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Ben,<br>
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:<br>
<blockquote><tt>cat: xxalloc4.tmp: No such file or directory<br>
cat: xxalloc5.tmp: No such file or directory<br>
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</tt><br>
</blockquote>
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.<br>
-Ian<br>
<br>
Bolker,Benjamin Michael wrote:
<blockquote
cite="mid:2180B808CDA3404B8FF30C1EA0AC09EE01E8FFEE43@UFEXCH-MBXCL03.ad.ufl.edu"
type="cite">
<pre wrap=""> thanks for the quick reply.
no luck, though:
ben@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 [<a class="moz-txt-link-abbreviated" href="mailto:s.martell@fisheries.ubc.ca">s.martell@fisheries.ubc.ca</a>]
Sent: Tuesday, August 04, 2009 11:35 AM
To: Bolker,Benjamin Michael
Cc: <a class="moz-txt-link-abbreviated" href="mailto:users@admb-project.org">users@admb-project.org</a>
Subject: Re: [ADMB Users] "xxglobal.tmp" error with tpl2rem
Ben,
Try using the scripts that Arni posted at:
<a class="moz-txt-link-freetext" href="http://admb-project.org/community/editing-tools/admb-ide/scripts-linux.zip/view?searchterm=Scripts">http://admb-project.org/community/editing-tools/admb-ide/scripts-linux.zip/view?searchterm=Scripts</a>
Steve
On 3-Aug-09, at 10:09 PM, Bolker,Benjamin Michael wrote:
</pre>
<blockquote type="cite">
<pre wrap=""> 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)));
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</pre>
</blockquote>
<pre wrap=""><!---->
Steve Martell
<a class="moz-txt-link-abbreviated" href="mailto:s.martell@fisheries.ubc.ca">s.martell@fisheries.ubc.ca</a>
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</pre>
</blockquote>
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