From 1cacfdf59b7aa9df088f2414d8d829a7f26763e1 Mon Sep 17 00:00:00 2001
From: Mark Abraham <mark.j.abraham@gmail.com>
Date: Fri, 7 Aug 2015 23:40:18 +0200
Subject: [PATCH] Require tune_pme to take -mdrun parameter

The transition away from many binaries in 5.0, and the removal of
symlinks in 5.1 mean there is even less chance that a sensible default
command line for calling mdrun can be provided. In general, mdrun
might be in either precision, with or without MPI, with or without
some custom suffix, inside the wrapper binary or from an mdrun-only
build, or from a custom directory.

Thus, the user is now required to say what command to call to run the
simulation they want to optimize. The MDRUN environment variable
remains as an undocumented and deprecated convenience feature for 5.1.

Fixes #1754

Change-Id: Ia2c278732ef2a79d7304967b230149eca4597888
---
 src/gromacs/gmxana/gmx_tune_pme.c | 39 ++++++++++++++++++++++++++-------------
 1 file changed, 26 insertions(+), 13 deletions(-)

diff --git a/src/gromacs/gmxana/gmx_tune_pme.c b/src/gromacs/gmxana/gmx_tune_pme.c
index b293179c07..f1f96dca5a 100644
--- a/src/gromacs/gmxana/gmx_tune_pme.c
+++ b/src/gromacs/gmxana/gmx_tune_pme.c
@@ -596,7 +596,6 @@ static void get_program_paths(gmx_bool bThreads, char *cmd_mpirun[], char *cmd_m
     char      *cp;
     FILE      *fp;
     const char def_mpirun[]   = "mpirun";
-    const char def_mdrun[]    = "mdrun";
 
     const char empty_mpirun[] = "";
 
@@ -617,13 +616,19 @@ static void get_program_paths(gmx_bool bThreads, char *cmd_mpirun[], char *cmd_m
         *cmd_mpirun = gmx_strdup(empty_mpirun);
     }
 
-    if ( (cp = getenv("MDRUN" )) != NULL)
+    if (*cmd_mdrun == NULL)
     {
-        *cmd_mdrun  = gmx_strdup(cp);
-    }
-    else
-    {
-        *cmd_mdrun  = gmx_strdup(def_mdrun);
+        /* The use of MDRUN is deprecated, but made available in 5.1
+           for backward compatibility. It may be removed in a future
+           version. */
+        if ( (cp = getenv("MDRUN" )) != NULL)
+        {
+            *cmd_mdrun = gmx_strdup(cp);
+        }
+        else
+        {
+            gmx_fatal(FARGS, "The way to call mdrun must be set in the -mdrun command-line flag.");
+        }
     }
 }
 
@@ -2133,14 +2138,20 @@ int gmx_tune_pme(int argc, char *argv[])
         "part of the Ewald sum. ",
         "Simply pass your [REF].tpr[ref] file to [THISMODULE] together with other options",
         "for [gmx-mdrun] as needed.[PAR]",
-        "Which executables are used can be set in the environment variables",
-        "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",
+        "[THISMODULE] needs to call [gmx-mdrun] and so requires that you",
+        "specify how to call mdrun with the argument to the [TT]-mdrun[tt]",
+        "parameter. Depending how you have built GROMACS, values such as",
+        "'gmx mdrun', 'gmx_d mdrun', or 'mdrun_mpi' might be needed.[PAR]",
+        "The program that runs MPI programs can be set in the environment variable",
+        "MPIRUN (defaults to 'mpirun'). 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.[PAR]",
-        "[TT]export MPIRUN=\"/usr/local/mpirun -machinefile hosts\"[tt][PAR]",
+        "[TT]export MPIRUN=\"/usr/local/mpirun -machinefile hosts\"[tt]",
+        "Note that in such cases it is normally necessary to compile",
+        "and/or run [THISMODULE] without MPI support, so that it can call",
+        "the MPIRUN program.[PAR]",
         "Before doing the actual benchmark runs, [THISMODULE] will do a quick",
-        "check whether mdrun works as expected with the provided parallel settings",
+        "check whether [gmx-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",
@@ -2308,6 +2319,8 @@ int gmx_tune_pme(int argc, char *argv[])
         /***********************/
         /* g_tune_pme options: */
         /***********************/
+        { "-mdrun",    FALSE, etSTR,  {&cmd_mdrun},
+          "Command line to run a simulation, e.g. 'gmx mdrun' or 'mdrun_mpi'" },
         { "-np",       FALSE, etINT,  {&nnodes},
           "Number of ranks to run the tests on (must be > 2 for separate PME ranks)" },
         { "-npstring", FALSE, etENUM, {procstring},
-- 
2.11.4.GIT