Fix GEKKOFS script and join environments

#!/usr/bin/env bash

echo "GEKKOFS Script Called"

#!/usr/bin/bash

echo "GEKKOFS Script Called" $HOSTNAME $SLURM_JOBID

# example of a script that can be called by the adhoc service

# [2023-11-23 09:37:32.583868] [scord-ctl] [2199567] [info] rpc => id: 0 name: "ADM_deploy_adhoc_storage" from: "ofi+tcp;ofi_rxm://127.0.0.1:52000" body: {uuid: "gekkofs-JR4ny5xHMhmlwh6KqThfYt71IaoR9cH5", type: ADM_ADHOC_STORAGE_GEKKOFS, resources: {nodes: [{hostname: "broadwell-001", type: regular}, {hostname: "broadwell-002", type: regular}, {hostname: "broadwell-003", type: regular}, {hostname: "broadwell-004", type: regular}]}}

# option: start --hosts "broadwell-001,broadwell-002,broadwell-003,broadwell-004" --workdir /tmp/gekkofs/gekkofs-JR4ny5xHMhmlwh6KqThfYt71IaoR9cH5 --datadir /tmp/gekkofs/gekkofs-JR4ny5xHMhmlwh6KqThfYt71IaoR9cH5/data --mountdir /tmp/gekkofs/gekkofs-JR4ny5xHMhmlwh6KqThfYt71IaoR9cH5/mnt

# code to count the number of elements in a comma separated list environment variable (called $nodes) and store in $num_nodes

if ($1 == "start") then

if [ "$1" == "start" ]; then

    echo "Starting GEKKOFS"

    $nodes = $3

    . /beegfs/home/r.nou/spack/share/spack/setup-env.sh

    spack load gekkofs

    spack load slurm@23.02.6

    nodes=$3

    num_nodes=$(echo $nodes | awk -F, '{print NF-1}')

    # If num_nodes is >40, we are on the testing environment

    if ($num_nodes > 40) then

    # If num_nodes is greater than 40, we are on the testing environment

    if [ $num_nodes -gt 40 ]; then

        exit 0

    end

    $workdir = $5

    $datadir = $7

    $mountdir = $9

    fi

    workdir=$5

    datadir=$7

    mountdir=$9

    mkdir -p $5

    srun -N $num_nodes -n $num_nodes --oversubscribe --cpus-per-task=1 --mem-per-task=1 --export=ALL bash -c "gkfs_daemon --rootdir $datadir --mountdir $mountdir" & 

else if ($1 == "stop") then

    mkdir -p $workdir

    /opt/slurm/bin/srun -N $num_nodes -n $num_nodes --oversubscribe --cpus-per-task=1 --mem-per-cpu=1 --export=ALL bash -c "gkfs_daemon --rootdir $datadir --mountdir $mountdir" &

   sleep 2

elif [ "$1" == "stop" ]; then

    echo "Stopping GEKKOFS"

    srun -N $num_nodes -n $num_nodes --oversubscribe --cpus-per-task=1 --mem-per-task=1 --export=ALL bash -c "pkill -9 gkfs_daemon"

    . /beegfs/home/r.nou/spack/share/spack/setup-env.sh

    spack load gekkofs

    spack load slurm@23.02.6

    /opt/slurm/bin/srun -N $num_nodes -n $num_nodes --oversubscribe --cpus-per-task=1 --mem-per-task=1 pkill -9 gkfs_daemon

else

    echo "Unknown command"

    exit 1

fi

exit 0

    return tmp;

}

// Function to join two sets of environment variables

char**

joinEnvironments(char** env1, const char** env2) {

    // Count the number of variables in each environment

    int count1 = 0;

    while(env1[count1] != nullptr) {

        ++count1;

    }

    int count2 = 0;

    while(env2[count2] != nullptr) {

        ++count2;

    }

    // Allocate memory for the combined environment

    char** combinedEnv = new char*[count1 + count2 + 1];

    // Copy the variables from the first environment

    for(int i = 0; i < count1; ++i) {

        combinedEnv[i] = strdup(env1[i]);

    }

    // Copy the variables from the second environment

    for(int i = 0; i < count2; ++i) {

        combinedEnv[count1 + i] = strdup(env2[i]);

    }

    // Null-terminate the combined environment

    combinedEnv[count1 + count2] = nullptr;

    return combinedEnv;

}

void

command::exec() const {

    switch(const auto pid = ::fork()) {

        case 0: {

            // Join the environments

            char** combinedEnv = joinEnvironments(environ, envp.get());

            ::execvpe(argv[0], const_cast<char* const*>(argv.get()),

                      const_cast<char* const*>(envp.get()));

                      const_cast<char* const*>(combinedEnv));

            // We cannot use the default logger in the child process because it

            // is not fork-safe, and even though we received a copy of the

            // global logger, it is not valid because the child process does

#include <net/utilities.hpp>

#include "rpc_server.hpp"

extern char** environ;

using namespace std::literals;

        const auto& adhoc_cfg = it->second;

        LOGGER_DEBUG("deploy \"{:e}\" (ID: {})", adhoc_type, adhoc_uuid);

        for (int i = 0; environ[i] != nullptr; ++i) {

        std::cout << environ[i] << std::endl;

    }

        // 1. Create a working directory for the adhoc storage instance

        adhoc_dir = adhoc_cfg.working_directory() / adhoc_uuid;

        const auto cmd = adhoc_cfg.startup_command().eval(

                adhoc_uuid, *adhoc_dir, hostnames);

        // Fill environment

        // 4. Execute the startup command

        try {