If you are installing MPI yourself, we recommend Argonne's MPICH 1.2 -or 2.0 or OpenMPI. MPICH can be downloaded from the Argonne MPI -site. OpenMPI can be downloaded the -OpenMPI site. LAM MPI should also work. If -you are running on a big parallel platform, your system people or the -vendor should have already installed a version of MPI, which will be -faster than MPICH or OpenMPI or LAM, so find out how to build and link -with it. If you use MPICH or OpenMPI or LAM, you will have to +
If you are installing MPI yourself, we recommend Argonne's MPICH2 +or OpenMPI. MPICH can be downloaded from the Argonne MPI +site. OpenMPI can +be downloaded from the OpenMPI site. +Other MPI packages should also work. If you are running on a big +parallel platform, your system people or the vendor should have +already installed a version of MPI, which is likely to be faster +than a self-installed MPICH or OpenMPI, so find out how to build +and link with it. If you use MPICH or OpenMPI, you will have to configure and build it for your platform. The MPI configure script should have compiler options to enable you to use the same compiler you are using for the LAMMPS build, which can avoid problems that can diff --git a/doc/Section_start.txt b/doc/Section_start.txt index 5b8e082868..fad3959e79 100644 --- a/doc/Section_start.txt +++ b/doc/Section_start.txt @@ -243,14 +243,15 @@ Failing this, with these 3 variables you can specify where the mpi.h file (MPI_INC) and the MPI library file (MPI_PATH) are found and the name of the library file (MPI_LIB). -If you are installing MPI yourself, we recommend Argonne's MPICH 1.2 -or 2.0 or OpenMPI. MPICH can be downloaded from the "Argonne MPI -site"_http://www-unix.mcs.anl.gov/mpi. OpenMPI can be downloaded the -"OpenMPI site"_http://www.open-mpi.org. LAM MPI should also work. If -you are running on a big parallel platform, your system people or the -vendor should have already installed a version of MPI, which will be -faster than MPICH or OpenMPI or LAM, so find out how to build and link -with it. If you use MPICH or OpenMPI or LAM, you will have to +If you are installing MPI yourself, we recommend Argonne's MPICH2 +or OpenMPI. MPICH can be downloaded from the "Argonne MPI +site"_http://www.mcs.anl.gov/research/projects/mpich2/. OpenMPI can +be downloaded from the "OpenMPI site"_http://www.open-mpi.org. +Other MPI packages should also work. If you are running on a big +parallel platform, your system people or the vendor should have +already installed a version of MPI, which is likely to be faster +than a self-installed MPICH or OpenMPI, so find out how to build +and link with it. If you use MPICH or OpenMPI, you will have to configure and build it for your platform. The MPI configure script should have compiler options to enable you to use the same compiler you are using for the LAMMPS build, which can avoid problems that can diff --git a/doc/fix_imd.html b/doc/fix_imd.html index 529fa96864..1d89148879 100644 --- a/doc/fix_imd.html +++ b/doc/fix_imd.html @@ -50,10 +50,11 @@ visualization program, so that it can monitor the progress of the simulation and interactively apply forces to selected atoms.
If LAMMPS is compiled with the preprocessor flag -DLAMMPS_ASYNC_IMD -then fix imd will use posix threads to spawn a thread on MPI rank 0 in -order to offload data reading and writing from the main execution -thread and potentiall lower the inferred latencies for slow -communication links. This feature has only been tested under linux. +then fix imd will use POSIX threads to spawn a IMD communication +thread on MPI rank 0 in order to offload data reading and writing +from the main execution thread and potentially lower the inferred +latencies for slow communication links. This feature has only been +tested under linux.
There are example scripts for using this package with LAMMPS in examples/USER/imd. Additional examples and a driver for use with the @@ -155,13 +156,6 @@ This fix is not invoked during energy minimization LAMMPS was built with that package. See the Making LAMMPS section for more info.
-On platforms that support multi-threading, this fix can be compiled in -a way that the coordinate transfers to the IMD client can be handled -from a separate thread, when LAMMPS is compiled with the --DLAMMPS_ASYNC_IMD preprocessor flag. This should to keep MD loop -times low and transfer rates high, especially for systems with many -atoms and for slow connections. -
When used in combination with VMD, a topology or coordinate file has to be loaded, which matches (in number and ordering of atoms) the group the fix is applied to. The fix internally sorts atom IDs by diff --git a/doc/fix_imd.txt b/doc/fix_imd.txt index 246cb36e0c..283755a796 100644 --- a/doc/fix_imd.txt +++ b/doc/fix_imd.txt @@ -42,10 +42,11 @@ visualization program"_VMD, so that it can monitor the progress of the simulation and interactively apply forces to selected atoms. If LAMMPS is compiled with the preprocessor flag -DLAMMPS_ASYNC_IMD -then fix imd will use posix threads to spawn a thread on MPI rank 0 in -order to offload data reading and writing from the main execution -thread and potentiall lower the inferred latencies for slow -communication links. This feature has only been tested under linux. +then fix imd will use POSIX threads to spawn a IMD communication +thread on MPI rank 0 in order to offload data reading and writing +from the main execution thread and potentially lower the inferred +latencies for slow communication links. This feature has only been +tested under linux. There are example scripts for using this package with LAMMPS in examples/USER/imd. Additional examples and a driver for use with the @@ -125,7 +126,7 @@ If IMD control messages are received, a line of text describing the message and its effect will be printed to the LAMMPS output screen, if screen output is active. -:link(VMD,http://www.ks.uiuc.edu/Research/vmd)x +:link(VMD,http://www.ks.uiuc.edu/Research/vmd) :link(imdvmd,http://www.ks.uiuc.edu/Research/vmd/imd/) :link(vrpnicms,http://sites.google.com/site/akohlmey/software/vrpn-icms) @@ -145,13 +146,6 @@ This fix is part of the USER-MISC package. It is only enabled if LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. -On platforms that support multi-threading, this fix can be compiled in -a way that the coordinate transfers to the IMD client can be handled -from a separate thread, when LAMMPS is compiled with the --DLAMMPS_ASYNC_IMD preprocessor flag. This should to keep MD loop -times low and transfer rates high, especially for systems with many -atoms and for slow connections. - When used in combination with VMD, a topology or coordinate file has to be loaded, which matches (in number and ordering of atoms) the group the fix is applied to. The fix internally sorts atom IDs by diff --git a/doc/pair_lj.html b/doc/pair_lj.html index 53a058b324..9283346637 100644 --- a/doc/pair_lj.html +++ b/doc/pair_lj.html @@ -35,8 +35,12 @@
Syntax:
pair_style style args diff --git a/doc/pair_lj.txt b/doc/pair_lj.txt index 09441a9d56..fb97f627d1 100644 --- a/doc/pair_lj.txt +++ b/doc/pair_lj.txt @@ -19,7 +19,9 @@ pair_style lj/cut/coul/debye/cuda command :h3 pair_style lj/cut/coul/long command :h3 pair_style lj/cut/coul/long/cuda command :h3 pair_style lj/cut/coul/long/gpu command :h3 +pair_style lj/cut/coul/long/opt command :h3 pair_style lj/cut/coul/long/tip4p command :h3 +pair_style lj/cut/coul/long/tip4p/opt command :h3 [Syntax:]