yum become unavailable if I set LD_LIBRARY_PATH=pitchfork/deployment/lib

[TakashiKoyama]

Hi,

I'm using CentOS7.
I set

export LD_LIBRARY_PATH=/path/to/pitchfork/deployment/lib:$LD_LIBRARY_PATH

in /etc/profile to make pitchfork libraries be available .

However if I do so, yum become unavailable with saying that

# yum --help
There was a problem importing one of the Python modules
required to run yum. The error leading to this problem was:

   No module named yum

Please install a package which provides this module, or
verify that the module is installed correctly.

It's possible that the above module doesn't match the
current version of Python, which is:
2.7.10 (default, Apr  7 2017, 00:55:54) 
[GCC 5.3.1 20160406 (Red Hat 5.3.1-6)]

If you cannot solve this problem yourself, please go to 
the yum faq at:
  http://yum.baseurl.org/wiki/Faq

How can I solve this problem?
Thank you for your kind helps!

Takashi

[mhsieh]

Hello Takashi,
You might not want to use pitchfork environment all the time, it's not recommended to write that setting to your ~/.bashrc or ~/.bash_profile or ~/.profile files. But if you really want to use yum under pitchfork environment, I will need to investigate a little bit and go back to you.

[mhsieh]

Hello Takashi,
You might not want to use pitchfork environment all the time, it's not recommended to write that setting to your ~/.bashrc or ~/.bash_profile or ~/.profile files. But if you really want to use yum under pitchfork environment, I will need to investigate a little bit and go back to you.

[mhsieh]

Dear Takashi,
Can you check your yum really quick for me? Can you post the output of this command for us?

head $(which yum)

[mhsieh]

Dear Takashi,
Can you check your yum really quick for me? Can you post the output of this command for us?

head $(which yum)

[TakashiKoyama]

Dear mhsieh

Thank you for your comments!
Here is the output.

$ head $(which yum)
#!/usr/bin/python
import sys
try:
    import yum
except ImportError:
    print >> sys.stderr, """\
There was a problem importing one of the Python modules
required to run yum. The error leading to this problem was:

   %s

Takashi

[TakashiKoyama]

Dear mhsieh

Thank you for your comments!
Here is the output.

$ head $(which yum)
#!/usr/bin/python
import sys
try:
    import yum
except ImportError:
    print >> sys.stderr, """\
There was a problem importing one of the Python modules
required to run yum. The error leading to this problem was:

   %s

Takashi

[mjhsieh]

That's very interesting, I am not sure how it could be the case of pitchfork could possibly interfere with your system yum. Can you try env -u LD_LIBRARY_PATH yum --help? Let's see if your system yum still has similar error without LD_LIBRARY_PATH.

[mjhsieh]

That's very interesting, I am not sure how it could be the case of pitchfork could possibly interfere with your system yum. Can you try env -u LD_LIBRARY_PATH yum --help? Let's see if your system yum still has similar error without LD_LIBRARY_PATH.

[TakashiKoyama]

Hi,

yum works withenv -u LD_LIBRARY_PATH yum --help and so yum works without LD_LIBRARY_PATH.

I think the cause of this phenomena might be from change of sys.path in python environment as shown below.

# env -u LD_LIBRARY_PATH python
Python 2.7.5 (default, Nov  6 2016, 00:28:07) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-11)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys
>>> sys.path
['', '/usr/lib64/python27.zip', '/usr/lib64/python2.7', '/usr/lib64/python2.7/plat-linux2', '/usr/lib64/python2.7/lib-tk', '/usr/lib64/python2.7/lib-old', '/usr/lib64/python2.7/lib-dynload', '/usr/lib64/python2.7/site-packages', '/usr/lib64/python2.7/site-packages/gtk-2.0', '/usr/lib/python2.7/site-packages']
>>> quit()
# python
Python 2.7.10 (default, Apr  7 2017, 00:55:54) 
[GCC 5.3.1 20160406 (Red Hat 5.3.1-6)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys
>>> sys.path
['', '/home/samba/Suijitsu_Public/software/pitchfork/deployment/lib/python27.zip', '/home/samba/Suijitsu_Public/software/pitchfork/deployment/lib/python2.7', '/home/samba/Suijitsu_Public/software/pitchfork/deployment/lib/python2.7/plat-linux2', '/home/samba/Suijitsu_Public/software/pitchfork/deployment/lib/python2.7/lib-tk', '/home/samba/Suijitsu_Public/software/pitchfork/deployment/lib/python2.7/lib-old', '/home/samba/Suijitsu_Public/software/pitchfork/deployment/lib/python2.7/lib-dynload', '/home/samba/Suijitsu_Public/software/pitchfork/deployment/lib/python2.7/site-packages']
>>> quit()

As you can see, version of python and sys.path is changed between with and without LD_LIBRARY_PATH.

Takashi

[TakashiKoyama]

Hi,

yum works withenv -u LD_LIBRARY_PATH yum --help and so yum works without LD_LIBRARY_PATH.

I think the cause of this phenomena might be from change of sys.path in python environment as shown below.

# env -u LD_LIBRARY_PATH python
Python 2.7.5 (default, Nov  6 2016, 00:28:07) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-11)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys
>>> sys.path
['', '/usr/lib64/python27.zip', '/usr/lib64/python2.7', '/usr/lib64/python2.7/plat-linux2', '/usr/lib64/python2.7/lib-tk', '/usr/lib64/python2.7/lib-old', '/usr/lib64/python2.7/lib-dynload', '/usr/lib64/python2.7/site-packages', '/usr/lib64/python2.7/site-packages/gtk-2.0', '/usr/lib/python2.7/site-packages']
>>> quit()
# python
Python 2.7.10 (default, Apr  7 2017, 00:55:54) 
[GCC 5.3.1 20160406 (Red Hat 5.3.1-6)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys
>>> sys.path
['', '/home/samba/Suijitsu_Public/software/pitchfork/deployment/lib/python27.zip', '/home/samba/Suijitsu_Public/software/pitchfork/deployment/lib/python2.7', '/home/samba/Suijitsu_Public/software/pitchfork/deployment/lib/python2.7/plat-linux2', '/home/samba/Suijitsu_Public/software/pitchfork/deployment/lib/python2.7/lib-tk', '/home/samba/Suijitsu_Public/software/pitchfork/deployment/lib/python2.7/lib-old', '/home/samba/Suijitsu_Public/software/pitchfork/deployment/lib/python2.7/lib-dynload', '/home/samba/Suijitsu_Public/software/pitchfork/deployment/lib/python2.7/site-packages']
>>> quit()

As you can see, version of python and sys.path is changed between with and without LD_LIBRARY_PATH.

Takashi

[mhsieh]

I see. I would recommend removal of any reference pitchfork in /etc/profile if it's possible for you. The libpython*.so is what causes the problem. Some suggestion will follow after I finish my day job work.

[mhsieh]

I see. I would recommend removal of any reference pitchfork in /etc/profile if it's possible for you. The libpython*.so is what causes the problem. Some suggestion will follow after I finish my day job work.

[mhsieh]

Sorry I was spent last night, here are my suggestions for the solution:

1. First solution would be rethinking your strategy and avoid putting pitchfork setting in your /etc/profile or user profile, instead of that you can design a wrapper as an entry point of your commands. For example a command wrapper call mypb:

#!/bin/bash
source /home/samba/Suijitsu_Public/software/pitchfork/deployment/setup-env.sh
$@

add this mypb to your PATH, suppose you put it in your $HOME/bin/mypb and your $PATH includes $HOME/bin, then you should be able to do this easily:

$ mypb blasr --version
blasr   5.3.da161e5

2. Second solution would still be removing pitchfork settings from your /etc/profile and user's profile, to use bash --init-file /home/samba/Suijitsu_Public/software/pitchfork/deployment/setup-env.sh (I call this "pitchfork shell") when you want to use pitchfork build just like what we wrote in the documentation. But this time I recommend you to rebuild your pitchfork with this:

cd ~/pitchfork
yes | make _startover
echo HAVE_PYTHON=/usr/bin/python >> settings.mk
make <your software>

so you can still run yum under "pitchfork shell".

Of course you can do both suggestions at the same time.

[mhsieh]

Sorry I was spent last night, here are my suggestions for the solution:

1. First solution would be rethinking your strategy and avoid putting pitchfork setting in your /etc/profile or user profile, instead of that you can design a wrapper as an entry point of your commands. For example a command wrapper call mypb:

#!/bin/bash
source /home/samba/Suijitsu_Public/software/pitchfork/deployment/setup-env.sh
$@

add this mypb to your PATH, suppose you put it in your $HOME/bin/mypb and your $PATH includes $HOME/bin, then you should be able to do this easily:

$ mypb blasr --version
blasr   5.3.da161e5

2. Second solution would still be removing pitchfork settings from your /etc/profile and user's profile, to use bash --init-file /home/samba/Suijitsu_Public/software/pitchfork/deployment/setup-env.sh (I call this "pitchfork shell") when you want to use pitchfork build just like what we wrote in the documentation. But this time I recommend you to rebuild your pitchfork with this:

cd ~/pitchfork
yes | make _startover
echo HAVE_PYTHON=/usr/bin/python >> settings.mk
make <your software>

so you can still run yum under "pitchfork shell".

Of course you can do both suggestions at the same time.

[TakashiKoyama]

Hi,

Sorry for late reply.
Thank you so much for the solutions.
Both of them works fine!

Takashi

[TakashiKoyama]

Hi,

Sorry for late reply.
Thank you so much for the solutions.
Both of them works fine!

Takashi

[mhsieh]

cleaning up old issues, if yo'all find issue I haven't solved, feel free to re-open it, thanks!

[mhsieh]

cleaning up old issues, if yo'all find issue I haven't solved, feel free to re-open it, thanks!