I found another server on which the code works as on your computer :

Using cuDNN version 5110 on context None
Preallocating 9151/11439 Mb (0.800000) on cuda0
Mapped name None to device cuda0: Tesla K80 (0000:83:00.0)
GpuEye{dtype='float32', context_name=None} [id A] ''   
 |x [id B]
 |y [id C]
Compiling
GpuEye{dtype='float32', context_name=None} [id A] ''   0
 |x [id B]
 |y [id C]
Results
[[ 1.  0.  0.]
 [ 0.  1.  0.]
 [ 0.  0.  1.]



To reproduce the segmentation fault :

*conda install pygpu* 

Fetching package metadata .........
Solving package specifications: .

Package plan for installation in environment /root/miniconda2:

The following packages will be UPDATED:

    libgpuarray: 0.6.4-0      --> 0.6.8-0     
    pygpu:       0.6.4-py27_1 --> 0.6.8-py27_0

Proceed ([y]/n)? y 


And then you can run again :

import theano
from theano.gpuarray.basic_ops import GpuEye
x = theano.tensor.iscalar('x')
y = theano.tensor.iscalar('y')
z = GpuEye(dtype='float32', context_name=None)(x,y, 
theano.tensor.constant(0))
theano.printing.debugprint(z)
print("Compiling")
f = theano.function( [x,y], z)
theano.printing.debugprint(f)
print("Results")
print(f(3, 3))

Using cuDNN version 5110 on context None
Preallocating 9151/11439 Mb (0.800000) on cuda0
Mapped name None to device cuda0: Tesla K80 (0000:83:00.0)
GpuEye{dtype='float32', context_name=None} [id A] ''   
 |x [id B]
 |y [id C]
Compiling
Segmentation fault (core dumped)

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