Remove unnecessary config.h includes

[alexxy/gromacs.git] / src / gromacs / commandline / pargs.cpp

diff --git a/src/gromacs/commandline/pargs.cpp b/src/gromacs/commandline/pargs.cpp
index 151c3b9e504e6b8f5d3a818753844eb32ba76e1a..d0184d1a8302927112416ac263f93a298110eb2a 100644 (file)
--- a/src/gromacs/commandline/pargs.cpp
+++ b/src/gromacs/commandline/pargs.cpp
@@ -34,27 +34,16 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
-/* This file is completely threadsafe - keep it that way! */
-#include "gromacs/commandline/pargs.h"
+#include "gmxpre.h"
 
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gromacs/commandline/pargs.h"
 
-#include <cctype>
-#include <cstdio>
 #include <cstdlib>
 #include <cstring>
 
 #include <algorithm>
 #include <list>
 
-#ifdef HAVE_UNISTD_H
-#include <unistd.h>
-#endif
-
-#include "thread_mpi/threads.h"
-
 #include "gromacs/commandline/cmdlinehelpcontext.h"
 #include "gromacs/commandline/cmdlinehelpwriter.h"
 #include "gromacs/commandline/cmdlineparser.h"
@@ -423,10 +412,6 @@ void OptionsAdapter::copyValues(bool bReadNode)
     std::list<FileNameData>::const_iterator file;
     for (file = fileNameOptions_.begin(); file != fileNameOptions_.end(); ++file)
     {
-        // FIXME: FF_NOT_READ_NODE should also skip all fexist() calls in
-        // FileNameOption.  However, it is not currently used, and other
-        // commented out code for using it is also outdated, so left this for
-        // later.
         if (!bReadNode && (file->fnm->flag & ffREAD))
         {
             continue;
@@ -439,8 +424,7 @@ void OptionsAdapter::copyValues(bool bReadNode)
         snew(file->fnm->fns, file->fnm->nfiles);
         for (int i = 0; i < file->fnm->nfiles; ++i)
         {
-            // TODO: Check for out-of-memory.
-            file->fnm->fns[i] = strdup(file->values[i].c_str());
+            file->fnm->fns[i] = gmx_strdup(file->values[i].c_str());
         }
     }
     std::list<ProgramArgData>::const_iterator arg;
@@ -493,7 +477,6 @@ gmx_bool parse_common_args(int *argc, char *argv[], unsigned long Flags,
 
     try
     {
-        int                        nicelevel = 0, debug_level = 0;
         double                     tbegin    = 0.0, tend = 0.0, tdelta = 0.0;
         bool                       bView     = false;
         int                        xvgFormat = 0;
@@ -502,16 +485,10 @@ gmx_bool parse_common_args(int *argc, char *argv[], unsigned long Flags,
         gmx::Options               options(NULL, NULL);
         gmx::FileNameOptionManager fileOptManager;
 
-        options.setDescription(gmx::ConstArrayRef<const char *>(desc, ndesc));
-        options.addOption(
-                gmx::IntegerOption("debug").store(&debug_level).hidden()
-                    .description("Write file with debug information, "
-                                 "1: short, 2: also x and f"));
-
-        options.addOption(
-                gmx::IntegerOption("nice").store(&nicelevel)
-                    .defaultValue(FF(PCA_BE_NICE) ? 19 : 0)
-                    .description("Set the nicelevel"));
+        fileOptManager.disableInputOptionChecking(
+                FF(PCA_NOT_READ_NODE) || FF(PCA_DISABLE_INPUT_FILE_CHECKING));
+        options.addManager(&fileOptManager);
+        options.setDescription(gmx::constArrayRefFromArray<const char *>(desc, ndesc));
 
         if (FF(PCA_CAN_SET_DEFFNM))
         {
@@ -572,20 +549,18 @@ gmx_bool parse_common_args(int *argc, char *argv[], unsigned long Flags,
             adapter.pargsToOptions(&options, &pa[i]);
         }
 
-        setManagerForFileNameOptions(&options, &fileOptManager);
-
         const gmx::CommandLineHelpContext *context =
             gmx::GlobalCommandLineHelpContext::get();
         if (context != NULL)
         {
-            if (!(FF(PCA_QUIET)))
-            {
-                gmx::CommandLineHelpWriter(options)
-                    .setShowDescriptions(true)
-                    .setTimeUnitString(timeUnitManager.timeUnitAsString())
-                    .setKnownIssues(gmx::ConstArrayRef<const char *>(bugs, nbugs))
-                    .writeHelp(*context);
-            }
+            GMX_RELEASE_ASSERT(gmx_node_rank() == 0,
+                               "Help output should be handled higher up and "
+                               "only get called only on the master rank");
+            gmx::CommandLineHelpWriter(options)
+                .setShowDescriptions(true)
+                .setTimeUnitString(timeUnitManager.timeUnitAsString())
+                .setKnownIssues(gmx::constArrayRefFromArray(bugs, nbugs))
+                .writeHelp(*context);
             return FALSE;
         }
 
@@ -597,49 +572,7 @@ gmx_bool parse_common_args(int *argc, char *argv[], unsigned long Flags,
         /* set program name, command line, and default values for output options */
         output_env_init(oenv, gmx::getProgramContext(),
                         (time_unit_t)(timeUnitManager.timeUnit() + 1), bView,
-                        (xvg_format_t)(xvgFormat + 1), 0, debug_level);
-
-        /* 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__);
-        }
-
-        /* Set the nice level */
-#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)
-        {
-            static gmx_bool            nice_set   = FALSE; /* only set it once */
-            static tMPI_Thread_mutex_t init_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
-            tMPI_Thread_mutex_lock(&init_mutex);
-            if (!nice_set)
-            {
-                if (nice(nicelevel) == -1)
-                {
-                    /* Do nothing, but use the return value to avoid warnings. */
-                }
-                nice_set = TRUE;
-            }
-            tMPI_Thread_mutex_unlock(&init_mutex);
-        }
-#endif
-#endif
+                        (xvg_format_t)(xvgFormat + 1), 0);
 
         timeUnitManager.scaleTimeOptions(&options);
 
@@ -649,11 +582,11 @@ gmx_bool parse_common_args(int *argc, char *argv[], unsigned long Flags,
         {
             setTimeValue(TBEGIN, tbegin);
         }
-        if (FF(PCA_CAN_END) && options.isSet("-e"))
+        if (FF(PCA_CAN_END) && options.isSet("e"))
         {
             setTimeValue(TEND, tend);
         }
-        if (FF(PCA_CAN_DT) && options.isSet("-dt"))
+        if (FF(PCA_CAN_DT) && options.isSet("dt"))
         {
             setTimeValue(TDELTA, tdelta);
         }