forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8615 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
3fea520ef9
commit
6908ce6e9d
|
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@ -85,38 +85,18 @@ that Python checks.
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<P>The first is the environment variable PYTHONPATH. It needs
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to include the directory where the python/lammps.py file is.
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</P>
|
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<P>For the csh or tcsh shells, you could add something like this to your
|
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~/.cshrc file:
|
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<P>For the csh or tcsh shells, add something like this to your ~/.cshrc
|
||||
file:
|
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</P>
|
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<PRE>setenv PYTHONPATH $<I>PYTHONPATH</I>:/home/sjplimp/lammps/python
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</PRE>
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<P>The second is the environment variable LD_LIBRARY_PATH, which is used
|
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by the operating system to find dynamic shared libraries when it loads
|
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them. It needs to include the directory where the shared LAMMPS
|
||||
library will be. Normally this is the LAMMPS src dir, as explained in
|
||||
the following section.
|
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them. See the discussion in <A HREF = "Section_start.html#start_5">Section_start
|
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5</A> of the manual about building LAMMPS as a
|
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shared library, for instructions on how to set the LD_LIBRARY_PATH
|
||||
variable appropriately.
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</P>
|
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<P>For the csh or tcsh shells, you could add something like this to your
|
||||
~/.cshrc file:
|
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</P>
|
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<PRE>setenv LD_LIBRARY_PATH $<I>LD_LIBRARY_PATH</I>:/home/sjplimp/lammps/src
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</PRE>
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<P>As discussed below, if your LAMMPS build includes auxiliary libraries,
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they must also be available as shared libraries for Python to
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successfully load LAMMPS. If they are not in default places where the
|
||||
operating system can find them, then you also have to add their paths
|
||||
to the LD_LIBRARY_PATH environment variable.
|
||||
</P>
|
||||
<P>For example, if you are using the dummy MPI library provided in
|
||||
src/STUBS, you need to add something like this to your ~/.cshrc file:
|
||||
</P>
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<PRE>setenv LD_LIBRARY_PATH $<I>LD_LIBRARY_PATH</I>:/home/sjplimp/lammps/src/STUBS
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</PRE>
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<P>If you are using the LAMMPS USER-ATC package, you need to add
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something like this to your ~/.cshrc file:
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</P>
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<PRE>setenv LD_LIBRARY_PATH $<I>LD_LIBRARY_PATH</I>:/home/sjplimp/lammps/lib/atc
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</PRE>
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<HR>
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<A NAME = "py_2"></A><H4>11.2 Building LAMMPS as a shared library
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@ -126,11 +106,11 @@ something like this to your ~/.cshrc file:
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that is dynamically loadable, which is what Python requires. On Linux
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this is a library file that ends in ".so", not ".a".
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</P>
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<P>>From the src directory, type
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</P>
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<P>make makeshlib
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make -f Makefile.shlib foo
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<P>From the src directory, type
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</P>
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<PRE>make makeshlib
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make -f Makefile.shlib foo
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</PRE>
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<P>where foo is the machine target name, such as linux or g++ or serial.
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This should create the file liblmp_foo.so in the src directory, as
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well as a soft link liblmp.so which is what the Python wrapper will
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|
|
@ -138,47 +118,7 @@ load by default. If you are building multiple machine versions of the
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shared library, the soft link is always set to the most recently built
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version.
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</P>
|
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<P>Note that as discussed in below, a LAMMPS build may depend on several
|
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auxiliary libraries, which are specified in your low-level
|
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src/Makefile.foo file. For example, an MPI library, the FFTW library,
|
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a JPEG library, etc. Depending on what LAMMPS packages you have
|
||||
installed, the build may also require additional libraries from the
|
||||
lib directories, such as lib/atc/libatc.so or lib/reax/libreax.so.
|
||||
</P>
|
||||
<P>You must insure that each of these libraries exist in shared library
|
||||
form (*.so file for Linux systems), or either the LAMMPS shared
|
||||
library build or the Python load of the library will fail. For the
|
||||
load to be successful all the shared libraries must also be in
|
||||
directories that the operating system checks. See the discussion in
|
||||
the preceding section about the LD_LIBRARY_PATH environment variable
|
||||
for how to insure this.
|
||||
</P>
|
||||
<P>Note that some system libraries, such as MPI, if you installed it
|
||||
yourself, may not be built by default as shared libraries. The build
|
||||
instructions for the library should tell you how to do this.
|
||||
</P>
|
||||
<P>For example, here is how to build and install the <A HREF = "http://www-unix.mcs.anl.gov/mpi">MPICH
|
||||
library</A>, a popular open-source version of MPI, distributed by
|
||||
Argonne National Labs, as a shared library in the default
|
||||
/usr/local/lib location:
|
||||
</P>
|
||||
|
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|
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<PRE>./configure --enable-shared
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make
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make install
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</PRE>
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<P>You may need to use "sudo make install" in place of the last line if
|
||||
you do not have write priveleges for /usr/local/lib. The end result
|
||||
should be the file /usr/local/lib/libmpich.so.
|
||||
</P>
|
||||
<P>Note that not all of the auxiliary libraries provided with LAMMPS have
|
||||
shared-library Makefiles in their lib directories. Typically this
|
||||
simply requires a Makefile.foo that adds a -fPIC switch when files are
|
||||
compiled and a "-fPIC -shared" switches when the library is linked
|
||||
with a C++ (or Fortran) compiler, as well as an output target that
|
||||
ends in ".so", like libatc.o. As we or others create and contribute
|
||||
these Makefiles, we will add them to the LAMMPS distribution.
|
||||
<P>See <A HREF = "Section_start.html#start_5">Section_start 5</A> for more details.
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</P>
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<HR>
|
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|
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|
@ -197,7 +137,7 @@ as a library and allow MPI functions to be called from Python.
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<LI><A HREF = "http://code.google.com/p/maroonmpi/">maroonmpi</A>
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<LI><A HREF = "http://code.google.com/p/mpi4py/">mpi4py</A>
|
||||
<LI><A HREF = "http://nbcr.sdsc.edu/forum/viewtopic.php?t=89&sid=c997fefc3933bd66204875b436940f16">myMPI</A>
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||||
<LI><A HREF = "http://datamining.anu.edu.au/~ole/pypar">Pypar</A>
|
||||
<LI><A HREF = "http://code.google.com/p/pypar">Pypar</A>
|
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</UL>
|
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<P>All of these except pyMPI work by wrapping the MPI library (which must
|
||||
be available on your system as a shared library, as discussed above),
|
||||
|
|
@ -272,7 +212,7 @@ and type:
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|||
<P>If you get no errors, you're ready to use LAMMPS from Python.
|
||||
If the load fails, the most common error to see is
|
||||
</P>
|
||||
<P>"CDLL: asdfasdfasdf"
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<P>OSError: Could not load LAMMPS dynamic library
|
||||
</P>
|
||||
<P>which means Python was unable to load the LAMMPS shared library. This
|
||||
can occur if it can't find the LAMMMPS library; see the environment
|
||||
|
|
|
|||
|
|
@ -81,37 +81,17 @@ that Python checks.
|
|||
The first is the environment variable PYTHONPATH. It needs
|
||||
to include the directory where the python/lammps.py file is.
|
||||
|
||||
For the csh or tcsh shells, you could add something like this to your
|
||||
~/.cshrc file:
|
||||
For the csh or tcsh shells, add something like this to your ~/.cshrc
|
||||
file:
|
||||
|
||||
setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/python :pre
|
||||
|
||||
The second is the environment variable LD_LIBRARY_PATH, which is used
|
||||
by the operating system to find dynamic shared libraries when it loads
|
||||
them. It needs to include the directory where the shared LAMMPS
|
||||
library will be. Normally this is the LAMMPS src dir, as explained in
|
||||
the following section.
|
||||
|
||||
For the csh or tcsh shells, you could add something like this to your
|
||||
~/.cshrc file:
|
||||
|
||||
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src :pre
|
||||
|
||||
As discussed below, if your LAMMPS build includes auxiliary libraries,
|
||||
they must also be available as shared libraries for Python to
|
||||
successfully load LAMMPS. If they are not in default places where the
|
||||
operating system can find them, then you also have to add their paths
|
||||
to the LD_LIBRARY_PATH environment variable.
|
||||
|
||||
For example, if you are using the dummy MPI library provided in
|
||||
src/STUBS, you need to add something like this to your ~/.cshrc file:
|
||||
|
||||
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src/STUBS :pre
|
||||
|
||||
If you are using the LAMMPS USER-ATC package, you need to add
|
||||
something like this to your ~/.cshrc file:
|
||||
|
||||
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/lib/atc :pre
|
||||
them. See the discussion in "Section_start
|
||||
5"_Section_start.html#start_5 of the manual about building LAMMPS as a
|
||||
shared library, for instructions on how to set the LD_LIBRARY_PATH
|
||||
variable appropriately.
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -122,10 +102,10 @@ Instructions on how to build LAMMPS as a shared library are given in
|
|||
that is dynamically loadable, which is what Python requires. On Linux
|
||||
this is a library file that ends in ".so", not ".a".
|
||||
|
||||
>From the src directory, type
|
||||
From the src directory, type
|
||||
|
||||
make makeshlib
|
||||
make -f Makefile.shlib foo
|
||||
make -f Makefile.shlib foo :pre
|
||||
|
||||
where foo is the machine target name, such as linux or g++ or serial.
|
||||
This should create the file liblmp_foo.so in the src directory, as
|
||||
|
|
@ -134,47 +114,7 @@ load by default. If you are building multiple machine versions of the
|
|||
shared library, the soft link is always set to the most recently built
|
||||
version.
|
||||
|
||||
Note that as discussed in below, a LAMMPS build may depend on several
|
||||
auxiliary libraries, which are specified in your low-level
|
||||
src/Makefile.foo file. For example, an MPI library, the FFTW library,
|
||||
a JPEG library, etc. Depending on what LAMMPS packages you have
|
||||
installed, the build may also require additional libraries from the
|
||||
lib directories, such as lib/atc/libatc.so or lib/reax/libreax.so.
|
||||
|
||||
You must insure that each of these libraries exist in shared library
|
||||
form (*.so file for Linux systems), or either the LAMMPS shared
|
||||
library build or the Python load of the library will fail. For the
|
||||
load to be successful all the shared libraries must also be in
|
||||
directories that the operating system checks. See the discussion in
|
||||
the preceding section about the LD_LIBRARY_PATH environment variable
|
||||
for how to insure this.
|
||||
|
||||
Note that some system libraries, such as MPI, if you installed it
|
||||
yourself, may not be built by default as shared libraries. The build
|
||||
instructions for the library should tell you how to do this.
|
||||
|
||||
For example, here is how to build and install the "MPICH
|
||||
library"_mpich, a popular open-source version of MPI, distributed by
|
||||
Argonne National Labs, as a shared library in the default
|
||||
/usr/local/lib location:
|
||||
|
||||
:link(mpich,http://www-unix.mcs.anl.gov/mpi)
|
||||
|
||||
./configure --enable-shared
|
||||
make
|
||||
make install :pre
|
||||
|
||||
You may need to use "sudo make install" in place of the last line if
|
||||
you do not have write priveleges for /usr/local/lib. The end result
|
||||
should be the file /usr/local/lib/libmpich.so.
|
||||
|
||||
Note that not all of the auxiliary libraries provided with LAMMPS have
|
||||
shared-library Makefiles in their lib directories. Typically this
|
||||
simply requires a Makefile.foo that adds a -fPIC switch when files are
|
||||
compiled and a "-fPIC -shared" switches when the library is linked
|
||||
with a C++ (or Fortran) compiler, as well as an output target that
|
||||
ends in ".so", like libatc.o. As we or others create and contribute
|
||||
these Makefiles, we will add them to the LAMMPS distribution.
|
||||
See "Section_start 5"_Section_start.html#start_5 for more details.
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -193,7 +133,7 @@ These include
|
|||
"maroonmpi"_http://code.google.com/p/maroonmpi/
|
||||
"mpi4py"_http://code.google.com/p/mpi4py/
|
||||
"myMPI"_http://nbcr.sdsc.edu/forum/viewtopic.php?t=89&sid=c997fefc3933bd66204875b436940f16
|
||||
"Pypar"_http://datamining.anu.edu.au/~ole/pypar :ul
|
||||
"Pypar"_http://code.google.com/p/pypar :ul
|
||||
|
||||
All of these except pyMPI work by wrapping the MPI library (which must
|
||||
be available on your system as a shared library, as discussed above),
|
||||
|
|
@ -229,6 +169,11 @@ sudo python setup.py install :pre
|
|||
The "sudo" is only needed if required to copy Numpy files into your
|
||||
Python distribution's site-packages directory.
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
To install Pypar (version pypar-2.1.0_66 as of April 2009), unpack it
|
||||
and from its "source" directory, type
|
||||
|
||||
|
|
@ -268,7 +213,10 @@ and type:
|
|||
If you get no errors, you're ready to use LAMMPS from Python.
|
||||
If the load fails, the most common error to see is
|
||||
|
||||
"CDLL: asdfasdfasdf"
|
||||
|
||||
OSError: Could not load LAMMPS dynamic library
|
||||
|
||||
|
||||
|
||||
which means Python was unable to load the LAMMPS shared library. This
|
||||
can occur if it can't find the LAMMMPS library; see the environment
|
||||
|
|
|
|||
|
|
@ -785,15 +785,15 @@ more info on wrapping and running LAMMPS from Python.
|
|||
make -f Makefile.lib foo
|
||||
</PRE>
|
||||
<P>where foo is the machine name. This kind of library is typically used
|
||||
to statically link a driver application to all of LAMMPS, so that you
|
||||
can insure all dependencies are satisfied at compile time. Note that
|
||||
to statically link a driver application to LAMMPS, so that you can
|
||||
insure all dependencies are satisfied at compile time. Note that
|
||||
inclusion or exclusion of any desired optional packages should be done
|
||||
before typing "make makelib". The first "make" command will create a
|
||||
current Makefile.lib with all the file names in your src dir. The 2nd
|
||||
"make" command will use it to build LAMMPS as a static library, using
|
||||
the ARCHIVE and ARFLAGS settings in src/MAKE/Makefile.foo. The build
|
||||
will create the file liblmp_foo.a which another application can link
|
||||
to.
|
||||
current Makefile.lib with all the file names in your src dir. The
|
||||
second "make" command will use it to build LAMMPS as a static library,
|
||||
using the ARCHIVE and ARFLAGS settings in src/MAKE/Makefile.foo. The
|
||||
build will create the file liblmp_foo.a which another application can
|
||||
link to.
|
||||
</P>
|
||||
<P>To build LAMMPS as a shared library (*.so file on Linux), which can be
|
||||
dynamically loaded, type
|
||||
|
|
@ -806,7 +806,7 @@ wrapping LAMMPS with Python; see <A HREF = "Section_python.html">Section_python<
|
|||
for details. Again, note that inclusion or exclusion of any desired
|
||||
optional packages should be done before typing "make makelib". The
|
||||
first "make" command will create a current Makefile.shlib with all the
|
||||
file names in your src dir. The 2nd "make" command will use it to
|
||||
file names in your src dir. The second "make" command will use it to
|
||||
build LAMMPS as a shared library, using the SHFLAGS and SHLIBFLAGS
|
||||
settings in src/MAKE/Makefile.foo. The build will create the file
|
||||
liblmp_foo.so which another application can link to dyamically, as
|
||||
|
|
@ -815,15 +815,87 @@ default.
|
|||
</P>
|
||||
<P>Note that for a shared library to be usable by a calling program, all
|
||||
the auxiliary libraries it depends on must also exist as shared
|
||||
libraries, and be find-able by the operating system. Else you will
|
||||
get a run-time error when the shared library is loaded. For LAMMPS,
|
||||
this includes all libraries needed by main LAMMPS (e.g. MPI or FFTW or
|
||||
JPEG), system libraries needed by main LAMMPS (e.g. extra libs needed
|
||||
by MPI), or packages you have installed that require libraries
|
||||
libraries, and the operating system must be able to find them. For
|
||||
LAMMPS, this includes all libraries needed by main LAMMPS (e.g. MPI or
|
||||
FFTW or JPEG), system libraries needed by main LAMMPS (e.g. extra libs
|
||||
needed by MPI), or packages you have installed that require libraries
|
||||
provided with LAMMPS (e.g. the USER-ATC package require
|
||||
lib/atc/libatc.so) or system libraries (e.g. BLAS or Fortran-to-C
|
||||
libraries) listed in the lib/package/Makefile.lammps file. See the
|
||||
discussion about the LAMMPS shared library in
|
||||
libraries) listed in the lib/package/Makefile.lammps file.
|
||||
</P>
|
||||
<P>If one of these auxiliary libraries does not exist as a shared
|
||||
library, the second make command should generate a build error. The
|
||||
build will not generate an error, if a needed library is simply
|
||||
missing from the link list; this will generate a run-time error when
|
||||
the library is loaded, so be sure all needed libraries are listed,
|
||||
as they would be when building LAMMPS as a stand-alone code.
|
||||
</P>
|
||||
<P>Note that if you install them yourself, some libraries, such as MPI,
|
||||
may not build by default as shared libraries. The build instructions
|
||||
for the library should tell you how to do this.
|
||||
</P>
|
||||
<P>For example, here is how to build and install the <A HREF = "http://www-unix.mcs.anl.gov/mpi">MPICH
|
||||
library</A>, a popular open-source version of MPI, distributed by
|
||||
Argonne National Labs, as a shared library in the default
|
||||
/usr/local/lib location:
|
||||
</P>
|
||||
|
||||
|
||||
<PRE>./configure --enable-shared
|
||||
make
|
||||
make install
|
||||
</PRE>
|
||||
<P>You may need to use "sudo make install" in place of the last line if
|
||||
you do not have write priveleges for /usr/local/lib. The end result
|
||||
should be the file /usr/local/lib/libmpich.so.
|
||||
</P>
|
||||
<P>Also note that not all of the auxiliary libraries provided with LAMMPS
|
||||
include Makefiles in their lib directories for building them as shared
|
||||
libraries. Typically this simply requires adding a -fPIC switch when
|
||||
files are compiled and "-fPIC -shared" switches when the library is
|
||||
linked with a C++ (or Fortran) compiler, and creating an output target
|
||||
that ends in ".so", like libatc.o. As we or others create and
|
||||
contribute these Makefiles, we will add them to the LAMMPS
|
||||
distribution.
|
||||
</P>
|
||||
<P>You must insure that each of these libraries exist in shared library
|
||||
form (*.so file for Linux systems), or either the LAMMPS shared
|
||||
library build or the Python load of the library will fail. For the
|
||||
load to be successful all the shared libraries must also be in
|
||||
directories that the operating system checks. See the discussion in
|
||||
the preceding section about the LD_LIBRARY_PATH environment variable
|
||||
for how to insure this.
|
||||
</P>
|
||||
<P>The second is the environment variable LD_LIBRARY_PATH, which is used
|
||||
by the operating system to find dynamic shared libraries when it loads
|
||||
them.
|
||||
</P>
|
||||
<P>It needs to include the directory where the shared LAMMPS
|
||||
library will be. Normally this is the LAMMPS src dir, as explained in
|
||||
the following section.
|
||||
</P>
|
||||
<P>For the csh or tcsh shells, you could add something like this to your
|
||||
~/.cshrc file:
|
||||
</P>
|
||||
<PRE>setenv LD_LIBRARY_PATH $<I>LD_LIBRARY_PATH</I>:/home/sjplimp/lammps/src
|
||||
</PRE>
|
||||
<P>As discussed below, if your LAMMPS build includes auxiliary libraries,
|
||||
they must also be available as shared libraries for Python to
|
||||
successfully load LAMMPS. If they are not in default places where the
|
||||
operating system can find them, then you also have to add their paths
|
||||
to the LD_LIBRARY_PATH environment variable.
|
||||
</P>
|
||||
<P>For example, if you are using the dummy MPI library provided in
|
||||
src/STUBS, you need to add something like this to your ~/.cshrc file:
|
||||
</P>
|
||||
<PRE>setenv LD_LIBRARY_PATH $<I>LD_LIBRARY_PATH</I>:/home/sjplimp/lammps/src/STUBS
|
||||
</PRE>
|
||||
<P>If you are using the LAMMPS USER-ATC package, you need to add
|
||||
something like this to your ~/.cshrc file:
|
||||
</P>
|
||||
<PRE>setenv LD_LIBRARY_PATH $<I>LD_LIBRARY_PATH</I>:/home/sjplimp/lammps/lib/atc
|
||||
</PRE>
|
||||
<P>See the discussion about the LAMMPS shared library in
|
||||
<A HREF = "Section_python.html">Section_python</A> for details about how to build
|
||||
shared versions of these libraries, and how to insure the operating
|
||||
system can find them, by setting the LD_LIBRARY_PATH environment
|
||||
|
|
|
|||
|
|
@ -779,15 +779,15 @@ make makelib
|
|||
make -f Makefile.lib foo :pre
|
||||
|
||||
where foo is the machine name. This kind of library is typically used
|
||||
to statically link a driver application to all of LAMMPS, so that you
|
||||
can insure all dependencies are satisfied at compile time. Note that
|
||||
to statically link a driver application to LAMMPS, so that you can
|
||||
insure all dependencies are satisfied at compile time. Note that
|
||||
inclusion or exclusion of any desired optional packages should be done
|
||||
before typing "make makelib". The first "make" command will create a
|
||||
current Makefile.lib with all the file names in your src dir. The 2nd
|
||||
"make" command will use it to build LAMMPS as a static library, using
|
||||
the ARCHIVE and ARFLAGS settings in src/MAKE/Makefile.foo. The build
|
||||
will create the file liblmp_foo.a which another application can link
|
||||
to.
|
||||
current Makefile.lib with all the file names in your src dir. The
|
||||
second "make" command will use it to build LAMMPS as a static library,
|
||||
using the ARCHIVE and ARFLAGS settings in src/MAKE/Makefile.foo. The
|
||||
build will create the file liblmp_foo.a which another application can
|
||||
link to.
|
||||
|
||||
To build LAMMPS as a shared library (*.so file on Linux), which can be
|
||||
dynamically loaded, type
|
||||
|
|
@ -800,7 +800,7 @@ wrapping LAMMPS with Python; see "Section_python"_Section_python.html
|
|||
for details. Again, note that inclusion or exclusion of any desired
|
||||
optional packages should be done before typing "make makelib". The
|
||||
first "make" command will create a current Makefile.shlib with all the
|
||||
file names in your src dir. The 2nd "make" command will use it to
|
||||
file names in your src dir. The second "make" command will use it to
|
||||
build LAMMPS as a shared library, using the SHFLAGS and SHLIBFLAGS
|
||||
settings in src/MAKE/Makefile.foo. The build will create the file
|
||||
liblmp_foo.so which another application can link to dyamically, as
|
||||
|
|
@ -809,20 +809,106 @@ default.
|
|||
|
||||
Note that for a shared library to be usable by a calling program, all
|
||||
the auxiliary libraries it depends on must also exist as shared
|
||||
libraries, and be find-able by the operating system. Else you will
|
||||
get a run-time error when the shared library is loaded. For LAMMPS,
|
||||
this includes all libraries needed by main LAMMPS (e.g. MPI or FFTW or
|
||||
JPEG), system libraries needed by main LAMMPS (e.g. extra libs needed
|
||||
by MPI), or packages you have installed that require libraries
|
||||
libraries, and the operating system must be able to find them. For
|
||||
LAMMPS, this includes all libraries needed by main LAMMPS (e.g. MPI or
|
||||
FFTW or JPEG), system libraries needed by main LAMMPS (e.g. extra libs
|
||||
needed by MPI), or packages you have installed that require libraries
|
||||
provided with LAMMPS (e.g. the USER-ATC package require
|
||||
lib/atc/libatc.so) or system libraries (e.g. BLAS or Fortran-to-C
|
||||
libraries) listed in the lib/package/Makefile.lammps file. See the
|
||||
discussion about the LAMMPS shared library in
|
||||
libraries) listed in the lib/package/Makefile.lammps file.
|
||||
|
||||
If one of these auxiliary libraries does not exist as a shared
|
||||
library, the second make command should generate a build error. The
|
||||
build will not generate an error, if a needed library is simply
|
||||
missing from the link list; this will generate a run-time error when
|
||||
the library is loaded, so be sure all needed libraries are listed,
|
||||
as they would be when building LAMMPS as a stand-alone code.
|
||||
|
||||
Note that if you install them yourself, some libraries, such as MPI,
|
||||
may not build by default as shared libraries. The build instructions
|
||||
for the library should tell you how to do this.
|
||||
|
||||
For example, here is how to build and install the "MPICH
|
||||
library"_mpich, a popular open-source version of MPI, distributed by
|
||||
Argonne National Labs, as a shared library in the default
|
||||
/usr/local/lib location:
|
||||
|
||||
:link(mpich,http://www-unix.mcs.anl.gov/mpi)
|
||||
|
||||
./configure --enable-shared
|
||||
make
|
||||
make install :pre
|
||||
|
||||
You may need to use "sudo make install" in place of the last line if
|
||||
you do not have write priveleges for /usr/local/lib. The end result
|
||||
should be the file /usr/local/lib/libmpich.so.
|
||||
|
||||
Also note that not all of the auxiliary libraries provided with LAMMPS
|
||||
include Makefiles in their lib directories for building them as shared
|
||||
libraries. Typically this simply requires adding a -fPIC switch when
|
||||
files are compiled and "-fPIC -shared" switches when the library is
|
||||
linked with a C++ (or Fortran) compiler, and creating an output target
|
||||
that ends in ".so", like libatc.o. As we or others create and
|
||||
contribute these Makefiles, we will add them to the LAMMPS
|
||||
distribution.
|
||||
|
||||
|
||||
You must insure that each of these libraries exist in shared library
|
||||
form (*.so file for Linux systems), or either the LAMMPS shared
|
||||
library build or the Python load of the library will fail. For the
|
||||
load to be successful all the shared libraries must also be in
|
||||
directories that the operating system checks. See the discussion in
|
||||
the preceding section about the LD_LIBRARY_PATH environment variable
|
||||
for how to insure this.
|
||||
|
||||
|
||||
|
||||
The second is the environment variable LD_LIBRARY_PATH, which is used
|
||||
by the operating system to find dynamic shared libraries when it loads
|
||||
them.
|
||||
|
||||
It needs to include the directory where the shared LAMMPS
|
||||
library will be. Normally this is the LAMMPS src dir, as explained in
|
||||
the following section.
|
||||
|
||||
For the csh or tcsh shells, you could add something like this to your
|
||||
~/.cshrc file:
|
||||
|
||||
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src :pre
|
||||
|
||||
As discussed below, if your LAMMPS build includes auxiliary libraries,
|
||||
they must also be available as shared libraries for Python to
|
||||
successfully load LAMMPS. If they are not in default places where the
|
||||
operating system can find them, then you also have to add their paths
|
||||
to the LD_LIBRARY_PATH environment variable.
|
||||
|
||||
For example, if you are using the dummy MPI library provided in
|
||||
src/STUBS, you need to add something like this to your ~/.cshrc file:
|
||||
|
||||
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src/STUBS :pre
|
||||
|
||||
If you are using the LAMMPS USER-ATC package, you need to add
|
||||
something like this to your ~/.cshrc file:
|
||||
|
||||
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/lib/atc :pre
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
See the discussion about the LAMMPS shared library in
|
||||
"Section_python"_Section_python.html for details about how to build
|
||||
shared versions of these libraries, and how to insure the operating
|
||||
system can find them, by setting the LD_LIBRARY_PATH environment
|
||||
variable correctly.
|
||||
|
||||
|
||||
|
||||
Either flavor of library allows one or more LAMMPS objects to be
|
||||
instantiated from the calling program.
|
||||
|
||||
|
|
|
|||
|
|
@ -58,6 +58,11 @@ results from a unitless LJ simulation into physical quantities.
|
|||
<LI>electric field = force/charge, where E* = E (4 pi perm0 sigma epsilon)^1/2 sigma / epsilon
|
||||
<LI>density = mass/volume, where rho* = rho sigma^dim
|
||||
</UL>
|
||||
<P>Note that for LJ units, the default mode of thermodyamic output via
|
||||
the <A HREF = "thermo_style.html">thermo_style</A> command is to normalize energies
|
||||
by the number of atoms, i.e. energy/atom. This can be changed via the
|
||||
<A HREF = "therm_modify.html">thermo_modify norm</A> command.
|
||||
</P>
|
||||
<P>For style <I>real</I>, these are the units:
|
||||
</P>
|
||||
<UL><LI>mass = grams/mole
|
||||
|
|
|
|||
|
|
@ -55,6 +55,11 @@ dipole = reduced LJ dipole, moment where *mu = mu / (4 pi perm0 sigma^3 epsilon)
|
|||
electric field = force/charge, where E* = E (4 pi perm0 sigma epsilon)^1/2 sigma / epsilon
|
||||
density = mass/volume, where rho* = rho sigma^dim :ul
|
||||
|
||||
Note that for LJ units, the default mode of thermodyamic output via
|
||||
the "thermo_style"_thermo_style.html command is to normalize energies
|
||||
by the number of atoms, i.e. energy/atom. This can be changed via the
|
||||
"thermo_modify norm"_therm_modify.html command.
|
||||
|
||||
For style {real}, these are the units:
|
||||
|
||||
mass = grams/mole
|
||||
|
|
|
|||
Loading…
Reference in New Issue