I do have problems building static executables on OSX: the CCP4 guys seem to be better at it.
Specifically, when I build with a "static" flag, fatal error messages from program exceptions get lost, making it hard to understand some serious errors.
However I have put on our ftp site
ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless-1.8.7.osx10.8static
which may help
Phil
On 12 Aug 2013, at 11:01, "Sheena McGowan (Med)" <[log in to unmask]> wrote:
> Hi
>
> Thanks for that. The latest build of OSX pointless gave us the same error (dyld: Symbol not found: __ZNSt11range_errorD1Ev) however the latest Aimless build was able to run successfully.
>
> Cheers
> Sheena
>
> On 12/08/2013, at 7:42 PM, Harry Powell <[log in to unmask]> wrote:
>
>> Hi
>>
>> I noticed last week that, although the CCP4 updater for OSX requires 64-bit (see CCP4 discussions passim), all the executables are 32-bit (or at least in my current copy, updated a few weeks ago). So there is an inconsistency - no doubt this will be sorted out shortly.
>>
>> If you want a 64-bit build of Pointless for OSX then see Phil Evans' ftp site -
>>
>> ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre
>>
>> Use the most recent version - it may solve your problem.
>>
>> On 12 Aug 2013, at 03:28, Bosch, Juergen wrote:
>>
>>> Hi Sheena,
>>>
>>> simple quickfix to your problem:
>>> a) Run CAD and limit the output resolution on that mtz file so you don't run into the memory allocation error of pointless.
>>> b) try phenix.xtriage also if it is not a CCP4 program
>>>
>>> Jürgen
>>>
>>> ......................
>>> Jürgen Bosch
>>> Johns Hopkins University
>>> Bloomberg School of Public Health
>>> Department of Biochemistry & Molecular Biology
>>> Johns Hopkins Malaria Research Institute
>>> 615 North Wolfe Street, W8708
>>> Baltimore, MD 21205
>>> Office: +1-410-614-4742
>>> Lab: +1-410-614-4894
>>> Fax: +1-410-955-2926
>>> http://lupo.jhsph.edu
>>>
>>>
>>>
>>>
>>> On Aug 11, 2013, at 9:54 PM, Sheena McGowan (Med) wrote:
>>>
>>>> Dear all
>>>>
>>>> We have been trying to run pointless on a large mtz file which seems to be allocating more than 1.5Gb of memory resulting in the following error:
>>>>
>>>> The program run with command: /Applications/ccp4-6.3.0/bin/pointless
>>>> has failed with error message
>>>> pointless(507) malloc: *** mmap(size=1577435136) failed (error code=12)
>>>> *** error: can't allocate region
>>>> *** set a breakpoint in malloc_error_break to debug
>>>>
>>>> We are using OSX 10.8.4 and believe that we need a 64bit version of pointless.
>>>>
>>>> Looking at the pre release ftp site, we found the latest versions of pointless compiled for OSX 10.8, however they do not run.
>>>>
>>>> dyld: Symbol not found: __ZNSt11range_errorD1Ev
>>>> Referenced from: /Applications/ccp4-6.3.0/bin/pointless-1.8.7.osx10.8
>>>> Expected in: /usr/lib/libstdc++.6.dylib
>>>> in /Applications/ccp4-6.3.0/bin/pointless-1.8.7.osx10.8
>>>>
>>>> Any help would be greatly appreciated (and any know if there is a upcoming release of a pre-compiled CCP4 OSX-64bit??)
>>>>
>>>> Regards
>>>> Sheena
>>>>
>>>>
>>>>
>>>> SHEENA McGOWAN | ARC Future Fellow
>>>> Department of Biochemistry and Molecular Biology
>>>> MONASH UNIVERSITY
>>>> Rm 243, Building 77, Wellington Rd, Clayton
>>>> Victoria, AUSTRALIA 3800
>>>> T + 61 3 9902 9309 | F + 61 3 9902 9500
>>>> E [log in to unmask] | Skype s.mcgowan
>>>> W http://www.med.monash.edu.au/biochem/staff/mcgowan.html
>>>>
>>>> Australian Society for Biochemistry and Molecular Biology (State Representative) http://www.asbmb.org.au/
>>>>
>>>> 39th Lorne Conference for Protein Structure and Function http://www.lorneproteins.org
>>>> February 9-13, 2014. Mantra Lorne, Lorne, AUSTRALIA
>>>>
>>>
>>>
>>
>> Harry
>> --
>> ** note change of address **
>> Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH
>> Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
>>
>>
>>
>>
>>
>>
>>
>>
>>
>
>
>
>
> SHEENA McGOWAN | ARC Future Fellow
> Department of Biochemistry and Molecular Biology
> MONASH UNIVERSITY
> Rm 243, Building 77, Wellington Rd, Clayton
> Victoria, AUSTRALIA 3800
> T + 61 3 9902 9309 | F + 61 3 9902 9500
> E [log in to unmask] | Skype s.mcgowan
> W http://www.med.monash.edu.au/biochem/staff/mcgowan.html
>
> Australian Society for Biochemistry and Molecular Biology (State Representative) http://www.asbmb.org.au/
>
> 39th Lorne Conference for Protein Structure and Function http://www.lorneproteins.org
> February 9-13, 2014. Mantra Lorne, Lorne, AUSTRALIA
>
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