pyximport fail on linux

[Alex Pitchford]

After a seemingly successful install on a linux (CentOS) cluster under Anaconda It get the following error when import qutip.

ImportError: Building module qutip.cy.spmatfuncs failed: ['ImportError: /home/alexander.pitchford/.pyxbld/lib.linux-x86_64-3.5/qutip/cy/spmatfuncs.cpython-35m-x86_64-linux-gnu.so: undefined symbol: __intel_sse4_strchr\n']

Anyone have any ideas of things I can try?

[Alex Pitchford]

pause on this one. Looks like I may have resolved the issue by switching to gnu compiler. Or just removing the cached file. Difficult to say which

[nonher...@gmail.com]

Try removing -mtune=native in the compiler flags and see if that changes anything.  Maybe others might have to be removed as well. 

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[nonher...@gmail.com]

What was your previous compiler?

[Alex Pitchford]

Thanks Paul,

I was trying various versions of the intel compiler, but I am not sure what compiler Python was built against on this cluster. They used to have a specific python with numpy that was built with intel compiler v13. But they recently rebuilt the whole thing with Centos upgrade. I tried using the intel compiled python with numpy, but had some other issue that I forget now. I noticed that they now had an anaconda install on there, so I tried using that, which was when these errors appeared. After which I tried using the gcc compiler, and it seemed ok, but I still have work to do.

I will have another go with the intel compiled python and see how I get on.

Alex

[Alex Pitchford]

I had another go at trying to use the intel compiler on this cluster.

I could not install qutip under the python numpy setup that they had on there. So I installed anaconda in the user directory. I am quite happy with this, as it gives us control over the python env.

qutip installed fine under anaconda. I noticed it was using the icc compiler.

However, on first import I got a similar error to:

ImportError: Building module qutip.cy.spmatfuncs failed: ['ImportError: /home/alexander.pitchford/.pyxbld/lib.linux-x86_64-3.5/qutip/cy/spmatfuncs.cpython-35m-x86_64-linux-gnu.so: undefined symbol: __intel_sse4_strchr\n']

It seems like there is some confusion there, as 'gnu' is in the filename.

I fixed the problem by reinstalling qutip using the gnu compiler.

I am wondering whether the Anaconda cython is somehow using the gnu compiler to make the .so.

Anyway, it doesn't really matter. I just thought I would report it for interests sake.

On Sunday, 29 May 2016 22:34:02 UTC+1, Alex Pitchford wrote:

Thanks Paul,

I was trying various versions of the intel compiler, but I am not sure what compiler Python was built against on this cluster. They used to have a specific python with numpy that was built with intel compiler v13. But they recently rebuilt the whole thing with Centos upgrade. I tried using the intel compiled python with numpy, but had some other issue that I forget now. I noticed that they now had an anaconda install on there, so I tried using that, which was when these errors appeared. After which I tried using the gcc compiler, and it seemed ok, but I still have work to do.

I will have another go with the intel compiled python and see how I get on.

Alex

On 27 May 2016 at 22:11, <nonher...@gmail.com> wrote:

What was your previous compiler?

On May 27, 2016, at 14:29, Alex Pitchford <alex.pi...@gmail.com> wrote:

pause on this one. Looks like I may have resolved the issue by switching to gnu compiler. Or just removing the cached file. Difficult to say which

On Friday, 27 May 2016 21:21:26 UTC+1, Alex Pitchford wrote:

After a seemingly successful install on a linux (CentOS) cluster under Anaconda It get the following error when import qutip.

ImportError: Building module qutip.cy.spmatfuncs failed: ['ImportError: /home/alexander.pitchford/.pyxbld/lib.linux-x86_64-3.5/qutip/cy/spmatfuncs.cpython-35m-x86_64-linux-gnu.so: undefined symbol: __intel_sse4_strchr\n']

Anyone have any ideas of things I can try?

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