Dear Nick, thanks for your answer. Unfortunately, I still end up in an error no matter what computer I use (but both are VMs). On the one, I just have one CPU, on the other I tried with setting the nproc = 1 and =4, but the result is the same (please see below). And no matter what I set, it's always just one CPU busy with ~100% (RAM is always some free left), so I guess it's one thread, right? the pprocess package is installed (version: 0.5-1+nd0~nd13.10+1 +nd14.04+1).
I'd be happy for any advice on this. Thanks Lydia ############ Traceback ############### Running searchlight with radius: 0 ... [SLC] DBG: Starting computing block for 338688 elements Traceback (most recent call last): File "load.py2", line 81, in <module> sl_map = sl(ds_copy) File "/usr/lib/python2.7/dist-packages/mvpa2/base/learner.py", line 258, in __call__ return super(Learner, self).__call__(ds) File "/usr/lib/python2.7/dist-packages/mvpa2/base/node.py", line 137, in __call__ result = self._call(ds, **(_call_kwargs or self._get_call_kwargs(ds))) File "/usr/lib/python2.7/dist-packages/mvpa2/measures/searchlight.py", line 154, in _call results = self._sl_call(dataset, roi_ids, nproc) File "/usr/lib/python2.7/dist-packages/mvpa2/measures/searchlight.py", line 375, in _sl_call self._proc_block(roi_ids, dataset, self.__datameasure)] File "/usr/lib/python2.7/dist-packages/mvpa2/measures/searchlight.py", line 471, in _proc_block res = measure(roi) File "/usr/lib/python2.7/dist-packages/mvpa2/base/learner.py", line 258, in __call__ return super(Learner, self).__call__(ds) File "/usr/lib/python2.7/dist-packages/mvpa2/base/node.py", line 137, in __call__ result = self._call(ds, **(_call_kwargs or self._get_call_kwargs(ds))) File "/usr/lib/python2.7/dist-packages/mvpa2/measures/base.py", line 514, in _call return super(CrossValidation, self)._call(ds) File "/usr/lib/python2.7/dist-packages/mvpa2/measures/base.py", line 337, in _call result = node(sds) File "/usr/lib/python2.7/dist-packages/mvpa2/base/learner.py", line 258, in __call__ return super(Learner, self).__call__(ds) File "/usr/lib/python2.7/dist-packages/mvpa2/base/node.py", line 137, in __call__ result = self._call(ds, **(_call_kwargs or self._get_call_kwargs(ds))) File "/usr/lib/python2.7/dist-packages/mvpa2/measures/base.py", line 619, in _call measure.train(dstrain) File "/usr/lib/python2.7/dist-packages/mvpa2/base/learner.py", line 137, in train self._train(ds) File "/usr/lib/python2.7/dist-packages/mvpa2/clfs/libsvmc/svm.py", line 147, in _train svmprob = _svm.SVMProblem(labels, src ) File "/usr/lib/python2.7/dist-packages/mvpa2/clfs/libsvmc/_svm.py", line 221, in __init__ svmc.double_setitem(y_array, i, y[i]) TypeError: in method 'double_setitem', argument 3 of type 'double' Exception AttributeError: "SVMProblem instance has no attribute 'data'" in <bound method SVMProblem.__del__ of <SVMProblem: size = 90>> ignored Von: Nick Oosterhof <n.n.ooster...@googlemail.com> An: Development and support of PyMVPA <pkg-exppsy-pymvpa@lists.alioth.debian.org> Datum: 10/06/2017 11:11 Betreff: Re: [pymvpa] searchlight analysis fails Gesendet von: "Pkg-ExpPsy-PyMVPA" <pkg-exppsy-pymvpa-bounces +lydia.hellrung=econ.uzh...@lists.alioth.debian.org> On 9 June 2017 at 18:03, <lydia.hellr...@econ.uzh.ch> wrote: I'm trying to run a searchlight analysis, but I just end up in error messages. I followed your searchlight example from the tutorial (detrend, z-score and kick out non-used conditions) and then calling the sl function exactly as in your tutorial (sl_map = sl(ds_copy)). I'm running it on a computer with lots of memory and several CPUs now. When I load the full dataset (size 180,338688), I end up with traceback #1 (please see below). When I load a mask I have less data (size180, 213), I end up with traceback #2 (also below). I just found such an issue in your mail archive with 3D nifti, but here it's 4D nifti. What am I missing here? Not sure what's causing this, but I wonder if it may be related to a high number of threads that may not play well with pprocess. Could you try to run the searchlight with as additional parameter in the call: nproc=1 (disabling multiple processes), and maybe also some other values (e.g. nproc=4 or 8)? Do you know how many threads the searchlight runs with? _______________________________________________ Pkg-ExpPsy-PyMVPA mailing list Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa
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