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Martin Kurečka
Plumed AlphaFold
Commits
88ae60c0
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Commit
88ae60c0
authored
6 years ago
by
Giovanni Bussi
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Improved changelog v2.5
parent
906ee939
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CHANGES/v2.5.md
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88ae60c0
...
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@@ -94,13 +94,32 @@ Changes from version 2.4 which are relevant for developers:
in the core parts of the code have been eliminated.
-
Exceptions cannot be disabled (
`--disable-cxx-exceptions`
option has been removed from
`./configure`
).
-
Every exception thrown in PLUMED now also writes its message on PLUMED log.
-
Runtime loader in
`Plumed.c`
now works also when linked without
`-rdynamic`
(that is,
its names are not exported). Notice that all the combinations are expected to
work, that is:
`Plumed.c`
from
<
=2.4
or
>
=2.5 combined with libplumedKernel
from
<
=2.4
or
>
=2.5. In order to achieve this the following changes are implemented:
-
libplumedKernel does not depend anymore on
`Plumed.c`
. This allows loading it even
in cases where names in the loader are not visible. The relevant function needed
to be compatible with
`Plumed.c`
<=2.4 are found using
`dlsym`
.
-
`Plumed.c`
does not need anymore libplumedKernel to register itself, but rather
searches the relevant functions using
`dlsym`
. In addition, if it is not able to
load
`libplumedKernel`
since the latter is <=2.4 and needs
`Plumed.c`
to be visible,
it just uses as a fallback
`libplumed`
, which should load properly.
-
In addition to the capability mentioned above, the MD-code interface has been significantly
improved and allows for:
-
Translation of exception (allowing to mix PLUMED and an MD-code linked against a different C++ library).
-
Possibility to choose the path to the PLUMED kernel while instantiating a Plumed object.
See the developer documentation for more information.
-
The installation layout of shared libraries has been modified. In particular,
both
`libplumed.so`
and
`plumed`
links to
`libplumedKernel.so`
.
This reduces considerably the size of the installed package. In addition, it allows
using two-level namespace on OSX. Notice that this implies that on Linux one should
always set the
`LD_LIBRARY_PATH`
flag to have a working executable.
-
A smaller number of header files is installed. In particular, all the files that were historically generated in subdirectories
(such as
`plumed/core/tools/Vector.h', just including `
plumed/tools/Vector.h
`) are not installed and the related include
statements are fixed. This makes the installed package smaller.
- List of preferred compilers (used when `
CXX
` or `
CC
` are not set) has been changed. On OSX, `
./configure
` will try `
clang++/clang
` as first choices.
-
Added
`--enable-static-archive`
to
`./configure`
to build a
`libplumed.a`
static library.
- Added `
--enable-static-archive
` to `
./configure
` to build a `
libplumed.a
` static library
(yes by default)
.
- Stop setting `
DYLD_LIBRARY_PATH
` in `
sourceme.sh
` and in modulefile. Notice that as of PLUMED v2.3.3
it should not be needed.
- Coverage scan is not anymore contained in developer manual. It can be found in a separate repository
...
...
@@ -109,21 +128,9 @@ Changes from version 2.4 which are relevant for developers:
- It is not possible anymore to use `
make install prefix=/path
`. Prefix can only be changed during `
./configure
` (see \issue{332}).
- Exception class has been rewritten to allow more extensive messages. Now also function name is shown.
- On linux, library is linked with `
-Bsymbolic
`.
-
A small number of header files is installed
- When launching `
plumed
`, flags `
--no-mpi
` and `
--mpi
` can appear multiple times. The last appearence is the effective one.
- Internal blas and lapack libraries updated to gromacs 2018.
- Choosing `
./configure --prefix=$PWD
` does not lead anymore to deletion of all header files.
-
Runtime loader in
`Plumed.c`
now works also when linked without
`-rdynamic`
(that is,
its names are not exported). Notice that all the combinations are expected to
work, that is:
`Plumed.c`
from
<
=2.4
or
>
=2.5 combined with libplumedKernel
from
<
=2.4
or
>
=2.5. In order to achieve this the following changes are implemented:
-
libplumedKernel does not depend anymore on
`Plumed.c`
. This allows loading it even
in cases where names in the loader are not visible. The relevant function needed
to be compatible with
`Plumed.c`
<=2.4 are found using
`dlsym`
.
-
`Plumed.c`
does not need anymore libplumedKernel to register itself, but rather
searches the relevant functions using
`dlsym`
. In addition, if it is not able to
load
`libplumedKernel`
since the latter is <=2.4 and needs
`Plumed.c`
to be visible,
it just uses as a fallback
`libplumed`
, which should load properly.
- A copy of `
plumed-runtime
` is installed in `
prefix/lib/plumed
` and can be used for testing.
- Absolute/relative soname/install_name can be configured on linux/OSX. This feature is only
for testing, the default choice is the typical one used on the respective operating system.
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