Memory usage with conda installation (on Travis) #1197
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I'd have to dig into this with memory_profiler to see what is happening. The one thing that is known to sometimes use a lot of memory is the dependency resolution algorithm, but it doesn't look like you are using the tricky parts of it (there is only one Can you reproduce this on a local machine? |
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Thanks Aaron! I kind of have the same behaviour on my desktop. These are the steps: I have repeated that twice, with consistent results:
Please note that you will need: for it to be fully reproducible on your end. Best regards, |
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I'm not able to reproduce it. How does Something you could do that might help is to run memory_profiler ( |
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Hi Aaron, Here is a nice explanation of how Here is the plot generated with memory_profiler on my Linux desktop: I have written a small Bash script: and then run Just in case this is relevant, here is an interesting article on how Python manages memory: On the other hand, I have added: to our Travis builds and the memory usage has decreased so they can now finish. Please let me know if I can try something else. Many thanks, |
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I am encountering a similar problem. The following command causes 1.3GB memory use on a Ubuntu 14.04 x64 VM: conda install -c ufechner -c janharms -c mutirri freekitesimSince the system only has 2GB, conda failed to complete the installation because it does not have enough memory to fork. Failing at a FYI: conda version 3.12.0 |
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I recently saw the same issue on a Linux VM where |
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@asmeurer, here: $ conda install -c ufechner -c janharms -c mutirri freekitesim
Fetching package metadata: ..........
Solving package specifications: ...............................
Warning: 2 possible package resolutions (only showing differing packages):
[u'freeglut-2.8.1-py27_0.tar.bz2'],
[u'freeglut-2.8.1-0.tar.bz2'],
Package plan for installation in environment /home/builder/miniconda/envs/kitesim:
The following packages will be downloaded:
package | build
---------------------------|-----------------
boost-1.55.0 | 1 13.6 MB
freetype-2.4.10 | 0 2.0 MB
jpeg-8d | 0 699 KB
lcms-1.19 | 0 595 KB
lib3ds-1.3.0 | 1 304 KB
libsodium-0.4.5 | 0 529 KB
qt-4.8.5 | 0 32.8 MB
sdl-1.2.15 | 0 2.0 MB
cairo-1.12.18 | 0 593 KB
zeromq-4.0.5 | 0 2.6 MB
cgkit-2.0.0 | py27_1 11.5 MB
distribute-0.6.45 | py27_1 517 KB
ipython-3.1.0 | py27_0 3.4 MB
pil-1.1.7 | py27_1 587 KB
pygame-patched-1.9.1 | py27_1 2.6 MB
pyopengl-py27-3.1.0b1 | py27_0 603 KB
freeglut-2.8.1 | py27_0 534 KB
pyparsing-2.0.3 | py27_0 63 KB
pytz-2015.4 | py27_0 174 KB
pyzmq-14.6.0 | py27_0 657 KB
scipy-0.15.1 | np19py27_0 37.0 MB
scons-2.3.0 | py27_0 714 KB
shiboken-1.2.1 | py27_0 883 KB
sip-4.15.5 | py27_0 243 KB
six-1.9.0 | py27_0 17 KB
dateutil-2.4.1 | py27_0 218 KB
protobuf-linux64-2.5.0 | py27_0 177 KB
pyqt-4.10.4 | py27_0 4.4 MB
pyside-1.2.1 | py27_1 5.7 MB
matplotlib-1.4.3 | np19py27_0 44.6 MB
pandas-0.16.1 | np19py27_0 10.7 MB
pyqtgraph-0.9.10 | np19py27_0 864 KB
assimulo-2.5 | np19py27_1 4.1 MB
freekitesim-0.4 | np19py27_0 2 KB
------------------------------------------------------------
Total: 185.9 MB
The following NEW packages will be INSTALLED:
assimulo: 2.5-np19py27_1
boost: 1.55.0-1
cairo: 1.12.18-0
cgkit: 2.0.0-py27_1
dateutil: 2.4.1-py27_0
distribute: 0.6.45-py27_1
enum34: 1.0.4-py27_0
freeglut: 2.8.1-py27_0
freekitesim: 0.4-np19py27_0
freetype: 2.4.10-0
funcsigs: 0.4-py27_0
ipython: 3.1.0-py27_0
jpeg: 8d-0
lcms: 1.19-0
lib3ds: 1.3.0-1
libpng: 1.5.13-1
libsodium: 0.4.5-0
llvmlite: 0.4.0-py27_0
matplotlib: 1.4.3-np19py27_0
numba: 0.18.2-np19py27_1
numpy: 1.9.2-py27_0
pandas: 0.16.1-np19py27_0
pil: 1.1.7-py27_1
pixman: 0.26.2-0
protobuf-linux64: 2.5.0-py27_0
py2cairo: 1.10.0-py27_2
pygame-patched: 1.9.1-py27_1
pyopengl-py27: 3.1.0b1-py27_0
pyparsing: 2.0.3-py27_0
pyqt: 4.10.4-py27_0
pyqtgraph: 0.9.10-np19py27_0
pyside: 1.2.1-py27_1
python-dateutil: 2.4.2-py27_0
pytz: 2015.4-py27_0
pyzmq: 14.6.0-py27_0
qt: 4.8.5-0
scipy: 0.15.1-np19py27_0
scons: 2.3.0-py27_0
sdl: 1.2.15-0
shiboken: 1.2.1-py27_0
sip: 4.15.5-py27_0
six: 1.9.0-py27_0
zeromq: 4.0.5-0
Proceed ([y]/n)? y
Fetching packages ...
boost-1.55.0-1 100% |######################################################| Time: 0:00:03 4.56 MB/s
freetype-2.4.1 100% |######################################################| Time: 0:00:00 2.89 MB/s
jpeg-8d-0.tar. 100% |######################################################| Time: 0:00:00 1.95 MB/s
lcms-1.19-0.ta 100% |######################################################| Time: 0:00:00 1.68 MB/s
lib3ds-1.3.0-1 100% |######################################################| Time: 0:00:00 1.26 MB/s
libsodium-0.4. 100% |######################################################| Time: 0:00:00 1.66 MB/s
qt-4.8.5-0.tar 100% |######################################################| Time: 0:00:10 3.21 MB/s
sdl-1.2.15-0.t 100% |######################################################| Time: 0:00:00 3.78 MB/s
cairo-1.12.18- 100% |######################################################| Time: 0:00:00 1.65 MB/s
zeromq-4.0.5-0 100% |######################################################| Time: 0:00:00 3.15 MB/s
cgkit-2.0.0-py 100% |######################################################| Time: 0:00:02 4.07 MB/s
distribute-0.6 100% |######################################################| Time: 0:00:17 30.44 kB/s
ipython-3.1.0- 100% |######################################################| Time: 0:00:01 2.79 MB/s
pil-1.1.7-py27 100% |######################################################| Time: 0:00:00 1.53 MB/s
pygame-patched 100% |######################################################| Time: 0:00:00 3.35 MB/s
pyopengl-py27- 100% |######################################################| Time: 0:00:00 1.61 MB/s
freeglut-2.8.1 100% |######################################################| Time: 0:00:00 1.52 MB/s
pyparsing-2.0. 100% |######################################################| Time: 0:00:00 528.28 kB/s
pytz-2015.4-py 100% |######################################################| Time: 0:00:04 41.64 kB/s
pyzmq-14.6.0-p 100% |######################################################| Time: 0:00:00 1.55 MB/s
scipy-0.15.1-n 100% |######################################################| Time: 0:00:10 3.75 MB/s
scons-2.3.0-py 100% |######################################################| Time: 0:00:00 966.36 kB/s
shiboken-1.2.1 100% |######################################################| Time: 0:00:00 1.83 MB/s
sip-4.15.5-py2 100% |######################################################| Time: 0:00:00 876.04 kB/s
six-1.9.0-py27 100% |######################################################| Time: 0:00:00 391.91 kB/s
dateutil-2.4.1 100% |######################################################| Time: 0:00:00 750.81 kB/s
protobuf-linux 100% |######################################################| Time: 0:00:00 1.02 MB/s
pyqt-4.10.4-py 100% |######################################################| Time: 0:00:03 1.21 MB/s
pyside-1.2.1-p 100% |######################################################| Time: 0:00:02 2.67 MB/s
matplotlib-1.4 100% |######################################################| Time: 0:00:13 3.51 MB/s
pandas-0.16.1- 100% |######################################################| Time: 0:00:03 3.13 MB/s
pyqtgraph-0.9. 100% |######################################################| Time: 0:00:00 973.30 kB/s
assimulo-2.5-n 100% |######################################################| Time: 0:00:01 3.01 MB/s
freekitesim-0. 100% |######################################################| Time: 0:00:00 1.79 MB/s
Extracting packages ...
[ COMPLETE ]|#########################################################################| 100%
Linking packages ...
An unexpected error has occurred, please consider sending the | 0%
following traceback to the conda GitHub issue tracker at:
https://github.com/conda/conda/issues
Include the output of the command 'conda info' in your report.
Traceback (most recent call last):
File "/home/builder/miniconda/envs/kitesim/bin/conda", line 5, in <module>
sys.exit(main())
File "/home/builder/miniconda/lib/python2.7/site-packages/conda/cli/main.py", line 203, in main
args_func(args, p)
File "/home/builder/miniconda/lib/python2.7/site-packages/conda/cli/main.py", line 208, in args_func
args.func(args, p)
File "/home/builder/miniconda/lib/python2.7/site-packages/conda/cli/common.py", line 609, in inner
return func(args, parser)
File "/home/builder/miniconda/lib/python2.7/site-packages/conda/cli/main_install.py", line 46, in execute
install.install(args, parser, 'install')
File "/home/builder/miniconda/lib/python2.7/site-packages/conda/cli/install.py", line 413, in install
plan.execute_actions(actions, index, verbose=not args.quiet)
File "/home/builder/miniconda/lib/python2.7/site-packages/conda/plan.py", line 531, in execute_actions
inst.execute_instructions(plan, index, verbose)
File "/home/builder/miniconda/lib/python2.7/site-packages/conda/instructions.py", line 156, in execute_instructions
cmd(state, arg)
File "/home/builder/miniconda/lib/python2.7/site-packages/conda/instructions.py", line 93, in LINK_CMD
link(state['prefix'], arg, index=state['index'])
File "/home/builder/miniconda/lib/python2.7/site-packages/conda/instructions.py", line 89, in link
install.link(pkgs_dir, prefix, dist, lt, index=index)
File "/home/builder/miniconda/lib/python2.7/site-packages/conda/install.py", line 568, in link
if not run_script(prefix, dist, 'post-link'):
File "/home/builder/miniconda/lib/python2.7/site-packages/conda/install.py", line 350, in run_script
subprocess.check_call(args, env=env)
File "/home/builder/miniconda/lib/python2.7/subprocess.py", line 535, in check_call
retcode = call(*popenargs, **kwargs)
File "/home/builder/miniconda/lib/python2.7/subprocess.py", line 522, in call
return Popen(*popenargs, **kwargs).wait()
File "/home/builder/miniconda/lib/python2.7/subprocess.py", line 710, in __init__
errread, errwrite)
File "/home/builder/miniconda/lib/python2.7/subprocess.py", line 1231, in _execute_child
self.pid = os.fork()
OSError: [Errno 12] Cannot allocate memory |
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Ah, some package has a post-link script. That explains why os.fork is used. |
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The code import logging
logging.disable(logging.NOTSET)
logging.basicConfig(level=logging.DEBUG)
from conda.cli.install import check_install
check_install(['freekitesim'], platform='linux-64', channel_urls=('ufechner', 'janharms', 'mutirri', 'defaults'), prepend=False)will reproduce this on any machine (not just Linux). If I run that on OS X I get very low memory usage (no more than 600 MB), and the memory usage drops a few times when things are garbage collected. I can maybe see it getting that big if nothing was ever garbage collected. Maybe using memory profiler to produce a memory graph from that script on Ubuntu and on OS X and comparing them would give some insight. |
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Thanks for the tip about Instruments @sklam. The issue was a @sebastian-luna-valero I noticed you are also using Python 2. Can you report back if this doesn't fix it after we release (or alternately, if Miniconda3 fixes your problems)? |
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Thanks @asmeurer I have just re-run the script above: This is the output: and this is the result: Any other suggestions? Many thanks, |
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@sebastian-luna-valero I guess your issue was something else. |
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Dear all,
We are using Travis for continuous integration. Our code base depends on a number of Python and R/Bioconductor packages that I am installing with Conda.
As you may know, Travis builds for open-source projects come with resource restrictions:
http://docs.travis-ci.com/user/ci-environment/#The-Build-Machine
namely, 3GB RAM + 1.5GB swap with 2 cores.
My problem here is with RAM usage. Our Travis builds fail due to the target system running out of memory and after some troubleshooting I have realised that the command:
consumes most of the RAM but in a non-deterministic fashion.
In a failed Travis build the amount of RAM, as reported by
free, goes from 1.2GB to 4.5GB (maximum allowed by Travis). Please see beforeconda create:https://travis-ci.org/CGATOxford/cgat/jobs/54262464#L124
and after:
https://travis-ci.org/CGATOxford/cgat/jobs/54262464#L571
This is the error reported by Travis:
https://travis-ci.org/CGATOxford/cgat/jobs/54262464#L682
In a successful Travis build the amount of RAM goes from 1.2GB to 1.8GB. Please see before
conda create:https://travis-ci.org/CGATOxford/cgat/jobs/54262465#L124
and after:
https://travis-ci.org/CGATOxford/cgat/jobs/54262465#L571
I have also found this thread:
travis-ci/travis-ci#2904
kindly asking for higher amount of resources for Travis builds but that is not going to happen soon.
I have used
conda clean --index-cachewith no success. I was wondering whether you could provide advice on this or do you think I need to ask to Travis forum instead?PS: My Conda recipes for R/Bioconductor packages are not uploaded to Git Hub yet but I am willing to do so soon, just in case anyone is interested in having them.
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