3 * This source code is part of
7 * GROningen MAchine for Chemical Simulations
10 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
11 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
12 * Copyright (c) 2001-2004, The GROMACS development team,
13 * check out http://www.gromacs.org for more information.
15 * This program is free software; you can redistribute it and/or
16 * modify it under the terms of the GNU General Public License
17 * as published by the Free Software Foundation; either version 2
18 * of the License, or (at your option) any later version.
20 * If you want to redistribute modifications, please consider that
21 * scientific software is very special. Version control is crucial -
22 * bugs must be traceable. We will be happy to consider code for
23 * inclusion in the official distribution, but derived work must not
24 * be called official GROMACS. Details are found in the README & COPYING
25 * files - if they are missing, get the official version at www.gromacs.org.
27 * To help us fund GROMACS development, we humbly ask that you cite
28 * the papers on the package - you can find them in the top README file.
30 * For more info, check our website at http://www.gromacs.org
33 * GROningen Mixture of Alchemy and Childrens' Stories
40 #include <thread_mpi.h>
48 #include <cuda_runtime_api.h>
54 /* This file is completely threadsafe - keep it that way! */
69 #include "buildinfo.h"
70 #include "gmx_cpuid.h"
72 static void pr_two(FILE *out,int c,int i)
75 fprintf(out,"%c0%1d",c,i);
77 fprintf(out,"%c%2d",c,i);
80 void pr_difftime(FILE *out,double dt)
82 int ndays,nhours,nmins,nsecs;
83 gmx_bool bPrint,bPrinted;
86 dt = dt-24*3600*ndays;
95 fprintf(out,"%d",ndays);
96 bPrint=bPrint || (nhours > 0);
99 pr_two(out,'d',nhours);
101 fprintf(out,"%d",nhours);
103 bPrinted=bPrinted || bPrint;
104 bPrint=bPrint || (nmins > 0);
107 pr_two(out,'h',nmins);
109 fprintf(out,"%d",nmins);
111 bPrinted=bPrinted || bPrint;
113 pr_two(out,':',nsecs);
115 fprintf(out,"%ds",nsecs);
120 gmx_bool be_cool(void)
122 /* Yes, it is bad to check the environment variable every call,
123 * but we dont call this routine often, and it avoids using
124 * a mutex for locking the variable...
130 return (getenv("GMX_NO_QUOTES") == NULL);
134 void space(FILE *out, int n)
136 fprintf(out,"%*s",n,"");
148 static void sp_print(FILE *out,const char *s)
153 space(out,(80-slen)/2);
154 fprintf(out,"%s\n",s);
157 static void ster_print(FILE *out,const char *s)
162 snprintf(buf,128,":-) %s (-:",s);
164 space(out,(80-slen)/2);
165 fprintf(out,"%s\n",buf);
169 static void pukeit(const char *db,const char *defstring, char *retstring,
170 int retsize, int *cqnum)
177 if (be_cool() && ((fp = low_libopen(db,FALSE)) != NULL)) {
178 nhlp=fget_lines(fp,&help);
179 /* for libraries we can use the low-level close routines */
182 *cqnum=nhlp*rando(&seed);
183 if (strlen(help[*cqnum]) >= STRLEN)
184 help[*cqnum][STRLEN-1] = '\0';
185 strncpy(retstring,help[*cqnum],retsize);
187 for(i=0; (i<nhlp); i++)
192 strncpy(retstring,defstring,retsize);
195 void bromacs(char *retstring, int retsize)
199 pukeit("bromacs.dat",
200 "Groningen Machine for Chemical Simulation",
201 retstring,retsize,&dum);
204 void cool_quote(char *retstring, int retsize, int *cqnum)
215 /* protect audience from explicit lyrics */
216 snew(tmpstr,retsize+1);
217 pukeit("gurgle.dat","Thanx for Using GROMACS - Have a Nice Day",
220 if ((ptr = strchr(tmpstr,'_')) != NULL) {
223 sprintf(retstring,"\"%s\" %s",tmpstr,ptr);
226 strcpy(retstring,tmpstr);
231 void CopyRight(FILE *out,const char *szProgram)
233 /* Dont change szProgram arbitrarily - it must be argv[0], i.e. the
234 * name of a file. Otherwise, we won't be able to find the library dir.
236 #define NCR (int)asize(CopyrightText)
238 #define NGPL 0 /*FAH has an exception permission from GPL to allow digital signatures in Gromacs*/
240 #define NGPL (int)asize(GPLText)
243 char buf[256],tmpstr[1024];
247 set_program_name("Gromacs");
249 set_program_name(szProgram);
252 ster_print(out,"G R O M A C S");
255 bromacs(tmpstr,1023);
256 sp_print(out,tmpstr);
259 ster_print(out,GromacsVersion());
262 /* fprintf(out,"\n");*/
264 /* sp_print(out,"PLEASE NOTE: THIS IS A BETA VERSION\n");
266 fprintf(out,"\n"); */
268 for(i=0; (i<NCR); i++)
269 sp_print(out,CopyrightText[i]);
270 for(i=0; (i<NGPL); i++)
271 sp_print(out,GPLText[i]);
275 snprintf(buf,256,"%s",Program());
277 strcat(buf," (double precision)");
289 /* protect the audience from suggestive discussions */
290 cool_quote(cq,1023,&cqnum);
293 fprintf(fp,"\ngcq#%d: %s\n\n",cqnum,cq);
295 fprintf(fp,"\n%s\n\n",cq);
307 void please_cite(FILE *fp,const char *key)
309 static const t_citerec citedb[] = {
311 "M. P. Allen and D. J. Tildesley",
312 "Computer simulation of liquids",
313 "Oxford Science Publications",
316 "H. J. C. Berendsen, D. van der Spoel and R. van Drunen",
317 "GROMACS: A message-passing parallel molecular dynamics implementation",
321 "H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak",
322 "Molecular dynamics with coupling to an external bath",
324 81, 1984, "3684-3690" },
326 "J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen",
327 "Numerical Integration of the Cartesian Equations of Motion of a System with Constraints; Molecular Dynamics of n-Alkanes",
329 23, 1977, "327-341" },
331 "S. Miyamoto and P. A. Kollman",
332 "SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid Water Models",
334 13, 1992, "952-962" },
336 "D. T. Cromer & J. B. Mann",
337 "X-ray scattering factors computed from numerical Hartree-Fock wave functions",
341 "E. Barth and K. Kuczera and B. Leimkuhler and R. D. Skeel",
342 "Algorithms for Constrained Molecular Dynamics",
344 16, 1995, "1192-1209" },
346 "U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen ",
347 "A smooth particle mesh Ewald method",
349 103, 1995, "8577-8592" },
351 "A. E. Torda and R. M. Scheek and W. F. van Gunsteren",
352 "Time-dependent distance restraints in molecular dynamics simulations",
354 157, 1989, "289-294" },
356 "I. G. Tironi and R. Sperb and P. E. Smith and W. F. van Gunsteren",
357 "Generalized reaction field method for molecular dynamics simulations",
359 102, 1995, "5451-5459" },
361 "B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije",
362 "LINCS: A Linear Constraint Solver for molecular simulations",
364 18, 1997, "1463-1472" },
367 "P-LINCS: A Parallel Linear Constraint Solver for molecular simulation",
368 "J. Chem. Theory Comput.",
369 4, 2008, "116-122" },
371 "B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl",
372 "GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation",
373 "J. Chem. Theory Comput.",
374 4, 2008, "435-447" },
376 "J. S. Hub, B. L. de Groot and D. van der Spoel",
377 "g_wham - A free weighted histogram analysis implementation including robust error and autocorrelation estimates",
378 "J. Chem. Theory Comput.",
379 6, 2010, "3713-3720"},
381 "Y. In-Chul and M. L. Berkowitz",
382 "Ewald summation for systems with slab geometry",
384 111, 1999, "3155-3162" },
386 "B. L. de Groot and D. M. F. van Aalten and R. M. Scheek and A. Amadei and G. Vriend and H. J. C. Berendsen",
387 "Prediction of Protein Conformational Freedom From Distance Constrains",
389 29, 1997, "240-251" },
391 "D. van der Spoel and P. J. van Maaren and H. J. C. Berendsen",
392 "A systematic study of water models for molecular simulation. Derivation of models optimized for use with a reaction-field.",
394 108, 1998, "10220-10230" },
396 "D. S. Wishart and A. M. Nip",
397 "Protein Chemical Shift Analysis: A Practical Guide",
398 "Biochem. Cell Biol.",
399 76, 1998, "153-163" },
401 "V. N. Maiorov and G. M. Crippen",
402 "Size-Independent Comparison of Protein Three-Dimensional Structures",
403 "PROTEINS: Struct. Funct. Gen.",
404 22, 1995, "273-283" },
406 "K. A. Feenstra and B. Hess and H. J. C. Berendsen",
407 "Improving Efficiency of Large Time-scale Molecular Dynamics Simulations of Hydrogen-rich Systems",
409 20, 1999, "786-798" },
411 "N. Timneanu and C. Caleman and J. Hajdu and D. van der Spoel",
412 "Auger Electron Cascades in Water and Ice",
414 299, 2004, "277-283" },
416 "T. A. Pascal and S. T. Lin and W. A. Goddard III",
417 "Thermodynamics of liquids: standard molar entropies and heat capacities of common solvents from 2PT molecular dynamics",
418 "Phys. Chem. Chem. Phys.",
419 13, 2011, "169-181" },
421 "C. Caleman and P. J. van Maaren and M. Hong and J. S. Hub and L. T. da Costa and D. van der Spoel",
422 "Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant",
423 "J. Chem. Theo. Comp.",
426 "E. Lindahl and B. Hess and D. van der Spoel",
427 "GROMACS 3.0: A package for molecular simulation and trajectory analysis",
429 7, 2001, "306-317" },
431 "J. Wang and W. Wang and S. Huo and M. Lee and P. A. Kollman",
432 "Solvation model based on weighted solvent accessible surface area",
434 105, 2001, "5055-5067" },
436 "D. Eisenberg and A. D. McLachlan",
437 "Solvation energy in protein folding and binding",
439 319, 1986, "199-203" },
441 "Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and Michael Scharf",
442 "The Double Cube Lattice Method: Efficient Approaches to Numerical Integration of Surface Area and Volume and to Dot Surface Contouring of Molecular Assemblies",
444 16, 1995, "273-284" },
446 "B. Hess, H. Saint-Martin and H.J.C. Berendsen",
447 "Flexible constraints: an adiabatic treatment of quantum degrees of freedom, with application to the flexible and polarizable MCDHO model for water",
449 116, 2002, "9602-9610" },
451 "Csaba Hetenyi and David van der Spoel",
452 "Efficient docking of peptides to proteins without prior knowledge of the binding site.",
454 11, 2002, "1729-1737" },
456 "B. Hess and R.M. Scheek",
457 "Orientation restraints in molecular dynamics simulations using time and ensemble averaging",
459 164, 2003, "19-27" },
461 "A. K. Rappe and W. A. Goddard III",
462 "Charge Equillibration for Molecular Dynamics Simulations",
464 95, 1991, "3358-3363" },
466 "Y. Mu, P. H. Nguyen and G. Stock",
467 "Energy landscape of a small peptide revelaed by dihedral angle principal component analysis",
468 "Prot. Struct. Funct. Bioinf.",
471 "T. Okabe and M. Kawata and Y. Okamoto and M. Mikami",
472 "Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble",
474 335, 2001, "435-439" },
476 "K. Hukushima and K. Nemoto",
477 "Exchange Monte Carlo Method and Application to Spin Glass Simulations",
478 "J. Phys. Soc. Jpn.",
479 65, 1996, "1604-1608" },
482 "Dipolar Relaxation and Nuclear Overhauser effects in nonrigid molecules: The effect of fluctuating internuclear distances",
484 72, 1980, "6035-6043" },
486 "P. Bultinck and W. Langenaeker and P. Lahorte and F. De Proft and P. Geerlings and M. Waroquier and J. P. Tollenaere",
487 "The electronegativity equalization method I: Parametrization and validation for atomic charge calculations",
489 106, 2002, "7887-7894" },
491 "Q. Y. Yang and K. A. Sharp",
492 "Atomic charge parameters for the finite difference Poisson-Boltzmann method using electronegativity neutralization",
493 "J. Chem. Theory Comput.",
494 2, 2006, "1152-1167" },
496 "D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen",
497 "GROMACS: Fast, Flexible and Free",
499 26, 2005, "1701-1719" },
501 "D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu",
502 "Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media",
504 110, 2006, "4393-4398" },
506 "D. van der Spoel and M. M. Seibert",
507 "Protein folding kinetics and thermodynamics from atomistic simulations",
508 "Phys. Rev. Letters",
509 96, 2006, "238102" },
512 "Transverse-current autocorrelation-function calculations of the shear viscosity for molecular liquids",
514 49, 1994, "359-366" },
516 "G. Bussi, D. Donadio and M. Parrinello",
517 "Canonical sampling through velocity rescaling",
519 126, 2007, "014101" },
521 "J. S. Hub and B. L. de Groot",
522 "Does CO2 permeate through Aquaporin-1?",
524 91, 2006, "842-848" },
526 "J. S. Hub and B. L. de Groot",
527 "Mechanism of selectivity in aquaporins and aquaglyceroporins",
529 105, 2008, "1198-1203" },
531 "M. S. Friedrichs, P. Eastman, V. Vaidyanathan, M. Houston, S. LeGrand, A. L. Beberg, D. L. Ensign, C. M. Bruns, and V. S. Pande",
532 "Accelerating Molecular Dynamic Simulation on Graphics Processing Units",
534 30, 2009, "864-872" },
536 "O. Engin, A. Villa, M. Sayar and B. Hess",
537 "Driving Forces for Adsorption of Amphiphilic Peptides to Air-Water Interface",
539 114, 2010, "11093" },
541 "S. Fritsch, C. Junghans and K. Kremer",
542 "Adaptive molecular simulation study on structure formation of toluene around C60 using Gromacs",
543 "J. Chem. Theo. Comp.",
546 "C. Junghans and S. Poblete",
547 "A reference implementation of the adaptive resolution scheme in ESPResSo",
551 "H. Wang, F. Dommert, C.Holm",
552 "Optimizing working parameters of the smooth particle mesh Ewald algorithm in terms of accuracy and efficiency",
554 133, 2010, "034117" },
556 "Y. Sugita, Y. Okamoto",
557 "Replica-exchange molecular dynamics method for protein folding",
559 314, 1999, "141-151" },
561 "C. Kutzner and J. Czub and H. Grubmuller",
562 "Keep it Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS",
563 "J. Chem. Theory Comput.",
564 7, 2011, "1381-1393" },
566 "M. Hoefling, N. Lima, D. Haenni, C.A.M. Seidel, B. Schuler, H. Grubmuller",
567 "Structural Heterogeneity and Quantitative FRET Efficiency Distributions of Polyprolines through a Hybrid Atomistic Simulation and Monte Carlo Approach",
571 "R. W. Hockney and J. W. Eastwood",
572 "Computer simulation using particles",
576 "V. Ballenegger, J.J. Cerda, and C. Holm",
577 "How to Convert SPME to P3M: Influence Functions and Error Estimates",
578 "J. Chem. Theory Comput.",
579 8, 2012, "936-947" },
581 "Garmay Yu, Shvetsov A, Karelov D, Lebedev D, Radulescu A, Petukhov M, Isaev-Ivanov V",
582 "Correlated motion of protein subdomains and large-scale conformational flexibility of RecA protein filament",
583 "Journal of Physics: Conference Series",
584 340, 2012, "012094" }
586 #define NSTR (int)asize(citedb)
591 #define LINE_WIDTH 79
596 for(index=0; (index<NSTR) && (strcmp(citedb[index].key,key) != 0); index++)
599 fprintf(fp,"\n++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++\n");
601 /* Insert newlines */
602 author = wrap_lines(citedb[index].author,LINE_WIDTH,0,FALSE);
603 title = wrap_lines(citedb[index].title,LINE_WIDTH,0,FALSE);
604 fprintf(fp,"%s\n%s\n%s %d (%d) pp. %s\n",
605 author,title,citedb[index].journal,
606 citedb[index].volume,citedb[index].year,
607 citedb[index].pages);
612 fprintf(fp,"Entry %s not found in citation database\n",key);
614 fprintf(fp,"-------- -------- --- Thank You --- -------- --------\n\n");
619 /* Version information generated at compile time. */
622 /* Fall back to statically defined version. */
623 static const char _gmx_ver_string[]="VERSION " VERSION;
626 const char *GromacsVersion()
628 return _gmx_ver_string;
631 void gmx_print_version_info(FILE *fp)
634 int cuda_driver,cuda_runtime;
637 fprintf(fp, "Gromacs version: %s\n", _gmx_ver_string);
639 fprintf(fp, "GIT SHA1 hash: %s\n", _gmx_full_git_hash);
640 /* Only print out the branch information if present.
641 * The generating script checks whether the branch point actually
642 * coincides with the hash reported above, and produces an empty string
644 if (_gmx_central_base_hash[0] != 0)
646 fprintf(fp, "Branched from: %s\n", _gmx_central_base_hash);
651 fprintf(fp, "Precision: double\n");
653 fprintf(fp, "Precision: single\n");
656 #ifdef GMX_THREAD_MPI
657 fprintf(fp, "MPI library: thread_mpi\n");
658 #elif defined(GMX_MPI)
659 fprintf(fp, "MPI library: MPI\n");
661 fprintf(fp, "MPI library: none\n");
664 fprintf(fp, "OpenMP support: enabled\n");
666 fprintf(fp, "OpenMP support: disabled\n");
669 fprintf(fp, "GPU support: enabled\n");
671 fprintf(fp, "GPU support: disabled\n");
673 /* A preprocessor trick to avoid duplicating logic from vec.h */
674 #define gmx_stringify2(x) #x
675 #define gmx_stringify(x) gmx_stringify2(x)
676 fprintf(fp, "invsqrt routine: %s\n", gmx_stringify(gmx_invsqrt(x)));
677 fprintf(fp, "CPU acceleration: %s\n", GMX_CPU_ACCELERATION_STRING);
679 /* TODO: Would be nicer to wrap this in a gmx_fft_version() call, but
680 * since that is currently in mdlib, can wait for master. */
681 #ifdef GMX_FFT_FFTPACK
682 fprintf(fp, "FFT library: fftpack (built-in)\n");
683 #elif defined(GMX_FFT_FFTW3) && defined(GMX_NATIVE_WINDOWS)
684 fprintf(fp, "FFT library: %s\n", "fftw3");
685 #elif defined(GMX_FFT_FFTW3) && defined(GMX_DOUBLE)
686 fprintf(fp, "FFT library: %s\n", fftw_version);
687 #elif defined(GMX_FFT_FFTW3)
688 fprintf(fp, "FFT library: %s\n", fftwf_version);
689 #elif defined(GMX_FFT_MKL)
690 fprintf(fp, "FFT library: MKL\n");
692 fprintf(fp, "FFT library: unknown\n");
694 #ifdef GMX_LARGEFILES
695 fprintf(fp, "Large file support: enabled\n");
697 fprintf(fp, "Large file support: disabled\n");
700 fprintf(fp, "RDTSCP usage: enabled\n");
702 fprintf(fp, "RDTSCP usage: disabled\n");
705 fprintf(fp, "Built on: %s\n", BUILD_TIME);
706 fprintf(fp, "Built by: %s\n", BUILD_USER);
707 fprintf(fp, "Build OS/arch: %s\n", BUILD_HOST);
708 fprintf(fp, "Build CPU vendor: %s\n", BUILD_CPU_VENDOR);
709 fprintf(fp, "Build CPU brand: %s\n", BUILD_CPU_BRAND);
710 fprintf(fp, "Build CPU family: %d Model: %d Stepping: %d\n",
711 BUILD_CPU_FAMILY, BUILD_CPU_MODEL, BUILD_CPU_STEPPING);
712 /* TODO: The below strings can be quite long, so it would be nice to wrap
713 * them. Can wait for later, as the master branch has ready code to do all
715 fprintf(fp, "Build CPU features: %s\n", BUILD_CPU_FEATURES);
716 fprintf(fp, "C compiler: %s\n", BUILD_C_COMPILER);
717 fprintf(fp, "C compiler flags: %s\n", BUILD_CFLAGS);
718 if (BUILD_CXX_COMPILER[0] != '\0')
720 fprintf(fp, "C++ compiler: %s\n", BUILD_CXX_COMPILER);
721 fprintf(fp, "C++ compiler flags: %s\n", BUILD_CXXFLAGS);
724 /* MKL might be used for LAPACK/BLAS even if FFTs use FFTW, so keep it separate */
725 fprintf(fp, "Linked with Intel MKL version %s.%s.%s.\n",
726 __INTEL_MKL__,__INTEL_MKL_MINOR__,__INTEL_MKL_UPDATE__);
729 fprintf(fp, "CUDA compiler: %s\n",CUDA_NVCC_COMPILER_INFO);
731 cudaDriverGetVersion(&cuda_driver);
733 cudaRuntimeGetVersion(&cuda_runtime);
734 fprintf(fp, "CUDA driver: %d.%d\n",cuda_driver/1000, cuda_driver%100);
735 fprintf(fp, "CUDA runtime: %d.%d\n",cuda_runtime/1000, cuda_runtime%100);