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installing MCsim
|
From: |
Jason Boyd |
|
Subject: |
installing MCsim |
|
Date: |
Sun, 09 Jun 2002 19:09:59 GMT |
Dear Sirs:
I recently dl'd MCsim to my Mac from your site. I am
using Mac OS 10.1.5 (although I dl'd MCsim when I had
Mac OS 10.1.4, if it makes any difference). After figuring
out that I needed to make aliases point to my compiler
(Mac 10 compiler called cc and language c++ instead
of gcc and g++) I finally used the make utility on the
makefile (I will include the terminal image of that
instance at the end of this mail). When using 'make
install' I have a problem. I'm new to unix programming
but have poked around in my system and have found
no 'install' option to my make utility. However there is
an 'install' utility which seems to copy a file from one
place to the next; for some reason this doesn't sound
like the install utility that I need; I tried it but when I tried
to invoke the mod utility at the terminal (and by double
clicking in the Aqua gui) it reported an error.
Nonetheless, I'd like to use MCsim on a pbpk model
I've worked on and need your help.
Included below is the history of the terminal wherein I
'made' the makefile and also the history of my (mis-
)uses of 'install'. Incidentally, after it didn't work, I
thought I would cat mod just to see if there was
anything there: I have included in this email the output
of cat mod in case you may find it useful. Any help you
may have would be extremely appreciated!!
Thanks in advance for your help,
Jason L. Boyd
PhD Candidate
Interdisciplinary Program in Toxicology
Department of Pharmaceutical and Biomedical
Sciences, College of Pharmacy
University of Georgia
706-542-5254
enc1:make history:
<note that the MCsim dl'd as the Unix variant, the html
manual for mcsim said I would have different directory
structures than these>
[localhost:/Users/Shared] ugajlb% cd /Users/Shared/
mcsim
[localhost:/Users/Shared/mcsim] ugajlb% ls
doc mod sim
[localhost:/Users/Shared/mcsim] ugajlb% cd /Users/
Shared/mcsim/mod
[localhost:Shared/mcsim/mod] ugajlb% ls
1cpt.model lex.h lexfn.h modd.c modiface.h
strutil.c
Makefile lexerr.c linear.model model.c modo.c
strutil.h
hungtype.h lexerr.h mod.c modelu.h
perc.model
lex.c lexfn.c mod.h modi.c ref_model.c
[localhost:Shared/mcsim/mod] ugajlb% make
gcc -O -DNDEBUG -I . -Wall -DMODGEN -c -o lex.o
lex.c
lex.c: In function `GetStatement':
lex.c:672: warning: suggest explicit braces to avoid
ambiguous `else'
gcc -O -DNDEBUG -I . -Wall -DMODGEN -c -o lexerr.o
lexerr.c
lexerr.c: In function `ReportError':
lexerr.c:53: warning: suggest explicit braces to avoid
ambiguous `else'
gcc -O -DNDEBUG -I . -Wall -DMODGEN -c -o lexfn.o
lexfn.c
gcc -O -DNDEBUG -I . -Wall -DMODGEN -c -o mod.o
mod.c
gcc -O -DNDEBUG -I . -Wall -DMODGEN -c -o modd.o
modd.c
gcc -O -DNDEBUG -I . -Wall -DMODGEN -c -o modi.o
modi.c
gcc -O -DNDEBUG -I . -Wall -DMODGEN -c -o modo.o
modo.c
modo.c: In function `ForAllVar':
modo.c:81: warning: suggest explicit braces to avoid
ambiguous `else'
gcc -O -DNDEBUG -I . -Wall -DMODGEN -c -o strutil.o
strutil.c
Linking mod...
* Created executable "mod".
***************************************
enc2:installing mod history:
[localhost:Shared/mcsim/mod] ugajlb% make install
mod
make: *** No rule to make target `install'. Stop.
[localhost:Shared/mcsim/mod] ugajlb% .
/Users/Shared/mcsim/mod
[localhost:Shared/mcsim/mod] ugajlb% make install
make: *** No rule to make target `install'. Stop.
[localhost:Shared/mcsim/mod] ugajlb% sudo install
mod
Password:
usage: install [-cps] [-f flags] [-m mode] [-o owner] [-g
group] [-l linkflags] [-S stripflags] file1 file2
install [-cps] [-f flags] [-m mode] [-o owner] [-g
group] [-l linkflags] [-S stripflags] file1 ... fileN directory
install -pd [-m mode] [-o owner] [-g group] directory
...
[localhost:Shared/mcsim/mod] ugajlb% ls
1cpt.model lexerr.c linear.model modd.o modo.c
strutil.o
Makefile lexerr.h mod model.c modo.o
hungtype.h lexerr.o mod.c modelu.h
perc.model
lex.c lexfn.c mod.h modi.c ref_model.c
lex.h lexfn.h mod.o modi.o strutil.c
lex.o lexfn.o modd.c modiface.h strutil.h
*****************************************
enc3:cat mod output:
[localhost:Shared/mcsim/sim] ugajlb% cat mod
?
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__dyld_mod_term_funcs__dyld_make_delayed_modu
le_initializer_callsThe kernel support for the dynamic
linker is not present to run this program.
quoted-stringinvalid lexical typepunctuationnumber-or-
idnumberfloat-or-idfloating-pointinteger-or-
idintegeridentifiernull-type??Unexpected end of
file.r%crvalue to assignmentWarning: Error: line %d:
'%s'...
Unknown error code %x: %sInitialization error.File not
found "%s".Cannot open file "%s".Unexpected
character '%c' in input file.Unexpected number %s in
input file.Expected '%c' before '%c'.Expected <%s>
before '%s''%s' used in invalid context.Duplicate
declaration of model variable '%s'.Out of memory in
%s() !'%s' redefined.Equation is too long. Possibly
missing terminator.Invalid state identifier
'%s'.Undefined identifier '%s'.Input '%s' is not
initialized.State variable '%s' has no dynamics.Too
many %s declarations. Limit is %d.
Bad definition of experiment %d
Experiment %d has no outputs specified
Experiment %d has no output times specified
DifSub() returned error %ld: %s
in specification: %s
Insufficient points in file "%s"
Already defining other experiment %s
Max is less than min
%s
One or more fatal errors: Exiting...
NDosesPerExpPerRatePerDoseinput-specpositive-
integerGetNDosesSyntax: GetNDoses (nDoses, <n
Magnitudes>, <n T0's>, <n Texposure's>)
Model Generator Program v4.0
Copyright (c) 1993-96. Don Maszle, Frederic Bois. All
rights reserved.
Usage: %s [input-file [output-file]]
Creates file 'model.c' according to input-file specs
NormalRandomUniformRandomlnGammalnDFNorma
lerfcCDFNormaltanhtansqrtsinhsinpowlog10logfmodfl
oorfabsexpcoshcosceilatan2atanasinacost.. in
equation* .. creating new equation in AddEquation* ..
defining equation in CopyString Inputs and parameters
cannot be assigned in Dynamics
* IgnoringJacobian equation handler not
implementedNon-standard assignment in Dynamics
section. Potential state discontinuity.
Only outputs can be defined in CalcOutputs{}
section.Model variable initialized before
declarationEnddtCalcOutputsJacobScaleDynamicsOut
putsInputsStates* Section must be delimited by curly
braces.ReadModelIFN_NDOSESIFN_PEREXPIFN_PE
RRATEIFN_PERDOSEIFN_CONSTANTIFN_NULL /* ??
*/ %s %s %s
:=->0.0 is an input function
/* %s
___________________________________________
________
Model File: %s
Date: %s
Created by: "%s-%s"
v4.0 -- a model preprocessor by Don Maszle
Copyright (c) 1993-96. Don Maszle, Frederic Bois. All
rights reserved.
Model calculations for compartmental model:
%d States:
%d Outputs:
%d Inputs:
%d Parameters:
*/
#include <stdlib.h>
#include <stdio.h>
#include <math.h>
#include <string.h>
#include <float.h>
#include "modelu.h"
#include "random.h"
double %s;
#define ID_%s 0x%04x
0x0000
/*----- Indices to Global Variables */
/* Model variables: States and other outputs */
/* Inputs */
/* Parameters */
/*----- Global Variables */
/* For export. Keep track of who we are. */
char szModelDescFilename[] = "%s";
char szModelSourceFilename[] = __FILE__;
char szModelGenAndVersion[] = "%s-%s";
/* Externs */
extern BOOL vbModelReinitd;
/* Model Dimensions */
int vnStates = %d;
int vnOutputs = %d;
int vnModelVars = %d;
int vnInputs = %d;
int vnParms = %d;
/* States and Outputs*/
double %s[%d];
/* Inputs */
IFN %s[%d];
vrgInputs[ID_%s]%s[ID_%s]vrgModelVars[ID_%s]%s
{"", NULL, 0} /* End flag */
{"%s", (PVOID) &%s, ID_%s | ID_%s},
OUTPUTSTATEINPUTPARM
/*----- Global Variable Map */
VMMAPSTRCT vrgvmGlo[] = {
}; /* vrgpvmGlo[] */
%s.iType = %s;
%s.dTStartPeriod = 0.0;
%s.bOn = FALSE;
%s.dMag = %f;
%s.dT0 = %f;
%s.dTexp = %f;
%s.dDecay = %f;
%s.dTper = %f;
%s.hMag = %#x;
%s.hT0 = %#x;
%s.hTexp = %#x;
%s.hDecay = %#x;
%s.hTper = %#x;
%s.dVal = 0.0;
%s.nDoses = 0;
%s = %s;
/* InitModel
Should be called to initialize model variables at
the beginning of experiment before reading
variants from the simulation spec file.
*/
void InitModel()
{
/*-- Initialize things in the order that they appear in
model definition file so that dependencies are
handled correctly. */
vbModelReinitd = TRUE; /* Flag is initialized */
} /* InitModel */
rgDerivs(*pdTime)rgModelVars.dMag.dVal0.0; /* NULL
EQN!?? */ ;
Error: input '%s' used in Scale context.
%s%s = %s = No Dynamics{} equations.
/* Dynamics section */
void CalcDeriv (double rgModelVars[],
double rgDerivs[],
PDOUBLE pdTime)
{
/* Local variables */
CalcInputs (pdTime); /* Get new input vals */
} /* CalcDeriv */
No Scale{} equations. Null function defined.
/* Model scaling */
void ScaleModel (void)
} /* ScaleModel */
/* Jacobian calculation */
void CalcJacob (double rgModelVars[], double *
rgdSave[], PDOUBLE pdTime)
} /* CalcJacob */
No CalcOutput{} equations. Null function defined.
/* Outputs calculation */
void CalcOutputs (double rgModelVars[],
double rgDerivs[],
PDOUBLE pdTime)
} /* CalcOutputs */
stateinputoutputparameterState equations
missing.cError: No Dynamics, no outputs or no global
variables defined
w
* Created model file '%s'
...in WriteModel ()?B?}h?=k??? }??9k N? ?B?}h?=
k????}??9k?N? ?B?}h?=k???`}??9k`N? ?B?}h?=
address@hidden@N? ?B?}h?=k??? }??9k N? ?B?}h?=
k???}??9kN? ?B?}h?=k?????9k? ?B?}h?=
k??????9k?? ?B?}h?=k??? }??9k N? ?B?}h?=
k????}??9k?N? ?B?}h?=k???`}??9k`N? ?B?}h?=
address@hidden@N? ?B?}h?=k??? }??9k N? ?B?}h?=
k???}??9kN? ?B?}h?=k?????9k? ?B?}h?=
k??????9k?? ?B?}h?=k??? }??9k N? ?B?}h?=
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address@hidden@N? ?B?}h?=k??? }??9k N? ?B?}h?=
k???}??9kN? ?B?}h?=k?????9k? ?B?}h?=
k??????9k?? ?B?}h?=k??? }??9k N? ?B?}h?=
k????}??9k?N?
u??8?0v?v?v?v?v°v?v?v?v?vhvhvhvhvhvhvhvXu?+-/*()><
?:,!={z?z??z?u?}
}|?|?|?|?|?|?|?|?|?|¸|´|°|¨|
|?|?|
?|?|t|l|\|Lu?0.0; /* Redefined later */
~?~?~?~?~?~¸~¬~¨~?du??vrgModelVarsvrgInputsh
address@hidden(model.cW?W¸[?p?m¸_?rh¬a??&?&?&?&
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?&?&??t??????x?p?|&?6qHHrtIH?G?YW??O?=
,?L?J?I?$M?4L
DN?3?1??4X¬'t¸)0gV?#<DÏ6¨?+P.><Al?Q0?P¸H? S?r^
??,|?3<?3?4?*?TH?_I{m¸?n(,`<¨?QxkC??s8((??up?
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,%X?2Z|Ad?¸s¨Q[_h¬q[??a???W¸¢_??j?`??
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on_init__cplus_init__cthread_init_routine__mh_execut
e_header__objcInit_atexit_catch_exception_raise_catc
h_exception_raise_state_catch_exception_raise_state
_identity_clock_alarm_reply_do_mach_notify_dead_na
me_do_mach_notify_no_senders_do_mach_notify_po
rt_deleted_do_mach_notify_send_once_do_seqnos_
mach_notify_dead_name_do_seqnos_mach_notify_n
o_senders_do_seqnos_mach_notify_port_deleted_do
_seqnos_mach_notify_send_once_errno_exit_mach_i
nit_routine_main_receive_samples_EGetPunct_ENext
Lex_EatStatement_FillBuffer_FlushBuffer_GetFuncArg
s_GetIdentifier_GetNumber_GetOptPunct_GetPunct_G
etStatement_GetString_InitBuffer_MakeStringBuffer_Ne
xtChar_NextLex_NextListItem_PreventLexSplit_SkipCo
mment_SkipWhitespace_vrgszLexTypes_ReportError_
_CurrentRuneLocale__DefaultRuneLocale____runety
pe_fopen_fread_fseek_ftell_malloc_printf_strchr_strnc
py_DefDepParm_GetFnType_GetInputArgs_GetInputFn
_GetNDoses_GetNNumbers_InitIFN_vrgifmMap_Calc
ulateVarHandle_MyStrcmp___sF_atof_atoi_fprintf_Rea
dModel_WriteModel_AddEquation_CopyString_Declare
ModelVar_DefineCalcOutEqn_DefineDynamicsEqn_D
efineGlobalVar_DefineJacobEqn_DefineScaleEqn_Def
ineVariable_GetVarPTR_GetVarType_IsMathFunc_Set
Equation_SetVarType_VerifyEqn_vrgszMathFuncs_vsz
HasInitializer_GetKeywordCode_free_strcmp_strcpy_s
trlen_GetKeyword_InitInfo_ProcessWord_vrgkmKeywor
dMap_fclose_AdjustOneVar_AdjustVarHandles_Assert
ExistsEqn_CountOneDecl_ForAllVar_GetName_Index
OneVar_IndexVariables_MakeCodeFilename_Reverse
Pointers_TranslateEquation_TranslateID_VerifyEqns_
WriteCalcDeriv_WriteCalcJacob_WriteCalcOutputs_Wri
teDecls_WriteHeader_WriteIncludes_WriteInitModel_W
riteOneDecl_WriteOneEquation_WriteOneIndexDefine_
WriteOneInit_WriteOneName_WriteOneVMEntry_Write
Scale_WriteVarMap_vszIFNTypes_ctime_localtime_me
mcpy_sprintf_strcat_time_vnInputs_vnModelVars_vnO
utputs_vnParms_vnStates_vpvmGloVarList_pointer_to
_objcInit_pointer_to_carbon_init__call_mod_init_funcs
dyld_lazy_symbol_binding_entry_pointerror_message
dyld_func_lookup_pointer_vszEqnPunct.45_vpvmGlo_v
szModelFilename_vszModGenName_vszModelArrayNa
me_vszInputArrayName_vszVarName.42_vszFilename
Default.103[localhost:Shared/mcsim/sim] ugajlb%
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