C++ program is hanging when invoking 'mkfifo' (Lustre FS)

Question

I'm running the C++ program STAR (https://github.com/alexdobin/STAR) which is quite common in my field of research.

When I run this software on my server, everything goes fine.

When I run the very same software on another server (FS=lustre) the program is freezing

my command line is:

/path/to/star/STAR-2.7.1a/source/STAR --genomeDir /path/to/reference/ \
        --readFilesIn jeter1.fastq.gz jeter1.fastq.gz \
        --readFilesCommand gunzip -c  --outReadsUnmapped None --outSAMattributes All  |\
        head -n 1000

I used strace to see what's happening:

   (...)

   rt_sigprocmask(SIG_SETMASK, [], NULL, 8) = 0
   --- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_EXITED, si_pid=54748, si_uid=24382, si_status=0, si_utime=0, si_stime=0} ---
   getxattr("./_STARtmp//readFilesIn.info", "security.shook_state", 0x7ffd5a10b6c0, 1024) = -1 ENODATA (No data available)
   open("./_STARtmp//readFilesIn.info", O_RDONLY) = 7
   read(7, "-rw-r-----. 1 lindenbp fg0073 10"..., 8191) = 66
   read(7, "", 8191)                       = 0
   close(7)                                = 0
   write(6, "exec > \"./_STARtmp/tmp.fifo.read"..., 82) = 82
   lseek(6, 0, SEEK_SET)                   = 0
   read(6, "exec > \"./_STARtmp/tmp.fifo.read"..., 8191) = 82
   read(6, "", 8191)                       = 0
   write(3, "-rw-r-----. 1 lindenbp fg0073 10"..., 172) = 172
   close(6)                                = 0
   chmod("./_STARtmp//readsCommand_read1", 0700) = 0
   vfork()                                 = 54750
   --- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_EXITED, si_pid=54750, si_uid=24382, si_status=0, si_utime=0, si_stime=0} ---
   getxattr("./_STARtmp/tmp.fifo.read1", "security.shook_state", 0x7ffd5a10b6c0, 1024) = -1 ENODATA (No data available)
   open("./_STARtmp/tmp.fifo.read1", O_RDONLY ######### <= FREEZES HERE
   (...)

So I think it freezed somewhere here (?): https://github.com/alexdobin/STAR/blob/bb207df0cb62560c9194247a0480182ccbe1dca5/source/Parameters_openReadsFiles.cpp#L38 when the software create another process to gunzip -c the gzipped input files.

I also tried to use an option that specifies a tmp directory to '/tmp' but I got the same result.

What can explain this behavior and is there a way to fix it ?

Thanks

Answer 1

I got an answer from the author https://github.com/alexdobin/STAR/issues/687

The program generated a shell script that was missing a shebang delcaration: this prevented the fifo stream from working.