Hi all,
I have installed all prerequisites for IMP (even libTAU and openCV which IMP cannot find, but that problem can I deal with later) but IMP won't install.
In brief, I obtain following error message:
Makefile:127: recipe for target 'all' failed
make: *** [all] Error 2
All details of output from cmake and installation can be found in the attached log file.
Could someone help me with this?
Also, as you can see in the log file, I have received many warnings concerning PyObject.. Am I using a wrong version of swig? I have swig 2.0.12.
Could someone please help me out here?
Warm regards Dennis
On 5/23/15 11:37 AM, Dennis FoxLetterman wrote: > I have installed all prerequisites for IMP (even libTAU and openCV which > IMP cannot find, but that problem can I deal with later) but IMP won't > install. > > In brief, I obtain following error message: > > Makefile:127: recipe for target 'all' failed
You need to look further up in the output to see the real error - that's just the summary - grep for "error" and you'll see:
/usr/bin/ld: /usr/local/lib/libfftw3.a(mapflags.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libfftw3.a: error adding symbols: Bad value collect2: error: ld returned 1 exit status
The problem is that you only appear to have the static (.a) library for FFTW, but IMP needs the dynamic (.so) library. This is provided by the fftw3-dev package on Ubuntu (at least in 14.04, which we do build packages for). (Or possibly you have both but the one in /usr/local is found before the system version, in which case the simplest solution would be to delete the one in /usr/local.)
> Also, as you can see in the log file, I have received many warnings > concerning PyObject..
No, these are normal, but out of our control (since the code is generated by SWIG). In fact, in our nightly builds we filter out these warnings to reduce confusion.
Ben
Thanks Ben!
I had already fftw3-dev package installed. I updated this package and reinstalled the newest fttw3 and it worked! Thanks! I still don't know why imp cannot find opencv2 (i can import the package through python), but I will first test out IMP package to see whether anything else is missing before I start resolving this problem.
All the best
Dennis
2015-05-23 23:16 GMT+02:00 Ben Webb ben@salilab.org:
> On 5/23/15 11:37 AM, Dennis FoxLetterman wrote: > >> I have installed all prerequisites for IMP (even libTAU and openCV which >> IMP cannot find, but that problem can I deal with later) but IMP won't >> install. >> >> In brief, I obtain following error message: >> >> Makefile:127: recipe for target 'all' failed >> > > You need to look further up in the output to see the real error - that's > just the summary - grep for "error" and you'll see: > > /usr/bin/ld: /usr/local/lib/libfftw3.a(mapflags.o): relocation R_X86_64_32 > against `.rodata' can not be used when making a shared object; recompile > with -fPIC > /usr/local/lib/libfftw3.a: error adding symbols: Bad value > collect2: error: ld returned 1 exit status > > The problem is that you only appear to have the static (.a) library for > FFTW, but IMP needs the dynamic (.so) library. This is provided by the > fftw3-dev package on Ubuntu (at least in 14.04, which we do build packages > for). (Or possibly you have both but the one in /usr/local is found before > the system version, in which case the simplest solution would be to delete > the one in /usr/local.) > > Also, as you can see in the log file, I have received many warnings >> concerning PyObject.. >> > > No, these are normal, but out of our control (since the code is generated > by SWIG). In fact, in our nightly builds we filter out these warnings to > reduce confusion. > > Ben > -- > ben@salilab.org http://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle >
Hello,
I found the tutorial IMP2.4 that still use add_restraint attribute: (m, c) = IMP.example.create_model_and_particles() ps = IMP.core.DistancePairScore(IMP.core.HarmonicLowerBound(1, 1)) r = IMP.container.PairsRestraint(ps, IMP.container.ClosePairContainer(c, 2.0)) m.add_restraint(r) http://www.integrativemodeling.org/2.4.0/doc/html/kernel_2basic_optimization...
It is still convenient to use it while migrating from IMP 1.0 to 2.4, however "remove_restraint" won't work at all. Given the m.add_restraint(r), how can I achieve m.remove_restraint(r) in IMP 2.4?
Thank you.
Best, Harianto.
On 6/3/15 3:37 PM, harianto tjong wrote: > I found the tutorial IMP2.4 that still use add_restraint attribute:
While you could probably make things work using add_restraint(), I would advise against it. Both add_restraint() and remove_restraint() were deprecated in IMP a long time ago, and will be removed in the upcoming 2.5 release. See http://integrativemodeling.org/nightly/doc/ref/kernel_2basic_optimization_8p... for the latest recommended way to run that example. Just keep your restraints in a Python data structure (such as a list), or in a RestraintSet, and pass them to a RestraintsScoringFunction. To remove a restraint, just remove it from that list or RestraintSet.
> Given the m.add_restraint(r), how can I achieve m.remove_restraint(r) in > IMP 2.4?
If you really want to stick with add_restraint() for now, m.remove_restraint(r) is equivalent to m.get_root_restraint_set().remove_restraint(r) (which will also stop working when IMP 2.5 is released).
Ben
participants (3)
-
Ben Webb -
Dennis FoxLetterman -
harianto tjong