Re: Stop During PsN
Dear Kajsa,
Thanks very much for your reply. I found the answers you provided cleared
many unsolved problems. However, regarding below answer I found there might
be something different from the answer you provided.
*What if I use the unidentified relationships in the new run, and using a
mod file with relations in the scm logfile at the time of stop?*
* That will usually not work.*
While waiting for answers, I tested this method and found that it is
actually working. The procedure is as follows:
1. use the included relations at the time of crash as the base model, copy
it from m1 folder to the folder where scm file exists [change $DATA
location].
2. make a copy of the original scm file, and rename it to a different name.
Some changes were made to the scm file:
- change the mod file to the new base model mod;
- delete all the included relations;
- change the search direction from both to forward. [A full backward
process would be initiated after the full model was established.]
3. submit the scm file without the option of -directory.
I am still waiting for the final results. But up until now it seems that
this method actually works. New covariate-parameter relations were added on
top of the previous ones. From my understanding this should be the same as
the method using [included_relations] as you mentioned, although this might
be a little bit more complex.
Best Regards
Quoted reply history
On 20 May 2014 14:56, Kajsa Harling <[email protected]> wrote:
> Dear Xinting,
>
>
>
> Previously when I wanted to resume a PsN run I used the -directory= in
> the command, and according to the PsN project homepage, this would enable a
> resume of a PsN run after stop. Such a method works fine without the
> -clean=3 option, but initiated a new search for covariates if I have
> -clean=3 option. However, this method seems to be different from the above
> mentioned.
>
>
> Yes, it is a different method. Setting -clean=3 removes files that are
> needed to resume an interupted run. I will make this more clear in the
> documentation, it is not explained properly at the moment.
>
>
> It seems to me that the method you mentioned requires 2 steps. The first
> one is to have only the included relations at the time of stop in the scm
> file. Should I use the -directory= option in the command line?
>
>
> The steps you need to perform are as follows:
> 1) Make a copy of your original scm configuration file, give it a new name
> and save it in the same folder as the original scm config file
> 2) open the original scm log file in the top level of the orginal scm run
> folder and locate the *last* place where it says "Relations included after
> this step", and copy those log-file-relations to the new configuration file
> under a new [included_relations] section at the end of the new
> configuration file. An example of a [included_relations] section with
> correct syntax is found in
> http://psn.sourceforge.net/pdfdocs/config_template_backward.scm and other
> details are found in the scm userguide.
> 3) If you had set option directory in your original config file then
> change the setting of that option in the new config file to something
> different
> 4) start a new scm with the same command as you used for the original scm,
> except that you use the new config file instead of the old, and either set
> -directory to the name of a folder that does not yet exist or omit the
> -directory option completely in which case the program will select a unique
> name for you.
>
>
> Secondly, if I start a new run in a new directory, why should I use the
> exactly same original input?
>
> You do not use exactly the same input, you use a new setting of
> [included_relations]. The input model however should be exactly the same.
>
>
> By doing so, would be program being able to skip the already established
> covariates and start from there onwards?
>
>
> Yes, it will start from the set of relations specified in
> [included_relations].
>
> What if I use the unidentified relationships in the new run, and using a
> mod file with relations in the scm logfile at the time of stop?
>
> That will usually not work.
>
>
>
> One last small question is that a few days ago, an error message saying
> "psn.lst" is not created [something like this] was put forward by the
> program during the middle of searching. The cov-par relation was completed
> successfully before crush. Do you have any idea what might be the possible
> reasons of this?
>
> I need the complete error message in its context of the scm run
> messages to be able to answer your question.
>
> Best regards,
> Kajsa
>
>
>
> --
> -----------------------------------------------------------------
> Kajsa Harling, PhD
> System Developer
> Department of Pharmaceutical Biosciences
> Uppsala University
> [email protected]+46-(0)18-471 4308
> http://www.farmbio.uu.se/research/researchgroups/pharmacometrics/
> -----------------------------------------------------------------
>
>
--
Xinting