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Martin Kurečka
Plumed AlphaFold
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898b0095
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898b0095
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Giovanni Bussi
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I added information about compiling PLUMED on a cluster
I think this fixes #143 [makedoc]
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@@ -504,6 +504,62 @@ Once ALMOST is installed, PLUMED 2 can then be configured with ALMOST enabled:
\endverbatim
with ALMOST_INSTALL_PATH set to the full path to the ALMOST installation folder.
\section installingonacluster Installing PLUMED on a cluster
If you are installing PLUMED on a cluster and you want several users to take advantage of it
consider the following suggestions.
First of all, we highly recommend using the module file that PLUMED provides to set up the environment.
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.
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.
Try to patch all MD codes with the `--runtime` option. This will allow independent update of PLUMED and MD codes.
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).
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`,
`gromacs/4.6.7p2` and write somewhere in the module file which version of PLUMED you used. Alternatively, call them
something like `gromacs/4.6.7p2.2.0`. In this way, when we report a bug on the mailing list, users will know if the version
they are using is affected by it.
Usually it is not necessary to install both a MPI and a non-MPI PLUMED version. PLUMED library only calls MPI functions
when the MD code is compiled with MPI. PLUMED executable calls MPI functions only when it is invoked without `--no-mpi`.
In many machines it is thus sufficient to run the plumed executable on the login node as
\verbatim
> plumed --no-mpi
\endverbatim
even though PLUMED was compiled with MPI and the login node does not support MPI.
The only case where you might need two different PLUMED installation for compute
and login node is when you are cross compiling.
PLUMED needs to be well optimized to run efficiently.
If you need a single PLUMED binary to run efficiency on machines with different levels of hardware (e.g.: some
of your workstations support AVX and some do not), with intel compiler you can use something like
\verbatim
./configure CXX=mpicxx CXXFLAGS="-O3 -axSSE2,AVX"
\endverbatim
It will take more time to compile but it will allow you to use a single module. Otherwise, you should install two
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
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.
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.
\attention
In case you found out how to compile PLUMED on some fancy architecture please share your tricks! You can
either post it in your blog, send it to the mailing list, or ask as to update this paragraph in the manual, we will
be happy to do so.
\section installinghints Other hints
We here collect a list of suggestions that might be useful on particular
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