrightText)
+
// FAH has an exception permission from LGPL to allow digital signatures in Gromacs.
#ifdef GMX_FAHCORE
#define NLICENSE 0
#define NLICENSE (int)asize(LicenseText)
#endif
+ fprintf(fp, "GROMACS is written by:\n");
+ for (int i = 0; i < NCONTRIBUTORS; )
+ {
+ for (int j = 0; j < 4 && i < NCONTRIBUTORS; ++j, ++i)
+ {
+ fprintf(fp, "%-18s ", Contributors[i]);
+ }
+ fprintf(fp, "\n");
+ }
+ fprintf(fp, "and the project leaders:\n");
+ fprintf(fp, "Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n");
+ fprintf(fp, "\n");
for (int i = 0; i < NCR; ++i)
{
fprintf(fp, "%s\n", CopyrightText[i]);
"Garmay Yu, Shvetsov A, Karelov D, Lebedev D, Radulescu A, Petukhov M, Isaev-Ivanov V",
"Correlated motion of protein subdomains and large-scale conformational flexibility of RecA protein filament",
"Journal of Physics: Conference Series",
- 340, 2012, "012094" }
+ 340, 2012, "012094" },
+ { "Kutzner2011b",
+ "C. Kutzner, H. Grubmuller, B. L. de Groot, and U. Zachariae",
+ "Computational Electrophysiology: The Molecular Dynamics of Ion Channel Permeation and Selectivity in Atomistic Detail",
+ "Biophys. J.",
+ 101, 2011, "809-817"},
+ { "Lundborg2014",
+ "M. Lundborg, R. Apostolov, D. Spangberg, A. Gardenas, D. van der Spoel and E. Lindahl",
+ "An efficient and extensible format, library, and API for binary trajectory data from molecular simulations",
+ "J. Comput. Chem.",
+ 35, 2014, "260-269"},
+ { "Goga2012",
+ "N. Goga and A. J. Rzepiela and A. H. de Vries and S. J. Marrink and H. J. C. Berendsen",
+ "Efficient Algorithms for Langevin and DPD Dynamics",
+ "J. Chem. Theory Comput.",
+ 8, 2012, "3637--3649"}
};
#define NSTR (int)asize(citedb)
fflush(fp);
}
-#ifdef GMX_GIT_VERSION_INFO
-/* Version information generated at compile time. */
-#include "gromacs/utility/gitversion.h"
-#else
-/* Fall back to statically defined version. */
-static const char _gmx_ver_string[] = "VERSION " VERSION;
-#endif
-
const char *GromacsVersion()
{
- return _gmx_ver_string;
+ return gmx_version();
+}
+
+const char *ShortProgram(void)
+{
+ const char *programName = NULL;
+
+ try
+ {
+ // TODO: Use the display name once it doesn't break anything.
+ programName = gmx::getProgramContext().programName();
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+
+ return programName;
+}
+
+const char *Program(void)
+{
+ try
+ {
+ return gmx::getProgramContext().fullBinaryPath();
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
}
+
extern void gmx_print_version_info_gpu(FILE *fp);
static void gmx_print_version_info(FILE *fp)
{
- fprintf(fp, "Gromacs version: %s\n", _gmx_ver_string);
-#ifdef GMX_GIT_VERSION_INFO
- fprintf(fp, "GIT SHA1 hash: %s\n", _gmx_full_git_hash);
- /* Only print out the branch information if present.
- * The generating script checks whether the branch point actually
- * coincides with the hash reported above, and produces an empty string
- * in such cases. */
- if (_gmx_central_base_hash[0] != 0)
+ fprintf(fp, "Gromacs version: %s\n", gmx_version());
+ const char *const git_hash = gmx_version_git_full_hash();
+ if (git_hash[0] != '\0')
{
- fprintf(fp, "Branched from: %s\n", _gmx_central_base_hash);
+ fprintf(fp, "GIT SHA1 hash: %s\n", git_hash);
+ }
+ const char *const base_hash = gmx_version_git_central_base_hash();
+ if (base_hash[0] != '\0')
+ {
+ fprintf(fp, "Branched from: %s\n", base_hash);
}
-#endif
#ifdef GMX_DOUBLE
fprintf(fp, "Precision: double\n");
#else
fprintf(fp, "Precision: single\n");
#endif
- fprintf(fp, "Memory model: %lu bit\n", 8*sizeof(void *));
+ fprintf(fp, "Memory model: %u bit\n", (unsigned)(8*sizeof(void *)));
#ifdef GMX_THREAD_MPI
fprintf(fp, "MPI library: thread_mpi\n");
#define gmx_stringify2(x) #x
#define gmx_stringify(x) gmx_stringify2(x)
fprintf(fp, "invsqrt routine: %s\n", gmx_stringify(gmx_invsqrt(x)));
- fprintf(fp, "CPU acceleration: %s\n", GMX_CPU_ACCELERATION_STRING);
-
- fprintf(fp, "FFT library: %s\n", gmx_fft_get_version_info());
-#ifdef GMX_LARGEFILES
- fprintf(fp, "Large file support: enabled\n");
+#ifndef __MIC__
+ fprintf(fp, "SIMD instructions: %s\n", GMX_SIMD_STRING);
#else
- fprintf(fp, "Large file support: disabled\n");
+ fprintf(fp, "SIMD instructions: %s\n", "Intel MIC");
#endif
+
+ fprintf(fp, "FFT library: %s\n", gmx_fft_get_version_info());
#ifdef HAVE_RDTSCP
fprintf(fp, "RDTSCP usage: enabled\n");
#else
fprintf(fp, "RDTSCP usage: disabled\n");
#endif
+#ifdef GMX_CXX11
+ fprintf(fp, "C++11 compilation: enabled\n");
+#else
+ fprintf(fp, "C++11 compilation: disabled\n");
+#endif
+#ifdef GMX_USE_TNG
+ fprintf(fp, "TNG support: enabled\n");
+#else
+ fprintf(fp, "TNG support: disabled\n");
+#endif
+#ifdef HAVE_EXTRAE
+ unsigned major, minor, revision;
+ Extrae_get_version(&major, &minor, &revision);
+ fprintf(fp, "Tracing support: enabled. Using Extrae-%d.%d.%d\n", major, minor, revision);
+#else
+ fprintf(fp, "Tracing support: disabled\n");
+#endif
+
fprintf(fp, "Built on: %s\n", BUILD_TIME);
fprintf(fp, "Built by: %s\n", BUILD_USER);
fprintf(fp, "Linked with Intel MKL version %d.%d.%d.\n",
__INTEL_MKL__, __INTEL_MKL_MINOR__, __INTEL_MKL_UPDATE__);
#endif
+#ifdef GMX_EXTERNAL_BOOST
+ const bool bExternalBoost = true;
+#else
+ const bool bExternalBoost = false;
+#endif
+ fprintf(fp, "Boost version: %d.%d.%d%s\n", BOOST_VERSION / 100000,
+ BOOST_VERSION / 100 % 1000, BOOST_VERSION % 100,
+ bExternalBoost ? " (external)" : " (internal)");
#ifdef GMX_GPU
gmx_print_version_info_gpu(fp);
#endif
}
+#ifdef GMX_DOUBLE
+void gmx_is_double_precision()
+{
+ /* allow precision detection */
+}
+#else
+void gmx_is_single_precision()
+{
+ /* allow precision detection */
+}
+#endif
+
namespace gmx
{
{
}
-void printBinaryInformation(FILE *fp, const ProgramInfo &programInfo)
+void printBinaryInformation(FILE *fp,
+ const ProgramContextInterface &programContext)
{
- printBinaryInformation(fp, programInfo, BinaryInformationSettings());
+ printBinaryInformation(fp, programContext, BinaryInformationSettings());
}
-void printBinaryInformation(FILE *fp, const ProgramInfo &programInfo,
+void printBinaryInformation(FILE *fp,
+ const ProgramContextInterface &programContext,
const BinaryInformationSettings &settings)
{
const char *prefix = settings.prefix_;
#ifdef GMX_DOUBLE
precisionString = " (double precision)";
#endif
- const std::string &name = programInfo.displayName();
+ const char *const name = programContext.displayName();
if (settings.bGeneratedByHeader_)
{
fprintf(fp, "%sCreated by:%s\n", prefix, suffix);
// TODO: It would be nice to know here whether we are really running a
// Gromacs binary or some other binary that is calling Gromacs; we
// could then print "%s is part of GROMACS" or some alternative text.
- fprintf(fp, "%sGROMACS: %s, %s%s%s\n", prefix, name.c_str(),
- GromacsVersion(), precisionString, suffix);
+ fprintf(fp, "%sGROMACS: %s, %s%s%s\n", prefix, name,
+ gmx_version(), precisionString, suffix);
fprintf(fp, "\n");
printCopyright(fp);
fprintf(fp, "\n");
}
- fprintf(fp, "%sGROMACS: %s, %s%s%s\n", prefix, name.c_str(),
- GromacsVersion(), precisionString, suffix);
- fprintf(fp, "%sExecutable: %s%s\n", prefix,
- programInfo.fullBinaryPath().c_str(), suffix);
- fprintf(fp, "%sCommand line:%s\n%s %s%s\n",
- prefix, suffix, prefix, programInfo.commandLine().c_str(), suffix);
+ fprintf(fp, "%sGROMACS: %s, %s%s%s\n", prefix, name,
+ gmx_version(), precisionString, suffix);
+ const char *const binaryPath = programContext.fullBinaryPath();
+ if (binaryPath != NULL && binaryPath[0] != '\0')
+ {
+ fprintf(fp, "%sExecutable: %s%s\n", prefix, binaryPath, suffix);
+ }
+ const char *const libraryPath = programContext.defaultLibraryDataPath();
+ if (libraryPath != NULL && libraryPath[0] != '\0')
+ {
+ fprintf(fp, "%sLibrary dir: %s%s\n", prefix, libraryPath, suffix);
+ }
+ const char *const commandLine = programContext.commandLine();
+ if (commandLine != NULL && commandLine[0] != '\0')
+ {
+ fprintf(fp, "%sCommand line:%s\n%s %s%s\n",
+ prefix, suffix, prefix, commandLine, suffix);
+ }
if (settings.bExtendedInfo_)
{
GMX_RELEASE_ASSERT(prefix[0] == '\0' && suffix[0] == '\0',
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff