SCM issue with PsN 4.9.0?
dong1206 opened this issue · 10 comments
Hello PsN developer,
My OS is windows10, the version of nonmem is 7.4.4, and the version of PsN is 4.9.0. My output is as follow:
D:\subscm>scm twocomp_combined_rmQ_Emax_covariance_20220510.scm -threads=50
Calculating continuous covariate statistics
|....................................| ... done
Calculating categorical covariate statistics
|....................................| ... done
Starting scm forward search
Starting 39 NONMEM executions. 39 in parallel.
S:1 .. S:4 .. S:7 .. S:10 .. S:13 .. S:16 .. S:19 .. S:22 .. S:25 .. S:28 .. S:31 .. S:34 .. S:37 .. S:39 .. NONMEM run failed. Check the lst-file in NM_run4 for errors
Not restarting this model.
Waiting for all NONMEM runs to finish:
F:1 .. F:25 .. F:37 .. F:17 .. F:29 .. F:13 .. F:33 .. F:9 .. F:5 .. F:39 .. F:21 .. done
Adding SEX on V1 state 2
Taking a step forward
Starting 38 NONMEM executions. 38 in parallel.
S:1 .. S:4 .. S:7 .. S:10 .. S:13 .. S:16 .. S:19 .. S:22 .. S:25 .. S:28 .. S:31 .. S:34 .. S:37 .. S:38 .. NONMEM run failed. Check the lst-file in NM_run9 for errors
Not restarting this model.
Waiting for all NONMEM runs to finish:
F:9 .. F:1 .. F:13 .. F:37 .. F:38 .. F:29 .. F:21 .. F:17 .. F:25 .. F:5 .. F:33 .. done
Adding ADA on CL state 2
Taking a step forward
Starting 37 NONMEM executions. 37 in parallel.
S:1 .. S:4 .. S:7 .. S:10 .. S:13 .. S:16 .. S:19 .. S:22 .. S:25 .. S:28 .. S:31 .. S:34 .. S:37 .. Waiting for all NONMEM runs to finish:
F:17 .. F:25 .. F:9 .. F:21 .. F:37 .. F:33 .. F:1 .. F:29 .. F:5 .. F:13 .. done
Adding SEX on CL state 2
Taking a step forward
Starting 36 NONMEM executions. 36 in parallel.
S:1 .. S:4 .. S:7 .. S:10 .. S:13 .. S:16 .. S:19 .. S:22 .. S:25 .. S:28 .. S:31 .. S:34 .. S:36 .. Waiting for all NONMEM runs to finish:
F:9 .. F:21 .. F:5 .. F:29 .. F:25 .. F:33 .. F:1 .. F:36 .. F:13 .. F:17 .. done
Adding ADA on V1 state 2
Taking a step forward
Starting 35 NONMEM executions. 35 in parallel.
S:1 .. S:4 .. S:7 .. S:10 .. S:13 .. S:16 .. S:19 .. S:22 .. S:25 .. S:28 .. S:31 .. S:34 .. S:35 .. NONMEM run failed. Check the lst-file in NM_run3 for errors
Not restarting this model.
Waiting for all NONMEM runs to finish:
F:35 .. F:13 .. F:5 .. F:29 .. F:33 .. F:1 .. F:17 .. F:25 .. F:9 .. F:21 .. done
Adding ALBB on CL state 5
Taking a step forward
Starting 34 NONMEM executions. 34 in parallel.
S:1 .. S:4 .. S:7 .. S:10 .. S:13 .. S:16 .. S:19 .. S:22 .. S:25 .. S:28 .. S:31 .. S:34 .. Waiting for all NONMEM runs to finish:
F:5 .. F:21 .. F:33 .. F:13 .. F:1 .. F:17 .. F:25 .. F:29 .. F:34 .. F:9 .. done
Adding WTB on V1 state 5
Taking a step forward
Starting 33 NONMEM executions. 33 in parallel.
S:1 .. S:4 .. S:7 .. S:10 .. S:13 .. S:16 .. S:19 .. S:22 .. S:25 .. S:28 .. S:31 .. S:33 .. Waiting for all NONMEM runs to finish:
F:29 .. F:13 .. F:25 .. F:33 .. F:17 .. F:5 .. F:9 .. F:1 .. F:21 .. done
Adding TTYPE on EMAX state 2
Taking a step forward
Starting 32 NONMEM executions. 32 in parallel.
S:1 .. S:4 .. S:7 .. S:10 .. S:13 .. S:16 .. S:19 .. S:22 .. S:25 .. S:28 .. S:31 .. S:32 .. NONMEM run failed. Check the lst-file in NM_run2 for errors
Not restarting this model.
Waiting for all NONMEM runs to finish:
F:17 .. F:29 .. F:13 .. F:5 .. F:32 .. F:1 .. F:9 .. F:25 .. F:21 .. done
Adding WTB on CL state 5
Taking a step forward
Starting 31 NONMEM executions. 31 in parallel.
S:1 .. S:4 .. S:7 .. S:10 .. S:13 .. S:16 .. S:19 .. S:22 .. S:25 .. S:28 .. S:31 .. NONMEM run failed. Check the lst-file in NM_run11 for errors
Not restarting this model.
Waiting for all NONMEM runs to finish:
F:29 .. F:25 .. F:31 .. F:21 .. F:9 .. F:5 .. F:13 .. F:1 .. F:17 .. done
Adding TTYPE on V1 state 2
Taking a step forward
Starting 30 NONMEM executions. 30 in parallel.
S:1 .. S:4 .. S:7 .. S:10 .. S:13 .. S:16 .. S:19 .. S:22 .. S:25 .. S:28 .. S:30 .. Waiting for all NONMEM runs to finish:
F:29 .. F:25 .. F:5 .. F:13 .. F:9 .. F:21 .. F:30 .. F:17 .. F:1 .. done
Adding CRPB on CL state 5
Taking a step forward
Starting 29 NONMEM executions. 29 in parallel.
S:1 .. S:3 .. S:5 .. S:7 .. S:9 .. S:11 .. S:13 .. S:15 .. S:17 .. S:19 .. S:21 .. S:23 .. S:25 .. S:27 .. S:29 .. NONMEM run failed. Check the lst-file in NM_run6 for errors
Not restarting this model.
Waiting for all NONMEM runs to finish:
F:1 .. F:29 .. F:10 .. F:25 .. F:4 .. F:28 .. F:7 .. F:19 .. F:13 .. F:22 .. F:16 .. done
Adding GGTB on V1 state 5
Taking a step forward
Starting 28 NONMEM executions. 28 in parallel.
S:1 .. S:3 .. S:5 .. S:7 .. S:9 .. S:11 .. S:13 .. S:15 .. S:17 .. S:19 .. S:21 .. S:23 .. S:25 .. S:27 .. S:28 .. Waiting for all NONMEM runs to finish:
F:1 .. F:4 .. F:7 .. F:10 .. F:13 .. F:16 .. F:19 .. F:22 .. F:25 .. F:28 .. done
Adding CRPB on V1 state 5
Taking a step forward
Starting 27 NONMEM executions. 27 in parallel.
S:1 .. S:3 .. S:5 .. S:7 .. S:9 .. S:11 .. S:13 .. S:15 .. S:17 .. S:19 .. S:21 .. S:23 .. S:25 .. S:27 .. Waiting for all NONMEM runs to finish:
F:10 .. F:27 .. F:13 .. F:4 .. F:25 .. F:16 .. F:22 .. F:7 .. F:1 .. F:19 .. done
Adding RACE on V1 state 2
Taking a step forward
Starting 26 NONMEM executions. 26 in parallel.
S:1 .. S:3 .. S:5 .. S:7 .. S:9 .. S:11 .. S:13 .. S:15 .. S:17 .. S:19 .. S:21 .. S:23 .. S:25 .. S:26 .. Waiting for all NONMEM runs to finish:
F:13 .. F:25 .. F:26 .. F:16 .. F:22 .. F:4 .. F:19 .. F:7 .. F:10 .. F:1 .. done
Adding LDHB on CL state 5
Taking a step forward
Starting 25 NONMEM executions. 25 in parallel.
S:1 .. S:3 .. S:5 .. S:7 .. S:9 .. S:11 .. S:13 .. S:15 .. S:17 .. S:19 .. S:21 .. S:23 .. S:25 .. Waiting for all NONMEM runs to finish:
F:25 .. F:19 .. F:7 .. F:16 .. F:10 .. F:22 .. F:1 .. F:13 .. F:4 .. done
Adding ALPB on V1 state 5
Taking a step forward
Starting 24 NONMEM executions. 24 in parallel.
S:1 .. S:3 .. S:5 .. S:7 .. S:9 .. S:11 .. S:13 .. S:15 .. S:17 .. S:19 .. S:21 .. S:23 .. S:24 .. NMtran failed. There is no output for model 1. Contents of FMSG:
WARNINGS AND ERRORS (IF ANY) FOR PROBLEM 1
(WARNING 2) NM-TRAN INFERS THAT THE DATA ARE POPULATION.
(WARNING 97) A RANDOM QUANTITY IS RAISED TO A POWER. IF THE RESULT
AFFECTS
THE VALUE OF THE OBJECTIVE FUNCTION, THE USER SHOULD ENSURE THAT THE
RANDOM QUANTITY IS NEVER 0 WHEN THE POWER IS < 1.
AN ERROR WAS FOUND IN THE CONTROL STATEMENTS.
THE CHARACTERS IN ERROR ARE:
................***_NONMEMpaper_rmCWRES_v3_20220424.csv
33 INPUT DATA FILE DOES NOT EXIST OR CANNOT BE OPENED.
Not restarting this model.
Waiting for all NONMEM runs to finish:
F:1 .. NMtran failed. There is no output for model 2. Contents of FMSG:
WARNINGS AND ERRORS (IF ANY) FOR PROBLEM 1
(WARNING 2) NM-TRAN INFERS THAT THE DATA ARE POPULATION.
(WARNING 97) A RANDOM QUANTITY IS RAISED TO A POWER. IF THE RESULT
AFFECTS
THE VALUE OF THE OBJECTIVE FUNCTION, THE USER SHOULD ENSURE THAT THE
RANDOM QUANTITY IS NEVER 0 WHEN THE POWER IS < 1.
AN ERROR WAS FOUND IN THE CONTROL STATEMENTS.
THE CHARACTERS IN ERROR ARE:
................***_NONMEMpaper_rmCWRES_v3_20220424.csv
33 INPUT DATA FILE DOES NOT EXIST OR CANNOT BE OPENED.
Not restarting this model.
NMtran failed. There is no output for model 3
Not restarting this model.
NMtran failed. There is no output for model 4
Not restarting this model.
F:4 .. NMtran failed. There is no output for model 5
Not restarting this model.
NMtran failed. There is no output for model 6
Not restarting this model.
NMtran failed. There is no output for model 7
Not restarting this model.
F:7 .. NMtran failed. There is no output for model 8
Not restarting this model.
NMtran failed. There is no output for model 9
Not restarting this model.
NMtran failed. There is no output for model 10
Not restarting this model.
F:10 .. NMtran failed. There is no output for model 11
Not restarting this model.
NMtran failed. There is no output for model 12
Not restarting this model.
NMtran failed. There is no output for model 13
Not restarting this model.
F:13 .. NMtran failed. There is no output for model 14
Not restarting this model.
NMtran failed. There is no output for model 15
Not restarting this model.
NMtran failed. There is no output for model 16
Not restarting this model.
F:16 .. NMtran failed. There is no output for model 17
Not restarting this model.
NMtran failed. There is no output for model 18
Not restarting this model.
NMtran failed. There is no output for model 19
Not restarting this model.
F:19 .. NMtran failed. There is no output for model 20
Not restarting this model.
NMtran failed. There is no output for model 21
Not restarting this model.
NMtran failed. There is no output for model 22
Not restarting this model.
F:22 .. NMtran failed. There is no output for model 23
Not restarting this model.
NMtran failed. There is no output for model 24
Not restarting this model.
F:24 .. done
How to solve this error?
Thanks a lot,
Aaron.
What does the $DATA look like in the model that failed?
Hi rikardn,
This is a problem I often encounter when using SCM. When the data set is relatively large and there are many covariates, the forward inclusion can be carried out normally at the beginning. However, when the number of round or file path reaches a certain value, the above error will occur. To gain the number of rounds, we must execute SCM in the root directory (e.g., D:, D:\subscm), not in any subdirectory (e.g. D:\program***, D:\test******). This seems to be related to the number of characters in the entire path. When we execute the following configuration in D: \ subscm, the error is reported as above.
model=twocomp_combined_rmQ_Emax_covariance.ctl
search_direction=both
logfile=***log.txt
p_forward=0.01
p_backward=0.001
parallel_states=1
logit=EMAX
directory=***EMAXpaper_covariance
When we execute this configuration in D: \ , the error is as follow:
Adding ALPB on V1 state 5
Taking a step forward
Starting 24 NONMEM executions. 24 in parallel.
S:1 .. S:3 .. S:5 .. S:7 .. S:9 .. S:11 .. S:13 .. S:15 .. S:17 .. S:19 .. S:21 .. S:23 .. S:24 .. NMtran failed. There is no output for model 10
Not restarting this model.
Waiting for all NONMEM runs to finish:
F:10 .. NMtran failed. There is no output for model 11
Not restarting this model.
NMtran failed. There is no output for model 12
Not restarting this model.
NMtran failed. There is no output for model 13
Not restarting this model.
F:13 .. NMtran failed. There is no output for model 14
Not restarting this model.
NMtran failed. There is no output for model 15
Not restarting this model.
NMtran failed. There is no output for model 16
Not restarting this model.
F:16 .. NMtran failed. There is no output for model 17
Not restarting this model.
NMtran failed. There is no output for model 18
Not restarting this model.
NMtran failed. There is no output for model 19
Not restarting this model.
F:19 .. NMtran failed. There is no output for model 20
Not restarting this model.
NMtran failed. There is no output for model 21
Not restarting this model.
NMtran failed. There is no output for model 22
Not restarting this model.
F:22 .. NMtran failed. There is no output for model 23
Not restarting this model.
NMtran failed. There is no output for model 24
Not restarting this model.
F:24 .. F:7 .. F:1 .. F:4 .. done
Writing final models from the forward search.
forward search done.
Starting scm backward search inside forward top level directory
Starting 15 NONMEM executions. 15 in parallel.
S:1 .. S:2 .. S:3 .. S:4 .. S:5 .. S:6 .. S:7 .. S:8 .. S:9 .. S:10 .. S:11 .. S:12 .. S:13 .. S:14 .. S:15 .. Waiting for all NONMEM runs to finish:
F:3 .. F:5 .. F:15 .. F:9 .. F:7 .. F:1 .. F:13 .. F:11 .. done
Removing ALPB on V1 state 1.
When this configuration file is changed to the following, the operation is normal.
model=twocomp_combined_rmQ_Emax_covariance.ctl
search_direction=both
logfile=***log.txt
p_forward=0.01
p_backward=0.001
parallel_states=1
logit=EMAX
directory=***P
I am looking forward to your reply. Thank you.
Best regards,
Aaron.
You could try add the option -always_datafile_in_nmrun to reduce the path length in $DATA
Thank you for your reply！
Did the -always_datafile_in_nmrun option solve the issue?
Yes, the option solves the issue. Thanks.
Great! Thanks for the feedback.
Hi rikardn,
I'm in trouble again. The option -always_datafile_in_nmrun does not always solve the problem. When the number of covariates and samples increases, the following problems are encountered.
D:\subscm\#####paper>scm twocomp_combined_rmQ_Emax_covariance_20220521.scm -threads=40 -always_datafile_in_nmrun
Calculating continuous covariate statistics
|....................................| ... done
Calculating categorical covariate statistics
|....................................| ... done
Starting scm forward search
Starting 39 NONMEM executions. 39 in parallel.
S:1 .. S:4 .. S:7 .. S:10 .. S:13 .. S:16 .. S:19 .. S:22 .. S:25 .. S:28 .. S:31 .. S:34 .. S:37 .. S:39 .. NONMEM run failed. Check the lst-file in NM_run12 for errors
Not restarting this model.
Waiting for all NONMEM runs to finish:
F:37 .. F:25 .. F:29 .. F:39 .. F:17 .. F:5 .. F:13 .. F:1 .. F:33 .. F:9 .. F:21 .. done
Adding SEX on V1 state 2
Taking a step forward
Starting 38 NONMEM executions. 38 in parallel.
S:1 .. S:4 .. S:7 .. S:10 .. S:13 .. S:16 .. S:19 .. S:22 .. S:25 .. S:28 .. S:31 .. S:34 .. S:37 .. S:38 .. Waiting for all NONMEM runs to finish:
F:1 .. F:37 .. F:13 .. F:9 .. F:33 .. F:29 .. F:5 .. F:21 .. F:17 .. F:38 .. F:25 .. done
Adding SEX on CL state 2
Taking a step forward
Starting 37 NONMEM executions. 37 in parallel.
S:1 .. S:4 .. S:7 .. S:10 .. S:13 .. S:16 .. S:19 .. S:22 .. S:25 .. S:28 .. S:31 .. S:34 .. S:37 .. Waiting for all NONMEM runs to finish:
F:37 .. F:25 .. F:29 .. F:9 .. F:13 .. F:21 .. F:17 .. F:33 .. F:1 .. F:5 .. done
Adding CRCLB on V1 state 5
Taking a step forward
Starting 36 NONMEM executions. 36 in parallel.
S:1 .. S:4 .. S:7 .. S:10 .. S:13 .. S:16 .. S:19 .. S:22 .. S:25 .. S:28 .. S:31 .. S:34 .. S:36 .. Waiting for all NONMEM runs to finish:
F:1 .. F:33 .. F:21 .. F:29 .. F:9 .. F:13 .. F:5 .. F:17 .. F:25 .. F:36 .. done
Adding CRPB on CL state 5
Taking a step forward
Starting 35 NONMEM executions. 35 in parallel.
S:1 .. S:4 .. S:7 .. S:10 .. S:13 .. S:16 .. S:19 .. S:22 .. S:25 .. S:28 .. S:31 .. S:34 .. S:35 .. Waiting for all NONMEM runs to finish:
F:33 .. F:35 .. F:5 .. F:25 .. F:1 .. F:29 .. F:17 .. F:21 .. F:9 .. F:13 .. done
Adding RACE on CL state 2
Taking a step forward
Starting 34 NONMEM executions. 34 in parallel.
S:1 .. S:4 .. S:7 .. S:10 .. S:13 .. S:16 .. S:19 .. S:22 .. S:25 .. S:28 .. S:31 .. S:34 .. Waiting for all NONMEM runs to finish:
F:33 .. F:13 .. F:1 .. F:17 .. F:25 .. F:9 .. F:21 .. F:29 .. F:34 .. F:5 .. done
Adding WTB on V1 state 5
Taking a step forward
Starting 33 NONMEM executions. 33 in parallel.
S:1 .. S:4 .. S:7 .. S:10 .. S:13 .. S:16 .. S:19 .. S:22 .. S:25 .. S:28 .. S:31 .. S:33 .. Waiting for all NONMEM runs to finish:
F:5 .. F:13 .. F:9 .. F:25 .. F:17 .. F:33 .. F:1 .. F:21 .. F:29 .. done
Adding TTYPE on V1 state 2
Taking a step forward
Starting 32 NONMEM executions. 32 in parallel.
S:1 .. S:4 .. S:7 .. S:10 .. S:13 .. S:16 .. S:19 .. S:22 .. S:25 .. S:28 .. S:31 .. S:32 .. Waiting for all NONMEM runs to finish:
F:21 .. F:17 .. F:9 .. F:1 .. F:25 .. F:13 .. F:32 .. F:29 .. F:5 .. done
Adding CRPB on V1 state 5
Taking a step forward
Starting 31 NONMEM executions. 31 in parallel.
S:1 .. S:4 .. S:7 .. S:10 .. S:13 .. S:16 .. S:19 .. S:22 .. S:25 .. S:28 .. S:31 .. Waiting for all NONMEM runs to finish:
F:31 .. F:13 .. F:21 .. F:9 .. F:17 .. F:29 .. F:1 .. F:25 .. F:5 .. done
Adding ADA on CL state 2
Taking a step forward
Starting 30 NONMEM executions. 30 in parallel.
S:1 .. S:4 .. S:7 .. S:10 .. S:13 .. S:16 .. S:19 .. S:22 .. S:25 .. S:28 .. S:30 .. Waiting for all NONMEM runs to finish:
F:25 .. F:29 .. F:17 .. F:9 .. F:1 .. F:30 .. F:13 .. F:5 .. F:21 .. done
Adding GGTB on V1 state 5
Taking a step forward
Starting 29 NONMEM executions. 29 in parallel.
S:1 .. S:3 .. S:5 .. S:7 .. S:9 .. S:11 .. S:13 .. S:15 .. S:17 .. S:19 .. S:21 .. S:23 .. S:25 .. S:27 .. S:29 .. Waiting for all NONMEM runs to finish:
F:25 .. F:4 .. F:1 .. F:7 .. F:22 .. F:16 .. F:29 .. F:10 .. F:19 .. F:28 .. F:13 .. done
Adding WTB on CL state 5
Taking a step forward
Starting 28 NONMEM executions. 28 in parallel.
S:1 .. S:3 .. S:5 .. S:7 .. S:9 .. S:11 .. S:13 .. S:15 .. S:17 .. S:19 .. S:21 .. S:23 .. S:25 .. S:27 .. S:28 .. Waiting for all NONMEM runs to finish:
F:13 .. F:1 .. F:25 .. F:22 .. F:19 .. F:28 .. F:7 .. F:16 .. F:10 .. F:4 .. done
Adding TBILB on V1 state 5
Taking a step forward
Starting 27 NONMEM executions. 27 in parallel.
S:1 .. S:3 .. S:5 .. S:7 .. S:9 .. S:11 .. S:13 .. S:15 .. S:17 .. S:19 .. S:21 .. S:23 .. S:25 .. S:27 .. Waiting for all NONMEM runs to finish:
F:19 .. F:25 .. F:10 .. F:7 .. F:27 .. F:13 .. F:1 .. F:4 .. F:22 .. F:16 .. done
Adding TTYPE on EMAX state 2
Taking a step forward
Starting 26 NONMEM executions. 26 in parallel.
S:1 .. S:3 .. S:5 .. S:7 .. S:9 .. S:11 .. S:13 .. S:15 .. S:17 .. S:19 .. S:21 .. S:23 .. S:25 .. S:26 .. Waiting for all NONMEM runs to finish:
F:26 .. F:16 .. F:7 .. F:13 .. F:22 .. F:25 .. F:19 .. F:1 .. F:10 .. F:4 .. done
Adding LDHB on CL state 5
Taking a step forward
Starting 25 NONMEM executions. 25 in parallel.
S:1 .. S:3 .. S:5 .. S:7 .. S:9 .. S:11 .. S:13 .. S:15 .. S:17 .. S:19 .. S:21 .. S:23 .. S:25 .. Waiting for all NONMEM runs to finish:
F:1 .. F:13 .. F:22 .. F:16 .. F:25 .. F:19 .. F:7 .. F:4 .. F:10 .. done
Adding ADA on V1 state 2
Taking a step forward
Starting 24 NONMEM executions. 24 in parallel.
S:1 .. S:3 .. S:5 .. S:7 .. S:9 .. S:11 .. S:13 .. S:15 .. S:17 .. S:19 .. S:21 .. S:23 .. S:24 .. Waiting for all NONMEM runs to finish:
F:19 .. F:24 .. F:22 .. F:7 .. F:16 .. F:13 .. F:4 .. F:10 .. F:1 .. done
Adding ALPB on V1 state 5
Taking a step forward
Starting 23 NONMEM executions. 23 in parallel.
Setting data to D:\subscm\#####paper\#####EMAXpaper_covariance\forward_scm_dir1\scm_dir1\scm_dir1\scm_dir1\scm_dir1\scm_dir1\scm_dir1\scm_dir1\scm_dir1\scm_dir1\scm_dir1\scm_dir1\scm_dir1\scm_dir1\scm_dir1\scm_dir1\modelfit_dir1\NM_run1\#####_NONMEMpaper_rmCWRES_v3_20220520.csv in D:\subscm\#####paper\#####EMAXpaper_covariance\forward_scm_dir1\scm_dir1\scm_dir1\scm_dir1\scm_dir1\scm_dir1\scm_dir1\scm_dir1\scm_dir1\scm_dir1\scm_dir1\scm_dir1\scm_dir1\scm_dir1\scm_dir1\scm_dir1\modelfit_dir1\NM_run1\psn.mod but data file does not exist at C:\STRAWB~1\perl\site\lib\PsN_4_9_0/tool/modelfit.pm line 3016.
Does the dataset exist at the path PsN is trying to use?
Please open a new issue for further problems with the scm