convert h.264 avi container to mp4 with ffmpeg

I'd like to convert my h.264 avi container to a mp4 container with ffmpeg. I've found this works:

./ffmpeg -i myfile.avi -vcodec copy myfile.mp4
ffmpeg version N-51169-gcedf276 Copyright (c) 2000-2013 the FFmpeg developers
  built on Mar 21 2013 05:12:00 with gcc 4.6 (Debian 4.6.3-1)
  configuration: --prefix=/root/ffmpeg-static/32bit --arch=x86_32 --extra-cflags='-m32 -I/root/ffmpeg-static/32bit/include -static' --extra-ldflags='-m32 -L/root/ffmpeg-static/32bit/lib -static' --extra-libs='-lxml2 -lexpat -lfreetype' --enable-static --disable-shared --disable-ffserver --disable-doc --enable-bzlib --enable-zlib --enable-postproc --enable-runtime-cpudetect --enable-libx264 --enable-gpl --enable-libtheora --enable-libvorbis --enable-libmp3lame --enable-gray --enable-libass --enable-libfreetype --enable-libopenjpeg --enable-libspeex --enable-libvo-aacenc --enable-libvo-amrwbenc --enable-version3 --enable-libvpx
  libavutil      52. 22.100 / 52. 22.100
  libavcodec     55.  1.100 / 55.  1.100
  libavformat    55.  0.100 / 55.  0.100
  libavdevice    55.  0.100 / 55.  0.100
  libavfilter     3. 48.100 /  3. 48.100
  libswscale      2.  2.100 /  2.  2.100
  libswresample   0. 17.102 /  0. 17.102
  libpostproc    52.  2.100 / 52.  2.100
[avi @ 0x9fff660] non-interleaved AVI
Guessed Channel Layout for  Input Stream #0.1 : mono
Input #0, avi, from 'myfile.avi':
  Metadata:
    encoder         : Lavf52.64.2
  Duration: 00:00:10.40, start: 0.000000, bitrate: 409 kb/s
    Stream #0:0: Video: h264 (Baseline) (H264 / 0x34363248), yuvj420p, 640x480, 10 fps, 10 tbr, 10 tbn, 30 tbc
    Stream #0:1: Audio: pcm_s16le ([1][0][0][0] / 0x0001), 8000 Hz, mono, s16, 128 kb/s
Output #0, mp4, to 'myfile.mp4':
  Metadata:
    encoder         : Lavf55.0.100
    Stream #0:0: Video: h264 ([33][0][0][0] / 0x0021), yuvj420p, 640x480, q=2-31, 10 fps, 10240 tbn, 10 tbc
    Stream #0:1: Audio: aac ([64][0][0][0] / 0x0040), 8000 Hz, mono, s16, 128 kb/s
Stream mapping:
  Stream #0:0 -> #0:0 (copy)
  Stream #0:1 -> #0:1 (pcm_s16le -> libvo_aacenc)
Press [q] to stop, [?] for help
[mp4 @ 0xa006ea0] pts has no value
    Last message repeated 100 times
frame=  101 fps=0.0 q=-1.0 Lsize=     350kB time=00:00:11.06 bitrate= 259.3kbits/s
video:332kB audio:15kB subtitle:0 global headers:0kB muxing overhead 0.926809%

This generates a file that I can play with the HTML5 video player but for legacy browsers I'd like to use a flash player (Flowplayer). The file doesn't play with Flowplayer, in fact it causes it to crash.

However if I use:

./ffmpeg -i myfile.avi myfile2.mp4
ffmpeg version N-51169-gcedf276 Copyright (c) 2000-2013 the FFmpeg developers
  built on Mar 21 2013 05:12:00 with gcc 4.6 (Debian 4.6.3-1)
  configuration: --prefix=/root/ffmpeg-static/32bit --arch=x86_32 --extra-cflags='-m32 -I/root/ffmpeg-static/32bit/include -static' --extra-ldflags='-m32 -L/root/ffmpeg-static/32bit/lib -static' --extra-libs='-lxml2 -lexpat -lfreetype' --enable-static --disable-shared --disable-ffserver --disable-doc --enable-bzlib --enable-zlib --enable-postproc --enable-runtime-cpudetect --enable-libx264 --enable-gpl --enable-libtheora --enable-libvorbis --enable-libmp3lame --enable-gray --enable-libass --enable-libfreetype --enable-libopenjpeg --enable-libspeex --enable-libvo-aacenc --enable-libvo-amrwbenc --enable-version3 --enable-libvpx
  libavutil      52. 22.100 / 52. 22.100
  libavcodec     55.  1.100 / 55.  1.100
  libavformat    55.  0.100 / 55.  0.100
  libavdevice    55.  0.100 / 55.  0.100
  libavfilter     3. 48.100 /  3. 48.100
  libswscale      2.  2.100 /  2.  2.100
  libswresample   0. 17.102 /  0. 17.102
  libpostproc    52.  2.100 / 52.  2.100
[avi @ 0x9b02660] non-interleaved AVI
Guessed Channel Layout for  Input Stream #0.1 : mono
Input #0, avi, from 'myfile.avi':
  Metadata:
    encoder         : Lavf52.64.2
  Duration: 00:00:10.40, start: 0.000000, bitrate: 409 kb/s
    Stream #0:0: Video: h264 (Baseline) (H264 / 0x34363248), yuvj420p, 640x480, 10 fps, 10 tbr, 10 tbn, 30 tbc
    Stream #0:1: Audio: pcm_s16le ([1][0][0][0] / 0x0001), 8000 Hz, mono, s16, 128 kb/s
No pixel format specified, yuvj420p for H.264 encoding chosen.
Use -pix_fmt yuv420p for compatibility with outdated media players.
[libx264 @ 0x9b065a0] using cpu capabilities: MMX2 SSE2Fast SSSE3 FastShuffle SSE4.1 Cache64
[libx264 @ 0x9b065a0] profile High, level 2.2
[libx264 @ 0x9b065a0] 264 - core 129 r2230 1cffe9f - H.264/MPEG-4 AVC codec - Copyleft 2003-2012 - http://www.videolan.org/x264.html - options: cabac=1 ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=1 lookahead_threads=1 sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0 constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1 weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=10 scenecut=40 intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=23.0 qcomp=0.60 qpmin=0 qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
Output #0, mp4, to 'myfile2.mp4':
  Metadata:
    encoder         : Lavf55.0.100
    Stream #0:0: Video: h264 ([33][0][0][0] / 0x0021), yuvj420p, 640x480, q=-1--1, 10240 tbn, 10 tbc
    Stream #0:1: Audio: aac ([64][0][0][0] / 0x0040), 8000 Hz, mono, s16, 128 kb/s
Stream mapping:
  Stream #0:0 -> #0:0 (h264 -> libx264)
  Stream #0:1 -> #0:1 (pcm_s16le -> libvo_aacenc)
Press [q] to stop, [?] for help
frame=   47 fps=0.0 q=25.0 size=      21kB time=00:00:04.40 bitrate=  39.9kbits/s dup=3 dropframe=   59 fps= 56 q=25.0 size=      56kB time=00:00:05.68 bitrate=  80.2kbits/s dup=3 dropframe=   71 fps= 45 q=25.0 size=      89kB time=00:00:06.84 bitrate= 106.9kbits/s dup=3 dropframe=   83 fps= 40 q=25.0 size=     124kB time=00:00:08.12 bitrate= 124.9kbits/s dup=3 dropframe=   94 fps= 36 q=25.0 size=     157kB time=00:00:09.14 bitrate= 140.4kbits/s dup=4 dropframe=  105 fps= 23 q=25.0 Lsize=     309kB time=00:00:11.06 bitrate= 228.8kbits/s dup=4 drop=0
video:291kB audio:15kB subtitle:0 global headers:0kB muxing overhead 1.108651%
[libx264 @ 0x9b065a0] frame I:1     Avg QP:17.65  size: 12772
[libx264 @ 0x9b065a0] frame P:94    Avg QP:19.46  size:  2868
[libx264 @ 0x9b065a0] frame B:10    Avg QP:21.58  size:  1464
[libx264 @ 0x9b065a0] consecutive B-frames: 82.9% 13.3%  0.0%  3.8%
[libx264 @ 0x9b065a0] mb I  I16..4: 16.6% 66.3% 17.1%
[libx264 @ 0x9b065a0] mb P  I16..4:  4.2%  6.3%  0.5%  P16..4: 27.0%  9.5%  5.1%  0.0%  0.0%    skip:47.4%
[libx264 @ 0x9b065a0] mb B  I16..4:  0.8%  1.0%  0.0%  B16..8: 39.1%  4.6%  0.5%  direct: 2.4%  skip:51.7%  L0:39.8% L1:56.4% BI: 3.9%
[libx264 @ 0x9b065a0] 8x8 transform intra:58.0% inter:74.7%
[libx264 @ 0x9b065a0] coded y,uvDC,uvAC intra: 47.3% 0.0% 0.0% inter: 16.6% 0.0% 0.0%
[libx264 @ 0x9b065a0] i16 v,h,dc,p: 29% 19% 10% 42%
[libx264 @ 0x9b065a0] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 31% 21% 29%  2%  3%  4%  4%  3%  3%
[libx264 @ 0x9b065a0] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 39% 28% 18%  2%  3%  3%  3%  2%  2%
[libx264 @ 0x9b065a0] i8c dc,h,v,p: 100%  0%  0%  0%
[libx264 @ 0x9b065a0] Weighted P-Frames: Y:5.3% UV:0.0%
[libx264 @ 0x9b065a0] ref P L0: 67.9% 12.0% 12.6%  6.8%  0.6%
[libx264 @ 0x9b065a0] ref B L0: 76.9% 23.1%
[libx264 @ 0x9b065a0] ref B L1: 99.7%  0.3%
[libx264 @ 0x9b065a0] kb/s:226.31

This works great. But the timing is quite different not to mention CPU cycles. The first command is measured in milli-secs while the second can take quite some time (~5-40secs).

Is there another way I can convert the avi to a mp4 container quickly? Ideally by re-muxing as opposed to re-encoding.

EDIT

I'm using this right now which I find to be the fastest for re-encoding. But again I'd rather not do this. I just want to re-mux the code.

ffmpeg -loglevel quiet -i myfile.avi -vcodec libx264 -profile:v baseline -preset ultrafast myfile.mp4

I wouldn't have done it differently than you already did. I tried to remux the file with ffmpeg-1.2 on OS X 10.7:

ffmpeg --info
ffmpeg version 1.2 Copyright (c) 2000-2013 the FFmpeg developers
  built on Apr  8 2013 02:39:03 with Apple LLVM version 4.2 (clang-425.0.27) (based on LLVM 3.2svn)

I tried your commands and explicitly

ffmpeg -i myfile.avi -vcodec copy -acodec copy out.mp4

But I always got the following errors:

ffmpeg -i myfile.avi -vcodec copy -acodec copy out.mp4
ffmpeg version 1.2 Copyright (c) 2000-2013 the FFmpeg developers
  built on Apr  8 2013 02:39:03 with Apple LLVM version 4.2 (clang-425.0.27) (based on LLVM 3.2svn)
  configuration: --prefix=/usr/local/Cellar/ffmpeg/1.2 --enable-shared --enable-pthreads --enable-gpl --enable-version3 --enable-nonfree --enable-hardcoded-tables --enable-avresample --enable-vda --cc=cc --host-cflags= --host-ldflags= --enable-libx264 --enable-libfaac --enable-libmp3lame --enable-libxvid
  libavutil      52. 18.100 / 52. 18.100
  libavcodec     54. 92.100 / 54. 92.100
  libavformat    54. 63.104 / 54. 63.104
  libavdevice    54.  3.103 / 54.  3.103
  libavfilter     3. 42.103 /  3. 42.103
  libswscale      2.  2.100 /  2.  2.100
  libswresample   0. 17.102 /  0. 17.102
  libpostproc    52.  2.100 / 52.  2.100
[avi @ 0x7f9ef981ae00] non-interleaved AVI
Guessed Channel Layout for  Input Stream #0.1 : mono
Input #0, avi, from 'myfile.avi':
  Metadata:
    encoder         : Lavf52.64.2
  Duration: 00:00:10.40, start: 0.000000, bitrate: 409 kb/s
    Stream #0:0: Video: h264 (Baseline) (H264 / 0x34363248), yuvj420p, 640x480, 10 fps, 10 tbr, 10 tbn, 30 tbc
    Stream #0:1: Audio: pcm_s16le ([1][0][0][0] / 0x0001), 8000 Hz, mono, s16, 128 kb/s
[mp4 @ 0x7f9ef991ac00] Tag [1][0][0][0]/0x00000001 incompatible with output codec id '65536' ([0][0][0][0])
Output #0, mp4, to 'out.mp4':
  Metadata:
    encoder         : Lavf52.64.2
    Stream #0:0: Video: h264 ([33][0][0][0] / 0x0021), yuvj420p, 640x480, q=2-31, 10 fps, 90k tbn, 10 tbc
    Stream #0:1: Audio: pcm_s16le ([1][0][0][0] / 0x0001), 8000 Hz, mono, 128 kb/s
Stream mapping:
  Stream #0:0 -> #0:0 (copy)
  Stream #0:1 -> #0:1 (copy)
Could not write header for output file #0 (incorrect codec parameters ?): Invalid data found when processing input

So I did a quick research for the error number and found out pcm_s16le isn't compatible with mp4. See this bug report on the ffmpeg tracker.

This would possibly explain the different results with both of your commands - although it's strange that it did not yield an error in your case (old ffmpeg snapshot?).

So I guess the solution could/would be to provide a different audio codec from the beginning or to convert the audio track to a different codec. As a quick test I tried:

ffmpeg -i myfile.avi -vcodec copy -acodec mp2 out.mp4

The output file was written immediately to disk - no errors were yielded. Unfortunately I don't have the possibility to verify the result with a flash player.