CMake Chem and Chem+KPP Build

[islas]

TYPE: enhancement

KEYWORDS: cmake, chem, kpp

SOURCE: internal

DESCRIPTION OF CHANGES:
Problem:
Current CMake build does not build chem or chem+kpp configurations

Solution:
Build kpp and associated tools, and cmake commands to facilitate simplified logic of the configure_wkc and compile_wkc scripts. As with all CMake builds, all auto-generated source code is placed in the out-of-source build directory.

Notable differences to make build :

• Use of Bison instead of Yacc as it is more easily accessible for install and usage as well as backward compatible
• Allow -j N parallel jobs to generate KPP sources up to a limit
• Use KPP-generated source file original names (not renamed to module_kpp_*
• Pass tuv_kpp a directory to locate where include file is to be generated, and allow control of file IO mode*
• Allow integration decomp rewrite to specify file locations rather than hard-coded*
• registry uses -DWRF_CHEM and -DWRF_KPP defines passed at command line instead of getenv() to match all other options*

*Affects make build in subtle ways but do not change user instructions

LIST OF MODIFIED FILES:
M CMakeLists.txt
M chem/CMakeLists.txt
A chem/KPP/CMakeLists.txt
M chem/KPP/compile_wkc
A chem/KPP/kpp/kpp-2.1/CMakeLists.txt
A chem/KPP/util/wkc/CMakeLists.txt
M chem/KPP/util/wkc/gen_kpp.c
M chem/KPP/util/wkc/protos_kpp.h
M chem/KPP/util/wkc/tuv_kpp.c
A chem/KPP/util/write_decomp/CMakeLists.txt
M chem/KPP/util/write_decomp/Makefile
M chem/KPP/util/write_decomp/integr_edit.c
M chem/chem_driver.F
M tools/CMakeLists.txt
M tools/data.h
M tools/registry.c

TESTS CONDUCTED:

1. Reproduction of chem and chem+kpp regtests with cmake is possible now

RELEASE NOTE:
CMake Chem and Chem+KPP Build

[weiwangncar]

The Jenkins test results:

Test Type              | Expected  | Received |  Failed
= = = = = = = = = = = = = = = = = = = = = = = =  = = = =
Number of Tests        : 23           24
Number of Builds       : 60           57
Number of Simulations  : 158           150        0
Number of Comparisons  : 95           86        0

Failed Simulations are: 
None
Which comparisons are not bit-for-bit: 
None

[islas]

Requires #2056, #2053, #2086, #2087, and #2088

[amstokely]

While replacing the call to system(cp_command) with a safer alternative would be a good improvement, this system call was not introduced in this PR. Addressing it might be better suited for a future PR.

[amstokely]

Calling system() with a command-line-provided argument introduces significant security risks, as it can allow command injection if the input is not carefully sanitized. Could we replace system(cp_command) with a safer alternative that avoids directly invoking the shell?

For example, the following implementation securely copies files using fork() and execlp():

#include <unistd.h>
#include <sys/wait.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>

void copy_file(const char *source, const char *destination) {
    pid_t pid = fork();
    if (pid == 0) {
        // Child process: Securely execute the `cp` command
        execlp("cp", "cp", source, destination, NULL);
        perror("execlp failed"); // If exec fails
        exit(EXIT_FAILURE);
    } else if (pid > 0) {
        // Parent process: Wait for the child to complete
        int status;
        waitpid(pid, &status, 0);
        if (WIFEXITED(status)) {
            printf("Copy completed with exit code %d\n", WEXITSTATUS(status));
        } else {
            fprintf(stderr, "Copy process terminated abnormally\n");
        }
    } else {
        perror("fork failed");
        exit(EXIT_FAILURE);
    }
}

int main(int argc, char *argv[]) {
    if (argc != 2) {
        fprintf(stderr, "Usage: %s \"<source_file> <destination_file>\"\n", argv[0]);
        return EXIT_FAILURE;
    }

    // Parse the cp_command argument into source and destination
    char *cp_command = argv[1];
    char *source = strtok(cp_command, " ");
    char *destination = strtok(NULL, " ");

    if (!source || !destination) {
        fprintf(stderr, "Error: Invalid command. Provide source and destination files.\n");
        return EXIT_FAILURE;
    }

    // Call the copy_file function
    printf("Copying '%s' to '%s'...\n", source, destination);
    copy_file(source, destination);

    return EXIT_SUCCESS;
}

[mgduda]

Everything seems to compile successfully if I select chem and kpp as additional configuration options, though I actually have no idea how to run anything with chem+kpp to verify that the compiled model includes chemistry functionality.