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regression from libblas-3.8.0-12_openblas to 3.8.0-13_openblas residuum of eigenvalue problem became worse #40

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marscher opened this issue Nov 20, 2019 · 2 comments
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regression from libblas-3.8.0-12_openblas to 3.8.0-13_openblas residuum of eigenvalue problem became worse #40

marscher opened this issue Nov 20, 2019 · 2 comments

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@marscher
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marscher commented Nov 20, 2019 •
edited by isuruf
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Issue: When upgrading libblas to the new build number, I can not get the prior precision of my BLAS computation as before. The convergence criteria are unchanged. I have attached a script (requiring pyemma from Conda-Forge) to produce the error.
There was an issue in the past, where a certain build causes wrong results on Intel CPU's xref: markovmodel/PyEMMA#1426
The solution back then was to mark this particular build as broken on CF, as the bug was fixed in a new version (e.g. the function dgemm was broken). But I do not know, if this is a similar issue now.
Please tell me, if I should file this one upstream.

failing env:

$ conda list
# packages in environment at /srv/public/marscher/software/miniconda3/envs/pyemma:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main  
attrs                     19.3.0                     py_0    conda-forge
backcall                  0.1.0                      py_0    conda-forge
bhmm                      0.6.3           py37h3010b51_1002    conda-forge
bleach                    3.1.0                      py_0    conda-forge
blosc                     1.17.0               he1b5a44_1    conda-forge
bzip2                     1.0.8                h516909a_1    conda-forge
ca-certificates           2019.9.11            hecc5488_0    conda-forge
certifi                   2019.9.11                py37_0    conda-forge
cffi                      1.13.2           py37h8022711_0    conda-forge
chardet                   3.0.4                 py37_1003    conda-forge
cmarkgfm                  0.4.2            py37h516909a_2    conda-forge
coverage                  4.5.4            py37h516909a_0    conda-forge
cryptography              2.8              py37h72c5cf5_0    conda-forge
cycler                    0.10.0                     py_2    conda-forge
cython                    0.29.14          py37he1b5a44_0    conda-forge
dbus                      1.13.6               he372182_0    conda-forge
decorator                 4.4.1                      py_0    conda-forge
defusedxml                0.6.0                      py_0    conda-forge
dill                      0.3.1.1                  py37_0    conda-forge
docutils                  0.15.2                   py37_0    conda-forge
entrypoints               0.3                   py37_1000    conda-forge
expat                     2.2.5             he1b5a44_1004    conda-forge
fontconfig                2.13.1            h86ecdb6_1001    conda-forge
freetype                  2.10.0               he983fc9_1    conda-forge
future                    0.18.2                   py37_0    conda-forge
gettext                   0.19.8.1          hc5be6a0_1002    conda-forge
glib                      2.58.3          py37h6f030ca_1002    conda-forge
gst-plugins-base          1.14.5               h0935bb2_0    conda-forge
gstreamer                 1.14.5               h36ae1b5_0    conda-forge
h5py                      2.10.0          nompi_py37h513d04c_100    conda-forge
hdf5                      1.10.5          nompi_h3c11f04_1104    conda-forge
icu                       64.2                 he1b5a44_1    conda-forge
idna                      2.8                   py37_1000    conda-forge
importlib_metadata        0.23                     py37_0    conda-forge
ipykernel                 5.1.3            py37h5ca1d4c_0    conda-forge
ipython                   7.9.0            py37h5ca1d4c_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.5.1                      py_0    conda-forge
jedi                      0.15.1                   py37_0    conda-forge
jinja2                    2.10.3                     py_0    conda-forge
joblib                    0.14.0                     py_0    conda-forge
jpeg                      9c                h14c3975_1001    conda-forge
jsonschema                3.2.0                    py37_0    conda-forge
jupyter_client            5.3.3                    py37_1    conda-forge
jupyter_core              4.6.1                    py37_0    conda-forge
kiwisolver                1.1.0            py37hc9558a2_0    conda-forge
libblas                   3.8.0               13_openblas    conda-forge
libcblas                  3.8.0               13_openblas    conda-forge
libclang                  9.0.0           default_hde54327_4    conda-forge
libffi                    3.2.1             he1b5a44_1006    conda-forge
libgcc-ng                 9.1.0                hdf63c60_0  
libgfortran-ng            7.3.0                hdf63c60_2    conda-forge
libiconv                  1.15              h516909a_1005    conda-forge
liblapack                 3.8.0               13_openblas    conda-forge
libllvm9                  9.0.0                hc9558a2_3    conda-forge
libopenblas               0.3.7                h6e990d7_3    conda-forge
libpng                    1.6.37               hed695b0_0    conda-forge
libsodium                 1.0.17               h516909a_0    conda-forge
libstdcxx-ng              9.1.0                hdf63c60_0  
libuuid                   2.32.1            h14c3975_1000    conda-forge
libxcb                    1.13              h14c3975_1002    conda-forge
libxkbcommon              0.9.1                hebb1f50_0    conda-forge
libxml2                   2.9.10               hee79883_0    conda-forge
lzo                       2.10              h14c3975_1000    conda-forge
markupsafe                1.1.1            py37h516909a_0    conda-forge
matplotlib                3.1.2                    py37_1    conda-forge
matplotlib-base           3.1.2            py37h250f245_1    conda-forge
mdtraj                    1.9.3            py37h00575c5_0    conda-forge
mistune                   0.8.4           py37h516909a_1000    conda-forge
mock                      3.0.5                    py37_0    conda-forge
more-itertools            7.2.0                      py_0    conda-forge
msmtools                  1.2.5            py37hc1659b7_0    conda-forge
multiprocess              0.70.9           py37h516909a_0    conda-forge
nbconvert                 5.6.1                    py37_0    conda-forge
nbformat                  4.4.0                      py_1    conda-forge
ncurses                   6.1               hf484d3e_1002    conda-forge
notebook                  6.0.1                    py37_0    conda-forge
nspr                      4.23                 he1b5a44_0    conda-forge
nss                       3.47                 he751ad9_0    conda-forge
numexpr                   2.7.0            py37hb3f55d8_0    conda-forge
numpy                     1.17.3           py37h95a1406_0    conda-forge
openssl                   1.1.1d               h516909a_0    conda-forge
packaging                 19.2                       py_0    conda-forge
pandas                    0.25.3           py37hb3f55d8_0    conda-forge
pandoc                    2.7.3                         0    conda-forge
pandocfilters             1.4.2                      py_1    conda-forge
parso                     0.5.1                      py_0    conda-forge
pathos                    0.2.5                      py_0    conda-forge
pcre                      8.43                 he1b5a44_0    conda-forge
pexpect                   4.7.0                    py37_0    conda-forge
pickleshare               0.7.5                 py37_1000    conda-forge
pip                       19.3.1                   py37_0    conda-forge
pkginfo                   1.5.0.1                    py_0    conda-forge
pluggy                    0.13.0                   py37_0    conda-forge
pox                       0.2.7                      py_0    conda-forge
ppft                      1.6.6.1                  py37_0    conda-forge
prometheus_client         0.7.1                      py_0    conda-forge
prompt_toolkit            2.0.10                     py_0    conda-forge
psutil                    5.6.5            py37h516909a_0    conda-forge
pthread-stubs             0.4               h14c3975_1001    conda-forge
ptyprocess                0.6.0                   py_1001    conda-forge
py                        1.8.0                      py_0    conda-forge
pycparser                 2.19                     py37_1    conda-forge
pyemma                    2.5.7            py37hb3f55d8_0    conda-forge
pyfiglet                  0.8.post1                pypi_0    pypi
pygments                  2.4.2                      py_0    conda-forge
pyopenssl                 19.0.0                   py37_0    conda-forge
pyparsing                 2.4.5                      py_0    conda-forge
pyqt                      5.12.3           py37hcca6a23_1    conda-forge
pyqt5-sip                 4.19.18                  pypi_0    pypi
pyqtwebengine             5.12.1                   pypi_0    pypi
pyrsistent                0.15.5           py37h516909a_0    conda-forge
pysocks                   1.7.1                    py37_0    conda-forge
pytables                  3.6.1            py37h9f153d1_0    conda-forge
pytest                    5.3.0                    py37_0    conda-forge
pytest-cov                2.8.1                      py_0    conda-forge
python                    3.7.3                h33d41f4_1    conda-forge
python-dateutil           2.8.1                      py_0    conda-forge
pytz                      2019.3                     py_0    conda-forge
pyyaml                    5.1.2            py37h516909a_0    conda-forge
pyzmq                     18.1.1           py37h1768529_0    conda-forge
qt                        5.12.5               hd8c4c69_1    conda-forge
readline                  8.0                  hf8c457e_0    conda-forge
readme_renderer           24.0                       py_0    conda-forge
requests                  2.22.0                   py37_1    conda-forge
requests-toolbelt         0.9.1                      py_0    conda-forge
ruamel-yaml               0.16.5                   pypi_0    pypi
ruamel-yaml-clib          0.2.0                    pypi_0    pypi
scikit-ci                 0.21.0                   pypi_0    pypi
scikit-learn              0.21.3           py37hcdab131_0    conda-forge
scipy                     1.3.2            py37h921218d_0    conda-forge
send2trash                1.5.0                      py_0    conda-forge
setuptools                41.6.0                   py37_1    conda-forge
six                       1.13.0                   py37_0    conda-forge
sqlite                    3.30.1               hcee41ef_0    conda-forge
terminado                 0.8.3                    py37_0    conda-forge
testpath                  0.4.4                      py_0    conda-forge
tk                        8.6.9             hed695b0_1003    conda-forge
tornado                   6.0.3            py37h516909a_0    conda-forge
tqdm                      4.38.0                     py_2    conda-forge
traitlets                 4.3.3                    py37_0    conda-forge
twine                     2.0.0                      py_0    conda-forge
urllib3                   1.25.7                   py37_0    conda-forge
wcwidth                   0.1.7                      py_1    conda-forge
webencodings              0.5.1                      py_1    conda-forge
wheel                     0.33.6                   py37_0    conda-forge
widgetsnbextension        3.5.1                    py37_0    conda-forge
xorg-libxau               1.0.9                h14c3975_0    conda-forge
xorg-libxdmcp             1.1.3                h516909a_0    conda-forge
xz                        5.2.4             h14c3975_1001    conda-forge
yaml                      0.1.7             h14c3975_1001    conda-forge
zeromq                    4.3.2                he1b5a44_2    conda-forge
zipp                      0.6.0                      py_0    conda-forge
zlib                      1.2.11            h516909a_1006    conda-forge

Details

$ conda info
     active environment : pyemma
    active env location : /srv/public/marscher/software/miniconda3/envs/pyemma
            shell level : 2
       user config file : /home/mi/marscher/.condarc
 populated config files : /home/mi/marscher/.condarc
          conda version : 4.7.12
    conda-build version : 3.18.10
         python version : 3.7.3.final.0
       virtual packages : __cuda=10.1
       base environment : /srv/public/marscher/software/miniconda3  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /srv/public/marscher/software/miniconda3/pkgs
                          /home/mi/marscher/.conda/pkgs
       envs directories : /srv/public/marscher/software/miniconda3/envs
                          /home/mi/marscher/.conda/envs
               platform : linux-64
             user-agent : conda/4.7.12 requests/2.22.0 CPython/3.7.3 Linux/4.19.0-6-amd64 debian/10 glibc/2.28
                UID:GID : 238651:10615
             netrc file : None
           offline mode : Fals
@marscher marscher mentioned this issue Nov 20, 2019
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@isuruf
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isuruf commented Nov 20, 2019

Can you compare the version of libopenblas in the two environments?

@marscher
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Sorry for the noise, my issue is unrelated to BLAS libraries.

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@marscher @isuruf