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60
doc/Section_start.html
View File

@ -148,13 +148,24 @@ sub-section.
<P>These are the issues you need to address when editing a low-level
Makefile for your machine. The only portion of the file you should
need to edit is the first line and the "System-specific Settings"
section.
section, which has two parts. The first part lists additional system
libraries needed by certain LAMMPS libraries; see (2). The second
part is compiler and linker settings, as well as MPI and FFT settings;
see (3-9).
</P>
<P>(1) Change the first line of Makefile.foo to list the word "foo" after
the "#", and whatever other options you set. This is the line you
will see if you just type "make".
</P>
<P>(2) Set the paths and flags for your C++ compiler, including
<P>(2) The system library section can be ignored unless you are building
LAMMPS with one or more of the listed LAMMPS packages that use these
libraries. See the <A HREF = "#2_3_4">section below</A> for more details. The
SYSLIB settings are the libraries themselves. The SYSLIBPATH settings
are where they are located on your machine, which is typically only
needed if they are in some non-standard place, that is not in your
library search path.
</P>
<P>(3) Set the paths and flags for your C++ compiler, including
optimization flags. You can use g++, the open-source GNU compiler,
which is available on all Unix systems. Vendor compilers often
produce faster code. On boxes with Intel CPUs, we suggest using the
@ -163,7 +174,7 @@ site</A>.
</P>
<P>(3) If you want LAMMPS to run in parallel, you must have an MPI
<P>(4) If you want LAMMPS to run in parallel, you must have an MPI
library installed on your platform. If you do not use "mpicc" as your
compiler/linker, then Makefile.foo needs to specify where the mpi.h
file (-I switch) and the libmpi.a library (-L switch) is found. If
@ -179,7 +190,7 @@ to enable you to use the same compiler you are using for the LAMMPS
build, which can avoid problems that may arise when linking LAMMPS to
the MPI library.
</P>
<P>(4) If you just want LAMMPS to run on a single processor, you can use
<P>(5) If you just want LAMMPS to run on a single processor, you can use
the STUBS library in place of MPI, since you don't need an MPI library
installed on your system. See the Makefile.serial file for how to
specify the -I and -L switches. You will also need to build the STUBS
@ -194,7 +205,7 @@ you'll need to insert code to call another timer. Note that the
ANSI-standard function clock() rolls over after an hour or so, and is
therefore insufficient for timing long LAMMPS simulations.
</P>
<P>(5) If you want to use the particle-particle particle-mesh (PPPM)
<P>(6) If you want to use the particle-particle particle-mesh (PPPM)
option in LAMMPS for long-range Coulombics, you must have a 1d FFT
library installed on your platform. This is specified by a switch of
the form -DFFT_XXX where XXX = INTEL, DEC, SGI, SCSL, or FFTW. All
@ -212,11 +223,11 @@ places. If you successfully add a new FFT option, like -DFFT_IBM,
please send the <A HREF = "http://lammps.sandia.gov">developers</A> an email; we'd
like to add it to LAMMPS.
</P>
<P>(6) If you don't plan to use PPPM, you don't need an FFT library. Use
<P>(7) If you don't plan to use PPPM, you don't need an FFT library. Use
a -DFFT_NONE switch in the CCFLAGS setting of Makefile.foo, or exclude
the KSPACE package (see below).
</P>
<P>(7) There are a few other -D compiler switches you can set as part of
<P>(8) There are a few other -D compiler switches you can set as part of
CCFLAGS. The read_data and dump commands will read/write gzipped
files if you compile with -DLAMMPS_GZIP. It requires that your Unix
support the "popen" command. Using one of the -DPACK_ARRAY,
@ -228,7 +239,7 @@ format. This is only necessary if your platform does have its own XDR
files available. See the Restrictions section of the <A HREF = "dump.html">dump</A>
command for details.
</P>
<P>(8) The DEPFLAGS setting is how the C++ compiler creates a dependency
<P>(9) The DEPFLAGS setting is how the C++ compiler creates a dependency
file for each source file. This speeds re-compilation when source
(*.cpp) or header (*.h) files are edited. Some compilers do not
support dependency file creation, or may use a different switch than
@ -237,17 +248,6 @@ files (a long list of errors involving *.d files), then you'll need to
create a Makefile.foo patterned after Makefile.tflop, which uses
different rules that do not involve dependency files.
</P>
<P>(9) The comments after the "System-specific Settings" heading refer to
Fortran, BLAS, GPU, etc system libraries. You only need to include
these settings if you intend to build LAMMPS with the optional
packages that use add-on LAMMPS libraries that need these system
libraries. See the <A HREF = "#2_3_3">section below</A> for more details. If you
are not using these packages and their associated LAMMPS libraries,
then you can either comment out the relevant lines in the Makefile, or
leave the setting blank. If you do not do this, and your system does
not have the specified system library (e.g. a BLAS or CUDA library)
then you will get an error when you build LAMMPS.
</P>
<P>That's it. Once you have a correct Makefile.foo and you have
pre-built the MPI and FFT libraries it will use, all you need to do
from the src directory is type one of these 2 commands:
@ -517,24 +517,26 @@ make g++
LAMMPS. You must also include the package that uses and wraps the
library before you build LAMMPS itself.
</P>
<P>As discussed in point (9) of <A HREF = "#2_2_4">this section</A> above, there are
<P>As discussed in point (2) of <A HREF = "#2_2_4">this section</A> above, there are
settings in the low-level Makefile that specify additional system
libraries needed by individual LAMMPS add-on libraries. These are the
settings you must specify correctly in your low-level Makefile in
lammps/src/MAKE, such as Makefile.foo:
</P>
<P>To use the user-atc package and library, the settings for LINKBLAS and
BLASLIB must be correct. This is so that the appropriate BLAS and
LAPACK libs, used by the user-atc library, can be found.
</P>
<P>To use the gpu package and library, the settings for LINKGPU and
GPULIB must be correct. These are specific to the NVIDIA CUDA
<P>To use the gpu package and library, the settings for gpu_SYSLIB and
gpu_SYSLIBPATH must be correct. These are specific to the NVIDIA CUDA
software which must be installed on your system.
</P>
<P>To use the meam or reax packages and their libraries which are Fortran
based, the settings for LINKFORT and FORTLIB must be correct. This is
so that the C++ compiler can perform a cross-language link using the
appropriate system Fortran libraries.
based, the settings for meam_SYSLIB, reax_SYSLIB, meam_SYSLIBPATH, and
reax_SYSLIBPATH must be correct. This is so that the C++ compiler can
perform a cross-language link using the appropriate system Fortran
libraries.
</P>
<P>To use the user-atc package and library, the settings for
user-atc_SYSLIB and user-atc_SYSLIBPATH must be correct. This is so
that the appropriate BLAS and LAPACK libs, used by the user-atc
library, can be found.
</P>
<HR>

60
doc/Section_start.txt
View File

@ -143,13 +143,24 @@ sub-section.
These are the issues you need to address when editing a low-level
Makefile for your machine. The only portion of the file you should
need to edit is the first line and the "System-specific Settings"
section.
section, which has two parts. The first part lists additional system
libraries needed by certain LAMMPS libraries; see (2). The second
part is compiler and linker settings, as well as MPI and FFT settings;
see (3-9).
(1) Change the first line of Makefile.foo to list the word "foo" after
the "#", and whatever other options you set. This is the line you
will see if you just type "make".
(2) Set the paths and flags for your C++ compiler, including
(2) The system library section can be ignored unless you are building
LAMMPS with one or more of the listed LAMMPS packages that use these
libraries. See the "section below"_#2_3_4 for more details. The
SYSLIB settings are the libraries themselves. The SYSLIBPATH settings
are where they are located on your machine, which is typically only
needed if they are in some non-standard place, that is not in your
library search path.
(3) Set the paths and flags for your C++ compiler, including
optimization flags. You can use g++, the open-source GNU compiler,
which is available on all Unix systems. Vendor compilers often
produce faster code. On boxes with Intel CPUs, we suggest using the
@ -158,7 +169,7 @@ site"_intel.
:link(intel,http://www.intel.com/software/products/noncom)
(3) If you want LAMMPS to run in parallel, you must have an MPI
(4) If you want LAMMPS to run in parallel, you must have an MPI
library installed on your platform. If you do not use "mpicc" as your
compiler/linker, then Makefile.foo needs to specify where the mpi.h
file (-I switch) and the libmpi.a library (-L switch) is found. If
@ -174,7 +185,7 @@ to enable you to use the same compiler you are using for the LAMMPS
build, which can avoid problems that may arise when linking LAMMPS to
the MPI library.
(4) If you just want LAMMPS to run on a single processor, you can use
(5) If you just want LAMMPS to run on a single processor, you can use
the STUBS library in place of MPI, since you don't need an MPI library
installed on your system. See the Makefile.serial file for how to
specify the -I and -L switches. You will also need to build the STUBS
@ -189,7 +200,7 @@ you'll need to insert code to call another timer. Note that the
ANSI-standard function clock() rolls over after an hour or so, and is
therefore insufficient for timing long LAMMPS simulations.
(5) If you want to use the particle-particle particle-mesh (PPPM)
(6) If you want to use the particle-particle particle-mesh (PPPM)
option in LAMMPS for long-range Coulombics, you must have a 1d FFT
library installed on your platform. This is specified by a switch of
the form -DFFT_XXX where XXX = INTEL, DEC, SGI, SCSL, or FFTW. All
@ -207,11 +218,11 @@ places. If you successfully add a new FFT option, like -DFFT_IBM,
please send the "developers"_http://lammps.sandia.gov an email; we'd
like to add it to LAMMPS.
(6) If you don't plan to use PPPM, you don't need an FFT library. Use
(7) If you don't plan to use PPPM, you don't need an FFT library. Use
a -DFFT_NONE switch in the CCFLAGS setting of Makefile.foo, or exclude
the KSPACE package (see below).
(7) There are a few other -D compiler switches you can set as part of
(8) There are a few other -D compiler switches you can set as part of
CCFLAGS. The read_data and dump commands will read/write gzipped
files if you compile with -DLAMMPS_GZIP. It requires that your Unix
support the "popen" command. Using one of the -DPACK_ARRAY,
@ -223,7 +234,7 @@ format. This is only necessary if your platform does have its own XDR
files available. See the Restrictions section of the "dump"_dump.html
command for details.
(8) The DEPFLAGS setting is how the C++ compiler creates a dependency
(9) The DEPFLAGS setting is how the C++ compiler creates a dependency
file for each source file. This speeds re-compilation when source
(*.cpp) or header (*.h) files are edited. Some compilers do not
support dependency file creation, or may use a different switch than
@ -232,17 +243,6 @@ files (a long list of errors involving *.d files), then you'll need to
create a Makefile.foo patterned after Makefile.tflop, which uses
different rules that do not involve dependency files.
(9) The comments after the "System-specific Settings" heading refer to
Fortran, BLAS, GPU, etc system libraries. You only need to include
these settings if you intend to build LAMMPS with the optional
packages that use add-on LAMMPS libraries that need these system
libraries. See the "section below"_#2_3_3 for more details. If you
are not using these packages and their associated LAMMPS libraries,
then you can either comment out the relevant lines in the Makefile, or
leave the setting blank. If you do not do this, and your system does
not have the specified system library (e.g. a BLAS or CUDA library)
then you will get an error when you build LAMMPS.
That's it. Once you have a correct Makefile.foo and you have
pre-built the MPI and FFT libraries it will use, all you need to do
from the src directory is type one of these 2 commands:
@ -510,24 +510,26 @@ Note that simply building the library is not sufficient to use it from
LAMMPS. You must also include the package that uses and wraps the
library before you build LAMMPS itself.
As discussed in point (9) of "this section"_#2_2_4 above, there are
As discussed in point (2) of "this section"_#2_2_4 above, there are
settings in the low-level Makefile that specify additional system
libraries needed by individual LAMMPS add-on libraries. These are the
settings you must specify correctly in your low-level Makefile in
lammps/src/MAKE, such as Makefile.foo:
To use the user-atc package and library, the settings for LINKBLAS and
BLASLIB must be correct. This is so that the appropriate BLAS and
LAPACK libs, used by the user-atc library, can be found.
To use the gpu package and library, the settings for LINKGPU and
GPULIB must be correct. These are specific to the NVIDIA CUDA
To use the gpu package and library, the settings for gpu_SYSLIB and
gpu_SYSLIBPATH must be correct. These are specific to the NVIDIA CUDA
software which must be installed on your system.
To use the meam or reax packages and their libraries which are Fortran
based, the settings for LINKFORT and FORTLIB must be correct. This is
so that the C++ compiler can perform a cross-language link using the
appropriate system Fortran libraries.
based, the settings for meam_SYSLIB, reax_SYSLIB, meam_SYSLIBPATH, and
reax_SYSLIBPATH must be correct. This is so that the C++ compiler can
perform a cross-language link using the appropriate system Fortran
libraries.
To use the user-atc package and library, the settings for
user-atc_SYSLIB and user-atc_SYSLIBPATH must be correct. This is so
that the appropriate BLAS and LAPACK libs, used by the user-atc
library, can be found.
:line