forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3243 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
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commit
ac33e812e8
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@ -77,7 +77,7 @@ and build it yourself, as described in the next section.
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</P>
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<UL><LI><A HREF = "#2_2_1">Read this first</A>
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<LI><A HREF = "#2_2_2">Building a LAMMPS executable</A>
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<LI><A HREF = "#2_2_3">Errors that can occur when making LAMMPS</A>
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<LI><A HREF = "#2_2_3">Common errors that can occur when making LAMMPS</A>
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<LI><A HREF = "#2_2_4">Editing a new low-level Makefile</A>
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<LI><A HREF = "#2_2_5">Additional build tips</A>
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</UL>
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@ -127,7 +127,7 @@ produced, you're done; it's your lucky day.
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</P>
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<HR>
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<A NAME = "2_2_3"></A><B><I>Errors that can occur when making LAMMPS:</I></B>
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<A NAME = "2_2_3"></A><B><I>Common errors that can occur when making LAMMPS:</I></B>
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<P>(1) If the make command breaks immediately with errors that indicate
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it can't find files with a "*" in their names, this can be because
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@ -167,16 +167,39 @@ sub-section.
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<P>These are the issues you need to address when editing a low-level
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Makefile for your machine. The portions of the file you typically
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need to edit are the first line, the "system-specific settings"
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section, and the "compiler/linker settings" section.
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need to edit are the first line, the "compiler/linker settings"
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section, and the "system-specific settings" section.
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</P>
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<P>(1) Change the first line of Makefile.foo to list the word "foo" after
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the "#", and whatever other options you set. This is the line you
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will see if you just type "make".
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</P>
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<P>(2) The "system-specific settings" section has 4 parts.
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<P>(3) The "compiler/linker settings" section lists compiler and linker
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settings for your C++ compiler, including optimization flags. You can
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use g++, the open-source GNU compiler, which is available on all Unix
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systems. You can also use mpicc which will typically be available if
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MPI is installed on your system, though you should check which actual
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compiler it wraps. Vendor compilers often produce faster code. On
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boxes with Intel CPUs, we suggest using the free Intel icc compiler,
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which you can download from <A HREF = "http://www.intel.com/software/products/noncom">Intel's compiler site</A>.
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</P>
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<P>(2.1) The LMP_INC variable is used to include options that turn on
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<P>If building a C++ code on your machine requires additional libraries,
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then you should list them as part of the LIB variable.
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</P>
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<P>The DEPFLAGS setting is what triggers the C++ compiler to create a
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dependency list for a source file. This speeds re-compilation when
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source (*.cpp) or header (*.h) files are edited. Some compilers do
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not support dependency file creation, or may use a different switch
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than -D. GNU g++ works with -D. If your compiler can't create
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dependency files (a long list of errors involving *.d files), then
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you'll need to create a Makefile.foo patterned after Makefile.storm,
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which uses different rules that do not involve dependency files.
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</P>
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<P>(3) The "system-specific settings" section has 4 parts.
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</P>
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<P>(3.a) The LMP_INC variable is used to include options that turn on
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system-dependent ifdefs within the LAMMPS code.
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</P>
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<P>The read_data and dump commands will read/write gzipped files if you
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@ -189,15 +212,18 @@ files for doing particle dumps in XTC format. This is only necessary
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if your platform does have its own XDR files available. See the
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Restrictions section of the <A HREF = "dump.html">dump</A> command for details.
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</P>
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<P>(2.2) The 3 MPI variables are used to specify an MPI library to build
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<P>(3.b) The 3 MPI variables are used to specify an MPI library to build
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LAMMPS with.
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</P>
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<P>If you want LAMMPS to run in parallel, you must have an MPI library
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installed on your platform. If you do not use "mpicc" as your
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compiler/linker, then Makefile.foo needs to specify where the mpi.h
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file (MPI_INC) and the MPI library (MPI_PATH) is found and its name
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(MPI_LIB). If you are installing MPI yourself, we recommend Argonne's
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MPICH 1.2 or 2.0 which can be downloaded from the <A HREF = "http://www-unix.mcs.anl.gov/mpi">Argonne MPI
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installed on your platform. If you use an MPI-wrapped compiler, such
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as "mpicc" to build LAMMPS, you can probably leave these 3 variables
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blank. If you do not use "mpicc" as your compiler/linker, then you
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need to specify where the mpi.h file (MPI_INC) and the MPI library
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(MPI_PATH) is found and its name (MPI_LIB).
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</P>
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<P>If you are installing MPI yourself, we recommend Argonne's MPICH 1.2
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or 2.0 which can be downloaded from the <A HREF = "http://www-unix.mcs.anl.gov/mpi">Argonne MPI
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site</A>. LAM MPI should also work. If
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you are running on a big parallel platform, your system people or the
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vendor should have already installed a version of MPI, which will be
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@ -223,12 +249,12 @@ you'll need to insert code to call another timer. Note that the
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ANSI-standard function clock() rolls over after an hour or so, and is
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therefore insufficient for timing long LAMMPS simulations.
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</P>
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<P>(2.3) The 3 FFT variables are used to specify an FFT library which
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<P>(3.c) The 3 FFT variables are used to specify an FFT library which
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LAMMPS uses when using the particle-particle particle-mesh (PPPM)
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option in LAMMPS for long-range Coulombics via the
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<A HREF = "kspace_style.html">kspace_style</A> command.
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</P>
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<P>To use this opttion, you must have a 1d FFT library installed on your
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<P>To use this option, you must have a 1d FFT library installed on your
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platform. This is specified by a switch of the form -DFFT_XXX where
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XXX = INTEL, DEC, SGI, SCSL, or FFTW. All but the last one are native
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vendor-provided libraries. FFTW is a fast, portable library that
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@ -250,7 +276,7 @@ case you can set FFT_INC to -DFFT_NONE and leave the other 2 FFT
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variables blank. Or you can exclude the KSPACE package when you build
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LAMMPS (see below).
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</P>
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<P>(2.4) The several SYSLIB and SYSPATH variables can be ignored unless
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<P>(3.d) The several SYSLIB and SYSPATH variables can be ignored unless
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you are building LAMMPS with one or more of the LAMMPS packages that
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require these extra system libraries. The names of these packages are
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the prefixes on the SYSLIB and SYSPATH variables. See the <A HREF = "#2_3_4">section
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@ -259,30 +285,6 @@ libraries. The SYSPATH variables are where they are located on your
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machine, which is typically only needed if they are in some
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non-standard place, that is not in your library search path.
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</P>
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<P>(3) The "compiler/linker settings" section lists compiler and linker
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settings for your C++ compiler, including optimization flags. You can
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use g++, the open-source GNU compiler, which is available on all Unix
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systems. You can also use mpicc which will typically be available if
|
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MPI is installed on your system, though you should check which actual
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compiler it wraps. Vendor compilers often produce faster code. On
|
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boxes with Intel CPUs, we suggest using the free Intel icc compiler,
|
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which you can download from <A HREF = "http://www.intel.com/software/products/noncom">Intel's compiler site</A>.
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</P>
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<P>If building a C++ code on your machine requires additional libraries,
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then you should list them as part of the LIB variable, after
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EXTRA_LIB.
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</P>
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<P>The DEPFLAGS setting is what triggers the C++ compiler to create a
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dependency list for a source file. This speeds re-compilation when
|
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source (*.cpp) or header (*.h) files are edited. Some compilers do
|
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not support dependency file creation, or may use a different switch
|
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than -D. GNU g++ works with -D. If your compiler can't create
|
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dependency files (a long list of errors involving *.d files), then
|
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you'll need to create a Makefile.foo patterned after Makefile.tflop,
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which uses different rules that do not involve dependency files.
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</P>
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<P>That's it. Once you have a correct Makefile.foo and you have
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pre-built any other libraries it will use (e.g. MPI, FFT, package
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libraries), all you need to do from the src directory is type one of
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|
|
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@ -72,7 +72,7 @@ This section has the following sub-sections:
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"Read this first"_#2_2_1
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"Building a LAMMPS executable"_#2_2_2
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"Errors that can occur when making LAMMPS"_#2_2_3
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"Common errors that can occur when making LAMMPS"_#2_2_3
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"Editing a new low-level Makefile"_#2_2_4
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"Additional build tips"_#2_2_5 :ul
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@ -122,7 +122,7 @@ produced, you're done; it's your lucky day.
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:line
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[{Errors that can occur when making LAMMPS:}] :link(2_2_3)
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[{Common errors that can occur when making LAMMPS:}] :link(2_2_3)
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(1) If the make command breaks immediately with errors that indicate
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it can't find files with a "*" in their names, this can be because
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|
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@ -162,16 +162,39 @@ sub-section.
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|||
|
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These are the issues you need to address when editing a low-level
|
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Makefile for your machine. The portions of the file you typically
|
||||
need to edit are the first line, the "system-specific settings"
|
||||
section, and the "compiler/linker settings" section.
|
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need to edit are the first line, the "compiler/linker settings"
|
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section, and the "system-specific settings" section.
|
||||
|
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(1) Change the first line of Makefile.foo to list the word "foo" after
|
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the "#", and whatever other options you set. This is the line you
|
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will see if you just type "make".
|
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|
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(2) The "system-specific settings" section has 4 parts.
|
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(3) The "compiler/linker settings" section lists compiler and linker
|
||||
settings for your C++ compiler, including optimization flags. You can
|
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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
|
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compiler it wraps. Vendor compilers often produce faster code. On
|
||||
boxes with Intel CPUs, we suggest using the free Intel icc compiler,
|
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which you can download from "Intel's compiler site"_intel.
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(2.1) The LMP_INC variable is used to include options that turn on
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:link(intel,http://www.intel.com/software/products/noncom)
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||||
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If building a C++ code on your machine requires additional libraries,
|
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then you should list them as part of the LIB variable.
|
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|
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The DEPFLAGS setting is what triggers the C++ compiler to create a
|
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dependency list for a source file. This speeds re-compilation when
|
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source (*.cpp) or header (*.h) files are edited. Some compilers do
|
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not support dependency file creation, or may use a different switch
|
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than -D. GNU g++ works with -D. If your compiler can't create
|
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dependency files (a long list of errors involving *.d files), then
|
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you'll need to create a Makefile.foo patterned after Makefile.storm,
|
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which uses different rules that do not involve dependency files.
|
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|
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(3) The "system-specific settings" section has 4 parts.
|
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|
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(3.a) The LMP_INC variable is used to include options that turn on
|
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system-dependent ifdefs within the LAMMPS code.
|
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|
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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
|
||||
Restrictions section of the "dump"_dump.html command for details.
|
||||
|
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(2.2) The 3 MPI variables are used to specify an MPI library to build
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(3.b) The 3 MPI variables are used to specify an MPI library to build
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||||
LAMMPS with.
|
||||
|
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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 (MPI_INC) and the MPI library (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
|
||||
installed on your platform. If you use an MPI-wrapped compiler, such
|
||||
as "mpicc" to build LAMMPS, you can probably leave these 3 variables
|
||||
blank. If you do not use "mpicc" as your compiler/linker, then you
|
||||
need to specify where the mpi.h file (MPI_INC) and the MPI library
|
||||
(MPI_PATH) is found and its name (MPI_LIB).
|
||||
|
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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
|
||||
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
|
||||
|
|
@ -218,12 +244,12 @@ you'll need to insert code to call another timer. Note that the
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ANSI-standard function clock() rolls over after an hour or so, and is
|
||||
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)
|
||||
option in LAMMPS for long-range Coulombics via the
|
||||
"kspace_style"_kspace_style.html command.
|
||||
|
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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
|
||||
XXX = INTEL, DEC, SGI, SCSL, or FFTW. All but the last one are native
|
||||
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
|
||||
LAMMPS (see below).
|
||||
|
||||
(2.4) The several SYSLIB and SYSPATH variables can be ignored unless
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||||
(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
|
||||
require these extra system libraries. The names of these packages are
|
||||
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
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|||
machine, which is typically only needed if they are in some
|
||||
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
|
||||
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
|
||||
|
|
|
|||
Loading…
Reference in New Issue