Issues with VPC

Dear all, I have a question to ask regarding VPC. I used below command to run a VPC for my model, *vpc Final.nmctl -lnDV=1 -dv=LNDV -bin_by_count=1 -bin_array=0.375,0.75,1.5,2.5,4,6,8.5,12,17.5,24.5,35,49,63,77,91 -stratify_on=STRT -clean=3 -seed86 -samplesP0 -run_on_sge -sge_queue=all.q -parafile=template.pnm -nodes0 -sge_prepend="-pe mpich 30" -predcorr -varcorr* However, the system give me below error messages whose cause I am not aware of. Could anyone of you give me some hint as where should I looking for to solve the problem? Thanks a lot for your help. *File system problem or NMtran could not be initiated (the NMtran output* *file FDATA is missing). There is no lst-file for model 2. It is recommended* *to check cluster status, and cluster settings and remote_perl in psn.conf.* *Waiting for all NONMEM runs to finish:* *F:2 ..* *File system problem or NMtran could not be initiated (the NMtran output* *file FDATA is missing). There is no lst-file for model 1. It is recommended* *to check cluster status, and cluster settings and remote_perl in psn.conf.* *F:1 .. done* ​Best Regards​ -- Xinting

Dear all, I have a question to ask regarding VPC. I used below command to run a VPC for my model, *vpc Final.nmctl -lnDV=1 -dv=LNDV -bin_by_count=1 -bin_array=0.375,0.75,1.5,2.5,4,6,8.5,12,17.5,24.5,35,49,63,77,91 -stratify_on=STRT -clean=3 -seed=1986 -samples=500 -run_on_sge -sge_queue=all.q -parafile=template.pnm -nodes=30 -sge_prepend="-pe mpich 30" -predcorr -varcorr* However, the system give me below error messages whose cause I am not aware of. Could anyone of you give me some hint as where should I looking for to solve the problem? Thanks a lot for your help. *File system problem or NMtran could not be initiated (the NMtran output* *file FDATA is missing). There is no lst-file for model 2. It is recommended* *to check cluster status, and cluster settings and remote_perl in psn.conf.* *Waiting for all NONMEM runs to finish:* *F:2 ..* *File system problem or NMtran could not be initiated (the NMtran output* *file FDATA is missing). There is no lst-file for model 1. It is recommended* *to check cluster status, and cluster settings and remote_perl in psn.conf.* *F:1 .. done* ​Best Regards​ -- Xinting

Dear Xinting, The default sge message files in step 2) below could possibly also be called Final.nmctl.e<number> and Final.nmctl.o<number>. Best regards, Kajsa On 10/06/2014 12:28 PM, Kajsa Harling wrote: Dear Xinting, You do not say which PsN version you are using, but from the output I am guessing PsN3 something. In that case I recommend that you upgrade to PsN 4.2.0, which among other advantages gives more diagnostic information. There are many bugs in PsN3 that are fixed in PsN 4.2.0. As the error message says, either there is a file system problem or NMtran, which is called from NONMEM's nmfe script, could not be started, so something went wrong with starting nmfe remotely on your sge system. This results in missing NONMEM output (missing lst-file). There are a number of possible causes for this, for example that the path to NONMEM *to be used by the execution nodes* is not properly set in psn.conf or that the nmfe script cannot be run on the execution nodes on your sge cluster. Go to the modelfit_dir1/NM_run1 subdirectory of the vpc run directory. In that directory: 1) Check the contents of the file nmfe_output.txt for any information 2) check the contents of the default sge message files with names psn.e<some number> and psn.o<some number>, for example psn.e19080592 and psn.o19080592, and see if there is any information there. Best regards, Kajsa On 10/06/2014 04:43 AM, Xinting Wang wrote: Dear all, I have a question to ask regarding VPC. I used below command to run a VPC for my model, vpc Final.nmctl -lnDV=1 -dv=LNDV -bin_by_count=1 -bin_array=0.375,0.75,1.5,2.5,4,6,8.5,12,17.5,24.5,35,49,63,77,91 -stratify_on=STRT -clean=3 -seed=1986 -samples=500 -run_on_sge -sge_queue=all.q -parafile=template.pnm -nodes=30 -sge_prepend="-pe mpich 30" -predcorr -varcorr However, the system give me below error messages whose cause I am not aware of. Could anyone of you give me some hint as where should I looking for to solve the problem? Thanks a lot for your help. File system problem or NMtran could not be initiated (the NMtran output file FDATA is missing). There is no lst-file for model 2. It is recommended to check cluster status, and cluster settings and remote_perl in psn.conf. Waiting for all NONMEM runs to finish: F:2 .. File system problem or NMtran could not be initiated (the NMtran output file FDATA is missing). There is no lst-file for model 1. It is recommended to check cluster status, and cluster settings and remote_perl in psn.conf. F:1 .. done ​Best Regards​ -- Xinting -- ----------------------------------------------------------------- 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/

Dear Xinting, I think you should try to change the nonmem control stream name for the dependent variable, from DV=LNDV (which is what I assume you have right now on $INPUT?) to just read DV. The name for the DV column in the datafile can remain LNDV, so this is just a matter of changing on $INPUT in the control stream. Then, in the call to psn you change to -dv=DV (which is the default argument to this option). In general PsN has problems when one variable is assigned two different names (like DV=LNDV), but I can not say for sure this is what happened in your case. However, it is a quick change, so suggest you try it. Best regards Jakob PS. Technical questions, which are more related to PsN than nonmem; these are better held on the PsN-users list, rather than the nonmem-users list. DS.