Page 1 of 2
OpenMM 6.0 binary install OS X 10.9
Posted: Mon Jun 09, 2014 11:28 am
by dlucent
Hello Everybody,
I have a number of brand new iMacs (nvidia GT750M) running OS X 10.9, the latest X-Code, CUDA 5.5, the Anaconda python dist, and have installed OpenM 6.01. For some reason only the CPU and Reference platforms are detected. Is there something obvious that I'm missing? Thanks for your help!
-Del
Re: OpenMM 6.0 binary install OS X 10.9
Posted: Mon Jun 09, 2014 11:55 am
by peastman
OpenCL doesn't work on Macs. Apple's implement is seriously broken.
If CUDA isn't getting loaded, it's likely to be a library dependency issue. Try typing
otool -L /usr/local/openmm/lib/plugins/libOpenMMCUDA.dylib
That should tell you if it has any unresolved dependencies. Make sure you've installed the CUDA toolkit, not just the driver.
Peter
Re: OpenMM 6.0 binary install OS X 10.9
Posted: Mon Jun 09, 2014 12:38 pm
by dlucent
Ahh, that did it, problems with the wrong CUDA version! Thanks Peter.
Re: OpenMM 6.0 binary install OS X 10.9
Posted: Tue Jun 10, 2014 9:22 am
by dlucent
Hi Peter,
Unfortunately, I'm still running into problems using the CUDA platform. testInstallation.py seems to fail for the CUDA platform. A simple simulation of villin gives the following error when I try to use the CUDA platform:
Exception: Error launching CUDA compiler: 256
clang: error: unsupported option '-dumpspecs'
clang: error: no input files
I'm not sure how to go about debugging this. I have the CUDA 5.5 (and the sdk) installed and nvcc is in /usr/local/cuda/bin. Any thoughts? The full context of the error is pasted below:
Code: Select all
pdb = PDBFile('/Users/lucent/aaron.cabinaw/WorkshopTutorials/input.pdb')
forcefield = ForceField('amber99sb.xml', 'tip3p.xml')
platform = Platform.getPlatformByName('CUDA')
system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME, nonbondedCutoff=1.0*nanometer,
constraints=HBonds)
integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)
simulation = Simulation(pdb.topology, system, integrator,platform)
simulation.context.setPositions(pdb.positions)
---------------------------------------------------------------------------
Exception Traceback (most recent call last)
<ipython-input-13-d2565d5e77a2> in <module>()
1 # Creating simulation context
----> 2 simulation = Simulation(pdb.topology, system, integrator,platform)
3 simulation.context.setPositions(pdb.positions)
/Users/lucent/anaconda/lib/python2.7/site-packages/simtk/openmm/app/simulation.pyc in __init__(self, topology, system, integrator, platform, platformProperties)
75 self.context = mm.Context(system, integrator)
76 elif platformProperties is None:
---> 77 self.context = mm.Context(system, integrator, platform)
78 else:
79 self.context = mm.Context(system, integrator, platform, platformProperties)
/Users/lucent/anaconda/lib/python2.7/site-packages/simtk/openmm/openmm.pyc in __init__(self, *args)
4861
4862
-> 4863 this = _openmm.new_Context(*args)
4864 try: self.this.append(this)
4865 except: self.this = this
Exception: Error launching CUDA compiler: 256
clang: error: unsupported option '-dumpspecs'
clang: error: no input files
Re: OpenMM 6.0 binary install OS X 10.9
Posted: Tue Jun 10, 2014 11:28 am
by peastman
I haven't seen this problem, but it looks like other people have:
http://stackoverflow.com/questions/1964 ... ted-option
http://stackoverflow.com/questions/1935 ... -mavericks
In both of those threads, the answer is to upgrade to a newer version of the CUDA toolkit. What version do you have? For me,
/usr/local/cuda/bin/nvcc --version
gives
Code: Select all
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2013 NVIDIA Corporation
Built on Thu_Sep__5_10:17:14_PDT_2013
Cuda compilation tools, release 5.5, V5.5.0
Peter
Re: OpenMM 6.0 binary install OS X 10.9
Posted: Tue Jun 10, 2014 11:45 am
by dlucent
I have 5.5:
Code: Select all
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2013 NVIDIA Corporation
Built on Wed_Jul_10_11:16:01_PDT_2013
Cuda compilation tools, release 5.5, V5.5.0
If I upgrade to 6.0, won't that break binary compatibility? I suppose I could just try compiling from source against CUDA 6.0 but I thought this should work with 5.5? Thanks for your help!
Re: OpenMM 6.0 binary install OS X 10.9
Posted: Tue Jun 10, 2014 12:03 pm
by peastman
It looks like NVIDIA is being sloppy with version numbers. My version of the toolkit is newer than yours (built in Sept. rather than July), but they both claim to be "release 5.5, V5.5.0". Sigh.
Looking at their page for past CUDA versions, they list 5.5 as being from July 2013. Presumably that's what you downloaded? Yet at some point, there clearly were newer builds than that still listed as 5.5.
Your best bet might be to install CUDA 6.0 and compile from source.
Peter
Re: OpenMM 6.0 binary install OS X 10.9
Posted: Tue Jun 10, 2014 3:17 pm
by dlucent
Compiling from source with cuda 6 seemed to work. As always, thanks for the help Peter!
Re: OpenMM 6.0 binary install OS X 10.9
Posted: Sat Jul 05, 2014 9:44 am
by psahu92
Hi Peter,
We have a Mac OS X 10.8.5 with AMD Radeon. So OpenMM can't be installed in this is it?
Re: OpenMM 6.0 binary install OS X 10.9
Posted: Sat Jul 05, 2014 10:21 am
by jswails1
OpenMM works fine on macs. It's just the OpenCL platform that doesn't work.