Re: [NMusers] The system cannot execute the specified program

[Nick Holford]

Juergen, Thanks for these benchmark results. One thing that is missing from the results is the actual time to do each test and the additional time for a customized installation of figuring out what parameters are needed for SIZES and the time to recompile the customized NONMEM. This customization overhead should be considered when the only criterion for success is total runtime. Best wishes, Nick Jurgen Bulitta wrote: Dear Nick, Dear All,   Please find below the results of some benchmarking with a customized installation (i.e. std installation with no. of observations and no. of compartments set to the smallest values for the respective dataset) vs. the big installation with additionally no. of compartments increased to 50 and no. of observations increased to 1001. I did not test any intermediately sized installations, since the results were reasonably surprising, at least to me.   The bottom line is that, memory use did not seem to be the bottleneck, at least not on this test system. The benefit of the small installation was biggest for ADVAN1 and ADVAN3. However, one will probably only notice this benefit during bootstrapping.   I would interpret these differences in the benefit of the customized installation vs. the big installation that some parts of NONMEM are memory dependent whereas others (especially solving of differential equations) are not. As long as NONMEM does not return a memory overflow error and runs the job, I would not worry much about the size of the NONMEM installation.   Best wishes Juergen     Cases 1, 2, and 3: Customized installation: Virtual memory size: 84 MB BIG installation: Virtual memory size: 828 MB (nothing else ran on the server other than this one NONMEM VI version 6.2 run)   Case 1: Linear 1-Cmt model, ADVAN1, 15 observations, 50 subjects, 100 bootstrap resplicates with nmbs (in WFN): Customized installation finished 100 replicates BIG installation finished 61 replicates in the same time (run on a different, but identical computer) --> 64% advantage for the customized installation   Case 2: Linear 2-Cmt model, ADVAN3, 15 observations, 50 subjects, 100 bootstrap resplicates with nmbs (in WFN): Customized installation finished 100 replicates BIG installation finished 76 replicates in the same time (run on a different, but identical computer) --> 32% advantage for the customized installation   Case 3: Linear 3-Cmt model, ADVAN11, 15 observations, 50 subjects, 100 bootstrap resplicates with nmbs (in WFN): Customized installation finished 100 replicates BIG installation finished 89 replicates in the same time (run on a different, but identical computer) --> 12% advantage for the customized installation   Case 4: Population PK model, 5 compartments, ADVAN6, run as a single job Customized installation: 131 min, peak memory use: 75 MB, virtual memory size: 86 MB BIG installation: 140 min, peak memory use: 225 MB, virtual memory size: 724 MB --> 7% advantage for the customized installation   Case 5: same as 4, but with overloading of my laptop by running too many programs simultaneously --> 7% advantage for the customized installation (i.e. exactly the same benefit as in case 4)   Case 6: Population PK/PD model, ADVAN6, about 40 compartments, 15 observations, run as a single job Customized installation: 330.77 min BIG installation: 331.12 min --> 0.11% advantage for the customized installation       From: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@globomaxnm.com] On Behalf Of Nick Holford Sent: Sunday, October 18, 2009 12:04 AM To: nmusers Subject: Re: [NMusers] The system cannot execute the specified program   Juergen, I'd be interested to know of your experience of how much estimation time you save by making project specific installations. Given that you must take additional time to setup SIZES and recompile NONMEM for each project (say 10-15 minutes) how much time do you save per run compared with having regular and big installations of NONMEM? Nick Jurgen Bulitta wrote: Dear Tom, Dear All,   For those of us who prefer project specific NONMEM installations to save estimation time, it might be helpful, if ICON can provide some rough guidance on the main contributor to the RAM needs of NONMEM 7. I.e. is it primarily the number of observations, compartments, thetas, omegas, or another variable or some function of these variables?   The following might be very cumbersome: Would it be possible to include a switch during the installation which disables certain NONMEM 7 features to save RAM. (I recognize that this might cause a lot of unpredictable software issues.) Dual CPU servers currently have around 8-18 RAM slots. 2 and 4 GB RAM chips are reasonably priced. Thus, on the 64-bit server side, this is probably a minor issue.   Best wishes Juergen         From: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@globomaxnm.com] On Behalf Of Ludden, Thomas Sent: Friday, October 16, 2009 3:14 PM To: non...@optonline.net Cc: nmusers@globomaxnm.com Subject: RE: [NMusers] The system cannot execute the specified program   Pavel,   The message you describe is usually the result of not having enough memory available for the NONMEM 7 memory image.  If you are using the "big" version of SIZES you may need about 1.6-2 GB of available memory for each job.  For the efficient use of NONMEM 7's  new methods more variables are now stored in memory than was the case for NONMEM VI.  The memory image is larger even if one is not using the new methods.  When using NONMEM 7 and the "reg" SIZES, I have been able to run 8 jobs simultaneously on a dual processor dual core machine, but only 3-4 jobs when using the "big" version of SIZES depending upon what else is running.  I have 3 GB of memory and the task manager indicates a maximum of about 7.4 GB via paging.   Tom Thomas M. Ludden Ph.D. Vice-President, Pharmacometrics R&D ICON Development Solutions Tel: + 1 410 696 3040 Mob: + 1  410 258 2411 Fax:  + 1 410 480 0776 Email: thomas.lud...@iconplc.com Web: www.icondevsolutions.com   From: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@globomaxnm.com] On Behalf Of non...@optonline.net Sent: Friday, October 16, 2009 2:02 PM To: non...@optonline.net Cc: nmusers@globomaxnm.com Subject: [NMusers] The system cannot execute the specified program > Hello NONMEM Users, > We have a computer with 4 processors. When I try to run more > than 3 NONMEM7 jobs, I am getting the following message: > Starting nonmem execution ... > The system cannot execute the specified program. > KP9022.OUT > newline > 1 file(s) copied. > Could Not Find H:\4\output > > The message is code and directory independent. It always > appears when I try to run more than 3 codes. When I test > nonmem7 using a laptop, which also has 4 processors, I can > execute 4 programs. Also, when I had NONMEM6, I did not have > this problem on the same machine. > Do you familiar with this problem? Thanks. > Pavel > ICON plc made the following annotations. ------------------------------------------------------------------------------ This e-mail transmission may contain confidential or legally privileged information that is intended only for the individual or entity named in the e-mail address. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution, or reliance upon the contents of this e-mail is strictly prohibited. If you have received this e-mail transmission in error, please reply to the sender, so that ICON plc can arrange for proper delivery, and then please delete the message. Thank You, ICON plc South County Business Park Leopardstown Dublin 18 Ireland Registered number: 145835   -- Nick Holford, Professor Clinical Pharmacology Dept Pharmacology & Clinical Pharmacology University of Auckland, 85 Park Rd, Private Bag 92019, Auckland, New Zealand n.holf...@auckland.ac.nz tel:+64(9)923-6730 fax:+64(9)373-7090 mobile: +64 21 46 23 53 http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford -- Nick Holford, Professor Clinical Pharmacology Dept Pharmacology & Clinical Pharmacology University of Auckland,85 Park Rd,Private Bag 92019,Auckland,New Zealand tel:+64(9)923-6730 fax:+64(9)373-7090 mobile:+64(21)46 23 53 email: n.holf...@auckland.ac.nz http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford