Notice that although the file 'src/lib/plumed-shared' is not necessary, being
able to produce it means that it will be possible to link PLUMED dynamically
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@@ -222,7 +222,7 @@ native lapack libraries have problems.
As a final resort, you can also edit the resulting Makefile.conf file.
Notable variables in this file include:
- DYNAMIC_LIB : these are the libraries needed to compile the PLUMED
library (e.g. -L/path/to/matheval -lmatheval etc). Notice that for the
library (e.g. -L/path/to/xdrfile -lxdrfile etc). Notice that for the
PLUMED shared library to be compiled properly these should be dynamic
libraries. Also notice that PLUMED preferentially requires BLAS and LAPACK library;
see \ref BlasAndLapack for further info. Notice that the variables
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@@ -231,7 +231,7 @@ variable. This is a bit misleading but is required to keep the configuration
files compatible with PLUMED 2.0.
- LIBS : these are the libraries needed when patching an MD code; typically only "-ldl" (needed to have functions for dynamic loading).
- CPPFLAGS : add here definition needed to enable specific optional functions;
e.g. use -D__PLUMED_HAS_MATHEVAL to enable the matheval library
e.g. use -D__PLUMED_HAS_XDRFILE to enable the xdrfile library
- SOEXT : this gives the extension for shared libraries in your system, typically
"so" on unix, "dylib" on mac; If your system does not support dynamic libraries or, for some other reason, you would like only static executables you can
just set this variable to a blank ("SOEXT=").
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@@ -529,7 +529,7 @@ First of all, we highly recommend using the module file that PLUMED provides to
Just edit it as necessary to make it suitable for your environment.
Notice that PLUMED can take advantage of many additionaly features if specific libraries are available upon
compiling it. Install libmatheval first and check if PLUMED `./configure` is detecting it. Libmatheval is a must have with PLUMED.
compiling it.
If someone uses gromacs, install libxdrfile first and check if PLUMED `./configure` is detecting it.
PLUMED will be able to write trr/xtc file, simplifying analysis.
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@@ -537,7 +537,7 @@ Try to patch all MD codes with the `--runtime` option. This will allow independe
Users will be able to combine any of the installed gromacs/amber/etc versions with any of the installed PLUMED versions.
Notice that it is sometime claimed that statically linked codes are faster. In our experience, this is not true.
In case you absolutely need a static executable, be ready to face non trivial linking issues. PLUMED is written in C++,
thus required the appropriate C++ library to be linked, and might require additional libraries (e.g. libmatheval).
thus required the appropriate C++ library to be linked, and might require additional libraries (e.g. libxdrfile).
Sometime we make small fixes on the patches. For this reason, keep track of which version of PLUMED you used
to patch each of the MD code. Perhaps you can call the MD code modules with names such as `gromacs/4.6.7p1`,
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@@ -565,9 +565,9 @@ It will take more time to compile but it will allow you to use a single module.
PLUMED version with different optimization levels.
Using modules, it is not necessary to make the PLUMED module explicitly dependent on the used library. Imagine a
scenario where you first installed a module `libmatheval`, then load it while you compile PLUMED. If you
scenario where you first installed a module `libxdrfile`, then load it while you compile PLUMED. If you
provide the following option to configure `LDFLAGS="-Wl,-rpath,$LD_LIBRARY_PATH"`, the PLUMED executable and
library will remember where libmatheval is, without the need to load libmatheval module at runtime.
library will remember where libxdrfile is, without the need to load libxdrfile module at runtime.
Notice that this trick often does not work for fundamental libraries such as C++ and MPI library. As a consequence,
usually the PLUMED module should load the compiler and MPI modules.
