void printBinaryInformation(FILE *fp,
const ProgramContextInterface &programContext,
const BinaryInformationSettings &settings)
{
const char *prefix = settings.prefix_;
const char *suffix = settings.suffix_;
const char *precisionString = "";
#ifdef GMX_DOUBLE
precisionString = " (double precision)";
#endif
const char *const name = programContext.displayName();
if (settings.bGeneratedByHeader_)
{
fprintf(fp, "%sCreated by:%s\n", prefix, suffix);
}
if (settings.bCopyright_)
{
GMX_RELEASE_ASSERT(prefix[0] == '\0' && suffix[0] == '\0',
"Prefix/suffix not supported with copyright");
// This line is printed again after the copyright notice to make it
// appear together with all the other information, so that it is not
// necessary to read stuff above the copyright notice.
// The line above the copyright notice puts the copyright notice is
// context, though.
// 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,
gmx_version(), precisionString, suffix);
fprintf(fp, "\n");
printCopyright(fp);
fprintf(fp, "\n");
}
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',
"Prefix/suffix not supported with extended info");
fprintf(fp, "\n");
gmx_print_version_info(fp);
}
}
void gmx_log_open(const char *lognm, const t_commrec *cr, gmx_bool bMasterOnly,
gmx_bool bAppendFiles, FILE** fplog)
{
int len, testlen, pid;
char buf[256], host[256];
time_t t;
char timebuf[STRLEN];
FILE *fp = *fplog;
char *tmpnm;
debug_gmx();
/* Communicate the filename for logfile */
if (cr->nnodes > 1 && !bMasterOnly
#ifdef GMX_THREAD_MPI
/* With thread MPI the non-master log files are opened later
* when the files names are already known on all nodes.
*/
&& FALSE
#endif
)
{
if (MASTER(cr))
{
len = strlen(lognm) + 1;
}
gmx_bcast(sizeof(len), &len, cr);
if (!MASTER(cr))
{
snew(tmpnm, len+8);
}
else
{
tmpnm = gmx_strdup(lognm);
}
gmx_bcast(len*sizeof(*tmpnm), tmpnm, cr);
}
else
{
tmpnm = gmx_strdup(lognm);
}
debug_gmx();
if (!bMasterOnly && !MASTER(cr))
{
/* Since log always ends with '.log' let's use this info */
par_fn(tmpnm, efLOG, cr, FALSE, !bMasterOnly, buf, 255);
fp = gmx_fio_fopen(buf, bAppendFiles ? "a+" : "w+" );
}
else if (!bAppendFiles)
{
fp = gmx_fio_fopen(tmpnm, bAppendFiles ? "a+" : "w+" );
}
sfree(tmpnm);
gmx_fatal_set_log_file(fp);
/* Get some machine parameters */
gmx_gethostname(host, 256);
time(&t);
#ifndef NO_GETPID
# ifdef GMX_NATIVE_WINDOWS
pid = _getpid();
# else
pid = getpid();
# endif
#else
pid = 0;
#endif
if (bAppendFiles)
{
fprintf(fp,
"\n"
"\n"
"-----------------------------------------------------------\n"
"Restarting from checkpoint, appending to previous log file.\n"
"\n"
);
}
gmx_ctime_r(&t, timebuf, STRLEN);
fprintf(fp,
"Log file opened on %s"
"Host: %s pid: %d nodeid: %d nnodes: %d\n",
timebuf, host, pid, cr->nodeid, cr->nnodes);
gmx_print_version_info(fp);
fprintf(fp, "\n\n");
fflush(fp);
debug_gmx();
*fplog = fp;
}
void parse_common_args(int *argc,char *argv[],unsigned long Flags,
int nfile,t_filenm fnm[],int npargs,t_pargs *pa,
int ndesc,const char **desc,
int nbugs,const char **bugs,
output_env_t *oenv)
{
gmx_bool bHelp=FALSE,bHidden=FALSE,bQuiet=FALSE,bVersion=FALSE;
const char *manstr[] = { NULL, "no", "html", "tex", "nroff", "ascii",
"completion", "py", "xml", "wiki", NULL };
/* This array should match the order of the enum in oenv.h */
const char *xvg_format[] = { NULL, "xmgrace", "xmgr", "none", NULL };
/* This array should match the order of the enum in oenv.h */
const char *time_units[] = { NULL, "fs", "ps", "ns", "us", "ms", "s",
NULL };
int nicelevel=0,mantp=0,npri=0,debug_level=0,verbose_level=0;
char *deffnm=NULL;
real tbegin=0,tend=0,tdelta=0;
gmx_bool bView=FALSE;
t_pargs *all_pa=NULL;
t_pargs npri_pa = { "-npri", FALSE, etINT, {&npri},
"HIDDEN Set non blocking priority (try 128)" };
t_pargs nice_pa = { "-nice", FALSE, etINT, {&nicelevel},
"Set the nicelevel" };
t_pargs deffnm_pa = { "-deffnm", FALSE, etSTR, {&deffnm},
"Set the default filename for all file options" };
t_pargs begin_pa = { "-b", FALSE, etTIME, {&tbegin},
"First frame (%t) to read from trajectory" };
t_pargs end_pa = { "-e", FALSE, etTIME, {&tend},
"Last frame (%t) to read from trajectory" };
t_pargs dt_pa = { "-dt", FALSE, etTIME, {&tdelta},
"Only use frame when t MOD dt = first time (%t)" };
t_pargs view_pa = { "-w", FALSE, etBOOL, {&bView},
"View output xvg, xpm, eps and pdb files" };
t_pargs xvg_pa = { "-xvg", FALSE, etENUM, {xvg_format},
"xvg plot formatting" };
t_pargs time_pa = { "-tu", FALSE, etENUM, {time_units},
"Time unit" };
/* Maximum number of extra arguments */
#define EXTRA_PA 16
t_pargs pca_pa[] = {
{ "-h", FALSE, etBOOL, {&bHelp},
"Print help info and quit" },
{ "-version", FALSE, etBOOL, {&bVersion},
"Print version info and quit" },
{ "-verb", FALSE, etINT, {&verbose_level},
"HIDDENLevel of verbosity for this program" },
{ "-hidden", FALSE, etBOOL, {&bHidden},
"HIDDENPrint hidden options" },
{ "-quiet",FALSE, etBOOL, {&bQuiet},
"HIDDENDo not print help info" },
{ "-man", FALSE, etENUM, {manstr},
"HIDDENWrite manual and quit" },
{ "-debug",FALSE, etINT, {&debug_level},
"HIDDENWrite file with debug information, 1: short, 2: also x and f" },
};
#define NPCA_PA asize(pca_pa)
FILE *fp;
gmx_bool bPrint,bExit,bXvgr;
int i,j,k,npall,max_pa,cmdlength;
char *ptr,*newdesc;
const char *envstr;
#define FF(arg) ((Flags & arg)==arg)
snew(*oenv, 1);
cmdlength = strlen(argv[0]);
/* Check for double arguments */
for (i=1; (i<*argc); i++)
{
cmdlength += strlen(argv[i]);
if (argv[i] && (strlen(argv[i]) > 1) && (!isdigit(argv[i][1])))
{
for (j=i+1; (j<*argc); j++)
{
if ( (argv[i][0]=='-') && (argv[j][0]=='-') &&
(strcmp(argv[i],argv[j])==0) )
{
if (FF(PCA_NOEXIT_ON_ARGS))
fprintf(stderr,"Double command line argument %s\n",
argv[i]);
else
gmx_fatal(FARGS,"Double command line argument %s\n",
argv[i]);
}
}
}
}
debug_gmx();
set_program_name(argv[0]);
set_command_line(*argc, argv);
/* Handle the flags argument, which is a bit field
* The FF macro returns whether or not the bit is set
*/
bPrint = !FF(PCA_SILENT);
/* Check ALL the flags ... */
max_pa = NPCA_PA + EXTRA_PA + npargs+1;
snew(all_pa,max_pa);
for(i=npall=0; (i<NPCA_PA); i++)
npall = add_parg(npall,all_pa,&(pca_pa[i]));
#ifdef __sgi
envstr = getenv("GMXNPRIALL");
if (envstr)
npri=strtol(envstr,NULL,10);
if (FF(PCA_BE_NICE)) {
envstr = getenv("GMXNPRI");
if (envstr)
npri=strtol(envstr,NULL,10);
}
npall = add_parg(npall,all_pa,&npri_pa);
#endif
if (FF(PCA_BE_NICE))
nicelevel=19;
npall = add_parg(npall,all_pa,&nice_pa);
if (FF(PCA_CAN_SET_DEFFNM))
npall = add_parg(npall,all_pa,&deffnm_pa);
if (FF(PCA_CAN_BEGIN))
npall = add_parg(npall,all_pa,&begin_pa);
if (FF(PCA_CAN_END))
npall = add_parg(npall,all_pa,&end_pa);
if (FF(PCA_CAN_DT))
{
npall = add_parg(npall,all_pa,&dt_pa);
}
if (FF(PCA_TIME_UNIT)) {
npall = add_parg(npall,all_pa,&time_pa);
}
if (FF(PCA_CAN_VIEW))
npall = add_parg(npall,all_pa,&view_pa);
bXvgr = FALSE;
for(i=0; (i<nfile); i++)
{
bXvgr = bXvgr || (fnm[i].ftp == efXVG);
}
if (bXvgr)
{
npall = add_parg(npall,all_pa,&xvg_pa);
}
/* Now append the program specific arguments */
for(i=0; (i<npargs); i++)
npall = add_parg(npall,all_pa,&(pa[i]));
/* set etENUM options to default */
for(i=0; (i<npall); i++)
{
if (all_pa[i].type==etENUM)
{
all_pa[i].u.c[0]=all_pa[i].u.c[1];
}
}
set_default_time_unit(time_units,FF(PCA_TIME_UNIT));
set_default_xvg_format(xvg_format);
/* Now parse all the command-line options */
get_pargs(argc,argv,npall,all_pa,FF(PCA_KEEP_ARGS));
/* set program name, command line, and default values for output options */
output_env_init(*oenv, *argc, argv, (time_unit_t)nenum(time_units), bView,
(xvg_format_t)nenum(xvg_format), verbose_level, debug_level);
if (bVersion) {
printf("Program: %s\n",output_env_get_program_name(*oenv));
gmx_print_version_info(stdout);
exit(0);
}
if (FF(PCA_CAN_SET_DEFFNM) && (deffnm!=NULL))
set_default_file_name(deffnm);
/* Parse the file args */
parse_file_args(argc,argv,nfile,fnm,FF(PCA_KEEP_ARGS),!FF(PCA_NOT_READ_NODE));
/* Open the debug file */
if (debug_level > 0) {
char buf[256];
if (gmx_mpi_initialized())
sprintf(buf,"%s%d.debug",output_env_get_short_program_name(*oenv),
gmx_node_rank());
else
sprintf(buf,"%s.debug",output_env_get_short_program_name(*oenv));
init_debug(debug_level,buf);
fprintf(stderr,"Opening debug file %s (src code file %s, line %d)\n",
buf,__FILE__,__LINE__);
}
/* Now copy the results back... */
for(i=0,k=npall-npargs; (i<npargs); i++,k++)
memcpy(&(pa[i]),&(all_pa[k]),(size_t)sizeof(pa[i]));
for(i=0; (i<npall); i++)
all_pa[i].desc = mk_desc(&(all_pa[i]), output_env_get_time_unit(*oenv));
bExit = bHelp || (strcmp(manstr[0],"no") != 0);
#if (defined __sgi && USE_SGI_FPE)
doexceptions();
#endif
/* Set the nice level */
#ifdef __sgi
if (npri != 0 && !bExit) {
schedctl(MPTS_RTPRI,0,npri);
}
#endif
#ifdef HAVE_UNISTD_H
#ifndef GMX_NO_NICE
/* The some system, e.g. the catamount kernel on cray xt3 do not have nice(2). */
if (nicelevel != 0 && !bExit)
{
#ifdef GMX_THREADS
static gmx_bool nice_set=FALSE; /* only set it once */
tMPI_Thread_mutex_lock(&init_mutex);
if (!nice_set)
{
#endif
i=nice(nicelevel); /* assign ret value to avoid warnings */
#ifdef GMX_THREADS
nice_set=TRUE;
}
tMPI_Thread_mutex_unlock(&init_mutex);
#endif
}
#endif
#endif
/* Update oenv for parsed command line options settings. */
(*oenv)->xvg_format = (xvg_format_t)nenum(xvg_format);
(*oenv)->time_unit = (time_unit_t)nenum(time_units);
if (!(FF(PCA_QUIET) || bQuiet )) {
if (bHelp)
write_man(stderr,"help",output_env_get_program_name(*oenv),
ndesc,desc,nfile, fnm,npall,all_pa, nbugs,bugs,bHidden);
else if (bPrint) {
pr_fns(stderr,nfile,fnm);
print_pargs(stderr,npall,all_pa,FALSE);
}
}
if (strcmp(manstr[0],"no") != 0) {
if(!strcmp(manstr[0],"completion")) {
/* one file each for csh, bash and zsh if we do completions */
fp=man_file(*oenv,"completion-zsh");
write_man(fp,"completion-zsh",output_env_get_program_name(*oenv),
ndesc,desc,nfile, fnm, npall,all_pa,nbugs,bugs,bHidden);
gmx_fio_fclose(fp);
fp=man_file(*oenv,"completion-bash");
write_man(fp,"completion-bash",output_env_get_program_name(*oenv),
ndesc,desc,nfile, fnm, npall,all_pa,nbugs,bugs,bHidden);
gmx_fio_fclose(fp);
fp=man_file(*oenv,"completion-csh");
write_man(fp,"completion-csh",output_env_get_program_name(*oenv),
ndesc,desc,nfile, fnm, npall,all_pa,nbugs,bugs,bHidden);
gmx_fio_fclose(fp);
} else {
fp=man_file(*oenv,manstr[0]);
write_man(fp,manstr[0],output_env_get_program_name(*oenv),
ndesc,desc,nfile,fnm, npall, all_pa,nbugs,bugs,bHidden);
gmx_fio_fclose(fp);
}
}
/* convert time options, must be done after printing! */
for(i=0; i<npall; i++) {
if ((all_pa[i].type == etTIME) && (*all_pa[i].u.r >= 0)) {
*all_pa[i].u.r *= output_env_get_time_invfactor(*oenv);
}
}
/* Extract Time info from arguments */
if (FF(PCA_CAN_BEGIN) && opt2parg_bSet("-b",npall,all_pa))
setTimeValue(TBEGIN,opt2parg_real("-b",npall,all_pa));
if (FF(PCA_CAN_END) && opt2parg_bSet("-e",npall,all_pa))
setTimeValue(TEND,opt2parg_real("-e",npall,all_pa));
if (FF(PCA_CAN_DT) && opt2parg_bSet("-dt",npall,all_pa))
setTimeValue(TDELTA,opt2parg_real("-dt",npall,all_pa));
/* clear memory */
for (i = 0; i < npall; ++i)
sfree((void *)all_pa[i].desc);
sfree(all_pa);
if (!FF(PCA_NOEXIT_ON_ARGS)) {
if (*argc > 1) {
gmx_cmd(argv[1]);
}
}
if (bExit) {
if (gmx_parallel_env_initialized())
/*gmx_abort(gmx_node_rank(),gmx_node_num(),0);*/
gmx_finalize();
exit(0);
}
#undef FF
}
void printBinaryInformation(FILE *fp,
const ProgramContextInterface &programContext,
const BinaryInformationSettings &settings)
{
const char *prefix = settings.prefix_;
const char *suffix = settings.suffix_;
const char *precisionString = "";
#ifdef GMX_DOUBLE
precisionString = " (double precision)";
#endif
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.
std::string title
= formatString(":-) GROMACS - %s, %s%s (-:", name, gmx_version(), precisionString);
const int indent
= centeringOffset(78 - strlen(prefix) - strlen(suffix), title.length()) + 1;
fprintf(fp, "%s%*c%s%s\n", prefix, indent, ' ', title.c_str(), suffix);
fprintf(fp, "%s%s\n", prefix, suffix);
if (settings.bCopyright_)
{
GMX_RELEASE_ASSERT(prefix[0] == '\0' && suffix[0] == '\0',
"Prefix/suffix not supported with copyright");
printCopyright(fp);
fprintf(fp, "\n");
// This line is printed again after the copyright notice to make it
// appear together with all the other information, so that it is not
// necessary to read stuff above the copyright notice.
// The line above the copyright notice puts the copyright notice is
// context, though.
fprintf(fp, "%sGROMACS: %s, %s%s%s\n", prefix, name,
gmx_version(), precisionString, suffix);
}
const char *const binaryPath = programContext.fullBinaryPath();
if (!gmx::isNullOrEmpty(binaryPath))
{
fprintf(fp, "%sExecutable: %s%s\n", prefix, binaryPath, suffix);
}
const gmx::InstallationPrefixInfo installPrefix = programContext.installationPrefix();
if (!gmx::isNullOrEmpty(installPrefix.path))
{
fprintf(fp, "%sData prefix: %s%s%s\n", prefix, installPrefix.path,
installPrefix.bSourceLayout ? " (source tree)" : "", suffix);
}
const char *const commandLine = programContext.commandLine();
if (!gmx::isNullOrEmpty(commandLine))
{
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',
"Prefix/suffix not supported with extended info");
fprintf(fp, "\n");
gmx_print_version_info(fp);
}
}
