[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.
>
> _______________________________________________
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