Updates for C-language output by yantosca · Pull Request #53 · KineticPreProcessor/KPP

yantosca · 2022-06-27T20:57:32Z

This PR fixes several issues that were preventing KPP from generating C-language output code. Namely:

Change /* */ comment headers to //, which reads much more clearly
Restored and updated the drv/general.c and drv/general_adj.c driver programs
Added updates to gen.c:
- Where the _Function file is generated, we now wrap Fortran90 optional arguments with an if ( useLang == F90_LANG ). This prevents a compiler error when the target language is C.
- Where Vdot is added to _Function, we need to loop over elements of the Vdot array if the target language is C. We can only use array notation for Fortran90.
Added updates to code_c.c:
- In routine C_FunctionStart, set fncPrototipe=0. This will declare each C-language function so that arrays will have dimensions included in the function interface. This will avoid a compilation error.
I have also reorganized the ./ci_tests subfolders.
- Each subfolder begins with either C_ or F90_, to denote the target language. (The minimum version test folder has been renamed to X_minver so that it will come last.
- Also, the names of all subfolders in ci-tests are now specified in a single file that is sourced by the other CI test scripts. This will make it easier to add new CI tests.

NOTE: At present, the C-language code fails when trying to use a mechanism other than small_strato. I think this is due to a Makefile issue that happens when e.g. Hessian is turned off but the Makefile looks for the Hessian files. I can implement a similar fix as was done for Fortran90.

src/code.c - Update author list src/code_c.c - Update bprintf call to print out //-style commments Signed-off-by: Bob Yantosca <[email protected]>

drv/general.c - C-language driver program drv/general_adj.c - C-language adjoint driver program Signed-off-by: Bob Yantosca <[email protected]>

src/code.c - In WriteDelim, extend the number of ~ characters printed src/code_c.c - Fix error in previous commit in call to bprintf, remove the 2nd parameter (LINE_LENGTH) and add a \n to the format. Signed-off-by: Bob Yantosca <[email protected]>

src/gen.c - When generating the _Function file, wrap Fortran90 optional arguments in an "if ( useLang == F90_LANG )". This prevents a compiler error when the target language is C - In the equation for Vdot, we need to loop over elements of the Vdot array if the target language is C. We can only use array notation for Fortran90. - Trim trailing whitespace src/code_c.c - In routine C_FunctionStart, set fncPrototipe=0. This will declare each C-language function so that arrays will have dimensions included in the function interface. This will avoid a compilation error. - Trim trailing whitespace Signed-off-by: Bob Yantosca <[email protected]>

drv/general.c drv/general_adj.c - Add more comments for clarity - Trimmed trailing whitespace Signed-off-by: Bob Yantosca <[email protected]>

We have renamed the continuous integration test folders in ci_tests so that each test begins with either a C_ or F90_, to denote the target language of KPP-generated code. The minimum version test has been renamed to X_minver. ./ci-pipelines/ci-testing-list.sh - Added the names of all the CI test folders in this file, which is source-d by the other scripts. The list of folders is stored in the ALL_TESTS bash variable. ./ci-pipelines/ci-manual-cleanup-script.sh ./ci-pipelines/ci-manual-testing-script.sh ./ci-pipelines/ci-testing-script.sh - These scripts now issue a "source ./ci-testing-list.sh" command in order to get the ALL_TESTS variable (which contains the list of CI test folders). Signed-off-by: Bob Yantosca <[email protected]>

This commit brings the updates from the "cleanup_util" and "dev" branches branch (plus some documentation updates) into the C-language development steream. Resolved conflicts in: (1) .ci-pipelines/ci-manual-cleanup-script.sh (2) .ci-pipelines/ci-manual-testing-script.sh (3) .ci-pipelines/ci-testing-script.sh Signed-off-by: Bob Yantosca <[email protected]>

…gets util/Makefile_f90 util/Makefile_upper_f90 - Remove *.o and *.mod files instead of KPP_ROOT*.o and KPP_ROOT*.mod in the clean and distclean targets. This will prevent issues where files are not removed due to case-insensitivity. Signed-off-by: Bob Yantosca <[email protected]>

./ci-tests/F90_ros_autoreduce - Renamed (was originally ros_autoreduce) ./ci-pipelines/ci-testing/list.sh - Add F90_ros_autoreduce to list of tests drv/general_autoreduce - Set ICNTRL(15) = -1 to prevent rate constants from being updated within the integration step. This slows the autoreduce code down. Signed-off-by: Bob Yantosca <[email protected]>

util/Makefile_c - Typo: Remove KPP_ROOT*.map (was KPP_ROOT_*.map) util/Makefile.f90 util/Makefile_upper_F90 - Now remove *.o and *.mod in clean and distclean targets, in order to avoid uppercase/lowercase ambiguity Signed-off-by: Bob Yantosca <[email protected]>

RolfSander · 2022-06-28T06:18:14Z

Looks good.

Thanks for given the CI tests a nice structure!

yantosca · 2022-06-28T13:49:38Z

Still debugging a seg fault when I try to build a larger mechanism than small_strato. It seems to be in C_InitDeclare when we pass it the EQN_NAMES. Will dig into this a bit.

yantosca · 2022-06-28T13:58:14Z

gdb output says:

Program received signal SIGSEGV, Segmentation fault.
0x00002aaaaaf60f76 in __mempcpy_sse2 () from /lib64/libc.so.6
(gdb) where
#0  0x00002aaaaaf60f76 in __mempcpy_sse2 () from /lib64/libc.so.6
#1  0x00002aaaaaf4e06c in _IO_default_xsputn () from /lib64/libc.so.6
#2  0x00002aaaaaf1e033 in vfprintf () from /lib64/libc.so.6
#3  0x00002aaaaaf424cb in vsprintf () from /lib64/libc.so.6
#4  0x0000000000401b55 in bprintf (fmt=0x425ce4 "\"%s\"") at code.c:202
#5  0x0000000000404878 in C_InitDeclare (v=90, n=235, values=0x7ffffffda350)
    at code_c.c:333
#6  0x000000000040dd4d in GenerateMonitorData () at gen.c:525
#7  0x000000000041998c in Generate () at gen.c:3629
#8  0x000000000041c66e in main (argc=2, argv=0x7fffffffb938) at kpp.c:640

yantosca · 2022-06-28T14:35:58Z

@RolfSander, I think I see what is going on. In routine C_InitDeclare I put in a debug statement that only executes when the variable EQN_NAMES is passed:

  // debug
  if ( v==90 ) {
    printf("\n");
    for (i=0; i<n; i++) printf( "\n%d, %s\n", i, cval[i] );
    exit(1);
  }

which gives this output:

0,               NO2 --> O3P + NO                                                                                                                                                                                                                                                                                 O3P + AIR + O2 --> O3                                                                                                                                                                                                                                                                                             O3P + O3 --> 2 O2                                                                                                                                                                                                                                                                                     O3P + NO + AIR --> NO2                                                                                                                                                                                                                                                                                           O3P + NO2 --> NO                                                                                                                                                                                                                                                                                            O3P + NO2 --> NO3                                                                                                                                                                                                                                                                                             O3 + NO --> NO2

so for each index i, the cval[i] contains the list of equations from i to the end of the file. This is causing the seg fault as we eventually run out of memory.

This is called from GenerateMonitorData in gen.c here:

  p = bufeqn;
  for (i = 0; i < EqnNr; i++) {
    EqnString(i, p);
    seqn[i] = p;
    p += MAX_EQNLEN;
  }
  InitDeclare( EQN_NAMES, EqnNr, (void*)seqn );

If you have any ideas then let me know. Thanks!

RolfSander · 2022-06-28T16:55:03Z

I'm sorry but I don't know how to solve this problem.

Maybe the easiest quick&dirty fix is to deactive EQN_NAMES for the C
language? I think that would be okay because I don't even know a single
KPP user who creates output in C.

yantosca · 2022-06-28T18:32:21Z

Found a solution!

  switch( var->type ) {
    case VELM: bprintf( "  %s  %s[] = {\n%5s", C_types[var->baseType], var->name, " " );
               for( i = 0; i < n; i++ ) {
                 switch( var->baseType ) {
                   case INT:
		     bprintf( "%3d",  ival[i] );
		     maxCols=12;
		     break;
                   case DOUBLE:
                   case REAL:
		     bprintf( "%5lg", dval[i] );
		     maxCols=8;
		     break;
                   case STRING:
		     bprintf( "\"%s\"", cval[i] );
		     maxCols=8;
		     break;
		   case DOUBLESTRING:
		     // Bug fix: To avoid a segmentation fault, copy the
		     // string from cval[i] to string variable thisEqn
		     // before passing it to bprintf.
		     //  -- Bob Yantosca (28 Jun 2022)
		     strncpy( thisEqn, cval[i], MAX_EQNLEN+1 );
		     bprintf( "\"%s\"", thisEqn );
		     maxCols=1;
		     break;
                 }

In routine C_InitDeclare, in the switch statement for VELM and DOUBLESTRING, we first copy the cval[i] to a temporary string variable before passing that to bprintf. This avoids a segmentation fault. Also removed some leftover debug printout. Signed-off-by: Bob Yantosca <[email protected]>

This is needed in order to generate C-language code for the models/saprc99.eqn or models/saprcnov.eqn mechanisms. Signed-off-by: Bob Yantosca <[email protected]>

drv/general.c - Use floating point variables for TSTART and TEND - Fixed a typo ("3600/0" should be "3600.0") drv/general_adj.c - Use floating point constants 100.0 and 3600.0 models/saprcnov.def - Remove tabs - Trim trailing whitespace - Align entries in INLINE blocks Signed-off-by: Bob Yantosca <[email protected]>

./ci-pipelines/ci-testing-list.sh - Added C_rosadj to the ALL_TESTS variable ./ci_tests/C_rk/C_rk.kpp - Bug fix: #LANGUAGE should be C, not Fortran90 ./ci-tests/C_rosadj/C_rosadj.kpp - Added KPP definition file for the rosenbrock_adj test in C Signed-off-by: Bob Yantosca <[email protected]>

yantosca · 2022-06-28T19:00:55Z

I've since fixed the issue above. For now I only use the small_strato mechanism for all the C-language integration tests. KPP will now generate code with the other mechanisms (e.g. saprcnov.eqn) though. Good enough for the sake of continuity and for the KPP 3.0.0 version.

RolfSander

Great that you found a solution. Yes, go ahead and merge!

yantosca added 7 commits June 27, 2022 11:30

Change C-style "/* */" comment headers to //

13938a9

src/code.c - Update author list src/code_c.c - Update bprintf call to print out //-style commments Signed-off-by: Bob Yantosca <[email protected]>

Restore general.c and general_adj.c driver programs

185fdf6

drv/general.c - C-language driver program drv/general_adj.c - C-language adjoint driver program Signed-off-by: Bob Yantosca <[email protected]>

Further updates for comment output

d82e7ee

src/code.c - In WriteDelim, extend the number of ~ characters printed src/code_c.c - Fix error in previous commit in call to bprintf, remove the 2nd parameter (LINE_LENGTH) and add a \n to the format. Signed-off-by: Bob Yantosca <[email protected]>

Add comments to C-language driver programs

86a9425

drv/general.c drv/general_adj.c - Add more comments for clarity - Trimmed trailing whitespace Signed-off-by: Bob Yantosca <[email protected]>

yantosca added code / structural Related to structural source code updates target-languages Related to the language options for KPP-generated code labels Jun 27, 2022

yantosca self-assigned this Jun 27, 2022

yantosca added this to the 3.0.0 milestone Jun 27, 2022

yantosca added 3 commits June 27, 2022 17:07

yantosca added 4 commits June 28, 2022 14:45

Add ARR_ab, ARR_ac, ARR_abc rate law functions to UserRateLaws.c

c600007

This is needed in order to generate C-language code for the models/saprc99.eqn or models/saprcnov.eqn mechanisms. Signed-off-by: Bob Yantosca <[email protected]>

yantosca marked this pull request as ready for review June 28, 2022 18:58

yantosca requested review from RolfSander and jimmielin June 28, 2022 19:01

Merge branch 'dev' into c-lang

a8ec3be

RolfSander approved these changes Jun 28, 2022

View reviewed changes

yantosca merged commit a8ec3be into dev Jun 28, 2022

yantosca deleted the c-lang branch June 28, 2022 21:31

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Updates for C-language output#53

Updates for C-language output#53
yantosca merged 15 commits intodevfrom
c-lang

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