[ADMB Users] "xxglobal.tmp" error with tpl2rem
Steve Martell
s.martell at fisheries.ubc.ca
Tue Aug 4 09:36:27 PDT 2009
I get the same error message on Mac OS X, but it still seems to
compile and run ok.
S.
On 4-Aug-09, at 9:28 AM, Ian Taylor wrote:
> Ben,
> I just wanted to note that the error I get with the same platform
> using admb-9.0.202-linux64-gcc4.2.4 is similar:
> cat: xxalloc4.tmp: No such file or directory
> cat: xxalloc5.tmp: No such file or directory
> Error executing command cat xxglobal.tmp xxhtop.tmp header.tmp
> xxalloc1.tmp xxalloc2.tmp xxalloc3.tmp xxalloc4.tmp
> xxalloc5.tmp xxtopm.tmp xxalloc6.tmp > bolker.cpp
> I have no experience with ADMB-RE so I can't advise you on problems
> with the TPL file, but your model does run using tpl2cpp if the RE
> vector is changed to be an init_vector.
> -Ian
>
> Bolker,Benjamin Michael wrote:
>>
>> thanks for the quick reply.
>>
>> no luck, though:
>>
>> ben at bolker-lap2:~/downloads$ ./admb -r ~/students/mccoy/mccoypred3
>>
>> *** tpl2rem /home/ben/students/mccoy/mccoypred3
>> cat: xxalloc4.tmp: No such file or directory
>> Error executing command cat xxglobal.tmp xxhtop.tmp
>> header.tmp xxalloc1.tmp xxalloc2.tmp xxalloc3.tmp
>> xxalloc4.tmp xxalloc5.tmp xxtopm.tmp xxalloc6.tmp > /home/
>> ben/students/mccoy/mccoypred3.cpp
>>
>> is there something boneheaded/obviously wrong with the TPL file?
>> it takes me a long time to recognize such things, being so new to
>> ADMB.
>>
>> I did find that the simple2.tpl example posted on the google code
>> site, which is
>> basically a translation of the example in the ADMB-RE manual (taking
>> "simple.tpl" and adding some measurement error) provokes the same
>> response. The union.tpl example distributed with ADMB-RE works,
>> but I can provoke the same error
>> by deleting the following lines from union.tpl:
>>
>> < PRELIMINARY_CALCS_SECTION
>> < cout << setprecision(4);
>> <
>> < GLOBALS_SECTION
>> <
>>
>> Here's simple2.tpl:
>>
>> DATA_SECTION
>> init_int nobs
>> init_vector Y(1,nobs)
>> init_vector X(1,nobs)
>> PARAMETER_SECTION
>> init_number a
>> init_number b
>> init_number mu
>> vector pred_Y(1,nobs)
>> init_bounded_number sigma_Y(0.000001,10)
>> init_bounded_number sigma_x(0.000001,10)
>> random_effects_vector x(1,nobs)
>> objective_function_value f
>> PROCEDURE_SECTION // This section is pure C++
>> f = 0;
>> pred_Y=a*x+b; // Vectorized operations
>> // Prior part for random effects x
>> f += -nobs*log(sigma_x) - 0.5*norm2((x-mu)/sigma_x);
>> // Likelihood part
>> f += -nobs*log(sigma_Y) - 0.5*norm2((pred_Y-Y)/sigma_Y);
>> f += -0.5*norm2((X-x)/0.5);
>> f *= -1; // ADMB does minimization!
>>
>>
>> ________________________________________
>> From: Steve Martell [s.martell at fisheries.ubc.ca]
>> Sent: Tuesday, August 04, 2009 11:35 AM
>> To: Bolker,Benjamin Michael
>> Cc: users at admb-project.org
>> Subject: Re: [ADMB Users] "xxglobal.tmp" error with tpl2rem
>>
>> Ben,
>>
>> Try using the scripts that Arni posted at:
>>
>> http://admb-project.org/community/editing-tools/admb-ide/scripts-linux.zip/view?searchterm=Scripts
>>
>> Steve
>>
>> On 3-Aug-09, at 10:09 PM, Bolker,Benjamin Michael wrote:
>>
>>
>>> I'm just beginning to use AD Model Builder.
>>> I have successfully (after some struggles) created a few different
>>> likelihood models, with results matching previous model fits in R.
>>> Now I'm trying to add a random effect. Versions of the TPL file
>>> below compiled OK with tpl2cpp before I added the random effect;
>>> now, with tpl2rem, I'm getting
>>>
>>> cat: xxalloc4.tmp: No such file or directory
>>> cat: xxalloc5.tmp: No such file or directory
>>> Error executing command cat xxglobal.tmp xxhtop.tmp header.tmp
>>> xxalloc1.tmp xxalloc2.tmp xxalloc3.tmp xxalloc4.tmp
>>> xxalloc5.tmp xxtopm.tmp xxalloc6.tmp > mccoypred4.cpp
>>>
>>> There was an issue with similar keywords listed on the ADMB site,
>>> but it
>>> was listed as "resolved".
>>>
>>> I'm running on Ubuntu Linux 9.04, with a recent (?? can't find
>>> version number ??)
>>> version of ADMB. (Maybe 9.0.202 from the google code page?)
>>>
>>> I'd be happy to provide any other diagnostics/information if that
>>> will
>>> help solve / diagnose ...
>>>
>>> sincerely
>>> Ben Bolker
>>>
>>>
>>>
>>> -------------------------------------
>>> DATA_SECTION
>>>
>>> init_int nobs // # of observations
>>> init_int nblock // # of blocks
>>> init_vector killed(1,nobs) // # killed per trial
>>> init_vector size(1,nobs) // size of individuals
>>> init_vector initial(1,nobs) // starting density (# individuals)
>>> init_matrix Z(1,nobs,1,nblock) // random-effects model matrix
>>>
>>> PARAMETER_SECTION
>>>
>>> init_number c // *mean* c value
>>> init_number d
>>> init_bounded_number h(0.0,1.0,1)
>>> init_number g
>>> init_bounded_number sigma_c(0.00001,1.0,1)
>>> random_effects_vector u(1,nblock)
>>> vector prob(1,nobs)
>>> vector cvec(1,nobs)
>>> objective_function_value f
>>>
>>> PROCEDURE_SECTION
>>> // compute vector of c values
>>> cvec = c + sigma_c*(Z*u)
>>> // power-Ricker
>>> prob = 1/(1/(elem_prod(cvec,elem_prod(pow(size/d,g),exp(-size/d))))
>>> +h*initial);
>>> // binomial negative log-likelihood
>>> f -= sum( log_comb(initial,killed)+
>>> elem_prod(killed,log(prob))+
>>> elem_prod(initial-killed,log(1-prob)));
>>> _______________________________________________
>>> Users mailing list
>>> Users at admb-project.org
>>> http://lists.admb-project.org/mailman/listinfo/users
>>>
>>
>> Steve Martell
>> s.martell at fisheries.ubc.ca
>>
>>
>>
>> _______________________________________________
>> Users mailing list
>> Users at admb-project.org
>> http://lists.admb-project.org/mailman/listinfo/users
>>
Steve Martell
s.martell at fisheries.ubc.ca
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