QuantumATK Forum

QuantumATK => Installation and License Questions => Topic started by: sergio on October 8, 2010, 09:44

Title: Import error:.../_path.so: undefined symbol: _ZNSs4_Rep20_S_empty_rep_storageE
Post by: sergio on October 8, 2010, 09:44

Hi,
I have installed ATK 10.8.2. At the end of the calculation the following error appears:

Traceback (most recent call last):
  File "/tmp/0835619392553552.py", line 33, in <module>
    import pylab
  File "./build/atkpython/lib/python2.6/site-packages/pylab.py", line 1, in <module>
  File "./build/atkpython/lib/python2.6/site-packages/matplotlib/pylab.py", line 216, in <module>
  File "./build/atkpython/lib/python2.6/site-packages/matplotlib/mpl.py", line 1, in <module>
  File "./build/atkpython/lib/python2.6/site-packages/matplotlib/artist.py", line 6, in <module>
  File "./build/atkpython/lib/python2.6/site-packages/matplotlib/transforms.py", line 34, in <module>
ImportError: /home/scaliskan/QuantumWise/atk-10.8.2/atkpython/lib/python2.6/site-packages/matplotlib/_path.so: undefined symbol: _ZNSs4_Rep20_S_empty_rep_storageE
NanoLanguageScript execution failure

How can I resolve that problem?

Thanks,

Title: Re: Import error:.../_path.so: undefined symbol: _ZNSs4_Rep20_S_empty_rep_storageE
Post by: Anders Blom on October 8, 2010, 10:12

Is there any chance the directory into which you try to store something contains a non-7-bit ASCII character, i.e. non Latin character? Can you show the script (if you don't want it public, email it to me)?

Title: Re: Import error:.../_path.so: undefined symbol: _ZNSs4_Rep20_S_empty_rep_storageE
Post by: Anders Blom on October 8, 2010, 10:23

Which Linux distribution are you using, and which precise ATK package did you install?

Title: Re: Import error:.../_path.so: undefined symbol: _ZNSs4_Rep20_S_empty_rep_storageE
Post by: Anders Blom on October 8, 2010, 10:29

Please try the following for us:

1. Instead of running the script from the Job Manager, save it as a Python file (let's say in your home directory, we'll call it test.py).
2. Open a terminal, and write

Code

export LD_DEBUG=all

Then, run (copy exactly)

Code

atkpython test.py > test.log 2>&1 

and send us the contents of test.log.

Title: Re: Import error:.../_path.so: undefined symbol: _ZNSs4_Rep20_S_empty_rep_storageE
Post by: sergio on October 8, 2010, 14:53

Thanks for your quick reply,

I use RHEL 5 and I have just installed ATK 10.8.2 with floating license server. Actually in ATK 10.8.0 there was no such a problem and everything was OK.

By the way, I have done what you have indicated in your Reply#3.  But the log file that I get has a size of 33 MB! So I think it is impossible to send it.

I think the main problem originates from the pylab which is taken place at the end of my script, for which we use import pylab.

Thanks,

Title: Re: Import error:.../_path.so: undefined symbol: _ZNSs4_Rep20_S_empty_rep_storageE
Post by: Anders Blom on October 8, 2010, 15:07

Yes, if you use pylab, that is clearly the reason. We'll see if there is something we can do about it, but it might be a bit tricky. Can you use some Windows computer for example to just complete the plotting?

Title: Re: Import error:.../_path.so: undefined symbol: _ZNSs4_Rep20_S_empty_rep_storageE
Post by: Anders Blom on October 8, 2010, 15:08

Regarding the log file, if you do

Code

grep _ZNSs4_Rep20_S_empty_rep_storageE test.log > smaller.log

probably smaller.log is not so large, maybe you can send that.

Title: Re: Import error:.../_path.so: undefined symbol: _ZNSs4_Rep20_S_empty_rep_storageE
Post by: sergio on October 8, 2010, 15:24

Actually, of course, I can also use other plotting software but I have intended to employ the pylab in my script.
Upon using grep the log file (file2.log) is attached.

I hope the problem will be resolved soon.

Thanks,

Title: Re: Import error:.../_path.so: undefined symbol: _ZNSs4_Rep20_S_empty_rep_storageE
Post by: Anders Blom on October 8, 2010, 15:41

On your machine, do you have the library /usr/lib64/libstdc++.so.5?

If not, I think a workaround for now is to install the compat-libstdc++ library, which provides this file. Use the package manager to update your system; also see http://rpm.pbone.net/index.php3/stat/4/idpl/13943754/dir/centos_5/com/compat-libstdc++-33-3.2.3-61.x86_64.rpm.html.

If you do already, then I'm at a loss, for the moment...

Title: Re: Import error:.../_path.so: undefined symbol: _ZNSs4_Rep20_S_empty_rep_storageE
Post by: sergio on October 8, 2010, 15:54

Yes I have this library....