"MPIRUN and MDRUN. If these are not present, 'mpirun' and 'mdrun'",
"will be used as defaults. Note that for certain MPI frameworks you",
"need to provide a machine- or hostfile. This can also be passed",
- "via the MPIRUN variable, e.g.",
+ "via the MPIRUN variable, e.g.[PAR]",
"[TT]export MPIRUN=\"/usr/local/mpirun -machinefile hosts\"[tt][PAR]",
"Please call [TT]g_tune_pme[tt] with the normal options you would pass to",
"[TT]mdrun[tt] and add [TT]-np[tt] for the number of processors to perform the",
"[TT]g_tune_pme[tt] can test various real space / reciprocal space workloads",
"for you. With [TT]-ntpr[tt] you control how many extra [TT].tpr[tt] files will be",
"written with enlarged cutoffs and smaller fourier grids respectively.",
- "Typically, the first test (No. 0) will be with the settings from the input",
- "[TT].tpr[tt] file; the last test (No. [TT]ntpr[tt]) will have cutoffs multiplied",
+ "Typically, the first test (number 0) will be with the settings from the input",
+ "[TT].tpr[tt] file; the last test (number [TT]ntpr[tt]) will have cutoffs multiplied",
"by (and at the same time fourier grid dimensions divided by) the scaling",
- "factor [TT]-fac[tt] (default 1.2). The remaining [TT].tpr[tt] files will have about equally",
- "spaced values inbetween these extremes. Note that you can set [TT]-ntpr[tt] to 1",
+ "factor [TT]-fac[tt] (default 1.2). The remaining [TT].tpr[tt] files will have about ",
+ "equally-spaced values in between these extremes. [BB]Note[bb] that you can set [TT]-ntpr[tt] to 1",
"if you just want to find the optimal number of PME-only nodes; in that case",
"your input [TT].tpr[tt] file will remain unchanged.[PAR]",
"For the benchmark runs, the default of 1000 time steps should suffice for most",
"are by default reset after 100 steps. For large systems",
"(>1M atoms) you may have to set [TT]-resetstep[tt] to a higher value.",
"From the 'DD' load imbalance entries in the md.log output file you",
- "can tell after how many steps the load is sufficiently balanced.[PAR]"
- "Example call: [TT]g_tune_pme -np 64 -s protein.tpr -launch[tt][PAR]",
+ "can tell after how many steps the load is sufficiently balanced. Example call:[PAR]"
+ "[TT]g_tune_pme -np 64 -s protein.tpr -launch[tt][PAR]",
"After calling [TT]mdrun[tt] several times, detailed performance information",
- "is available in the output file perf.out. ",
- "Note that during the benchmarks a couple of temporary files are written",
+ "is available in the output file [TT]perf.out.[tt] ",
+ "[BB]Note[bb] that during the benchmarks, a couple of temporary files are written",
"(options [TT]-b[tt]*), these will be automatically deleted after each test.[PAR]",
"If you want the simulation to be started automatically with the",
"optimized parameters, use the command line option [TT]-launch[tt].[PAR]",
{ "-np", FALSE, etINT, {&nnodes},
"Number of nodes to run the tests on (must be > 2 for separate PME nodes)" },
{ "-npstring", FALSE, etENUM, {procstring},
- "Specify the number of processors to $MPIRUN using this string"},
+ "Specify the number of processors to [TT]$MPIRUN[tt] using this string"},
{ "-passall", FALSE, etBOOL, {&bPassAll},
- "HIDDENPut arguments unknown to [TT]mdrun[tt] at the end of the command line. Can e.g. be used for debugging purposes. "},
+ "HIDDENPut arguments unknown to [TT]mdrun[tt] at the end of the command line. Can be used for debugging purposes. "},
{ "-nt", FALSE, etINT, {&nthreads},
"Number of threads to run the tests on (turns MPI & mpirun off)"},
{ "-r", FALSE, etINT, {&repeats},
{ "-downfac", FALSE, etREAL, {&downfac},
"Lower limit for rcoulomb scaling factor" },
{ "-ntpr", FALSE, etINT, {&ntprs},
- "Number of [TT].tpr[tt] files to benchmark. Create these many files with scaling factors ranging from 1.0 to fac. If < 1, automatically choose the number of [TT].tpr[tt] files to test" },
+ "Number of [TT].tpr[tt] files to benchmark. Create this many files with scaling factors ranging from 1.0 to fac. If < 1, automatically choose the number of [TT].tpr[tt] files to test" },
{ "-four", FALSE, etREAL, {&fs},
"Use this fourierspacing value instead of the grid found in the [TT].tpr[tt] input file. (Spacing applies to a scaling factor of 1.0 if multiple [TT].tpr[tt] files are written)" },
{ "-steps", FALSE, etGMX_LARGE_INT, {&bench_nsteps},
- "Take timings for these many steps in the benchmark runs" },
+ "Take timings for this many steps in the benchmark runs" },
{ "-resetstep",FALSE, etINT, {&presteps},
- "Let dlb equilibrate these many steps before timings are taken (reset cycle counters after these many steps)" },
+ "Let dlb equilibrate this many steps before timings are taken (reset cycle counters after this many steps)" },
{ "-simsteps", FALSE, etGMX_LARGE_INT, {&new_sim_nsteps},
- "If non-negative, perform these many steps in the real run (overwrite nsteps from [TT].tpr[tt], add [TT].cpt[tt] steps)" },
+ "If non-negative, perform this many steps in the real run (overwrites nsteps from [TT].tpr[tt], add [TT].cpt[tt] steps)" },
{ "-launch", FALSE, etBOOL, {&bLaunch},
"Lauch the real simulation after optimization" },
/******************/
{ "-rerunvsite", FALSE, etBOOL, {&bRerunVSite},
"HIDDENRecalculate virtual site coordinates with [TT]-rerun[tt]" },
{ "-ionize", FALSE, etBOOL, {&bIonize},
- "Do a simulation including the effect of an X-Ray bombardment on your system" },
+ "Do a simulation including the effect of an X-ray bombardment on your system" },
{ "-confout", FALSE, etBOOL, {&bConfout},
"HIDDENWrite the last configuration with [TT]-c[tt] and force checkpointing at the last step" },
{ "-stepout", FALSE, etINT, {&nstepout},
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff