[GenABEL-dev] export.plink() uses too much memory in GenABEL v1.7-0 (beta)

[L.C. Karssen]

Dear Yurii,

We just tried svn revision 827 and had the same problem. We killed the 
program at 51% memory usage (32GB). So, unfortunately I think the 
problem is not solved yet.


Lennart



On 07-12-11 11:36, Yury Aulchenko wrote:
> Ok, should be fixed in r823 just committed.
>
> Let me know if the problem persist
>
> On Dec 7, 2011, at 11:13 AM, Yury Aulchenko wrote:
>
>> I think this is something I introduced in rev. 810-814 (a new without delete). Now (hopefully) fixed, will commit changes in next hour.
>> -------------------------------------------------------
>> Yurii Aulchenko, PhD, Dr. Habil.
>> Independent researcher and consultant
>> yurii [dot] aulchenko [at] gmail [dot] com
>>
>> On Dec 7, 2011, at 11:03 AM, L.C. Karssen wrote:
>>
>>> Dear list,
>>>
>>> We just tried to convert a GenABEL object to plink format using export.plink() from GenABEL v 1.7-0 (still under development, package built from SVN yesterday), and it nearly brought the machine to a halt because it used all available memory (RAM + swap).
>>>
>>> Our GenABEL object contained almost 3700 individuals and about 700k SNPS.
>>>
>>> Have others experienced this as well? I haven't looked at Yurii's latest implementation of the function in C++ yet. Hopefully I will be able to find some time later today. Does anyone here know how we could limit memory usage in C++?
>>>
>>>
>>> Thanks,
>>>
>>> Lennart.
>
>

-- 
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L.C. Karssen
Erasmus MC
Department of Epidemiology
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