Remove .tpa, .tpb, .tpx, .trj files. Part of #1500.

[alexxy/gromacs.git] / src / programs / mdrun / runner.cpp

diff --git a/src/programs/mdrun/runner.cpp b/src/programs/mdrun/runner.cpp
index d833b6fb23a3516bd4583583bfeda81fbbd370d9..864b2b729e6e2a2d462e0638b6d36a35ed75120e 100644 (file)
--- a/src/programs/mdrun/runner.cpp
+++ b/src/programs/mdrun/runner.cpp
@@ -35,9 +35,9 @@
  * the research papers on the package. Check out http://www.gromacs.org.
  */
 
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
 
 #include <algorithm>
 
@@ -49,36 +49,36 @@
 #include <unistd.h>
 #endif
 
-#include "typedefs.h"
-#include "oenv.h"
-#include "force.h"
-#include "mdrun.h"
-#include "md_logging.h"
-#include "md_support.h"
-#include "network.h"
-#include "names.h"
-#include "disre.h"
-#include "orires.h"
-#include "pme.h"
-#include "mdatoms.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/md_logging.h"
+#include "gromacs/legacyheaders/md_support.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/disre.h"
+#include "gromacs/legacyheaders/orires.h"
+#include "gromacs/legacyheaders/pme.h"
+#include "gromacs/legacyheaders/mdatoms.h"
 #include "repl_ex.h"
 #include "deform.h"
-#include "qmmm.h"
-#include "domdec.h"
-#include "coulomb.h"
-#include "constr.h"
-#include "mvdata.h"
-#include "checkpoint.h"
+#include "gromacs/legacyheaders/qmmm.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/coulomb.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/mvdata.h"
+#include "gromacs/legacyheaders/checkpoint.h"
 #include "gromacs/topology/mtop_util.h"
-#include "sighandler.h"
-#include "txtdump.h"
-#include "gmx_detect_hardware.h"
-#include "gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/sighandler.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/gmx_detect_hardware.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/gmxpreprocess/calc_verletbuf.h"
 #include "membed.h"
-#include "gmx_thread_affinity.h"
-#include "inputrec.h"
-#include "main.h"
+#include "gromacs/legacyheaders/gmx_thread_affinity.h"
+#include "gromacs/legacyheaders/inputrec.h"
+#include "gromacs/legacyheaders/main.h"
 
 #include "gromacs/essentialdynamics/edsam.h"
 #include "gromacs/fileio/tpxio.h"
@@ -98,8 +98,7 @@
 #include "corewrap.h"
 #endif
 
-#include "gpu_utils.h"
-#include "nbnxn_cuda_data_mgmt.h"
+#include "gromacs/legacyheaders/gpu_utils.h"
 
 typedef struct {
     gmx_integrator_t *func;
@@ -1039,47 +1038,6 @@ static void override_nsteps_cmdline(FILE            *fplog,
     }
 }
 
-/* Frees GPU memory and destroys the CUDA context.
- *
- * Note that this function needs to be called even if GPUs are not used
- * in this run because the PME ranks have no knowledge of whether GPUs
- * are used or not, but all ranks need to enter the barrier below.
- */
-static void free_gpu_resources(const t_forcerec *fr,
-                               const t_commrec  *cr)
-{
-    gmx_bool bIsPPrankUsingGPU;
-    char     gpu_err_str[STRLEN];
-
-    bIsPPrankUsingGPU = (cr->duty & DUTY_PP) && fr != NULL && fr->nbv != NULL && fr->nbv->bUseGPU;
-
-    if (bIsPPrankUsingGPU)
-    {
-        /* free nbnxn data in GPU memory */
-        nbnxn_cuda_free(fr->nbv->cu_nbv);
-
-        /* With tMPI we need to wait for all ranks to finish deallocation before
-         * destroying the context in free_gpu() as some ranks may be sharing
-         * GPU and context.
-         * Note: as only PP ranks need to free GPU resources, so it is safe to
-         * not call the barrier on PME ranks.
-         */
-#ifdef GMX_THREAD_MPI
-        if (PAR(cr))
-        {
-            gmx_barrier(cr);
-        }
-#endif  /* GMX_THREAD_MPI */
-
-        /* uninitialize GPU (by destroying the context) */
-        if (!free_gpu(gpu_err_str))
-        {
-            gmx_warning("On rank %d failed to free GPU #%d: %s",
-                        cr->nodeid, get_current_gpu_device_id(), gpu_err_str);
-        }
-    }
-}
-
 int mdrunner(gmx_hw_opt_t *hw_opt,
              FILE *fplog, t_commrec *cr, int nfile,
              const t_filenm fnm[], const output_env_t oenv, gmx_bool bVerbose,
@@ -1145,7 +1103,7 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
     if (SIMMASTER(cr))
     {
         /* Read (nearly) all data required for the simulation */
-        read_tpx_state(ftp2fn(efTPX, nfile, fnm), inputrec, state, NULL, mtop);
+        read_tpx_state(ftp2fn(efTPR, nfile, fnm), inputrec, state, NULL, mtop);
 
         if (inputrec->cutoff_scheme != ecutsVERLET &&
             ((Flags & MD_TESTVERLET) || getenv("GMX_VERLET_SCHEME") != NULL))
@@ -1414,16 +1372,9 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
         }
     }
 
-    if (((MASTER(cr) || (Flags & MD_SEPPOT)) && (Flags & MD_APPENDFILES))
-#ifdef GMX_THREAD_MPI
-        /* With thread MPI only the master node/thread exists in mdrun.c,
-         * therefore non-master nodes need to open the "seppot" log file here.
-         */
-        || (!MASTER(cr) && (Flags & MD_SEPPOT))
-#endif
-        )
+    if (MASTER(cr) && (Flags & MD_APPENDFILES))
     {
-        gmx_log_open(ftp2fn(efLOG, nfile, fnm), cr, !(Flags & MD_SEPPOT),
+        gmx_log_open(ftp2fn(efLOG, nfile, fnm), cr,
                      Flags, &fplog);
     }
 
@@ -1596,7 +1547,6 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
         /*init_forcerec(fplog,fr,fcd,inputrec,mtop,cr,box,FALSE,
            "nofile","nofile","nofile","nofile",FALSE,pforce);
          */
-        fr->bSepDVDL = ((Flags & MD_SEPPOT) == MD_SEPPOT);
 
         /* Initialize QM-MM */
         if (fr->bQMMM)
@@ -1795,8 +1745,7 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
      */
     finish_run(fplog, cr,
                inputrec, nrnb, wcycle, walltime_accounting,
-               fr != NULL && fr->nbv != NULL && fr->nbv->bUseGPU ?
-               nbnxn_cuda_get_timings(fr->nbv->cu_nbv) : NULL,
+               fr ? fr->nbv : NULL,
                EI_DYNAMICS(inputrec->eI) && !MULTISIM(cr));