[pyngl-talk] PyNIO fatal:NclMalloc Failed: errno=12

[Scott Shaw]

Hi all,
I completed the build process of compiling all of the required packages for ncl_ncarg-6.2.1 and PyNIO-1.3.0b1 successfully using the Intel v15.0 C/C++/Fort compilers.  When testing Nio I am able to do an "import Nio" but when performing a create, read or write I/O request python will Seg fault.

Python 2.6.8 (unknown, Jul 16 2013, 14:48:55)
[GCC 4.3.4 [gcc-4_3-branch revision 152973]] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import Nio
>>> import os
>>> print Nio.__version__
1.3.0b1
>>> filename = os.tempnam(None, 'test_')
>>> filename += '.nc'
>>> print 'Creating temporary file: ', filename

Creating temporary file:  /tmp/test_AfmnXH.nc
>>> f = Nio.open_file(filename, 'c')
fatal:NclMalloc Failed:[errno=12]
Segmentation fault (core dumped)

System info:
    Processors: 2 x 12 Cores Intel(R) Xeon(R) CPU E5-2690 v3 @ 2.60GHz 30720KB Cache
     Total Mem: 128 GB/per node,    Speed: 2133 MHz (0.5 ns)
    OS Release: SUSE Linux Enterprise Server 11 (x86_64) VERSION = 11 SP3
    Kernel Ver: 3.0.101-0.35.1.7253.0.PTF-default

> icc -v
icc version 15.0.1 (gcc version 4.3.0 compatibility)
> ifort -v
ifort version 15.0.1

Currently Loaded Modulefiles:
  1) intel-cc-15/15.0.1.133          3) intel-compilers-15/15.0.1.133
  2) intel-fc-15/15.0.1.133

When building PyNIO the following options were used.
NCAR_ROOT=/NCAR
NCAR_LOCAL_ROOT=/NCAR/local.intel
NCARG_ROOT=${ NCAR_LOCAL_ROOT}/ncarg
setenv LD_LIBRARY_PATH ${NCAR_LOCAL_ROOT}/lib:$LD_LIBRARY_PATH

> env | grep HAS
HAS_NETCDF4=1
HAS_HDFEOS5=1
NETCDF4_PREFIX==/NCAR/local.intel

I used the build_pynio_from_src.shtml webpage a  guide and everything appears to be correct with the build process but I am not sure why NCL is failing on the Malloc call.

Any ideas how to get around this issue would be great appreciated!  In the meantime I will try building the required packages with GNU compiler environment and see if things improve.

Thanks,
Scott Shaw
SGI - Apps Engineering

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