Demeter on Mac OS X

Juliana Fonseca de Lima

5 Jun 2014 5 Jun '14

5:09 a.m.

Hi all, I have used Athena on my Mac since last month, but from last week I have had the below problem to open the software. Could you help me to solve that? perl5.16(423,0x7fff75854310) malloc: *** mach_vm_map(size=18446744071562072064) failed (error code=3) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Out of memory! PS: I have 8 GB of physical memory. Cheers, Juliana

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Bruce Ravel

6 Jun 6 Jun

8:11 a.m.

On 06/05/2014 06:09 AM, Juliana Fonseca de Lima wrote:

...

Hi all,

I have used Athena on my Mac since last month, but from last week I have had the below problem to open the software. Could you help me to solve that?

perl5.16(423,0x7fff75854310) malloc: *** mach_vm_map(size=18446744071562072064) failed (error code=3)

*** error: can't allocate region

*** set a breakpoint in malloc_error_break to debug

Out of memory!

PS: I have 8 GB of physical memory.

Juliana, I suspect the reason no one has answered your post is that you have not provided much information to work with. /Something/ must have happened to your computer in the last week. Did you do a system update? Did you install new software? Perhaps a block of RAM went bad -- you could run a hardware test to find out. (That happened recently on one of my laptops.) The bottom line is that I cannot see any way to diagnose the problem simply on the basis of the information provided. That Athena worked one day and not the next suggests something changed on your computer. B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

Schima, Frank

12:16 p.m.

On Jun 6, 2014, at 7:11 AM, Bruce Ravel mailto:bravel@bnl.gov> wrote: On 06/05/2014 06:09 AM, Juliana Fonseca de Lima wrote: Hi all, I have used Athena on my Mac since last month, but from last week I have had the below problem to open the software. Could you help me to solve that? perl5.16(423,0x7fff75854310) malloc: *** mach_vm_map(size=18446744071562072064) failed (error code=3) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Out of memory! PS: I have 8 GB of physical memory. Juliana, I suspect the reason no one has answered your post is that you have not provided much information to work with. /Something/ must have happened to your computer in the last week. Did you do a system update? Did you install new software? Perhaps a block of RAM went bad -- you could run a hardware test to find out. (That happened recently on one of my laptops.) The bottom line is that I cannot see any way to diagnose the problem simply on the basis of the information provided. That Athena worked one day and not the next suggests something changed on your computer. Agreed. I can tell you that all of the programs launch fine for me on OS X 10.9.3 and 10.8.5 using the latest Demeter port in Macports. I would suggest making sure you are up to date in Macports: sudo port selfupdate sudo port upgrade outdated Cheers! Frank

Kevin Jorissen

2:08 p.m.

There was a recent update of XCode (5.1.1), which could be a suspect (depending on when you installed it) and might have broken some dependency? (I don't know what the Demeter port depends on.) E.g. it might update some of the libraries/compilers used in demeter (I'm not sure), and sometimes the command line tools need to be reinstalled to restore softlinks etc. The error message you see might be related to a changed c runtime library or something (just guessing). I tried a clean install of demeter today and I can open Athena properly. Have you tried reinstalling demeter? This is always a good thing to try. - Use "port" to remove demeter and dependencies. - Reinstall XCode command line tools ("xcode-select --install") if you haven't already. - sudo port install demeter Cheers, Kevin PS It's clearly harmless but I get a couple of these warnings: ~% /opt/local/bin/athena 2014-06-06 11:50:01.909 perl5.16[31186:303] CoreText performance note: Client called CTFontCreateWithName() using name "Lucida Grande" and got font with PostScript name "LucidaGrande". For best performance, only use PostScript names when calling this API. 2014-06-06 11:50:01.909 perl5.16[31186:303] CoreText performance note: Set a breakpoint on CTFontLogSuboptimalRequest to debug. 2014-06-06 11:50:01.989 perl5.16[31186:303] CoreText performance note: Client called CTFontCreateWithName() using name "Lucida Grande" and got font with PostScript name "LucidaGrande". For best performance, only use PostScript names when calling this API. 2014-06-06 11:50:02.040 perl5.16[31186:303] CoreText performance note: Client called CTFontCreateWithName() using name "Lucida Grande" and got font with PostScript name "LucidaGrande". For best performance, only use PostScript names when calling this API. 2014-06-06 11:50:02.085 perl5.16[31186:303] CoreText performance note: Client called CTFontCreateWithName() using name "Lucida Grande" and got font with PostScript name "LucidaGrande". For best performance, only use PostScript names when calling this API. 2014-06-06 11:50:02.091 perl5.16[31186:303] CoreText performance note: Client called CTFontCreateWithName() using name "Lucida Grande" and got font with PostScript name "LucidaGrande". For best performance, only use PostScript names when calling this API. 2014-06-06 11:50:02.096 perl5.16[31186:303] CoreText performance note: Client called CTFontCreateWithName() using name "Lucida Grande" and got font with PostScript name "LucidaGrande". For best performance, only use PostScript names when calling this API. 2014-06-06 11:50:02.404 perl5.16[31186:303] CoreText performance note: Client called CTFontCreateWithName() using name ".Lucida Grande UI" and got font with PostScript name ".LucidaGrandeUI". For best performance, only use PostScript names when calling this API. 2014-06-06 11:50:02.407 perl5.16[31186:303] CoreText performance note: Client called CTFontCreateWithName() using name ".Lucida Grande UI" and got font with PostScript name ".LucidaGrandeUI". For best performance, only use PostScript names when calling this API. 2014-06-06 11:50:03.202 perl5.16[31186:303] CoreText performance note: Client called CTFontCreateWithName() using name "Lucida Grande" and got font with PostScript name "LucidaGrande". For best performance, only use PostScript names when calling this API. ~% ~% On Fri, Jun 6, 2014 at 10:16 AM, Schima, Frank wrote:

...

On Jun 6, 2014, at 7:11 AM, Bruce Ravel wrote:

On 06/05/2014 06:09 AM, Juliana Fonseca de Lima wrote:

Hi all,

I have used Athena on my Mac since last month, but from last week I have had the below problem to open the software. Could you help me to solve that?

perl5.16(423,0x7fff75854310) malloc: *** mach_vm_map(size=18446744071562072064) failed (error code=3)

*** error: can't allocate region

*** set a breakpoint in malloc_error_break to debug

Out of memory!

PS: I have 8 GB of physical memory.

Juliana,

I suspect the reason no one has answered your post is that you have not provided much information to work with. /Something/ must have happened to your computer in the last week. Did you do a system update? Did you install new software? Perhaps a block of RAM went bad -- you could run a hardware test to find out. (That happened recently on one of my laptops.)

The bottom line is that I cannot see any way to diagnose the problem simply on the basis of the information provided. That Athena worked one day and not the next suggests something changed on your computer.

Agreed. I can tell you that all of the programs launch fine for me on OS X 10.9.3 and 10.8.5 using the latest Demeter port in Macports. I would suggest making sure you are up to date in Macports:

sudo port selfupdate sudo port upgrade outdated

Cheers! Frank

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Bruce Ravel

4:29 p.m.

On 06/06/2014 03:08 PM, Kevin Jorissen wrote:

...

There was a recent update of XCode (5.1.1), which could be a suspect (depending on when you installed it) and might have broken some dependency? (I don't know what the Demeter port depends on.) E.g. it might update some of the libraries/compilers used in demeter (I'm not sure), and sometimes the command line tools need to be reinstalled to restore softlinks etc. The error message you see might be related to a changed c runtime library or something (just guessing).

I tried a clean install of demeter today and I can open Athena properly.

Thanks, Kevin! That sounds like a likely candidate for Juliana's problem. The error messages she reported could plausibly have come from an updated library.

...

Have you tried reinstalling demeter? This is always a good thing to try.

- Use "port" to remove demeter and dependencies. - Reinstall XCode command line tools ("xcode-select --install") if you haven't already. - sudo port install demeter

Cheers,

Kevin

PS It's clearly harmless but I get a couple of these warnings:

~% /opt/local/bin/athena

2014-06-06 11:50:01.909 perl5.16[31186:303] CoreText performance note: Client called CTFontCreateWithName() using name "Lucida Grande" and got font with PostScript name "LucidaGrande". For best performance, only use PostScript names when calling this API.

This is almost certainly a problem coming from the wxWindows library, which is the library which creates all the GUI elements. It is almost certainly not something done wrongly in Demeter. A bit of google searching turns up quite a number of projects written in many different languages all showing the same warning. B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

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participants (4)

Bruce Ravel
Juliana Fonseca de Lima
Kevin Jorissen
Schima, Frank