Hello, I am trying to install OpenMM in Chimera to script some molecular dynamics. However, I am struggling to make it work, since the build fails with this error: g++ -pthread -fPIC -mtune=generic -m64 -I/home/chimera/chimeraBuild_X11/build/build/include -L/home/chimera/chimeraBuild_X11/build/build/lib -DUSE_DYLD_GLOBAL_NAMESPACE -shared -Wl,--hash-style=both build/temp.linux-x86_64-2.7/src/swig_doxygen/OpenMMSwig.o -L/lib -R/lib -lOpenMM -lOpenMMAmoeba -lOpenMMRPMD -lOpenMMDrude -o build/lib.linux-x86_64-2.7/simtk/openmm/_openmm.so g++: error: unrecognized command line option '-R' which is probably not related to Chimera at all. What I've done so far: 1. Download precompiled binaries for Linux from their site: https://simtk.org/project/xml/downloads.xml?group_id=161 2. Extract that file and merge the contents of the directories "include" and "lib" with those in Chimera root path. 3. Cd into the python directory of the extracted file and run: chimera --nogui --script "setup.py install". Has somebody been successful with this package? I know it seems more of a compiler issue, but maybe Chimera is doing some trickery with the build mechanism too. Thank you in advance, Jaime.
For compatibility with other ELF linkers, if the -R option is followed by a directory name, rather than a file name, it is treated as the -rpath option. So, you should change the -R/lib to be -Wl,-Rlib or -Wl,-rpath,/lib. I suspect that the -R is from SunOS, but as you found out, that is not
This is probably a bug in OpenMM's build script, but it could be in the Python distutils package that comes with Chimera (you don't say which version you're using). Try again with the Chimera daily build, since that comes with Python 2.7.10, the latest revision of Python 2.7. If that doesn't fix it, you will need to patch the appropriate source code -- OpenMM's build script or the Python distutils module. From the ld documentation: portable. If the above information is insufficient to get it to install, let me know, and I'll dig further. -- Greg On 11/30/2015 09:04 AM, Jaime Rodríguez-Guerra Pedregal wrote:
Hello,
I am trying to install OpenMM in Chimera to script some molecular dynamics. However, I am struggling to make it work, since the build fails with this error:
g++ -pthread -fPIC -mtune=generic -m64 -I/home/chimera/chimeraBuild_X11/build/build/include -L/home/chimera/chimeraBuild_X11/build/build/lib -DUSE_DYLD_GLOBAL_NAMESPACE -shared -Wl,--hash-style=both build/temp.linux-x86_64-2.7/src/swig_doxygen/OpenMMSwig.o -L/lib -R/lib -lOpenMM -lOpenMMAmoeba -lOpenMMRPMD -lOpenMMDrude -o build/lib.linux-x86_64-2.7/simtk/openmm/_openmm.so g++: error: unrecognized command line option ‘-R’
which is probably not related to Chimera at all.
What I've done so far:
1. Download precompiled binaries for Linux from their site: https://simtk.org/project/xml/downloads.xml?group_id=161
2. Extract that file and merge the contents of the directories "include" and "lib" with those in Chimera root path.
3. Cd into the python directory of the extracted file and run: chimera --nogui --script "setup.py install".
Has somebody been successful with this package? I know it seems more of a compiler issue, but maybe Chimera is doing some trickery with the build mechanism too.
Thank you in advance,
Jaime.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Jaime, You don’t say exactly what your goal is with the MD, but I feel like I should point out that in the daily build you can run MD via the included MMTK library. The code is in the “md” module and the interface in the the MD/Ensemble Analysis category of tools. Of course, OpenMM offers different capabilties and maybe you need those specifically… —Eric Eric Pettersen UCSF Computer Graphics Lab
On Nov 30, 2015, at 9:04 AM, Jaime Rodríguez-Guerra Pedregal <Jaime.RodriguezGuerra@uab.cat> wrote:
Hello,
I am trying to install OpenMM in Chimera to script some molecular dynamics. However, I am struggling to make it work, since the build fails with this error:
g++ -pthread -fPIC -mtune=generic -m64 -I/home/chimera/chimeraBuild_X11/build/build/include -L/home/chimera/chimeraBuild_X11/build/build/lib -DUSE_DYLD_GLOBAL_NAMESPACE -shared -Wl,--hash-style=both build/temp.linux-x86_64-2.7/src/swig_doxygen/OpenMMSwig.o -L/lib -R/lib -lOpenMM -lOpenMMAmoeba -lOpenMMRPMD -lOpenMMDrude -o build/lib.linux-x86_64-2.7/simtk/openmm/_openmm.so g++: error: unrecognized command line option ‘-R’
which is probably not related to Chimera at all.
What I've done so far:
1. Download precompiled binaries for Linux from their site: https://simtk.org/project/xml/downloads.xml?group_id=161 <https://simtk.org/project/xml/downloads.xml?group_id=161>
2. Extract that file and merge the contents of the directories "include" and "lib" with those in Chimera root path.
3. Cd into the python directory of the extracted file and run: chimera --nogui --script "setup.py install".
Has somebody been successful with this package? I know it seems more of a compiler issue, but maybe Chimera is doing some trickery with the build mechanism too.
Thank you in advance, Jaime. _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
Hi guys! Thanks for those tips! I managed to install it after patching unixccompiler.py in Chimera's distutils. I was using Chimera 1.10.2 with Python 2.7.8 so maybe that's already fixed in a more recent version, but I had installed a lot of packages a didn't feel like going through that hassle again. I detailed my adventure in a post in OpenMM forums, so if somebody is experiencing the same issue, go to: https://simtk.org/forums/viewtopic.php?f=161&t=6158&p=15787#p15787 Thanks again! PS: Eric, yes, I did know about MMTK in Chimera, but I am trying to do some GPU accelerated calculations. Thanks anyway! :) ________________________________ De: Eric Pettersen <pett@cgl.ucsf.edu> Enviado: martes, 1 de diciembre de 2015 2:36 Para: Jaime Rodríguez-Guerra Pedregal Cc: chimera-users@cgl.ucsf.edu Asunto: Re: [Chimera-users] Installing OpenMM in Chimera Hi Jaime, You don't say exactly what your goal is with the MD, but I feel like I should point out that in the daily build you can run MD via the included MMTK library. The code is in the "md" module and the interface in the the MD/Ensemble Analysis category of tools. Of course, OpenMM offers different capabilties and maybe you need those specifically... -Eric Eric Pettersen UCSF Computer Graphics Lab On Nov 30, 2015, at 9:04 AM, Jaime Rodríguez-Guerra Pedregal <Jaime.RodriguezGuerra@uab.cat<mailto:Jaime.RodriguezGuerra@uab.cat>> wrote: Hello, I am trying to install OpenMM in Chimera to script some molecular dynamics. However, I am struggling to make it work, since the build fails with this error: g++ -pthread -fPIC -mtune=generic -m64 -I/home/chimera/chimeraBuild_X11/build/build/include -L/home/chimera/chimeraBuild_X11/build/build/lib -DUSE_DYLD_GLOBAL_NAMESPACE -shared -Wl,--hash-style=both build/temp.linux-x86_64-2.7/src/swig_doxygen/OpenMMSwig.o -L/lib -R/lib -lOpenMM -lOpenMMAmoeba -lOpenMMRPMD -lOpenMMDrude -o build/lib.linux-x86_64-2.7/simtk/openmm/_openmm.so g++: error: unrecognized command line option '-R' which is probably not related to Chimera at all. What I've done so far: 1. Download precompiled binaries for Linux from their site: https://simtk.org/project/xml/downloads.xml?group_id=161 2. Extract that file and merge the contents of the directories "include" and "lib" with those in Chimera root path. 3. Cd into the python directory of the extracted file and run: chimera --nogui --script "setup.py install". Has somebody been successful with this package? I know it seems more of a compiler issue, but maybe Chimera is doing some trickery with the build mechanism too. Thank you in advance, Jaime. _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Eric Pettersen -
Greg Couch -
Jaime Rodríguez-Guerra Pedregal