int cmain(int argc,char *argv[])
{
const char *desc[] = {
- #ifdef GMX_OPENMM
- "This is an experimental release of GROMACS for accelerated",
- "Molecular Dynamics simulations on GPU processors. Support is provided",
- "by the OpenMM library (https://simtk.org/home/openmm).[PAR]",
- "*Warning*[BR]",
- "This release is targeted at developers and advanced users and",
- "care should be taken before production use. The following should be",
- "noted before using the program:[PAR]",
- " * The current release runs only on modern nVidia GPU hardware with CUDA support.",
- "Make sure that the necessary CUDA drivers and libraries for your operating system",
- "are already installed. The CUDA SDK also should be installed in order to compile",
- "the program from source (http://www.nvidia.com/object/cuda_home.html).[PAR]",
- " * Multiple GPU cards are not supported.[PAR]",
- " * Only a small subset of the GROMACS features and options are supported on the GPUs.",
- "See below for a detailed list.[PAR]",
- " * Consumer level GPU cards are known to often have problems with faulty memory.",
- "It is recommended that a full memory check of the cards is done at least once",
- "(for example, using the memtest=full option).",
- "A partial memory check (for example, memtest=15) before and",
- "after the simulation run would help spot",
- "problems resulting from processor overheating.[PAR]",
- " * The maximum size of the simulated systems depends on the available",
- "GPU memory,for example, a GTX280 with 1GB memory has been tested with systems",
- "of up to about 100,000 atoms.[PAR]",
- " * In order to take a full advantage of the GPU platform features, many algorithms",
- "have been implemented in a very different way than they are on the CPUs.",
- "Therefore numercal correspondence between properties of the state of",
- "simulated systems should not be expected. Moreover, the values will likely vary",
- "when simulations are done on different GPU hardware.[PAR]",
- " * Frequent retrieval of system state information such as",
- "trajectory coordinates and energies can greatly influence the performance",
- "of the program due to slow CPU<->GPU memory transfer speed.[PAR]",
- " * MD algorithms are complex, and although the Gromacs code is highly tuned for them,",
- "they often do not translate very well onto the streaming architetures.",
- "Realistic expectations about the achievable speed-up from test with GTX280:",
- "For small protein systems in implicit solvent using all-vs-all kernels the acceleration",
- "can be as high as 20 times, but in most other setups involving cutoffs and PME the",
- "acceleration is usually only ~4 times relative to a 3GHz CPU.[PAR]",
- "Supported features:[PAR]",
- " * Integrators: md/md-vv/md-vv-avek, sd/sd1 and bd.\n",
- " * Long-range interactions (option coulombtype): Reaction-Field, Ewald, PME, and cut-off (for Implicit Solvent only)\n",
- " * Temperature control: Supported only with the md/md-vv/md-vv-avek, sd/sd1 and bd integrators.\n",
- " * Pressure control: Supported.\n",
- " * Implicit solvent: Supported.\n",
- "A detailed description can be found on the GROMACS website:\n",
- "http://www.gromacs.org/gpu[PAR]",
-/* From the original mdrun documentaion */
- "The [TT]mdrun[tt] program reads the run input file ([TT]-s[tt])",
- "and distributes the topology over nodes if needed.",
- "[TT]mdrun[tt] produces at least four output files.",
- "A single log file ([TT]-g[tt]) is written, unless the option",
- "[TT]-seppot[tt] is used, in which case each node writes a log file.",
- "The trajectory file ([TT]-o[tt]), contains coordinates, velocities and",
- "optionally forces.",
- "The structure file ([TT]-c[tt]) contains the coordinates and",
- "velocities of the last step.",
- "The energy file ([TT]-e[tt]) contains energies, the temperature,",
- "pressure, etc, a lot of these things are also printed in the log file.",
- "Optionally coordinates can be written to a compressed trajectory file",
- "([TT]-x[tt]).[PAR]",
-/* openmm specific information */
- "Usage with OpenMM:[BR]",
- "[TT]mdrun -device \"OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=no\"[tt][PAR]",
- "Options:[PAR]",
- " [TT]platform[tt] = Cuda\t\t:\tThe only available value. OpenCL support will be available in future.\n",
- " [TT]memtest[tt] = 15\t\t:\tRun a partial, random GPU memory test for the given amount of seconds. A full test",
- "(recommended!) can be run with \"memtest=full\". Memory testing can be disabled with \"memtest=off\".\n",
- " [TT]deviceid[tt] = 0\t\t:\tSpecify the target device when multiple cards are present.",
- "Only one card can be used at any given time though.\n",
- " [TT]force-device[tt] = no\t\t:\tIf set to \"yes\" [TT]mdrun[tt] will be forced to execute on",
- "hardware that is not officially supported. GPU acceleration can also be achieved on older",
- "but Cuda capable cards, although the simulation might be too slow, and the memory limits too strict.",
-#else
"The [TT]mdrun[tt] program is the main computational chemistry engine",
"within GROMACS. Obviously, it performs Molecular Dynamics simulations,",
"but it can also perform Stochastic Dynamics, Energy Minimization,",
"forces and energies will be (re)calculated. Neighbor searching will be",
"performed for every frame, unless [TT]nstlist[tt] is zero",
"(see the [TT].mdp[tt] file).[PAR]",
- "ED (essential dynamics) sampling is switched on by using the [TT]-ei[tt]",
- "flag followed by an [TT].edi[tt] file.",
- "The [TT].edi[tt] file can be produced using options in the essdyn",
- "menu of the WHAT IF program. [TT]mdrun[tt] produces a [TT].xvg[tt] output file that",
+ "ED (essential dynamics) sampling and/or additional flooding potentials",
+ "are switched on by using the [TT]-ei[tt] flag followed by an [TT].edi[tt]",
+ "file. The [TT].edi[tt] file can be produced with the [TT]make_edi[tt] tool",
+ "or by using options in the essdyn menu of the WHAT IF program.",
+ "[TT]mdrun[tt] produces a [TT].xvg[tt] output file that",
"contains projections of positions, velocities and forces onto selected",
"eigenvectors.[PAR]",
"When user-defined potential functions have been selected in the",
"the [TT]mdrun[tt] process that is the parent of the others.",
"[PAR]",
"When [TT]mdrun[tt] is started with MPI, it does not run niced by default."
-#endif
};
t_commrec *cr;
t_filenm fnm[] = {
"HIDDENReset cycle counters after these many time steps" },
{ "-resethway", FALSE, etBOOL, {&bResetCountersHalfWay},
"HIDDENReset the cycle counters after half the number of steps or halfway [TT]-maxh[tt]" }
-#ifdef GMX_OPENMM
- ,
- { "-device", FALSE, etSTR, {&deviceOptions},
- "Device option string" }
-#endif
};
gmx_edsam_t ed;
unsigned long Flags, PCA_Flags;
ivec ddxyz;
int dd_node_order;
gmx_bool bAddPart;
- FILE *fplog,*fptest;
+ FILE *fplog,*fpmulti;
int sim_part,sim_part_fn;
const char *part_suffix=".part";
char suffix[STRLEN];
&sim_part_fn,NULL,cr,
bAppendFiles,NFILE,fnm,
part_suffix,&bAddPart);
- if (sim_part_fn==0 && MASTER(cr))
+ if (sim_part_fn==0 && MULTIMASTER(cr))
{
fprintf(stdout,"No previous checkpoint file present, assuming this is a new run.\n");
}
if (MULTISIM(cr) && MASTER(cr))
{
- check_multi_int(stdout,cr->ms,sim_part,"simulation part");
+ if (MULTIMASTER(cr))
+ {
+ /* Log file is not yet available, so if there's a
+ * problem we can only write to stderr. */
+ fpmulti = stderr;
+ }
+ else
+ {
+ fpmulti = NULL;
+ }
+ check_multi_int(fpmulti,cr->ms,sim_part,"simulation part",TRUE);
}
}
else
sprintf(suffix,"%s%04d",part_suffix,sim_part_fn);
add_suffix_to_output_names(fnm,NFILE,suffix);
- if (MASTER(cr))
+ if (MULTIMASTER(cr))
{
fprintf(stdout,"Checkpoint file is from part %d, new output files will be suffixed '%s'.\n",sim_part-1,suffix);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff