[pymvpa] hdf5

Eilbott, Jeffrey jeffrey.eilbott at yale.edu
Thu Apr 27 16:42:20 UTC 2017


I installed h5py and hdf5 packages and then built PyMVPA again. Same issue, still. Here’s the output of wtf().


Current date:   2017-04-27 12:39
PyMVPA:
 Version:       2.6.1.dev1
 Hash:          $Format:%H$
 Path:          /ysm-gpfs/home/je45/local/miniconda2/lib/python2.7/site-packages/mvpa2/__init__.pyc
 Version control (GIT):
 GIT information could not be obtained due "/ysm-gpfs/home/je45/local/miniconda2/lib/python2.7/site-packages/mvpa2/.. is not under GIT"
SYSTEM:
 OS:            posix Linux 3.10.0-327.36.3.el7.x86_64 #1 SMP Thu Oct 20 04:56:07 EDT 2016
 Distribution:  redhat/7.2/Maipo
EXTERNALS:
 Present:       cPickle, ctypes, good scipy.stats.rv_continuous._reduce_func(floc,fscale), good scipy.stats.rv_discrete.ppf, griddata, gzip, h5py, hdf5, ipython, libsvm, libsvm verbosity control, mass, matplotlib, nibabel, nipy, numpy, numpy_correct_unique, pylab, pylab plottable, rpy2, running ipython env, scipy, skl
 Absent:        afni-3dinfo, atlas_fsl, atlas_pymvpa, cran-energy, datalad, elasticnet, glmnet, good scipy.stats.rdist, hcluster, joblib, lars, liblapack.so, lxml, mdp, mdp ge 2.4, mock, nipy.neurospin, nose, numpydoc, openopt, pprocess, pywt, pywt wp reconstruct, pywt wp reconstruct fixed, reportlab, scipy.weave, sg ge 0.6.4, sg ge 0.6.5, sg_fixedcachesize, shogun, shogun.krr, shogun.lightsvm, shogun.mpd, shogun.svmocas, shogun.svrlight, statsmodels, weave
 Versions of critical externals:
  ctypes      : 1.1.0
  h5py        : 2.7.0
  hdf5        : 1.8.17
  ipython     : 5.3.0
  matplotlib  : 2.0.0
  nibabel     : 2.1.0
  nipy        : 0.4.1
  numpy       : 1.12.1
  rpy2        : 2.8.5
  scipy       : 0.19.0
  skl         : 0.18.1
 Matplotlib backend: Qt5Agg
RUNTIME:
 PyMVPA Environment Variables:
  PYTHONPATH          : "/ysm-gpfs/apps/software/prompt-toolkit/1.0.6-foss-2016a-Python-2.7.11/lib/python2.7/site-packages:/ysm-gpfs/apps/software/wcwidth/0.1.7-foss-2016a-Python-2.7.11/lib/python2.7/site-packages:/ysm-gpfs/apps/software/path.py/8.2.1-foss-2016a-Python-2.7.11/lib/python2.7/site-packages:/ysm-gpfs/apps/software/testpath/0.3-foss-2016a-Python-2.7.11/lib/python2.7/site-packages:/ysm-gpfs/apps/software/PyZMQ/15.4.0-foss-2016a-Python-2.7.11-zmq4/lib/python2.7/site-packages"
 PyMVPA Runtime Configuration:
  [general]
  verbose = 1
  
  [externals]
  have running ipython env = yes
  have ipython = yes
  have numpy = yes
  have scipy = yes
  have matplotlib = yes
  have afni-3dinfo = no
  have lxml = no
  have atlas_fsl = no
  have atlas_pymvpa = no
  have cpickle = yes
  have rpy2 = yes
  have cran-energy = no
  have ctypes = yes
  have datalad = no
  have elasticnet = no
  have glmnet = no
  have good scipy.stats.rdist = no
  have good scipy.stats.rv_continuous._reduce_func(floc,fscale) = yes
  have good scipy.stats.rv_discrete.ppf = yes
  have griddata = yes
  have gzip = yes
  have h5py = yes
  have hcluster = no
  have hdf5 = yes
  have joblib = no
  have lars = no
  have liblapack.so = no
  have libsvm = yes
  have libsvm verbosity control = yes
  have mass = yes
  have mdp = no
  have mdp ge 2.4 = no
  have mock = no
  have nibabel = yes
  have nipy = yes
  have nipy.neurospin = no
  have nose = no
  have numpy_correct_unique = yes
  have numpydoc = no
  have openopt = no
  have pprocess = no
  have pylab = yes
  have pylab plottable = yes
  have pywt = no
  have pywt wp reconstruct = no
  have pywt wp reconstruct fixed = no
  have reportlab = no
  have scipy.weave = no
  have sg ge 0.6.4 = no
  have sg ge 0.6.5 = no
  have sg_fixedcachesize = no
  have shogun = no
  have shogun.krr = no
  have shogun.lightsvm = no
  have shogun.mpd = no
  have shogun.svmocas = no
  have shogun.svrlight = no
  have skl = yes
  have statsmodels = no
  have weave = no
 Process Information:
  Name:	ipython
  State:	R (running)
  Tgid:	15695
  Ngid:	15695
  Pid:	15695
  PPid:	4695
  TracerPid:	0
  Uid:	12015	12015	12015	12015
  Gid:	10718	10718	10718	10718
  FDSize:	256
  Groups:	10594 10681 10718 
  VmPeak:	 1184060 kB
  VmSize:	 1125208 kB
  VmLck:	       0 kB
  VmPin:	       0 kB
  VmHWM:	  152620 kB
  VmRSS:	  152620 kB
  VmData:	  317772 kB
  VmStk:	     468 kB
  VmExe:	       4 kB
  VmLib:	  196340 kB
  VmPTE:	    1456 kB
  VmSwap:	       0 kB
  Threads:	4
  SigQ:	0/511608
  SigPnd:	0000000000000000
  ShdPnd:	0000000000000000
  SigBlk:	0000000000000000
  SigIgn:	0000000001001004
  SigCgt:	0000000180000002
  CapInh:	0000000000000000
  CapPrm:	0000000000000000
  CapEff:	0000000000000000
  CapBnd:	0000001fffffffff
  Seccomp:	0
  Cpus_allowed:	00008
  Cpus_allowed_list:	3
  Mems_allowed:	00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000003
  Mems_allowed_list:	0-1
  voluntary_ctxt_switches:	6873
  nonvoluntary_ctxt_switches:	476

> On Apr 27, 2017, at 12:25, Yaroslav Halchenko <yoh at onerussian.com> wrote:
> 
> On April 27, 2017 11:35:34 AM EDT, "Eilbott, Jeffrey" <jeffrey.eilbott at yale.edu> wrote:
>> Hi,
>> 
>> I’m trying to do the hyperalignment tutorial and am running into an
>> issue where h5load isn’t found. mvpa2.base.hdf5 doesn’t seem to exist. 
>> 
>> I built PyMVPA on RHEL 7 with python 2.7.13 (via miniconda).
>> 
>> Any idea what’s wrong?
>> 
>> Thanks,
>> Jeff
>> _______________________________________________
>> Pkg-ExpPsy-PyMVPA mailing list
>> Pkg-ExpPsy-PyMVPA at lists.alioth.debian.org
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.alioth.debian.org_cgi-2Dbin_mailman_listinfo_pkg-2Dexppsy-2Dpymvpa&d=DwIGaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=fh9o3kmRDnzHBfw_dO8G-HJXDnZP9HwBLvYAhNg_PwU&m=Lx8stIX01v8M6nhyhIcdqHucxqM_xLL0_MvJNZtD_Sg&s=pd0vwaJxbYrgqs2lkxoUCpyiKhIMFG0hjiDv8Jt-I5g&e= 
> 
> print(mvpa2.wtf())
> Might give an idea about missing module
> -- 
> Sent from a phone which beats iPhone.
> 
> _______________________________________________
> Pkg-ExpPsy-PyMVPA mailing list
> Pkg-ExpPsy-PyMVPA at lists.alioth.debian.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.alioth.debian.org_cgi-2Dbin_mailman_listinfo_pkg-2Dexppsy-2Dpymvpa&d=DwIGaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=fh9o3kmRDnzHBfw_dO8G-HJXDnZP9HwBLvYAhNg_PwU&m=Lx8stIX01v8M6nhyhIcdqHucxqM_xLL0_MvJNZtD_Sg&s=pd0vwaJxbYrgqs2lkxoUCpyiKhIMFG0hjiDv8Jt-I5g&e=



More information about the Pkg-ExpPsy-PyMVPA mailing list