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)" <sheena.mcgo...@monash.edu> 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 <ha...@mrc-lmb.cam.ac.uk> 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 sheena.mcgo...@monash.edu | 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 sheena.mcgo...@monash.edu | 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 >
