Merge release-4-6 into master

Change-Id: I86203d25d2e3c1bacdfa58207914830aadd61f4f

diff --git a/share/html/online/mdp_opt.html b/share/html/online/mdp_opt.html
index 637cd9561dcb30687f9c5d3b458f38ba818866df..88a27c21bf34d45a72144314c9157cfe4758afb1 100644 (file)
--- a/share/html/online/mdp_opt.html
+++ b/share/html/online/mdp_opt.html
@@ -443,9 +443,10 @@ while 99.99% of the particles are fine.
 </dl></dd>
 
 <dt><b>nstcalclr: (-1) [steps]</b></dt>
-<dd><dl compact>
-Controls the period between calculations of long-range forces. Useful
-only with <b>cutoff-scheme</b>=<b>group</b>.
+<dd>
+Controls the period between calculations of long-range forces when
+using the group cut-off scheme.
+<dl compact>
 <dt><b>1</b></dt>
 <dd>Calculate the long-range forces every single step. This is useful
 to have separate neighbor lists with buffers for electrostatics and Van
@@ -465,6 +466,7 @@ vary slower than electrostatics.</dd>
 <dd>Calculate long-range forces on steps where neighbor searching is
 performed. While this is the default value, you might want to consider
 updating the long-range forces more frequently.</dd>
+</dl>
 Note that twin-range force evaluation might be enabled automatically
 by PP-PME load balancing. This is done in order to maintain the chosen
 Van der Waals interaction radius even if the load balancing is
@@ -473,7 +475,7 @@ specifies twin-range interactions (e.g. to evaluate Lennard-Jones
 interactions with a longer cutoff than the PME electrostatics every
 2-3 steps), the load balancing will have also a small effect on
 Lennard-Jones, since the short-range cutoff (inside which forces are
-evaluated every step) is changed.</dl>
+evaluated every step) is changed.
 </dd>
 
 
@@ -1106,7 +1108,7 @@ the process ID number.
 <h3>Bonds</h3>
 
 <dl>
-<dt><b>constraints<!--QuietIdx-->constraint algorithms<!--QuietEIdx-->:</b></dt>
+<dt><b>constraints<!--QuietIdx-->constraint algorithms<!--EQuietIdx-->:</b></dt>
 <dd><dl compact>
 <dt><b>none</b></dt>
 <dd>No constraints except for those defined explicitly in the topology,

diff --git a/src/config.h.cmakein b/src/config.h.cmakein
index 6217bda9fa1ef25a22ec7019fbfb712341848c06..ade12fd5464b381d176cbf3cb067764574f5101e 100644 (file)
--- a/src/config.h.cmakein
+++ b/src/config.h.cmakein
@@ -155,9 +155,6 @@
 /* Use OpenMP multithreading */
 #cmakedefine GMX_OPENMP
 
-/* Use old threading (domain decomp force calc) code */
-#cmakedefine GMX_THREAD_SHM_FDECOMP 
-
 /* Ignore calls to nice(3) */
 #cmakedefine GMX_NO_NICE
 

diff --git a/src/contrib/pmetest.c b/src/contrib/pmetest.c
index 55f1d17350e0a9d81c828d962df18b2676e07b5f..494bc32d0f05b992cc9516742f2051be4db75b68 100644 (file)
--- a/src/contrib/pmetest.c
+++ b/src/contrib/pmetest.c
@@ -225,7 +225,6 @@ int main(int argc,char *argv[])
   static gmx_bool bSort=FALSE;
   static int  ewald_geometry=eewg3D;
   static int  nnodes=1;
-  static int  nthreads=1;
   static int  pme_order=0;
   static rvec grid = { -1, -1, -1 };
   static real rc   = 0.0;
@@ -234,8 +233,6 @@ int main(int argc,char *argv[])
   static t_pargs pa[] = {
     { "-np",      FALSE, etINT, {&nnodes},
       "Number of nodes, must be the same as used for [TT]grompp[tt]" },
-    { "-nt",      FALSE, etINT, {&nthreads},
-      "Number of threads to start on each node" },
     { "-v",       FALSE, etBOOL,{&bVerbose},  
       "Be loud and noisy" },
     { "-sort",    FALSE, etBOOL,{&bSort},  
@@ -287,10 +284,6 @@ int main(int argc,char *argv[])
   if (nnodes > 1) 
     gmx_fatal(FARGS,"GROMACS compiled without MPI support - can't do parallel runs");
 #endif
-#ifndef GMX_THREAD_SHM_FDECOMP
-  if(nthreads > 1)
-    gmx_fatal(FARGS,"GROMACS compiled without threads support - can only use one thread");
-#endif
 
   /* Open log files on all processors */
   open_log(ftp2fn(efLOG,NFILE,fnm),cr);

diff --git a/src/gromacs/legacyheaders/types/commrec.h b/src/gromacs/legacyheaders/types/commrec.h
index 1fd00e8ae43b81102e9d0d6317741a182008b931..dddbc4c998f01bff84d3a4401d0abae5f00dbfe6 100644 (file)
--- a/src/gromacs/legacyheaders/types/commrec.h
+++ b/src/gromacs/legacyheaders/types/commrec.h
@@ -258,10 +258,6 @@ typedef struct {
   
 } gmx_nodecomm_t;
 
-typedef struct {
-       int dummy;
-} gmx_commrec_thread_t;
-
 typedef struct {
   /* The nodeids in one sim are numbered sequentially from 0.
    * All communication within some simulation should happen
@@ -282,10 +278,6 @@ typedef struct {
   int nnodes_intra;         /* total number of intra nodes */
   int nnodes_pp_intra;      /* total number of PP intra nodes */
 
-#ifdef GMX_THREAD_SHM_FDECOMP
-  gmx_commrec_thread_t thread;
-#endif
-
   gmx_nodecomm_t nc;
   
   /* For domain decomposition */

diff --git a/src/gromacs/mdlib/ns.c b/src/gromacs/mdlib/ns.c
index 208773dc99a827fc13bb492cb7f90aed6e9caf2d..46a283f2f55f93e4ee38d6302ff6307305d0132a 100644 (file)
--- a/src/gromacs/mdlib/ns.c
+++ b/src/gromacs/mdlib/ns.c
@@ -37,10 +37,6 @@
 #include <config.h>
 #endif
 
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include <pthread.h> 
-#endif
-
 #include <math.h>
 #include <string.h>
 #include "sysstuff.h"
@@ -169,12 +165,6 @@ static void init_nblist(FILE *log, t_nblist *nl_sr,t_nblist *nl_lr,
             fprintf(debug,"Initiating neighbourlist (ielec=%d, ivdw=%d, free=%d) for %s interactions,\nwith %d SR, %d LR atoms.\n",
                     nl->ielec,nl->ivdw,nl->free_energy,gmx_nblist_geometry_names[nl->igeometry],maxsr,maxlr);
         }
-
-#ifdef GMX_THREAD_SHM_FDECOMP
-        nl->counter = 0;
-        snew(nl->mtx,1);
-        pthread_mutex_init(nl->mtx,NULL);
-#endif
     }
 }