openmm
Build openmm-plumed in a container
So I was trying to build the plugin on the container using cmake as following :
RUN cd /opt &&
git clone https://github.com/openmm/openmm-plumed.git &&
cd openmm-plumed &&
mkdir build &&
cd build &&
cmake .. &&
export OPENMM_DIR=/usr/local/lib/python3.10/dist-packages/openmm &&
export PLUMED_INCLUDE_DIR=/usr/local/lib/python3.10/dist-packages/openmm-plumed/include/plumed &&
export PLUMED_LIBRARY_DIR=/usr/local/lib/python3.10/dist-packages/openmm-plumed/lib &&
export CMAKE_INSTALL_PREFIX=$OPENMM_DIR
RUN cd /opt/openmm-plumed/build &&
make install
RUN make PythonInstall
and I was getting this error
`=> ERROR [ 8/17] RUN CD /opt/openmm-plumed/build && make install 0.5s
[ 8/17] RUN CD /opt/openmm-plumed/build && make install: 0.431 [ 11%] Building CXX object CMakeFiles/OpenMMPlumed.dir/openmmapi/src/PlumedForce.cpp.o 0.495 In file included from /opt/openmm-plumed/openmmapi/src/PlumedForce.cpp:34: 0.495 /opt/openmm-plumed/openmmapi/include/internal/PlumedForceImpl.h:38:10: fatal error: wrapper/Plumed.h: No such file or directory 0.495 38 | #include "wrapper/Plumed.h" 0.495 | ^~~~~~~~~~~~~~~~~~ 0.495 compilation terminated. 0.498 make[2]: *** [CMakeFiles/OpenMMPlumed.dir/build.make:76: CMakeFiles/OpenMMPlumed.dir/openmmapi/src/PlumedForce.cpp.o] Error 1 0.498 make[1]: *** [CMakeFiles/Makefile2:136: CMakeFiles/OpenMMPlumed.dir/all] Error 2 0.498 make: *** [Makefile:146: all] Error 2`
is there a way to fix this ?
Thanks.
Check whether you have PLUMED_INCLUDE_DIR set correctly. You have it set to /usr/local/lib/python3.10/dist-packages/openmm-plumed/include/plumed. If you look inside that directory, there should be a subdirectory called wrapper, and in that a file called Plumed.h. Is there?
No actually it is not there. well in this case what should I set Plumed_include and library directories to ?
I re-installed it
like that
RUN cd /opt &&
git clone https://github.com/plumed/plumed2.git
RUN pip install cython &&
cd /opt/plumed2/python &&
make pip &&
pip install .
then, found the wrapper file here
/opt/plumed2/src/include/plumed
and I set
export PLUMED_INCLUDE_DIR=/opt/plumed2/src/include/plumed &&
however i face the same error.
PLUMED_INCLUDE_DIR is a CMake variable, not an environment variable. You set it in ccmake.
oh, right !
Thanks
but i got this time a new error
RUN CD /opt/openmm-plumed/build && make install:
0.445 [ 11%] Building CXX object CMakeFiles/OpenMMPlumed.dir/openmmapi/src/PlumedForce.cpp.o
0.718 In file included from /opt/openmm-plumed/openmmapi/include/internal/PlumedForceImpl.h:38,
0.718 from /opt/openmm-plumed/openmmapi/src/PlumedForce.cpp:34:
0.718 /opt/plumed2/src/include/plumed/wrapper/Plumed.h:2995:10: error: 'unique_ptr' in namespace 'std' does not name a template type
0.718 2995 | std::unique_ptr<char[]> dynamic_buffer;
0.718 | ^~~~~~~~~~
0.718 In file included from /opt/openmm-plumed/openmmapi/include/internal/PlumedForceImpl.h:38,
0.718 from /opt/openmm-plumed/openmmapi/src/PlumedForce.cpp:34:
0.718 /opt/plumed2/src/include/plumed/wrapper/Plumed.h:1761:1: note: 'std::unique_ptr' is defined in header '
i don't know if the way i installed plumed made it install an old version !
That version should be fine. I have no idea. Does this only happen when building inside a container, not when building natively?
I don't know. Can you show the exact sequence of commands you execute for building natively and the full output from them?
git clone https://github.com/openmm/openmm-plumed.git
Cloning into 'openmm-plumed'... remote: Enumerating objects: 671, done. remote: Counting objects: 100% (104/104), done. remote: Compressing objects: 100% (18/18), done. remote: Total 671 (delta 91), reused 86 (delta 86), pack-reused 567 Receiving objects: 100% (671/671), 174.46
cd openmm-plumed/ cd build/ cmake .. -DOPENMM_DIR=/usr/local/openmm/ -DPLUMED_INCLUDE_DIR=/home/go/test2/plumed2/src/include/plumed -DPLUMED_LIBRARY_DIR=/home/go/test2/plumed2/src/lib -DCMAKE_INSTALL_PREFIX=/home/go/test2/openmm-plumed where this path /usr/local/openmm/ leads to openmm lib and include /home/go/test2/openmm-plumed is the path of openmm-plumed plugin file itself
the output for this CMake Warning (dev) in CMakeLists.txt: No project() command is present. The top-level CMakeLists.txt file must contain a literal, direct call to the project() command. Add a line of code such as
project(ProjectName)
near the top of the file, but after cmake_minimum_required().
CMake is pretending there is a "project(Project)" command on the first line. This warning is for project developers. Use -Wno-dev to suppress it.
CMake Deprecation Warning at CMakeLists.txt:5 (CMAKE_MINIMUM_REQUIRED): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake.
Update the VERSION argument
-- Configuring done -- Generating done -- Build files have been written to: /home/george/NEU/test2/openmm-plumed/build
make install
Consolidate compiler generated dependencies of target OpenMMPlumed
[ 11%] Building CXX object CMakeFiles/OpenMMPlumed.dir/openmmapi/src/PlumedForce.cpp.o
In file included from /home/george/NEU/test2/openmm-plumed/openmmapi/include/internal/PlumedForceImpl.h:38,
from /home/george/NEU/test2/openmm-plumed/openmmapi/src/PlumedForce.cpp:34:
/home/george/NEU/test2/plumed2/src/include/plumed/wrapper/Plumed.h:2995:10: error: ‘unique_ptr’ in namespace ‘std’ does not name a template type
2995 | std::unique_ptr<char[]> dynamic_buffer;
| ^~~~~~~~~~
In file included from /home/george/NEU/test2/openmm-plumed/openmmapi/include/internal/PlumedForceImpl.h:38,
from /home/george/NEU/test2/openmm-plumed/openmmapi/src/PlumedForce.cpp:34:
/home/george/NEU/test2/plumed2/src/include/plumed/wrapper/Plumed.h:1761:1: note: ‘std::unique_ptr’ is defined in header ‘
I've never seen that error before, including with recent versions of gcc, so I'm not sure. The specific error is
/home/george/NEU/test2/plumed2/src/include/plumed/wrapper/Plumed.h:2995:10: error: ‘unique_ptr’ in namespace ‘std’ does not name a template type
Plumed.h is the header file Plumed provides that allows other programs to call it. Apparently it uses the unique_ptr template, which is part of the C++ standard template library, and the compiler doesn't recognize it. This line may provide a clue:
/home/george/NEU/test2/plumed2/src/include/plumed/wrapper/Plumed.h:1761:1: note: ‘std::unique_ptr’ is defined in header ‘’; did you forget to ‘#include ’?
That's confusing, because according to the documentation it's actually defined in <memory>. I looked up the source for Plumed.h, and it does #include <memory> in a couple of different places depending on what macros are defined. I notice an inconsistency in how it uses them. The #include is guarded by
#if __cplusplus > 199711L && __PLUMED_WRAPPER_LIBCXX11
But when it actually uses unique_ptr at line 2995, it has a less restrictive guard:
#if __cplusplus > 199711L
So if __cplusplus > 199711L and __PLUMED_WRAPPER_LIBCXX11 is not set, it will try to use the type without including the required header first. That looks like a bug that should be reported to the Plumed developers.
That said, I don't know why this problem is appearing for you but not for our standard builds.
I have the same issue when I am trying to install within a conda environment. Any updates, @gorgW ?
