Undefined function or variable 'neff'. in diag/psrf.m

[YuHsiangLo]

Hi,

I got the following error while running the test code from LonGP:

>> lonGP('./test/output',1)
processing target 1: y.

in conStep1

Selecting 0th continuous variable.
toSelVarInds: 1
Resuming from rep=1 mcmc_round=4.
Undefined function or variable 'neff'.

Error in psrf (line 108)
neff=min(neff,N*M);

Error in runMCMC (line 97)
    R = psrf(thetaArr{:});

Error in runMcmcInfer (line 26)
    [R, rfull, flag] = runMCMC(gp,xmn,ymn,nRep,tmpresfile);

Error in conStep1 (line 44)
    runMcmcInfer(currVarFlagArr, 1);

Error in lonGP (line 173)
        currNextFun(currNextArg{:});

I think this was caused by the last line neff=min(neff,N*M); being outside the function definition in diag/psrf.m. I was running the code on MATLAB R2019a with macOS 10.15.7, using the gpstuff dev branch. Could you look into this? Thanks a lot!

[jpvanhat]

Hi,
The problem seems to be in the LonGP function that calls GPstuff function. Hence, maybe @avehtari can direct this issue to someone in LonGP team.

-Jarno

[avehtari]

I emailed Lu Cheng

[chengl7]

Hi YuHsiangLo,

Sorry for the long delay.

The problem is that the code needs to use 'SuiteSparse' in GPstuff to make inferences. There are two solutions.

1. use the file "LonGP/util/gpcf_cat.m.bak" to replace the file "gpstuff/gp/gpcf_cat.m"
2. install 'SuiteSparse', check the installation manual of GPstuff

Cheers,
Lu

Hi,

I got the following error while running the test code from LonGP:

>> lonGP('./test/output',1)
processing target 1: y.

in conStep1

Selecting 0th continuous variable.
toSelVarInds: 1
Resuming from rep=1 mcmc_round=4.
Undefined function or variable 'neff'.

Error in psrf (line 108)
neff=min(neff,N*M);

Error in runMCMC (line 97)
    R = psrf(thetaArr{:});

Error in runMcmcInfer (line 26)
    [R, rfull, flag] = runMCMC(gp,xmn,ymn,nRep,tmpresfile);

Error in conStep1 (line 44)
    runMcmcInfer(currVarFlagArr, 1);

Error in lonGP (line 173)
        currNextFun(currNextArg{:});

I think this was caused by the last line neff=min(neff,N*M); being outside the function definition in diag/psrf.m. I was running the code on MATLAB R2019a with macOS 10.15.7, using the gpstuff dev branch. Could you look into this? Thanks a lot!

[jpvanhat]

Hi @YuHsiangLo . Did the above answer solve your problem and can we close this issue?