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Bugfix: Resolve race condition with FIFO cleanup and child process termination #2636

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Bugfix: Resolve race condition with FIFO cleanup and child process termination #2636

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45d4baf
Resolve race condition with FIFO cleanup and child process termination
robsyme Jun 4, 2025
296e4db
Clean up processes BEFORE removing files
robsyme Jun 4, 2025
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25 changes: 23 additions & 2 deletions source/Parameters_closeReadsFiles.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -2,11 +2,32 @@
#include "ErrorWarning.h"
#include <fstream>
#include <sys/stat.h>
#include <sys/wait.h>
void Parameters::closeReadsFiles() {
for (uint imate=0; imate<readFilesIn.size(); imate++) {//open readIn files
if ( inOut->readIn[imate].is_open() )
inOut->readIn[imate].close();
if (readFilesCommandPID[imate]>0)
kill(readFilesCommandPID[imate],SIGKILL);
if (readFilesCommandPID[imate]>0) {
kill(readFilesCommandPID[imate],SIGTERM); // Use SIGTERM for graceful shutdown
int status;
waitpid(readFilesCommandPID[imate], &status, 0); // Wait for process to terminate

// Check if process had issues (but don't fail - this is cleanup)
if (WIFEXITED(status)) {
int exit_code = WEXITSTATUS(status);
if (exit_code != 0) {
warningMessage("readFilesCommand process for mate " + to_string(imate+1) +
" exited with non-zero code: " + to_string(exit_code),
std::cerr, inOut->logMain, *this);
}
} else if (WIFSIGNALED(status)) {
int signal_num = WTERMSIG(status);
if (signal_num != SIGTERM) { // Don't warn about our own SIGTERM
warningMessage("readFilesCommand process for mate " + to_string(imate+1) +
" was terminated by signal: " + to_string(signal_num),
std::cerr, inOut->logMain, *this);
}
}
}
};
};
3 changes: 2 additions & 1 deletion source/STAR.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -292,14 +292,15 @@ int main(int argInN, char *argIn[])
*P.inOut->logStdOut << timeMonthDayTime(g_statsAll.timeFinish) << " ..... finished successfully\n"
<< flush;

P.closeReadsFiles(); // Clean up processes BEFORE removing files

P.inOut->logMain << "ALL DONE!\n"
<< flush;
if (P.outTmpKeep == "None")
{
sysRemoveDir(P.outFileTmp);
};

P.closeReadsFiles(); // this will kill the readFilesCommand processes if necessary
// genomeMain.~Genome(); //need explicit call because of the 'delete P.inOut' below, which will destroy P.inOut->logStdOut
if (genomeMain.sharedMemory != NULL)
{ // need explicit call because this destructor will write to files which are deleted by 'delete P.inOut' below
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