problems with fermilite

[karinlag]

Hi!

I am able to install ariba without any issues, but, I do get the following error when I try to run it:

(ariba)[karinlag@abel ariba]$ ariba --help
Traceback (most recent call last):
  File "/work/projects/nn9305k/bin/virtenv/ariba/bin/ariba", line 3, in <module>
    import ariba
  File "/work/projects/nn9305k/bin/virtenv/ariba/lib/python3.5/site-packages/ariba/__init__.py", line 55, in <module>
    from ariba import *
  File "/work/projects/nn9305k/bin/virtenv/ariba/lib/python3.5/site-packages/ariba/assembly.py", line 6, in <module>
    import fermilite_ariba
ImportError: /cluster/software/VERSIONS/intel-2017.1/advisor_2017.1.1.486553/lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /work/projects/nn9305k/bin/virtenv/ariba/lib/python3.5/site-packages/fermilite_ariba.cpython-35m-x86_64-linux-gnu.so)
(ariba)[karinlag@abel ariba]$

I believe this is Heng Li's fermi-lite, is it not? If so, I will take the issue there. I have a sneaking suspicion this is down to which intel something-or-other that I have loaded, but no clue of how to figure out what I need...

[martinghunt]

This is an issue with compiling the C++ ariba code, not fermilite itself, so don't take the issue to fermi-lite. Can you try downloading the release tarball and running "python3 setup.py test". That compiles all the C/C++ code and runs the tests. I think the output will be more verbose than using pip, and also pip doesn't run the tests.

[karinlag]

Ahhhh! (definite lightbulb moment!). Now I understand a lot more! I will do that presently. Any specifics on compiler versions etc? I have around 11 available.

[martinghunt]

I deliberately didn't use any c++11, so old compilers should be ok. I'm using gcc 4.6.3, which is 5 years old. It's the oldest compiler I've tested ariba on.

First I would try whatever the default is on your system, by not changing anything and running python3 setup.py test. That will compile the code. If you try to change your compiler, then compile, you'll like run into errors like the one above when you run ariba.

[karinlag]

I forgot to say that I figured out what the problem is. The python3 that was on the cluster was compiled with icc, and that seemed to be incompatible with the things in ariba. But, I installed anaconda, and I managed to get it to work then.