Allow gmx tune_pme to skip the check for command-line health

Therefore, this patch adds the "-check" command line option, which is
TRUE by default, but can be switched to FALSE in problematic cases.
Documented its main use case in the error message that it would
circumvent.

Also corrected a few typos.

Fixes part of #1609

Change-Id: Id1cadd620438c36c123ff075c9a98ea7d1534d4d

diff --git a/src/gromacs/gmxana/gmx_tune_pme.c b/src/gromacs/gmxana/gmx_tune_pme.c
index 112e87273262698a714f1c5bdcbe1413eefca659..a4378039327b2f23e842dc8ec5bb3c1ce79ae3cc 100644 (file)
--- a/src/gromacs/gmxana/gmx_tune_pme.c
+++ b/src/gromacs/gmxana/gmx_tune_pme.c
@@ -1330,9 +1330,12 @@ static void make_sure_it_runs(char *mdrun_cmd_line, int length, FILE *fp,
     {
         /* To prevent confusion, do not again issue a gmx_fatal here since we already
          * get the error message from mdrun itself */
-        sprintf(msg,    "Cannot run the benchmark simulations! Please check the error message of\n"
+        sprintf(msg,
+                "Cannot run the first benchmark simulation! Please check the error message of\n"
                 "mdrun for the source of the problem. Did you provide a command line\n"
-                "argument that neither g_tune_pme nor mdrun understands? Offending command:\n"
+                "argument that neither gmx tune_pme nor mdrun understands? If you're\n"
+                "sure your command line should work, you can bypass this check with \n"
+                "gmx tune_pme -nocheck. The failing command was:\n"
                 "\n%s\n\n", command);
 
         fprintf(stderr, "%s", msg);
@@ -1363,7 +1366,7 @@ static void do_the_tests(
         int             npme_fixed,     /* If >= -1, test fixed number of PME
                                          * nodes only                             */
         const char     *npmevalues_opt, /* Which -npme values should be tested    */
-        t_perf        **perfdata,       /* Here the performace data is stored     */
+        t_perf        **perfdata,       /* Here the performance data is stored    */
         int            *pmeentries,     /* Entries in the nPMEnodes list          */
         int             repeats,        /* Repeat each test this often            */
         int             nnodes,         /* Total number of nodes = nPP + nPME     */
@@ -1376,7 +1379,8 @@ static void do_the_tests(
         const t_filenm *fnm,            /* List of filenames from command line    */
         int             nfile,          /* Number of files specified on the cmdl. */
         int             presteps,       /* DLB equilibration steps, is checked    */
-        gmx_int64_t     cpt_steps)      /* Time step counter in the checkpoint    */
+        gmx_int64_t     cpt_steps,      /* Time step counter in the checkpoint    */
+        gmx_bool        bCheck)         /* Check whether benchmark mdrun works    */
 {
     int      i, nr, k, ret, count = 0, totaltests;
     int     *nPMEnodes = NULL;
@@ -1476,8 +1480,11 @@ static void do_the_tests(
                         cmd_stub, pd->nPMEnodes, tpr_names[k], cmd_args_bench);
 
                 /* To prevent that all benchmarks fail due to a show-stopper argument
-                 * on the mdrun command line, we make a quick check first */
-                if (bFirst)
+                 * on the mdrun command line, we make a quick check first.
+                 * This check can be turned off in cases where the automatically chosen
+                 * number of PME-only ranks leads to a number of PP ranks for which no
+                 * decomposition can be found (e.g. for large prime numbers) */
+                if (bFirst && bCheck)
                 {
                     make_sure_it_runs(pd->mdrun_cmd_line, cmdline_length, fp, fnm, nfile);
                 }
@@ -2038,6 +2045,9 @@ int gmx_tune_pme(int argc, char *argv[])
         "need to provide a machine- or hostfile. This can also be passed",
         "via the MPIRUN variable, e.g.[PAR]",
         "[TT]export MPIRUN=\"/usr/local/mpirun -machinefile hosts\"[tt][PAR]",
+        "Before doing the actual benchmark runs, [THISMODULE] will do a quick",
+        "check whether mdrun works as expected with the provided parallel settings",
+        "if the [TT]-check[tt] option is activated (the default).",
         "Please call [THISMODULE] with the normal options you would pass to",
         "[gmx-mdrun] and add [TT]-np[tt] for the number of ranks to perform the",
         "tests on, or [TT]-ntmpi[tt] for the number of threads. You can also add [TT]-r[tt]",
@@ -2047,7 +2057,7 @@ int gmx_tune_pme(int argc, char *argv[])
         "written with enlarged cutoffs and smaller Fourier grids respectively.",
         "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 the Coulomb cutoff",
-        "specified by [TT]-rmax[tt] with a somwhat smaller PME grid at the same time. ",
+        "specified by [TT]-rmax[tt] with a somewhat smaller PME grid at the same time. ",
         "In this last test, the Fourier spacing is multiplied with [TT]rmax[tt]/rcoulomb. ",
         "The remaining [TT].tpr[tt] files will have equally-spaced Coulomb radii (and Fourier "
         "spacings) between these extremes. [BB]Note[bb] that you can set [TT]-ntpr[tt] to 1",
@@ -2057,7 +2067,7 @@ int gmx_tune_pme(int argc, char *argv[])
         "MD systems. The dynamic load balancing needs about 100 time steps",
         "to adapt to local load imbalances, therefore the time step counters",
         "are by default reset after 100 steps. For large systems (>1M atoms), as well as ",
-        "for a higher accuarcy of the measurements, you should set [TT]-resetstep[tt] to a higher value.",
+        "for a higher accuracy of the measurements, you should 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. Example call:[PAR]"
         "[TT]gmx tune_pme -np 64 -s protein.tpr -launch[tt][PAR]",
@@ -2184,6 +2194,7 @@ int gmx_tune_pme(int argc, char *argv[])
     gmx_bool     bKeepAndNumCPT        = FALSE;
     gmx_bool     bResetCountersHalfWay = FALSE;
     gmx_bool     bBenchmark            = TRUE;
+    gmx_bool     bCheck                = TRUE;
 
     output_env_t oenv = NULL;
 
@@ -2227,6 +2238,8 @@ int gmx_tune_pme(int argc, char *argv[])
           "Launch the real simulation after optimization" },
         { "-bench",    FALSE, etBOOL, {&bBenchmark},
           "Run the benchmarks or just create the input [TT].tpr[tt] files?" },
+        { "-check",    FALSE, etBOOL, {&bCheck},
+          "Before the benchmark runs, check whether mdrun works in parallel" },
         /******************/
         /* mdrun options: */
         /******************/
@@ -2478,7 +2491,7 @@ int gmx_tune_pme(int argc, char *argv[])
     {
         do_the_tests(fp, tpr_names, maxPMEnodes, minPMEnodes, npme_fixed, npmevalues_opt[0], perfdata, &pmeentries,
                      repeats, nnodes, ntprs, bThreads, cmd_mpirun, cmd_np, cmd_mdrun,
-                     cmd_args_bench, fnm, NFILE, presteps, cpt_steps);
+                     cmd_args_bench, fnm, NFILE, presteps, cpt_steps, bCheck);
 
         fprintf(fp, "\nTuning took%8.1f minutes.\n", (gmx_gettime()-seconds)/60.0);