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@ -77,7 +77,7 @@ and build it yourself, as described in the next section.
</P> </P>
<UL><LI><A HREF = "#2_2_1">Read this first</A> <UL><LI><A HREF = "#2_2_1">Read this first</A>
<LI><A HREF = "#2_2_2">Building a LAMMPS executable</A> <LI><A HREF = "#2_2_2">Building a LAMMPS executable</A>
<LI><A HREF = "#2_2_3">Errors that can occur when making LAMMPS</A> <LI><A HREF = "#2_2_3">Common errors that can occur when making LAMMPS</A>
<LI><A HREF = "#2_2_4">Editing a new low-level Makefile</A> <LI><A HREF = "#2_2_4">Editing a new low-level Makefile</A>
<LI><A HREF = "#2_2_5">Additional build tips</A> <LI><A HREF = "#2_2_5">Additional build tips</A>
</UL> </UL>
@ -127,7 +127,7 @@ produced, you're done; it's your lucky day.
</P> </P>
<HR> <HR>
<A NAME = "2_2_3"></A><B><I>Errors that can occur when making LAMMPS:</I></B> <A NAME = "2_2_3"></A><B><I>Common errors that can occur when making LAMMPS:</I></B>
<P>(1) If the make command breaks immediately with errors that indicate <P>(1) If the make command breaks immediately with errors that indicate
it can't find files with a "*" in their names, this can be because it can't find files with a "*" in their names, this can be because
@ -167,16 +167,39 @@ sub-section.
<P>These are the issues you need to address when editing a low-level <P>These are the issues you need to address when editing a low-level
Makefile for your machine. The portions of the file you typically Makefile for your machine. The portions of the file you typically
need to edit are the first line, the "system-specific settings" need to edit are the first line, the "compiler/linker settings"
section, and the "compiler/linker settings" section. section, and the "system-specific settings" section.
</P> </P>
<P>(1) Change the first line of Makefile.foo to list the word "foo" after <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 the "#", and whatever other options you set. This is the line you
will see if you just type "make". will see if you just type "make".
</P> </P>
<P>(2) The "system-specific settings" section has 4 parts. <P>(3) The "compiler/linker settings" section lists compiler and linker
settings for your C++ compiler, including optimization flags. You can
use g++, the open-source GNU compiler, which is available on all Unix
systems. You can also use mpicc which will typically be available if
MPI is installed on your system, though you should check which actual
compiler it wraps. Vendor compilers often produce faster code. On
boxes with Intel CPUs, we suggest using the free Intel icc compiler,
which you can download from <A HREF = "http://www.intel.com/software/products/noncom">Intel's compiler site</A>.
</P> </P>
<P>(2.1) The LMP_INC variable is used to include options that turn on
<P>If building a C++ code on your machine requires additional libraries,
then you should list them as part of the LIB variable.
</P>
<P>The DEPFLAGS setting is what triggers the C++ compiler to create a
dependency list for a 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 -D. GNU g++ works with -D. If your compiler can't create
dependency files (a long list of errors involving *.d files), then
you'll need to create a Makefile.foo patterned after Makefile.storm,
which uses different rules that do not involve dependency files.
</P>
<P>(3) The "system-specific settings" section has 4 parts.
</P>
<P>(3.a) The LMP_INC variable is used to include options that turn on
system-dependent ifdefs within the LAMMPS code. system-dependent ifdefs within the LAMMPS code.
</P> </P>
<P>The read_data and dump commands will read/write gzipped files if you <P>The read_data and dump commands will read/write gzipped files if you
@ -189,15 +212,18 @@ files for doing particle dumps in XTC format. This is only necessary
if your platform does have its own XDR files available. See the 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. Restrictions section of the <A HREF = "dump.html">dump</A> command for details.
</P> </P>
<P>(2.2) The 3 MPI variables are used to specify an MPI library to build <P>(3.b) The 3 MPI variables are used to specify an MPI library to build
LAMMPS with. LAMMPS with.
</P> </P>
<P>If you want LAMMPS to run in parallel, you must have an MPI library <P>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 installed on your platform. If you use an MPI-wrapped compiler, such
compiler/linker, then Makefile.foo needs to specify where the mpi.h as "mpicc" to build LAMMPS, you can probably leave these 3 variables
file (MPI_INC) and the MPI library (MPI_PATH) is found and its name blank. If you do not use "mpicc" as your compiler/linker, then you
(MPI_LIB). If you are installing MPI yourself, we recommend Argonne's need to specify where the mpi.h file (MPI_INC) and the MPI library
MPICH 1.2 or 2.0 which can be downloaded from the <A HREF = "http://www-unix.mcs.anl.gov/mpi">Argonne MPI (MPI_PATH) is found and its name (MPI_LIB).
</P>
<P>If you are installing MPI yourself, we recommend Argonne's MPICH 1.2
or 2.0 which can be downloaded from the <A HREF = "http://www-unix.mcs.anl.gov/mpi">Argonne MPI
site</A>. LAM MPI should also work. If site</A>. LAM MPI should also work. If
you are running on a big parallel platform, your system people or the 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 vendor should have already installed a version of MPI, which will be
@ -223,12 +249,12 @@ 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 ANSI-standard function clock() rolls over after an hour or so, and is
therefore insufficient for timing long LAMMPS simulations. therefore insufficient for timing long LAMMPS simulations.
</P> </P>
<P>(2.3) The 3 FFT variables are used to specify an FFT library which <P>(3.c) The 3 FFT variables are used to specify an FFT library which
LAMMPS uses when using the particle-particle particle-mesh (PPPM) LAMMPS uses when using the particle-particle particle-mesh (PPPM)
option in LAMMPS for long-range Coulombics via the option in LAMMPS for long-range Coulombics via the
<A HREF = "kspace_style.html">kspace_style</A> command. <A HREF = "kspace_style.html">kspace_style</A> command.
</P> </P>
<P>To use this opttion, you must have a 1d FFT library installed on your <P>To use this option, you must have a 1d FFT library installed on your
platform. This is specified by a switch of the form -DFFT_XXX where platform. This is specified by a switch of the form -DFFT_XXX where
XXX = INTEL, DEC, SGI, SCSL, or FFTW. All but the last one are native XXX = INTEL, DEC, SGI, SCSL, or FFTW. All but the last one are native
vendor-provided libraries. FFTW is a fast, portable library that vendor-provided libraries. FFTW is a fast, portable library that
@ -250,7 +276,7 @@ case you can set FFT_INC to -DFFT_NONE and leave the other 2 FFT
variables blank. Or you can exclude the KSPACE package when you build variables blank. Or you can exclude the KSPACE package when you build
LAMMPS (see below). LAMMPS (see below).
</P> </P>
<P>(2.4) The several SYSLIB and SYSPATH variables can be ignored unless <P>(3.d) The several SYSLIB and SYSPATH variables can be ignored unless
you are building LAMMPS with one or more of the LAMMPS packages that you are building LAMMPS with one or more of the LAMMPS packages that
require these extra system libraries. The names of these packages are require these extra system libraries. The names of these packages are
the prefixes on the SYSLIB and SYSPATH variables. See the <A HREF = "#2_3_4">section the prefixes on the SYSLIB and SYSPATH variables. See the <A HREF = "#2_3_4">section
@ -259,30 +285,6 @@ libraries. The SYSPATH variables are where they are located on your
machine, which is typically only needed if they are in some machine, which is typically only needed if they are in some
non-standard place, that is not in your library search path. non-standard place, that is not in your library search path.
</P> </P>
<P>(3) The "compiler/linker settings" section lists compiler and linker
settings for your C++ compiler, including optimization flags. You can
use g++, the open-source GNU compiler, which is available on all Unix
systems. You can also use mpicc which will typically be available if
MPI is installed on your system, though you should check which actual
compiler it wraps. Vendor compilers often produce faster code. On
boxes with Intel CPUs, we suggest using the free Intel icc compiler,
which you can download from <A HREF = "http://www.intel.com/software/products/noncom">Intel's compiler site</A>.
</P>
<P>If building a C++ code on your machine requires additional libraries,
then you should list them as part of the LIB variable, after
EXTRA_LIB.
</P>
<P>The DEPFLAGS setting is what triggers the C++ compiler to create a
dependency list for a 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 -D. GNU g++ works with -D. If your compiler can't create
dependency 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>That's it. Once you have a correct Makefile.foo and you have <P>That's it. Once you have a correct Makefile.foo and you have
pre-built any other libraries it will use (e.g. MPI, FFT, package pre-built any other libraries it will use (e.g. MPI, FFT, package
libraries), all you need to do from the src directory is type one of libraries), all you need to do from the src directory is type one of

80
doc/Section_start.txt
View File

@ -72,7 +72,7 @@ This section has the following sub-sections:
"Read this first"_#2_2_1 "Read this first"_#2_2_1
"Building a LAMMPS executable"_#2_2_2 "Building a LAMMPS executable"_#2_2_2
"Errors that can occur when making LAMMPS"_#2_2_3 "Common errors that can occur when making LAMMPS"_#2_2_3
"Editing a new low-level Makefile"_#2_2_4 "Editing a new low-level Makefile"_#2_2_4
"Additional build tips"_#2_2_5 :ul "Additional build tips"_#2_2_5 :ul
@ -122,7 +122,7 @@ produced, you're done; it's your lucky day.
:line :line
[{Errors that can occur when making LAMMPS:}] :link(2_2_3) [{Common errors that can occur when making LAMMPS:}] :link(2_2_3)
(1) If the make command breaks immediately with errors that indicate (1) If the make command breaks immediately with errors that indicate
it can't find files with a "*" in their names, this can be because it can't find files with a "*" in their names, this can be because
@ -162,16 +162,39 @@ sub-section.
These are the issues you need to address when editing a low-level These are the issues you need to address when editing a low-level
Makefile for your machine. The portions of the file you typically Makefile for your machine. The portions of the file you typically
need to edit are the first line, the "system-specific settings" need to edit are the first line, the "compiler/linker settings"
section, and the "compiler/linker settings" section. section, and the "system-specific settings" section.
(1) Change the first line of Makefile.foo to list the word "foo" after (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 the "#", and whatever other options you set. This is the line you
will see if you just type "make". will see if you just type "make".
(2) The "system-specific settings" section has 4 parts. (3) The "compiler/linker settings" section lists compiler and linker
settings for your C++ compiler, including optimization flags. You can
use g++, the open-source GNU compiler, which is available on all Unix
systems. You can also use mpicc which will typically be available if
MPI is installed on your system, though you should check which actual
compiler it wraps. Vendor compilers often produce faster code. On
boxes with Intel CPUs, we suggest using the free Intel icc compiler,
which you can download from "Intel's compiler site"_intel.
(2.1) The LMP_INC variable is used to include options that turn on :link(intel,http://www.intel.com/software/products/noncom)
If building a C++ code on your machine requires additional libraries,
then you should list them as part of the LIB variable.
The DEPFLAGS setting is what triggers the C++ compiler to create a
dependency list for a 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 -D. GNU g++ works with -D. If your compiler can't create
dependency files (a long list of errors involving *.d files), then
you'll need to create a Makefile.foo patterned after Makefile.storm,
which uses different rules that do not involve dependency files.
(3) The "system-specific settings" section has 4 parts.
(3.a) The LMP_INC variable is used to include options that turn on
system-dependent ifdefs within the LAMMPS code. system-dependent ifdefs within the LAMMPS code.
The read_data and dump commands will read/write gzipped files if you The read_data and dump commands will read/write gzipped files if you
@ -184,15 +207,18 @@ files for doing particle dumps in XTC format. This is only necessary
if your platform does have its own XDR files available. See the if your platform does have its own XDR files available. See the
Restrictions section of the "dump"_dump.html command for details. Restrictions section of the "dump"_dump.html command for details.
(2.2) The 3 MPI variables are used to specify an MPI library to build (3.b) The 3 MPI variables are used to specify an MPI library to build
LAMMPS with. LAMMPS with.
If you want LAMMPS to run in parallel, you must have an MPI library 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 installed on your platform. If you use an MPI-wrapped compiler, such
compiler/linker, then Makefile.foo needs to specify where the mpi.h as "mpicc" to build LAMMPS, you can probably leave these 3 variables
file (MPI_INC) and the MPI library (MPI_PATH) is found and its name blank. If you do not use "mpicc" as your compiler/linker, then you
(MPI_LIB). If you are installing MPI yourself, we recommend Argonne's need to specify where the mpi.h file (MPI_INC) and the MPI library
MPICH 1.2 or 2.0 which can be downloaded from the "Argonne MPI (MPI_PATH) is found and its name (MPI_LIB).
If you are installing MPI yourself, we recommend Argonne's MPICH 1.2
or 2.0 which can be downloaded from the "Argonne MPI
site"_http://www-unix.mcs.anl.gov/mpi. LAM MPI should also work. If site"_http://www-unix.mcs.anl.gov/mpi. LAM MPI should also work. If
you are running on a big parallel platform, your system people or the 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 vendor should have already installed a version of MPI, which will be
@ -218,12 +244,12 @@ 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 ANSI-standard function clock() rolls over after an hour or so, and is
therefore insufficient for timing long LAMMPS simulations. therefore insufficient for timing long LAMMPS simulations.
(2.3) The 3 FFT variables are used to specify an FFT library which (3.c) The 3 FFT variables are used to specify an FFT library which
LAMMPS uses when using the particle-particle particle-mesh (PPPM) LAMMPS uses when using the particle-particle particle-mesh (PPPM)
option in LAMMPS for long-range Coulombics via the option in LAMMPS for long-range Coulombics via the
"kspace_style"_kspace_style.html command. "kspace_style"_kspace_style.html command.
To use this opttion, you must have a 1d FFT library installed on your To use this option, you must have a 1d FFT library installed on your
platform. This is specified by a switch of the form -DFFT_XXX where platform. This is specified by a switch of the form -DFFT_XXX where
XXX = INTEL, DEC, SGI, SCSL, or FFTW. All but the last one are native XXX = INTEL, DEC, SGI, SCSL, or FFTW. All but the last one are native
vendor-provided libraries. FFTW is a fast, portable library that vendor-provided libraries. FFTW is a fast, portable library that
@ -245,7 +271,7 @@ case you can set FFT_INC to -DFFT_NONE and leave the other 2 FFT
variables blank. Or you can exclude the KSPACE package when you build variables blank. Or you can exclude the KSPACE package when you build
LAMMPS (see below). LAMMPS (see below).
(2.4) The several SYSLIB and SYSPATH variables can be ignored unless (3.d) The several SYSLIB and SYSPATH variables can be ignored unless
you are building LAMMPS with one or more of the LAMMPS packages that you are building LAMMPS with one or more of the LAMMPS packages that
require these extra system libraries. The names of these packages are require these extra system libraries. The names of these packages are
the prefixes on the SYSLIB and SYSPATH variables. See the "section the prefixes on the SYSLIB and SYSPATH variables. See the "section
@ -254,30 +280,6 @@ libraries. The SYSPATH variables are where they are located on your
machine, which is typically only needed if they are in some machine, which is typically only needed if they are in some
non-standard place, that is not in your library search path. non-standard place, that is not in your library search path.
(3) The "compiler/linker settings" section lists compiler and linker
settings for your C++ compiler, including optimization flags. You can
use g++, the open-source GNU compiler, which is available on all Unix
systems. You can also use mpicc which will typically be available if
MPI is installed on your system, though you should check which actual
compiler it wraps. Vendor compilers often produce faster code. On
boxes with Intel CPUs, we suggest using the free Intel icc compiler,
which you can download from "Intel's compiler site"_intel.
:link(intel,http://www.intel.com/software/products/noncom)
If building a C++ code on your machine requires additional libraries,
then you should list them as part of the LIB variable, after
EXTRA_LIB.
The DEPFLAGS setting is what triggers the C++ compiler to create a
dependency list for a 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 -D. GNU g++ works with -D. If your compiler can't create
dependency 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.
That's it. Once you have a correct Makefile.foo and you have That's it. Once you have a correct Makefile.foo and you have
pre-built any other libraries it will use (e.g. MPI, FFT, package pre-built any other libraries it will use (e.g. MPI, FFT, package
libraries), all you need to do from the src directory is type one of libraries), all you need to do from the src directory is type one of