I've got 10k+ files totaling over 20GB that I need to concatenate into one file.
Is there a faster way than
cat input_file* >> out
?
The preferred way would be a bash command, Python is acceptable too if not considerably slower.
2 Answers
Nope, cat is surely the best way to do this. Why use python when there is a program already written in C for this purpose? However, you might want to consider using xargs in case the command line length exceeds ARG_MAX and you need more than one cat. Using GNU tools, this is equivalent to what you already have:
find . -maxdepth 1 -type f -name 'input_file*' -print0 |
sort -z |
xargs -0 cat -- >>out
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1
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1Yes, because the output of
findis piped throughsort. Without this, the files would be listed in an arbitrary order (defined by the file system, which could be file creation order).– scaiMar 5, 2014 at 13:43 -
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1@Kiwy, the only case I can see is if the locale isn't properly set in the environment, then sort might behave differently from a
bashglob. Otherwise I don't see any cases wherexargsorcatwould not behave as expected.– GraemeMar 5, 2014 at 14:05 -
3@MarcvanLeeuwen,
xargswill call as maycatas is necessary to avoid an E2BIG error of execve(2). Mar 6, 2014 at 9:41
Allocating the space for the output file first may improve the overall speed as the system won't have to update the allocation for every write.
For instance, if on Linux:
size=$({ find . -maxdepth 1 -type f -name 'input_file*' -printf '%s+'; echo 0;} | bc)
fallocate -l "$size" out &&
find . -maxdepth 1 -type f -name 'input_file*' -print0 |
sort -z | xargs -r0 cat 1<> out
Another benefit is that if there's not enough free space, the copy will not be attempted.
If on btrfs, you could copy --reflink=always the first file (which implies no data copy and would therefore be almost instantaneous), and append the rest. If there are 10000 files, that probably won't make much difference though unless the first file is very big.
There's an API to generalise that to ref-copy all the files (the BTRFS_IOC_CLONE_RANGE ioctl), but I could not find any utility exposing that API, so you'd have to do it in C (or python or other languages provided they can call arbitrary ioctls).
If the source files are sparse or have large sequences of NUL characters, you could make a sparse output file (saving time and disk space) with (on GNU systems):
find . -maxdepth 1 -type f -name 'input_file*' -print0 |
sort -z | xargs -r0 cat | cp --sparse=always /dev/stdin out
answered Mar 5, 2014 at 14:57
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1@XTian, no, it should be neither
>nor>>, but1<>as I said to write into the file. Mar 5, 2014 at 16:41 -
5@grebneke,
<>is the standard Bourne/POSIX read+write redirection operator. See your shell manual or the POSIX spec for details. The defaultfdis0for the<>operator (<>is short for0<>, like<is short for0<and>short for1>), so you need the1to explicitly redirect stdout. Here, it's not so much that we need read+write (O_RDWR), but that we don't wantO_TRUNC(as in>) which would deallocate what we've just allocated. Mar 5, 2014 at 20:30 -
1@grebneke, unix.stackexchange.com/search?q=user%3A22565+%22%3C%3E%22 will give you a few. ksh93 has seek operators BTW, and you can seek forward with
ddor via reading. Mar 5, 2014 at 21:15 -
1@StephaneChazelas - thanks a lot, your help and knowledge is deeply appreciated!– grebnekeMar 5, 2014 at 21:19
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1I'm not convinced that there will be many cases where
fallocatewill negate the overhead of the extrafind, even though it will be faster the second time round.btrfscertainly opens up some interesting possibilities though.– GraemeMar 6, 2014 at 1:28
finddoes not sort files the same as a shell glob.outis located on another disk.