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<p><font size="2" face="sans-serif">Dear Nick, </font><br>
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<font size="2" face="sans-serif">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).</font><br>
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<font size="2" face="sans-serif">I'd be happy for any advice on this.</font><br>
<font size="2" face="sans-serif">Thanks</font><br>
<font size="2" face="sans-serif">Lydia </font><br>
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<font size="2" face="sans-serif">############ Traceback ###############</font><br>
<font size="2" face="sans-serif">Running searchlight with radius: 0 ...</font><br>
<font size="2" face="sans-serif">[SLC] DBG: Starting computing block for 338688 elements</font><br>
<font size="2" face="sans-serif">Traceback (most recent call last):</font><br>
<font size="2" face="sans-serif"> File "load.py2", line 81, in <module></font><br>
<font size="2" face="sans-serif"> sl_map = sl(ds_copy)</font><br>
<font size="2" face="sans-serif"> File "/usr/lib/python2.7/dist-packages/mvpa2/base/learner.py", line 258, in __call__</font><br>
<font size="2" face="sans-serif"> return super(Learner, self).__call__(ds)</font><br>
<font size="2" face="sans-serif"> File "/usr/lib/python2.7/dist-packages/mvpa2/base/node.py", line 137, in __call__</font><br>
<font size="2" face="sans-serif"> result = self._call(ds, **(_call_kwargs or self._get_call_kwargs(ds)))</font><br>
<font size="2" face="sans-serif"> File "/usr/lib/python2.7/dist-packages/mvpa2/measures/searchlight.py", line 154, in _call</font><br>
<font size="2" face="sans-serif"> results = self._sl_call(dataset, roi_ids, nproc)</font><br>
<font size="2" face="sans-serif"> File "/usr/lib/python2.7/dist-packages/mvpa2/measures/searchlight.py", line 375, in _sl_call</font><br>
<font size="2" face="sans-serif"> self._proc_block(roi_ids, dataset, self.__datameasure)]</font><br>
<font size="2" face="sans-serif"> File "/usr/lib/python2.7/dist-packages/mvpa2/measures/searchlight.py", line 471, in _proc_block</font><br>
<font size="2" face="sans-serif"> res = measure(roi)</font><br>
<font size="2" face="sans-serif"> File "/usr/lib/python2.7/dist-packages/mvpa2/base/learner.py", line 258, in __call__</font><br>
<font size="2" face="sans-serif"> return super(Learner, self).__call__(ds)</font><br>
<font size="2" face="sans-serif"> File "/usr/lib/python2.7/dist-packages/mvpa2/base/node.py", line 137, in __call__</font><br>
<font size="2" face="sans-serif"> result = self._call(ds, **(_call_kwargs or self._get_call_kwargs(ds)))</font><br>
<font size="2" face="sans-serif"> File "/usr/lib/python2.7/dist-packages/mvpa2/measures/base.py", line 514, in _call</font><br>
<font size="2" face="sans-serif"> return super(CrossValidation, self)._call(ds)</font><br>
<font size="2" face="sans-serif"> File "/usr/lib/python2.7/dist-packages/mvpa2/measures/base.py", line 337, in _call</font><br>
<font size="2" face="sans-serif"> result = node(sds)</font><br>
<font size="2" face="sans-serif"> File "/usr/lib/python2.7/dist-packages/mvpa2/base/learner.py", line 258, in __call__</font><br>
<font size="2" face="sans-serif"> return super(Learner, self).__call__(ds)</font><br>
<font size="2" face="sans-serif"> File "/usr/lib/python2.7/dist-packages/mvpa2/base/node.py", line 137, in __call__</font><br>
<font size="2" face="sans-serif"> result = self._call(ds, **(_call_kwargs or self._get_call_kwargs(ds)))</font><br>
<font size="2" face="sans-serif"> File "/usr/lib/python2.7/dist-packages/mvpa2/measures/base.py", line 619, in _call</font><br>
<font size="2" face="sans-serif"> measure.train(dstrain)</font><br>
<font size="2" face="sans-serif"> File "/usr/lib/python2.7/dist-packages/mvpa2/base/learner.py", line 137, in train</font><br>
<font size="2" face="sans-serif"> self._train(ds)</font><br>
<font size="2" face="sans-serif"> File "/usr/lib/python2.7/dist-packages/mvpa2/clfs/libsvmc/svm.py", line 147, in _train</font><br>
<font size="2" face="sans-serif"> svmprob = _svm.SVMProblem(labels, src )</font><br>
<font size="2" face="sans-serif"> File "/usr/lib/python2.7/dist-packages/mvpa2/clfs/libsvmc/_svm.py", line 221, in __init__</font><br>
<font size="2" face="sans-serif"> svmc.double_setitem(y_array, i, y[i])</font><br>
<font size="2" face="sans-serif">TypeError: in method 'double_setitem', argument 3 of type 'double'</font><br>
<font size="2" face="sans-serif">Exception AttributeError: "SVMProblem instance has no attribute 'data'" in <bound method SVMProblem.__del__ of <SVMProblem: size = 90>> ignored</font><br>
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<img width="16" height="16" src="cid:1__=4EBB0BAEDFA4C6148f9e8a93df9@lotus.uzh.ch" border="0" alt="Inactive hide details for Nick Oosterhof ---10/06/2017 11:11:21---On 9 June 2017 at 18:03, <lydia.hellrung@econ.uzh.ch> wrote: "><font size="2" color="#424282" face="sans-serif">Nick Oosterhof ---10/06/2017 11:11:21---On 9 June 2017 at 18:03, <lydia.hellrung@econ.uzh.ch> wrote: > I'm trying to run a searchlight analy</font><br>
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<font size="1" color="#5F5F5F" face="sans-serif">Von: </font><font size="1" face="sans-serif">Nick Oosterhof <n.n.oosterhof@googlemail.com></font><br>
<font size="1" color="#5F5F5F" face="sans-serif">An: </font><font size="1" face="sans-serif">Development and support of PyMVPA <pkg-exppsy-pymvpa@lists.alioth.debian.org></font><br>
<font size="1" color="#5F5F5F" face="sans-serif">Datum: </font><font size="1" face="sans-serif">10/06/2017 11:11</font><br>
<font size="1" color="#5F5F5F" face="sans-serif">Betreff: </font><font size="1" face="sans-serif">Re: [pymvpa] searchlight analysis fails</font><br>
<font size="1" color="#5F5F5F" face="sans-serif">Gesendet von: </font><font size="1" face="sans-serif">"Pkg-ExpPsy-PyMVPA" <pkg-exppsy-pymvpa-bounces+lydia.hellrung=econ.uzh.ch@lists.alioth.debian.org></font><br>
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<font size="3" face="serif">On 9 June 2017 at 18:03, <</font><a href="mailto:lydia.hellrung@econ.uzh.ch" target="_blank"><font size="3" color="#0000FF" face="serif"><u>lydia.hellrung@econ.uzh.ch</u></font></a><font size="3" face="serif">> wrote:</font>
<ul style="padding-left: 9pt"><font size="2" face="sans-serif">I'm trying to run a searchlight analysis, but I just end up in error messages. <br>
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)).<br>
I'm running it on a computer with lots of memory and several CPUs now. <br>
When I load the full dataset (size 180,338688), I end up with traceback #1 (please see below).<br>
When I load a mask I have less data (size180, 213), I end up with traceback #2 (also below).</font><font size="3" face="serif"><br>
</font><font size="2" face="sans-serif"><br>
I just found such an issue in your mail archive with 3D nifti, but here it's 4D nifti.<br>
What am I missing here?</font></ul>
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<font size="3" face="serif">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? </font><br>
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