Re: Segmentation fault

2011/11/25 Justin Wilkins <[email protected]> > Dear Maria, > > This could be the result of faulty or unprotected code in your control > stream, or a compiler issue. > > A segmentation fault is a crash that happens when a program (NONMEM in > this case) tries to access memory that cannot be accessed. This can happen > when a code error or non-optimal compiler setting (or flaw in the compiler > itself) leads to a faulty executable file being built. Your model is quite > numerically complex, and it's possible that it's exposed issues with the > compiler that had not been obvious before. It could also be masking a > numerical problem with your code. > > You could try the following: > > > - Since IPRED=LOG(F), I would add some code to make sure F can never > be 0. > - Check your data and code to make sure you don't have any other > illegal numerical actions taking place (e.g. divide by zero) - such an > issue might be masked by this kind of crash, if not handled properly by the > compiler - one simple way to do this is to implement the model in something > like Berkeley Madonna and see if it does what you expect. Does it behave > the same way with different initial estimates? > - Try a different compiler, ideally on a different system, and see if > the same thing happens. If it does, it's likely to be a numerical issue, > and I would try a different ADVAN, and adjust TOL settings > - If it works on another system, try less aggressive optimization > settings for the compiler (you can check these in the first few lines of > the nmfe* execution script) - this will require that NONMEM be recompiled, > however > > > Best > Justin > > On Nov 24, 2011, at 5:01 PM, Maria Matoses Osborne wrote: > > Dear Nonmem users, > > I just run a couple of times into the same problem, and still find myself > incapable of solving it, hopefully you might come with some new ideas for > this unusual problem (at least for the Navarra group). > > With NONMEM, I'm running a model of 12 compartments, the procedure used > was adding one compartment at the time and fixing the thetas previously > obtained before adding a new compartment. It went well until I reached the > compartment 12, when a message came out of NONMEM saying: > > * line 65: 8666 Segmentation fault ./nonmem $1 $3 -licfile=$lfile* > > Do you have any idea of why that happens? > > Thanks in advance, > > María Matoses Osborne > > The NONMEM script is as follows: > > > $PROBLEM RATS PK - IV ADM > $INPUT ID TIME AMT CMT CMTT DVV DV WEIG ORWE RUTE DRUG EVID > $DATA rat2.dta IGNORE= # > $SUBROUTINES ADVAN9 TOL=5 > $MODEL COMP (DPL) > COMP (MPL) > COMP (DBR) > COMP (MBR) > COMP (DBM) > COMP (MBM) > COMP (DSP) > COMP (MSP) > COMP (DLN) > COMP (DTRA) > COMP (MLN) > COMP (MTRA) > > $PK > > ;-------- DRUG AND MET IN PLASMA -------------- > > V1=THETA(1)*EXP(ETA(1)) > V2=THETA(2) > CLR=THETA(3) > CLM12=THETA(4) > CLM20=THETA(5) > > ;----------- DRUG IN BRAIN ------------ > > V3=THETA(6)/1000 > CL13=THETA(7) > CL30=THETA(8) > > ;----------- MET IN BRAIN -------------- > > V4=THETA(9) > CL24=THETA(10) > CL40=THETA(11) > > ;----------- DRUG IN BONE MARROW ----- > > V5=THETA(12) > CL15=THETA(13) > CL50=THETA(14) > > ;----------- MET IN BONE MARROW ------- > > V6=THETA(15)/1000 > CL26=THETA(16) > CL60=THETA(17) > > ;------------ DRUG IN SPLEEN ------- > > V7=THETA(18)/1000 > CL17=THETA(19) > CL70=THETA(20) > > ;----------- MET IN SPLEEN ------------- > > V8=THETA(21)/1000 > CL28=THETA(22) > CL80=THETA(23)/1000 > > ;---------- DRUG IN LYMPN NODE ---------- > > V9=THETA(24)/100000 > CL19=THETA(25) > CL90=THETA(26) > > ;----------- MET IN LYMPH NODE ---------- > > V11=THETA(27) > CL211=THETA(28) > CL110=THETA(29) > > > S1=V1/1000 > S2=V2/1000 > S3=V3/1000 > S4=V4/1000 > S5=V5/1000 > S6=V6/1000 > S7=V7/1000 > S8=V8/1000 > S9=V9/1000 > S11=V11/1000 > > $DES > > DADT(1)=-((CLR*CLM12)/V1)*A(1) > DADT(2)=(CLM12/V1)*A(1)-(CLM20/V2)*A(2) > DADT(3)=(CL13/V1)*A(1)-(CL30/V3)*A(3) > DADT(4)=(CL24/V2)*A(2)-(CL40/V4)*A(4) > DADT(5)=(CL15/V1)*A(1)-(CL50/V5)*A(5) > DADT(6)=(CL26/V2)*A(2)-(CL60/V6)*A(6) > DADT(7)=(CL17/V1)*A(1)-(CL70/V7)*A(7) > DADT(8)=(CL28/V2)*A(2)-(CL80/V8)*A(8) > DADT(9)=(CL19/V1)*A(10)-(CL90/V9)*A(9) > DADT(10)=(CL19/V1)*A(1)-(CL19/V1)*A(10) > DADT(11)=(CL211/V2)*A(12)-(CL110/V11)*A(11) > DADT(12)=(CL211/V2)*A(2)-(CL211/V2)*A(12) > > > $ERROR(OBSERVATION ONLY) > > IPRED=LOG(F) > > Y=IPRED+EPS(1) > IF (CMT.EQ.2) Y=IPRED+EPS(2) > IF (CMT.EQ.3) Y=IPRED+EPS(3) > IF (CMT.EQ.4) Y=IPRED+EPS(4) > IF (CMT.EQ.5) Y=IPRED+EPS(5) > IF (CMT.EQ.6) Y=IPRED+EPS(6) > IF (CMT.EQ.7) Y=IPRED+EPS(7) > IF (CMT.EQ.8) Y=IPRED+EPS(8) > IF (CMT.EQ.9) Y=IPRED+EPS(9) > IF (CMT.EQ.11) Y=IPRED+EPS(10) > > > $ESTIMATION MAXEVAL=9999 PRINT=5 METHOD=1 INTERACTION NOABORT > $COV > > $THETA 2.9 FIX ; V1 > $THETA 5.8 FIX ; V2 > $THETA 1.22 FIX ; CLR > $THETA 0.3 FIX ; CLM12 > $THETA 0.526 FIX ; CLM20 > > $THETA 0.8 FIX ; V3 > $THETA 1.65 FIX ; CL13 > $THETA 0.2 FIX ; CL30 > > $THETA 0.0129 FIX ; V4 > $THETA 0.82 FIX ; CL24 > $THETA 0.0289 FIX ; CL40 > > $THETA 0.244 FIX ; V5 > $THETA 1.13 FIX ; CL15 > $THETA 1.55 FIX ; CL50 > > $THETA 0.925 FIX ; V6 > $THETA 1.9 FIX ; CL26 > $THETA 3.67 FIX ; CL60 > > $THETA 6.67 FIX ; V7 > $THETA 0.5 FIX ; CL17 > $THETA 0.0112 FIX ; CL70 > > $THETA 1.23 FIX ; V8 > $THETA 0.09 FIX ; CL28 > $THETA 1.74 FIX ; CL80 > > $THETA 0.959 FIX ; V9 > $THETA 5.77 FIX ; CL19 > $THETA 0.0544 FIX ; CL90 > > $THETA (0,1) ; V11 > $THETA (0,1) ; CL211 > $THETA (0,1) ; CL110 > > > > $OMEGA 0 FIX > $SIGMA 0.1 > $SIGMA 0.187 > $SIGMA 0.15 > $SIGMA 0.37 > $SIGMA 0.22 > $SIGMA 0.64 > $SIGMA 0.212 > $SIGMA 0.2 > $SIGMA 0.167 > $SIGMA 0.1 > > > $TABLE ID TIME CMTT CMT EVID ONEHEADER NOPRINT FILE=sdtab46 > > And the dataset head is: > > #ID TIME AMT CMTT CMT DVV DV WEIG ORWE RUTE DRUG EVID 1 0 0.165 1 1 0 > 0 220 . 1 1 4 1 0.16 . 1 1 82.13 4.41 220 . 1 1 0 1 0.16 . 2 2 0.864 > -0.15 220 . 1 2 0 1 0.16 . 3 3 635.8 6.45 220 2.1 1 1 0 1 0.16 . 4 3 > 4.761 1.56 220 2.1 1 2 0 1 0.16 . 5 3 21.04 3.05 220 . 1 1 0 1 0.16 . 6 > 3 0.864 -0.15 220 . 1 2 0 1 0.16 . 7 3 708.13 6.56 220 1.03 1 1 0 1 0.16 > . 8 3 2.35 0.85 220 1.03 1 2 0 1 0.16 . 9 3 1942.59 7.57 220 0.21 1 1 0 > 1 0.16 . 11 3 1.728 0.55 220 0.21 1 2 0 2 0 0.159 1 1 0 0 212 . 1 1 4 2 > 0.16 . 1 1 57.62 4.05 212 . 1 1 0 2 0.16 . 2 2 0.864 -0.15 212 . 1 2 0 2 > 0.16 . 3 3 414.11 6.03 212 2 1 1 0 2 0.16 . 4 3 4.761 1.56 212 2 1 2 0 2 > 0.16 . 5 3 15.56 2.74 212 . 1 1 0 2 0.16 . 6 3 0.864 -0.15 212 . 1 2 0 2 > 0.16 . 7 3 481.66 6.18 212 1.1 1 1 0 2 0.16 . 8 3 4.95 1.6 212 1.1 1 2 0 > 2 0.16 . 9 3 2890.95 7.97 212 0.22 1 1 0 2 0.16 . 11 3 1.728 0.55 212 > 0.22 1 2 0 > > > > -- > > Justin Wilkins, PhD > > Exprimo NV > Tel:+41 (0) 81 599 23 82Mobile:+41 (0) 76 561 09 49E-mail: > [email protected]:www.exprimo.com > This e-mail is confidential. 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