The script is also finding out if function names have the final underscore added,
so this should be completely transparent to the user.
In case blas or lapack are not found, the internal versions are used.
If the functions of these libraries are not found, the compiler
looks for a version with final underscore added.
Finally, since blas and lapack are compulsory in PLUMED,
if also this second search fails an internal replacement is used.
Notice that this procedure is transparent to the user.
In case one wants to disable the search for external libraries
(e.g. because the system libraries have problems) this can be done with
\verbatim
> ./configure --disable-external-lapack
\endverbatim
As a final resort, you may also edit the resulting Makefile.conf file.
Notable variables there:
...
...
@@ -107,19 +156,57 @@ e.g. use -D__PLUMED_HAS_MATHEVAL to enable matheval library
"so" on unix, "dylib" on mac; in case 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=").
Also notice that a new file sourceme.sh
appears in the main PLUMED directory.
This file should be "sourced" (presently only working for bash shell)
if you want to use PLUMED *without installing it* (i.e. from the compilation
directory. It is a good idea to source it now:
\verbatim
> source sourceme.sh
\endverbatim
\subsection BlasAndLapack BLAS and LAPACK
Then compile PLUMED
We tried to keep PLUMED as independent as possible from external libraries.
Moreover, some libraries (e.g. Almost and Matheval) providing
extra features are optional. However, to have a properly working PLUMED
you need BLAS and LAPACK libraries.
In case you cannot manage to install blas and lapack, you can use the internal
ones. Just add to the CPPFLAGS the flags -D__PLUMED_INTERNAL_BLAS
-D__PLUMED_INTERNAL_LAPACK.
The automatic configure should be able to choose automatically the internal
libraries when necessary.
Some additional notes follow.
First of all, the DYNAMIC_LIB variable in the Makefile.conf
should contain the flag necessary to load these libraries
(typically -llapack -lblas, in some case followed by -lgfortran
but full path specification with -L should be necessary depending on your system configuration).
Even though you can incur in some problem.
- If the linker complains and suggest to recompiled lapack with -fPIC, it means that you have static lapack libraries. Either install dynamic lapack libraries
or switch to static compilation of PLUMED (by unsetting the SOEXT variable
in configuration file).
- If the linker complains that dsyevr_ cannot be found, try to add
-DF77_NO_UNDERSCORE to CPPFLAGS
- If the linker complains about other missing functions (typically starting with
"for_" prefix) then you should link also Fortran libraries. Indeed, PLUMED
is written in C++ and often C++ linkers do not include by default Fortran libraries
which are required for lapack and blas to work. Please check the documentation of your compiler.
\section CompilingPlumed Compiling PLUMED
Once configured, PLUMED can be compiled using the following command:
\verbatim
> make -j 4
\endverbatim
This will compile the entire code and produce a number of files
in the 'src/lib' directory, including the executable
'src/lib/plumed'. In case shared libraries are enabled,
also a shared libraries should have been compiled, namely
'src/lib/libKernel.so'. Notice that the extension could be
'.dylib' on a Mac.
The file 'sourceme.sh' that has been created by
the configure script in the main PLUMED directory
can be "sourced" (presently only working for bash shell)
if you want to use PLUMED *without installing it* (i.e. from the compilation
directory). It is a good idea to source it now:
\verbatim
> source sourceme.sh
\endverbatim
If compilation is successful,
a "plumed" executable should be in your path. Try to type
...
...
@@ -127,6 +214,10 @@ a "plumed" executable should be in your path. Try to type
> plumed -h
\endverbatim
\warning In case you are cross compiling, the plumed executable
will not work. As a consequence, you won't be able to run regtests
or compile the manual.
You can also check if PLUMED is correctly compiled performing our regression tests.
Be warned that some of them just fails because of the different numerical accuracy of different machines.
\verbatim
...
...
@@ -142,7 +233,7 @@ This means that if you do not source "sourceme.sh" file, tests will fails. Moreo
another version of PLUMED installed somewhere regtests might use that one instead
of the just-compiled one.
Also notice that the compiled executable, which now sits in src/lib/plumed, relies
Also notice that the compiled executable, which now sits in 'src/lib/plumed', relies
on other resource files present in the compilation directory.
This directory should thus stay in the correct place, and one should not
rename or delete it. The path to the PLUMED root directory is indeed
...
...
@@ -166,36 +257,6 @@ You can force plumed to run anyway using the option --standalone-executable:
Anyway, many features will not be available in this way.
This is currently the only way to use a PLUMED static executable on Windows.
\section BlasAndLapack BLAS and LAPACK
We tried to keep PLUMED as independent as possible from external libraries.
Moreover, some libraries (e.g. Almost and Matheval) providing
extra features are optional. However, to have a properly working PLUMED
you need BLAS and LAPACK libraries.
In case you cannot manage to install blas and lapack, you can use the internal
ones. Just add to the CPPFLAGS the flags -D__PLUMED_INTERNAL_BLAS
-D__PLUMED_INTERNAL_LAPACK.
The automatic configure should be able to choose automatically the internal
libraries when necessary.
Some additional notes follow.
First of all, the DYNAMIC_LIB variable in the Makefile.conf
should contain the flag necessary to load these libraries
(typically -llapack -lblas, in some case followed by -lgfortran
but full path specification with -L should be necessary depending on your system configuration).
Even though you can incur in some problem.
- If the linker complains and suggest to recompiled lapack with -fPIC, it means that you have static lapack libraries. Either install dynamic lapack libraries
or switch to static compilation of PLUMED (by unsetting the SOEXT variable
in configuration file).
- If the linker complains that dsyevr_ cannot be found, try to add
-DF77_NO_UNDERSCORE to CPPFLAGS
- If the linker complains about other missing functions (typically starting with
"for_" prefix) then you should link also Fortran libraries. Indeed, PLUMED
is written in C++ and often C++ linkers do not include by default Fortran libraries
which are required for lapack and blas to work. Please check the documentation of your compiler.
\section Installing Installing PLUMED
It might be convenient to install PLUMED in a predefined location.
...
...
@@ -246,7 +307,7 @@ the following things:
header files such as "#include <plumed/tools/Vector.h>". this is also usefule to
exploit the PLUMED library in general purpose programs
As a final note, one may want to install several PLUMED version
As a final note, one may want to install several PLUMED versions
alongside without using modules.
An alternative is to also define the environment variable PLUMED_LIBSUFFIX. E.g. with
\verbatim
...
...
@@ -256,7 +317,7 @@ An alternative is to also define the environment variable PLUMED_LIBSUFFIX. E.g.
\endverbatim
will install plumed executable with name "plumed-v2.0". All the other files will be renamed accordingly,
e.g. the PLUMED library will be loaded with "-lplumed-v2.0" and the PLUMED header files
will be included with "\#include <plumed-v2.0/tools/Vector.h>". This trick is useful if you
will be included with "#include <plumed-v2.0/tools/Vector.h>". This trick is useful if you
do not want to set up modules, but we think using modules (see above) is more flexible.
\section Patching Patching your MD code
...
...
@@ -270,10 +331,10 @@ working. In particular, you should have the command "plumed" in your execution
path, either because it is installed or because you are using it
from the compilation directory.
Then, follow these steps
- Configure and compile your MD enginge
- Test if it is working properly
- Go to the root diretory of the MD engine
- Patch:
- Configure and compile your MD enginge (look for the instructions in its documentation).
- Test if it is working properly.
- Go to the root directory of the source code of the MD engine.
- Patch with PLUMED:
\verbatim
> plumed patch -p
\endverbatim
...
...
@@ -285,18 +346,22 @@ There are different options when patching, check them using
\verbatim
> plumed patch --help
\endverbatim
Interesing ones:
- --shared allows you to link PLUMED as a shared library. when PLUMED is updated, there will be no need to recompile the MD code
Interesting ones are:
- --static (default) just link PLUMED as a collection of object files.
- --shared allows you to link PLUMED as a shared library. when PLUMED is updated, there will be no need to recompile the MD code.
- --runtime allows you to choose the location of the PLUMED library at runtime, setting the variable PLUMED_KERNEL.
- --static (default) just link PLUMED as a collection of object files
Notice that it is not currently possible to link PLUMED as a static library (something like 'libplumed.a').
The reason is that PLUMED heavily relies on C++ static constructors that do not behave well in static libraries.
For this reason, the only we to produce a static executable with an MD code + PLUMED is
to link PLUMED as a collection of object files.
A note for cross compiling: in case you are compiling an executable from a different machine, then
"plumed" executable will not be available in the compilation environment. You can thus use the following command
\verbatim
> plumed-patch
\endverbatim
as a replacement of "plumed patch". This trick only works with those commands which are implemented as pure scripts
(e.g. there is no "plumed-help" available...).
as a replacement of "plumed patch".
If your MD code is not supported, you may want to implement an interface for
it. Refer to the <a href="../../developer-doc/html/index.html"> developer
