[ADMB Users] lgam in 10.0

Sun May 15 11:12:27 PDT 2011

Is this only a problem on Macs? I'd be surprised if others aren't trying to use log_negbinomial_density
thanks,
Mollie

On 15 May 2011, at 2:09 PM, Mollie Brooks wrote:

> Hi Ian,
> Talking to a friend last night, I learned that I had to use sudo to delete /usr/local/admb (I'm really new to this type of programming.) So I did that this morning and changed ./.bashrc to have 
> export ADMB_HOME= /Users/molliebrooks/Desktop/admb-10.1/build/admb-10.1-macos10.6.7-xcode3.2.5-64bit/
> 
> How do  I "rerun .bashrc"?
> After making these changes, I tried to run my program again (even thought I haven't debugged lgam yet) and I got this error:
> 
> mollie-brookss-macbook-4:~ molliebrooks$ cd /Users/molliebrooks/Desktop/UF\ ADMB\ May\ Workshop/examples/FirFecundity/
> mollie-brookss-macbook-4:FirFecundity molliebrooks$ admb firdbhfec
> /usr/local/bin/admb: fork: Resource temporarily unavailable
> 
> So I guess that means that specifying ADMB HOME does nothing? 
> Should I move some admb files to /usr/local/bin?
> thanks,
> Mollie
> 
> On 14 May 2011, at 8:06 PM, Ian Taylor wrote:
> 
>> Dave’s suggestion will hopefully fix everything.
>> But if you say that things are imbedded deeper, that could also be the reason it didn’t find the new version.
>> change ADMB_HOME to /Users/molliebrooks/Desktop/admb-10.1/build/admb-10.1-macos10.6.7-xcode3.2.5-64bit/
>> then rerun .bashrc
>> and then try again. ADMB_HOME/bin has to contain the admb, adcomp, and adlink.< mal>-Ian
>>  
>> From: Mollie Brooks [mailto:mbrooks at ufl.edu] 
>> Sent: Saturday, May 14, 2011 4:11 PM
>> To: Ian Taylor
>> Subject: Re: [ADMB Users] lgam in 10.0
>>  
>> Thanks Ian for trying to help. I can't get either of those solutions to work. 
>> I can't delete /usr/local/admb because I don't have permission and I can't mod
>>  
>> I tried to rename the files you suggested. They are imbedded deeper than I expected
>> /Users/molliebrooks/Desktop/admb-10.1/build/admb-10.1-macos10.6.7-xcode3.2.5-64bit/bin
>> When I tried to look for every instance of “adcomp” or “adlink” and change them to “adcompNew” and “adlinkNew” there was only one instance of "adlink" and none of "adcomp" in admbNEW.
>>  
>> I think I should just give up on this. I was hoping to show some students an example and exercise using log_negbinomial_densit this hard to get it working, then I can't expect them to get it and should put my efforts into other examples and exercises. I'll just avoid negative binomial data for a while.
>> -Mollie
>>  
>>  
>> On 14 May 2011, at 5:55 PM, Ian Taylor wrote:
>> 
>> 
>> Hi Mollie,
>> Thanks to your modifying the path, your computer now has two places where it can search for ADMB binaries:
>> /usr/local/, and the folder on your desktop. Unfortunately, when you call admb, it appears to go to /usr/local/ first and never sees the new version. You can tell this because the command
>>                 g++  -O3 -L/usr/local/admb/lib
>> includes the location /usr/local/ and does not include your new location.
>>  
>> What I would do is delete the entire /usr/local/admb/ you won’t have this problem.
>> An alternative is to go to /Users/molliebrooks/Desktop/admb-10.1//build/bin/ and rename 3 files
>>             admb to admbNew
>> &nbs ;       adcomp to adcompNew
>>             adlink to adlinkNew
>> (or whateve r). Then edit the file admbNew and look for every instance of “adcomp” or “adlink” and change them to “adcompNew” and “adlinkNew”. Now you should have two independent methods of compiling ADMB by calling either admb or admbNew.
>>  
>> -Ian
>>  
>>  
>> From: users-bounces at admb-project.org [mailto:users-bounces at admb-project.org] On Behalf Of Mollie Brooks
>> Sent: Saturday, May 14, 2011 2:11 PM
>> To: users at admb-project.org
>> Subject: Re: [ADMB Users] lgam in 10.0
>>  
>> Hi, 
>> Just swer my own question, I downloaded the source for 10.1 and followed the instructions in README.txt for Unix and GNU g++ since there weren't instructions for Macs. The install seems to have worked, but I no ace the version in /usr/local/
>> So I edited the file ./.bashrc to now have the lines
>>  
>> export ADMB_HOME=/Users/molliebrooks/Desktop/admb-10.1//build
>> export PATH=$ADMB_HOME/bin:$PATH
>>  
>> because I think that's the location of the necessary files. Then I reran the model and still got the error for lgam
>>  
>> *** Linking: adlink /div>
>> g++  -O3 -L/usr/local/admb/lib firdbhfec.o -ldf1b2o -ladmod -ladt -lado -ldf1b2o -ladmod -ladt -lado -o firdbhfec
>> ld: duplicate symbol lgam(double)in /usr/local/admb/lib/libado.a(cgamdev.obj) libdf1b2o.a(df13tester.obj)
>> collect2: ld returned 1 exit status
>>  
>> So I found all the instances of "lgam" in df13tester.cpp
>> How much of this should I comment out? Is it just the definition of lgam(double) lines 943 to 1050? What about lines 309 and 314?
>>  
>> double lgam ( double );
>> double lgam();
>>  
>>  
>> thanks,
>> Mollie
>>  
>> Mollie Brooks
>> Ph.D. Candidate
>> NSF IGERT Fellow
>> Biology Department
>> University of Florida
>> www.zoology.ufl.edu/mbrooks
>>  
>>  
>>  
>> On 14 May 2011, at 3:12 PM, Mollie Brooks wrote:
>> 
>> 
>> 
>> Hi ADMBers,
>> I'm running 10.0 on a mac and this old problem seems to have reoccurred
>> http://groups.google.com/group/admb-users/browse_thread/thread/2e82a6c63586c83e
>>  
>> 
>> The messag >
>> *** Linking: adlink firdbhfec
>> g++  -O3 -L/usr/local/admb/lib firdbhfec.o -ldf1b2o -ladmod -ladt -lado -ldf1b2o -ladmod -ladt -lado -o firdbhfec
>> ld: duplicate symbol lgam(double)in /usr/local/admb/lib/libado.a(cgamdev.obj) and /usr/local/admb/lib/libdf1b2o.a(df13tester.obj)
>> collect2: ld returned 1 exit status
>>  
>> Is this fixed in version 10.1? I saw in the readme.txt file that there was a fix to gammln functions.
>> thanks,
>>  
> 
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