CentOS - Apr 2018 - yum excludes

Valeri Galtsev wrote:
<snip>
>>> On Fri, 6 Apr 2018 17:25 , <m.roth at 5-cent.us> wrote:
>>>
>>>> CentOS 7 box. As there's no package in any of the repos,
we're trying
>>>> to install scikit-learn in the user's space. It refuses. My
late try
was,
>>>> after d/l a .whl from last year, hoping that would work with
the numpy
>>>> package in the regular repos, I did a pip install --user
>>>> scikit-learn..., and it still seems to want to write to system
space:
>>>>  OSError: [Errno 13] Permission denied:
>>>> '/usr/lib64/python2.7/site-packages/numpy-1.7.1.dist-info
>>>>
>>>> Anyone got any pointers?
<snip>
> Mark, python is a "sneaky snake" ;-) and some modules may require
> particular version of dependencies, therefore they may ignore your
> system wide numpy (even though it may just may be compatible with them),
> and may demand latest version of numpy. Which will explain pip (or
> other) attempting to pull dependencies which allegedly are available
> system wide already.
>
> Just speculating, your own research on your particular issue may give
> your better answer.
<snip>
Well, my manager came back, and he's got me using virtenv. Having read
about it, I like it.  Oh, and the issue with the system numpy in
site-packages was that, for some reason, it was *not* world-readable.
Fixed that.

So, I'm working on trying to install scipy in the virtenv... and for
unknown reasons, it simply can't find the system libs. I did this before
the last attempt to
export LAPACK=/usr/lib64/liblapack.so.3
export BLAS=/usr/lib64/libblas.so.3
and just added export LD_LIBRARY_PATH=/usr/lib64
Still can't find them.

Clues on this one?

        mark

On 06.04.2018 21:04, m.roth at 5-cent.us wrote:
> So, I'm working on trying to install scipy in the virtenv... and for
> unknown reasons, it simply can't find the system libs.
try to run 'pip install --upgrade pip' in your virtualenv. Fix the issue
for me.

best regards
Ulf

David Miller.

----- Original Message -----
> From: "m roth" <m.roth at 5-cent.us>
> To: "CentOS mailing list" <centos at centos.org>
> Sent: Friday, April 6, 2018 12:04:43 PM
> Subject: Re: [CentOS] Semi-OT: install python package in userspace
> Valeri Galtsev wrote:
> <snip>
>>>> On Fri, 6 Apr 2018 17:25 , <m.roth at 5-cent.us> wrote:
>>>>
>>>>> CentOS 7 box. As there's no package in any of the
repos, we're trying
>>>>> to install scikit-learn in the user's space. It
refuses. My late try
> was,
>>>>> after d/l a .whl from last year, hoping that would work
with the numpy
>>>>> package in the regular repos, I did a pip install --user
>>>>> scikit-learn..., and it still seems to want to write to
system space:
>>>>>  OSError: [Errno 13] Permission denied:
>>>>>
'/usr/lib64/python2.7/site-packages/numpy-1.7.1.dist-info
>>>>>
>>>>> Anyone got any pointers?
> <snip>
>> Mark, python is a "sneaky snake" ;-) and some modules may
require
>> particular version of dependencies, therefore they may ignore your
>> system wide numpy (even though it may just may be compatible with
them),
>> and may demand latest version of numpy. Which will explain pip (or
>> other) attempting to pull dependencies which allegedly are available
>> system wide already.
>>
>> Just speculating, your own research on your particular issue may give
>> your better answer.
> <snip>
> Well, my manager came back, and he's got me using virtenv. Having read
> about it, I like it.  Oh, and the issue with the system numpy in
> site-packages was that, for some reason, it was *not* world-readable.
> Fixed that.
> 
> So, I'm working on trying to install scipy in the virtenv... and for
> unknown reasons, it simply can't find the system libs. I did this
before
> the last attempt to
> export LAPACK=/usr/lib64/liblapack.so.3
> export BLAS=/usr/lib64/libblas.so.3
> and just added export LD_LIBRARY_PATH=/usr/lib64
> Still can't find them.
> 
> Clues on this one?
> 
>        mark
Mark,

You might also want to look at conda for managing a self contained python and
all the crazy external dependencies. Being in a research environment means these
people will probably come back with lots of requests for other modules and
external dependencies like tensorflow, qt5, hdf5, etc.  Conda handles building
the snowflake versions for all that junk.

David.

dear all

Every yum command returns "nvidia excluding" lines, and those items
are invisible for installation, see lower.
I have no idea where those excludes are defined.

Also, the flag  "--disableexcludes=all" does not remove the excludes.

any ideas?

thanks

mathy
------------------------------------------------------
[root at gbw-d-l0070 ~]# yum update
Loaded plugins: etckeeper, fastestmirror, langpacks, nvidia
Loading mirror speeds from cached hostfile
 * base: centos.cu.be
 * elrepo: ftp.nluug.nl
 * epel: fedora.cu.be
 * extras: centos.cu.be
 * updates: centos.cu.be
[nvidia]: excluding kmod-nvidia-367.57-3.el7.elrepo.x86_64
[nvidia]: excluding kmod-nvidia-390.25-1.el7_4.elrepo.x86_64
[nvidia]: excluding kmod-nvidia-390.42-1.el7_4.elrepo.x86_64
[nvidia]: excluding kmod-nvidia-390.48-1.el7_4.elrepo.x86_64
[nvidia]: excluding nvidia-x11-drv-367.57-1.el7.elrepo.x86_64
[nvidia]: excluding nvidia-x11-drv-390.25-1.el7.elrepo.x86_64
[nvidia]: excluding nvidia-x11-drv-390.42-1.el7.elrepo.x86_64
[nvidia]: excluding nvidia-x11-drv-390.48-1.el7_4.elrepo.x86_64
[nvidia]: excluding nvidia-x11-drv-32bit-367.57-1.el7.elrepo.x86_64
[nvidia]: excluding nvidia-x11-drv-32bit-390.25-1.el7.elrepo.x86_64
[nvidia]: excluding nvidia-x11-drv-32bit-390.42-1.el7.elrepo.x86_64
[nvidia]: excluding nvidia-x11-drv-32bit-390.48-1.el7_4.elrepo.x86_64
No packages marked for update

> 
> Every yum command returns "nvidia excluding" lines, and those
items
> are invisible for installation, see lower.
> I have no idea where those excludes are defined.
> 
> ------------------------------------------------------
> [root at gbw-d-l0070 ~]# yum update
> Loaded plugins: etckeeper, fastestmirror, langpacks, nvidia
They are from the nvidia plugin.
> 
> [nvidia]: excluding kmod-nvidia-367.57-3.el7.elrepo.x86_64
> [nvidia]: excluding kmod-nvidia-390.25-1.el7_4.elrepo.x86_64
> [nvidia]: excluding kmod-nvidia-390.42-1.el7_4.elrepo.x86_64
> [nvidia]: excluding kmod-nvidia-390.48-1.el7_4.elrepo.x86_64
> [nvidia]: excluding nvidia-x11-drv-367.57-1.el7.elrepo.x86_64
> [nvidia]: excluding nvidia-x11-drv-390.25-1.el7.elrepo.x86_64
> [nvidia]: excluding nvidia-x11-drv-390.42-1.el7.elrepo.x86_64
> [nvidia]: excluding nvidia-x11-drv-390.48-1.el7_4.elrepo.x86_64
> [nvidia]: excluding nvidia-x11-drv-32bit-367.57-1.el7.elrepo.x86_64
> [nvidia]: excluding nvidia-x11-drv-32bit-390.25-1.el7.elrepo.x86_64
> [nvidia]: excluding nvidia-x11-drv-32bit-390.42-1.el7.elrepo.x86_64
> [nvidia]: excluding nvidia-x11-drv-32bit-390.48-1.el7_4.elrepo.x86_64
> No packages marked for update
> 
The plugin excludes the drivers that are not compatible with the card
you have in your machine.

P.

ps please don't reply to an unrelated mailing list post and just change
the subject when creating a new question.  It really mucks up threading
if you do so.