fyi ... here is the output of strace when the Bad file descriptor error is generated ... $nohup ./run_shuffle.sh > /tmp/run_shuffle.log 2>&1 0>&- & execve("/usr/bin/shuf", ["shuf", "/nfs/digits/datasets/com-aosvapp"...], [/* 54 vars */]) = 0 brk(0) = 0x10dc000 access("/etc/ld.so.nohwcap", F_OK) = -1 ENOENT (No such file or directory) mmap(NULL, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7f9af2d5a000 access("/etc/ld.so.preload", R_OK) = -1 ENOENT (No such file or directory) open("tls/x86_64/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory) open("tls/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory) open("x86_64/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory) open("libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory) open("/usr/local/cuda-7.5/lib64/tls/x86_64/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory) stat("/usr/local/cuda-7.5/lib64/tls/x86_64", 0x7ffcc850b6c0) = -1 ENOENT (No such file or directory) open("/usr/local/cuda-7.5/lib64/tls/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory) stat("/usr/local/cuda-7.5/lib64/tls", 0x7ffcc850b6c0) = -1 ENOENT (No such file or directory) open("/usr/local/cuda-7.5/lib64/x86_64/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory) stat("/usr/local/cuda-7.5/lib64/x86_64", 0x7ffcc850b6c0) = -1 ENOENT (No such file or directory) open("/usr/local/cuda-7.5/lib64/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory) stat("/usr/local/cuda-7.5/lib64", {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0 open("/etc/ld.so.cache", O_RDONLY|O_CLOEXEC) = 0 fstat(0, {st_mode=S_IFREG|0644, st_size=78541, ...}) = 0 mmap(NULL, 78541, PROT_READ, MAP_PRIVATE, 0, 0) = 0x7f9af2d46000 close(0) = 0 access("/etc/ld.so.nohwcap", F_OK) = -1 ENOENT (No such file or directory) open("/lib/x86_64-linux-gnu/libc.so.6", O_RDONLY|O_CLOEXEC) = 0 read(0, "\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0P \2\0\0\0\0\0"..., 832) = 832 fstat(0, {st_mode=S_IFREG|0755, st_size=1840928, ...}) = 0 mmap(NULL, 3949248, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 0, 0) = 0x7f9af2775000 mprotect(0x7f9af292f000, 2097152, PROT_NONE) = 0 mmap(0x7f9af2b2f000, 24576, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 0, 0x1ba000) = 0x7f9af2b2f000 mmap(0x7f9af2b35000, 17088, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_ANONYMOUS, -1, 0) = 0x7f9af2b35000 close(0) = 0 mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7f9af2d45000 mmap(NULL, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7f9af2d43000 arch_prctl(ARCH_SET_FS, 0x7f9af2d43740) = 0 mprotect(0x7f9af2b2f000, 16384, PROT_READ) = 0 mprotect(0x60a000, 4096, PROT_READ) = 0 mprotect(0x7f9af2d5c000, 4096, PROT_READ) = 0 munmap(0x7f9af2d46000, 78541) = 0 brk(0) = 0x10dc000 brk(0x10fd000) = 0x10fd000 open("/usr/lib/locale/locale-archive", O_RDONLY|O_CLOEXEC) = 0 fstat(0, {st_mode=S_IFREG|0644, st_size=1607664, ...}) = 0 mmap(NULL, 1607664, PROT_READ, MAP_PRIVATE, 0, 0) = 0x7f9af2bba000 close(0) = 0 open("/nfs/digits/datasets/com-aosvapps-distracted-driving3/databases/TrainImagePathsAndLabels_AlpineTest1.csv", O_RDONLY) = 0 dup3(0, 0, 0) = -1 EINVAL (Invalid argument) dup2(0, 0) = 0 close(0) = 0 fadvise64(0, 0, 0, POSIX_FADV_SEQUENTIAL) = -1 EBADF (Bad file descriptor) fstat(0, 0x7ffcc850be10) = -1 EBADF (Bad file descriptor) fstat(0, 0x7ffcc850bcd0) = -1 EBADF (Bad file descriptor) mmap(NULL, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7f9af2d58000 read(0, 0x10dd030, 8192) = -1 EBADF (Bad file descriptor) open("/usr/share/locale/locale.alias", O_RDONLY|O_CLOEXEC) = 0 fstat(0, {st_mode=S_IFREG|0644, st_size=2570, ...}) = 0 mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7f9af2d57000 read(0, "# Locale name alias data base.\n#"..., 4096) = 2570 read(0, "", 4096) = 0 close(0) = 0 munmap(0x7f9af2d57000, 4096) = 0 open("/usr/share/locale/en_US.UTF-8/LC_MESSAGES/coreutils.mo", O_RDONLY) = -1 ENOENT (No such file or directory) open("/usr/share/locale/en_US.utf8/LC_MESSAGES/coreutils.mo", O_RDONLY) = -1 ENOENT (No such file or directory) open("/usr/share/locale/en_US/LC_MESSAGES/coreutils.mo", O_RDONLY) = -1 ENOENT (No such file or directory) open("/usr/share/locale/en.UTF-8/LC_MESSAGES/coreutils.mo", O_RDONLY) = -1 ENOENT (No such file or directory) open("/usr/share/locale/en.utf8/LC_MESSAGES/coreutils.mo", O_RDONLY) = -1 ENOENT (No such file or directory) open("/usr/share/locale/en/LC_MESSAGES/coreutils.mo", O_RDONLY) = -1 ENOENT (No such file or directory) open("/usr/share/locale-langpack/en_US.UTF-8/LC_MESSAGES/coreutils.mo", O_RDONLY) = -1 ENOENT (No such file or directory) open("/usr/share/locale-langpack/en_US.utf8/LC_MESSAGES/coreutils.mo", O_RDONLY) = -1 ENOENT (No such file or directory) open("/usr/share/locale-langpack/en_US/LC_MESSAGES/coreutils.mo", O_RDONLY) = -1 ENOENT (No such file or directory) open("/usr/share/locale-langpack/en.UTF-8/LC_MESSAGES/coreutils.mo", O_RDONLY) = -1 ENOENT (No such file or directory) open("/usr/share/locale-langpack/en.utf8/LC_MESSAGES/coreutils.mo", O_RDONLY) = -1 ENOENT (No such file or directory) open("/usr/share/locale-langpack/en/LC_MESSAGES/coreutils.mo", O_RDONLY) = -1 ENOENT (No such file or directory) write(2, "shuf: ", 6shuf: ) = 6 write(2, "read error", 10read error) = 10 open("/usr/share/locale/en_US.UTF-8/LC_MESSAGES/libc.mo", O_RDONLY) = -1 ENOENT (No such file or directory) open("/usr/share/locale/en_US.utf8/LC_MESSAGES/libc.mo", O_RDONLY) = -1 ENOENT (No such file or directory) open("/usr/share/locale/en_US/LC_MESSAGES/libc.mo", O_RDONLY) = -1 ENOENT (No such file or directory) open("/usr/share/locale/en.UTF-8/LC_MESSAGES/libc.mo", O_RDONLY) = -1 ENOENT (No such file or directory) open("/usr/share/locale/en.utf8/LC_MESSAGES/libc.mo", O_RDONLY) = -1 ENOENT (No such file or directory) open("/usr/share/locale/en/LC_MESSAGES/libc.mo", O_RDONLY) = -1 ENOENT (No such file or directory) open("/usr/share/locale-langpack/en_US.UTF-8/LC_MESSAGES/libc.mo", O_RDONLY) = -1 ENOENT (No such file or directory) open("/usr/share/locale-langpack/en_US.utf8/LC_MESSAGES/libc.mo", O_RDONLY) = -1 ENOENT (No such file or directory) open("/usr/share/locale-langpack/en_US/LC_MESSAGES/libc.mo", O_RDONLY) = -1 ENOENT (No such file or directory) open("/usr/share/locale-langpack/en.UTF-8/LC_MESSAGES/libc.mo", O_RDONLY) = -1 ENOENT (No such file or directory) open("/usr/share/locale-langpack/en.utf8/LC_MESSAGES/libc.mo", O_RDONLY) = -1 ENOENT (No such file or directory) open("/usr/share/locale-langpack/en/LC_MESSAGES/libc.mo", O_RDONLY) = -1 ENOENT (No such file or directory) write(2, ": Bad file descriptor", 21: Bad file descriptor) = 21 write(2, "\n", 1 ) = 1 close(1) = 0 close(2) = 0 exit_group(1) = ? +++ exited with 1 +++ On Fri, Nov 25, 2016 at 3:20 PM, Paul Eggert wrote: > I see no real evidence that this is a bug in 'shuf'. It looks like a bug > in the program that calls 'shuf'. You can verify this by using 'strace > shuf' instead of plain 'shuf'. > -- Alex Ryan https://www.linkedin.com/in/alexryan