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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/ directory, in which case 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 whatever naming scheme you prefer). 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.
On 14 May 2011, at 3:12 PM, Mollie Brooks wrote:
*** 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.
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first problme is that posfun must have a non negative second argument.
This is where the "positiveness" kicks in. If you make it 0.0 the
curvature is infinite. Best is to tune it as the model gets fitted.
Call it eps2 and begin with a bigger number in the first phase.
This is a typical technique to make the objective function well
behaved until you get near the solution.
will cause you trouble if p is too close to 0 or 1. so add a tiny number
and tune it as well.
Note the order of addition (eps1+(1-p)) ans figure out why (eps1+1-p)
may not work.
Then add a kludge variable with the number of phases that you want. I
always name if
kkludge so that I l know what its purpose is.
Now run the model and tune the values of eps1 eps2 to be small but the
model still converges.
I got into this and ended up with 5 phases. the value of eps1 has a
I ran with the CLO of -crit 1.e-8.
else if (current_phase()<3)
else if (current_phase()<4)
else if (current_phase()<5)
arrmblsize = 2147483647;
After you change the .bashrc (or whatever it is named) you need to close
and reopen it. (that works on Linux maybe with Macs you need to log out,
Then it should work. On Linux the system keeps track of where the
executable programs are
so if you remove one and don't refresh it somehow such as by logging in
or in Linux
typing the command
It may act confused as to where admb is.
In the good old days when this was closed source as God intended I
would have rebuilt the sources
and pointed the users at them and the lgam problem would have been fixed
Now we need a committee.