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Conda solver slowdown FAQ and recommendations #13774

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bgruening opened this Issue Feb 24, 2019 · 13 comments

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bgruening commented Feb 24, 2019

Hi all,

this issue is intended keep the community up-to-date about the recent state of the conda solver, how you can improve things, and what we are working on to make it better.

What is the problem?

Conda currently uses an SAT (boolean satisfiability) solver to figure out the correct, and hopefully working, set of packages required to construct a functional environment. This means downloading the package index, cutting down the search-space, iterating the graph, inspecting the pinnings and so on.

Conda/Bioconda is special in that we have 1000s of Python and R packages. Recently, we’ve begun adding entire Bioconductor releases, with thousands of packages. Conda supports mixed environments, like Python+R+Perl, and does not remove old packages from the index. On the one hand, this enables reproducibility in the future (Need an old version of an R package or deepTools? No problem.), on the other hand it results in an incredibly large search space for the dependency solver to traverse. So in contrast to other package managers, Conda is constantly growing and we are currently not cutting out dead wood.

So we do face a special situation in Conda. Please take this into account when considering Conda’s performance. Yes, Conda is slow and will probably never be as fast as other package managers because Conda is vastly larger and supports scientific use-cases that others do not support.
However, we are aware of this and multiple people are working on it. See our tips below.

How to improve solver performance

Conda is especially slow if R is involved. This has historical reasons, as most of the packages are in all 3 supported channels (anaconda, conda-forge, bioconda). This was our fault. However, things should improve dramatically if you install the latest version available, e.g. bioconductor-deseq2=1.22.1. We’ve learned from past issues and now pin to one particular R version. However, old packages are still around for the sake of reproducibility.

Use pins, install packages with versions. Even conda create -n foo python=3 deeptools will help. You will magically solve all your R envs by simply adding r-base=3.5.1 to your package install list.

Recommendations

A few recommendations, especially for environments with R inside:

conda install pycryptosat
conda config --set sat_solver pycryptosat
  • use --strict-channel-priority
conda config --set channel_priority strict
  • Do not use conda install use conda create
  • Use environment.yaml files where ever you can. These include exact package versions, removing much of the solver’s workload and drastically speeding things up.

* Different people from the community are trying to improve the solver or using different strategies to improve the situation. This is, and probably always be, a work in progress. Conda will grow and Anaconda and the community will improve things as we go.

cutting down the search space

Please have a look at https://github.com/regro/conda-metachannel. Conda Metachannels are work in progress but will allow users to specify the portion of the graph they care about upfront. It is very rare that users will actually need ALL of the packages in bioconda/conda-forge. Think about it like a constrained channel, only a specific set of your packages appear in this special channel. All others are not available, so you can not recreate a 3 years old environment with this channel. However, if you have this use case you can just switch back to the normal channels.

Maybe we should have this at some point for our community. The idea could be, having all recent (~2 years) packages in this space but all others still available to reproduce old envs. Start a discussion!

Bioconda is prepared

Very early on we recognised the special challenges that Conda is trying to face and we are prepared for the special use-case of long-term reproducibility - BioContainers. The containers are frozen sets of conda environments. A BioContainer is created for every Bioconda package, but you can also create your own. https://usegalaxy.eu is maintaining 1034 environments currently using BioContainers and it works well in that demanding environment.
Read more about this in our manuscript.

I recommend BioContainers for static/reproducible environments. For flexible environments we could use a metachannel in the future if we want to maintain this.

That said, I use conda on a daily basis and with the above recommendation I do not need a metachannel, as the normal conda solver is fast enough for me. However, I believe the conda community is prepared for the future.

Feedback

We would like to get feedback, benchmarks and examples do help us. What does slow mean? Considering what Conda is doing for you behind the scenes, is 30s or a minute really slow? Please provide numbers and the exact installation command.

Last but not least I would like to thank the conda-forge team, Anaconda and the
@bioconda/core team that are constantly working on all the packages and trying to keep things fast and reliable even with 100k packages.

@bgruening bgruening pinned this issue Feb 24, 2019

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msarahan commented Feb 24, 2019

Thanks for this. I'm working on a similar post for Anaconda. I'll link to this and also copy some of the suggestions here.

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chapmanb commented Feb 25, 2019

Björn and all;
This is incredible, thanks for the summary of the issues and current solutions. I'd like to explore the metachannel approach for bcbio. We're rearranging the current install and preparing to move to py3k as the default so this makes some of the updates especially slow. conda 4.6 and pycryptosat didn't make a big difference in these cases (see discussion here: bcbio/bcbio-nextgen#2676).

Is this something we want to host/do in a standard way? It might be useful for other projects as well and also would be nice to have a standard set of URLs for these channels. I'd be interested to hear if anyone else has explored this yet.

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dpryan79 commented Feb 25, 2019

We were discussing setting up a meta channel where only the last 1-2 years of packages would be included. In theory that could be setup for things like bcbio as well, though I expect that'd be done on the bcbio side (presumably after a convenient "step by step guide" was put together).

Are you using environment yaml files in bcbio to install things? I've been using them in snakePipes and it's generally worked pretty well for our rather complicated environments.

yesimon added a commit to broadinstitute/viral-ngs that referenced this issue Feb 25, 2019

yesimon added a commit to broadinstitute/viral-ngs that referenced this issue Feb 25, 2019

yesimon added a commit to broadinstitute/viral-ngs that referenced this issue Feb 25, 2019

yesimon added a commit to broadinstitute/viral-ngs that referenced this issue Feb 25, 2019

yesimon added a commit to broadinstitute/viral-ngs that referenced this issue Feb 25, 2019

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bgruening commented Feb 26, 2019

@chapmanb please let us know which exact command is slow and what means slow :)
I would like to try this, especially since 4.6.x was faster in all my tests.

Btw. are you not using environment.yaml files in bcbio? This should be super fast as the solver will not be stressed much.

gdv added a commit to gdv/dotfiles that referenced this issue Feb 27, 2019

bioconda priorities
According to bioconda/bioconda-recipes#13774
this should speed up conda resolutions

@apeltzer apeltzer referenced this issue Feb 27, 2019

Merged

Update Base to 4.6.7 conda #271

2 of 5 tasks complete
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mmiladi commented Mar 1, 2019

Hello @bioconda/core,

Is there any statistics about the popularity and usage level of the R packages, e.g. the ratio of bioconda recipes that depend on the R packages or number of downloads?

Usually simple solutions win, like the Conda itself! Wouldn't it work to simply(?) split and clone the latest version of the recipes into 2-3 new spawned channels like bioconda-R, bioconda-core, ... and halt/leave the bioconda channel for reproduciblity?

From my solo experience, bioconda has been much more about the python scripts&libs, pre-compiled C++ tools and also some perl dependencies. Also I guess hardcore R devs typically prefer sticking to R's specific packaging solutions.

tomkinsc added a commit to broadinstitute/viral-ngs that referenced this issue Mar 1, 2019

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jakevc commented Mar 4, 2019

After no resolution in an overnight conda solving fiasco, I simply removed conda-forge channel from my conda config and solved in under three minutes, creating a new environment with a package from bioconda.

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dpryan79 commented Mar 5, 2019

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jakevc commented Mar 5, 2019

conda create -n cnvkit -c bioconda cnvkit is what I was executing. As it turns out, it doesn't install the most recent version this way, so conda-forge is probably necessary to solve for the dependencies of the most recent version.

cnvkit 0.9.6a0 py36_2
---------------------
file name   : cnvkit-0.9.6a0-py36_2.tar.bz2
name        : cnvkit
version     : 0.9.6a0
build       : py36_2
build number: 2
size        : 232 KB
license     : Apache License 2.0
subdir      : linux-64
url         : https://conda.anaconda.org/bioconda/linux-64/cnvkit-0.9.6a0-py36_2.tar.bz2
md5         : 5b1130b128e862a68c16b5996999a830
timestamp   : 2019-01-30 01:34:08 UTC
dependencies:
  - bioconductor-dnacopy
  - biopython >=1.62
  - future >=0.15.2
  - matplotlib >=1.3.1
  - numpy >=1.9
  - pandas >=0.18.1
  - pyfaidx >=0.4.7
  - pysam >=0.10.0
  - python >=3.6,<3.7.0a0
  - python-dateutil >=2.5.0
  - r-base >=3.4.1
  - r-cghflasso
  - reportlab >=3.0
  - scipy >=0.15.0

With conda-forge in my channels and the following config, the solver was still running overnight:

$conda config --show
add_anaconda_token: True
add_pip_as_python_dependency: True
aggressive_update_packages:
  - ca-certificates
  - certifi
  - openssl
allow_conda_downgrades: False
allow_cycles: True
allow_non_channel_urls: False
allow_softlinks: False
always_copy: False
always_softlink: False
always_yes: None
anaconda_upload: None
auto_activate_base: True
auto_update_conda: True
bld_path:
changeps1: True
channel_alias: https://conda.anaconda.org
channel_priority: strict
channels:
  - bioconda
  - conda-forge
  - defaults
client_ssl_cert: None
client_ssl_cert_key: None
clobber: False
conda_build: {}
create_default_packages: []
croot: /home/groups/hoolock/u1/jvc/miniconda3/conda-bld
custom_channels:
  pkgs/main: https://repo.anaconda.com
  pkgs/free: https://repo.anaconda.com
  pkgs/r: https://repo.anaconda.com
  pkgs/pro: https://repo.anaconda.com
custom_multichannels:
  defaults:
    - https://repo.anaconda.com/pkgs/main
    - https://repo.anaconda.com/pkgs/free
    - https://repo.anaconda.com/pkgs/r
  local:
debug: False
default_channels:
  - https://repo.anaconda.com/pkgs/main
  - https://repo.anaconda.com/pkgs/free
  - https://repo.anaconda.com/pkgs/r
default_python: 3.6
deps_modifier: not_set
disallowed_packages: []
download_only: False
dry_run: False
enable_private_envs: False
env_prompt: ({default_env})
envs_dirs:
  - /home/groups/hoolock/u1/jvc/miniconda3/envs
  - /home/users/vancampe/.conda/envs
error_upload_url: https://conda.io/conda-post/unexpected-error
extra_safety_checks: False
force: False
force_32bit: False
force_reinstall: False
force_remove: False
ignore_pinned: False
json: False
local_repodata_ttl: 1
migrated_channel_aliases: []
migrated_custom_channels: {}
non_admin_enabled: True
notify_outdated_conda: True
offline: False
override_channels_enabled: True
path_conflict: clobber
pinned_packages: []
pip_interop_enabled: False
pkgs_dirs:
  - /home/groups/hoolock/u1/jvc/miniconda3/pkgs
  - /home/users/vancampe/.conda/pkgs
proxy_servers: {}
prune: False
quiet: False
remote_connect_timeout_secs: 9.15
remote_max_retries: 3
remote_read_timeout_secs: 60.0
report_errors: None
rollback_enabled: True
root_prefix: /home/groups/hoolock/u1/jvc/miniconda3
safety_checks: warn
sat_solver: pycryptosat
shortcuts: True
show_channel_urls: None
solver_ignore_timestamps: False
ssl_verify: True
subdir: linux-64
subdirs:
  - linux-64
  - noarch
target_prefix_override:
track_features: []
update_modifier: update_specs
use_index_cache: False
use_local: False
verbosity: 0
whitelist_channels: []
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bgruening commented Mar 5, 2019

@jakevc following the suggestions from above the following works on seconds for me: conda create -n cnvkit-r cnvkit r-base=3.5.1

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dpryan79 commented Mar 5, 2019

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PertuyF commented Mar 5, 2019

@jakevc the recommended channels order changed a few months back when using bioconda and conda-forge, could you reorder your channels as below?

channels:
  - conda-forge
  - bioconda
  - defaults
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jakevc commented Mar 5, 2019

The recommended channels order did make everything more responsive:

$time conda create -n cnvkit cnvkit
Collecting package metadata: done
Solving environment: done

## Package Plan ##

  environment location: /home/groups/hoolock/u1/jvc/miniconda3/envs/cnvkit

  added / updated specs:
    - cnvkit


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    atk-2.25.90                |    hf2eb9ee_1001         430 KB  conda-forge
    bioconductor-dnacopy-1.56.0|   r351h9ac9557_0         435 KB  bioconda
    biopython-1.73             |   py36h14c3975_0         2.5 MB  conda-forge
    bwidget-1.9.11             |                1         113 KB
    cairo-1.14.12              |    h80bd089_1005         1.4 MB  conda-forge
    cnvkit-0.9.6a0             |           py36_2         232 KB  bioconda
    curl-7.64.0                |       h646f8bb_0         143 KB  conda-forge
    gdk-pixbuf-2.36.12         |    h4f1c04b_1001         598 KB  conda-forge
    glib-2.56.2                |    had28632_1001         4.7 MB  conda-forge
    gobject-introspection-1.56.1|py36h9e29830_1001         1.3 MB  conda-forge
    gsl-2.2.1                  |blas_openblashddceaf2_6         2.1 MB  conda-forge
    gstreamer-1.12.5           |    h0cc0488_1000         3.7 MB  conda-forge
    gtk2-2.24.31               |    h5baeb44_1000         7.3 MB  conda-forge
    harfbuzz-1.9.0             |    he243708_1001         957 KB  conda-forge
    krb5-1.16.3                |    hc83ff2d_1000         1.4 MB  conda-forge
    libcurl-7.64.0             |       h01ee5af_0         586 KB  conda-forge
    libedit-3.1.20170329       |    hf8c457e_1001         172 KB  conda-forge
    libgfortran-3.0.0          |                1         281 KB  conda-forge
    libssh2-1.8.0              |    h1ad7b7a_1003         246 KB  conda-forge
    libtiff-4.0.10             |    h9022e91_1002         555 KB  conda-forge
    make-4.2.1                 |    h14c3975_2004         458 KB  conda-forge
    matplotlib-3.0.3           |           py36_0           6 KB  conda-forge
    matplotlib-base-3.0.3      |   py36h167e16e_0         6.7 MB  conda-forge
    numpy-1.16.2               |py36_blas_openblash1522bff_0         4.3 MB  conda-forge
    olefile-0.46               |             py_0          31 KB  conda-forge
    openblas-0.3.3             |    h9ac9557_1001        15.8 MB  conda-forge
    pandas-0.24.1              |   py36hf484d3e_0        11.1 MB  conda-forge
    pango-1.40.14              |    hf0c64fd_1003         532 KB  conda-forge
    pillow-5.4.1               |py36h00a061d_1000         614 KB  conda-forge
    pyfaidx-0.5.5.2            |             py_0          25 KB  bioconda
    pysam-0.15.2               |   py36h1671916_1         2.2 MB  bioconda
    qt-5.6.2                   |    hbe13537_1012        44.5 MB  conda-forge
    r-base-3.5.1               |       h391c2eb_5        37.6 MB  conda-forge
    r-cghflasso-0.2_1          |r351h9ac9557_1001         199 KB  conda-forge
    reportlab-3.5.13           |py36hbd3ef63_1000         2.4 MB  conda-forge
    samtools-1.9               |       h57cc563_7         636 KB  bioconda
    scipy-1.2.1                |py36_blas_openblash1522bff_0        18.1 MB  conda-forge
    tktable-2.10               |       h14c3975_0          88 KB
    tornado-6.0.1              |   py36h14c3975_0         635 KB  conda-forge
    zstd-1.3.3                 |                1        1023 KB  conda-forge
    ------------------------------------------------------------
                                           Total:       175.8 MB

The following NEW packages will be INSTALLED:

  _r-mutex           pkgs/r/linux-64::_r-mutex-1.0.0-anacondar_1
  atk                conda-forge/linux-64::atk-2.25.90-hf2eb9ee_1001
  bcftools           bioconda/linux-64::bcftools-1.9-h47928c2_2
  bioconductor-dnac~ bioconda/linux-64::bioconductor-dnacopy-1.56.0-r351h9ac9557_0
  biopython          conda-forge/linux-64::biopython-1.73-py36h14c3975_0
  blas               conda-forge/linux-64::blas-1.1-openblas
  bwidget            pkgs/main/linux-64::bwidget-1.9.11-1
  bzip2              conda-forge/linux-64::bzip2-1.0.6-h14c3975_1002
  ca-certificates    conda-forge/linux-64::ca-certificates-2018.11.29-ha4d7672_0
  cairo              conda-forge/linux-64::cairo-1.14.12-h80bd089_1005
  certifi            conda-forge/linux-64::certifi-2018.11.29-py36_1000
  cnvkit             bioconda/linux-64::cnvkit-0.9.6a0-py36_2
  curl               conda-forge/linux-64::curl-7.64.0-h646f8bb_0
  cycler             conda-forge/noarch::cycler-0.10.0-py_1
  dbus               conda-forge/linux-64::dbus-1.13.0-h4e0c4b3_1000
  expat              conda-forge/linux-64::expat-2.2.5-hf484d3e_1002
  fontconfig         conda-forge/linux-64::fontconfig-2.13.1-h2176d3f_1000
  freetype           conda-forge/linux-64::freetype-2.9.1-h94bbf69_1005
  future             conda-forge/linux-64::future-0.17.1-py36_1000
  gdk-pixbuf         conda-forge/linux-64::gdk-pixbuf-2.36.12-h4f1c04b_1001
  gettext            conda-forge/linux-64::gettext-0.19.8.1-h9745a5d_1001
  glib               conda-forge/linux-64::glib-2.56.2-had28632_1001
  gobject-introspec~ conda-forge/linux-64::gobject-introspection-1.56.1-py36h9e29830_1001
  graphite2          conda-forge/linux-64::graphite2-1.3.13-hf484d3e_1000
  gsl                conda-forge/linux-64::gsl-2.2.1-blas_openblashddceaf2_6
  gstreamer          conda-forge/linux-64::gstreamer-1.12.5-h0cc0488_1000
  gtk2               conda-forge/linux-64::gtk2-2.24.31-h5baeb44_1000
  harfbuzz           conda-forge/linux-64::harfbuzz-1.9.0-he243708_1001
  htslib             bioconda/linux-64::htslib-1.9-h47928c2_5
  icu                conda-forge/linux-64::icu-58.2-hf484d3e_1000
  jpeg               conda-forge/linux-64::jpeg-9c-h14c3975_1001
  kiwisolver         conda-forge/linux-64::kiwisolver-1.0.1-py36h6bb024c_1002
  krb5               conda-forge/linux-64::krb5-1.16.3-hc83ff2d_1000
  libcurl            conda-forge/linux-64::libcurl-7.64.0-h01ee5af_0
  libdeflate         bioconda/linux-64::libdeflate-1.0-h14c3975_1
  libedit            conda-forge/linux-64::libedit-3.1.20170329-hf8c457e_1001
  libffi             conda-forge/linux-64::libffi-3.2.1-hf484d3e_1005
  libgcc-ng          conda-forge/linux-64::libgcc-ng-7.3.0-hdf63c60_0
  libgfortran        conda-forge/linux-64::libgfortran-3.0.0-1
  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-7.2.0-hdf63c60_3
  libiconv           conda-forge/linux-64::libiconv-1.15-h14c3975_1004
  libpng             conda-forge/linux-64::libpng-1.6.36-h84994c4_1000
  libssh2            conda-forge/linux-64::libssh2-1.8.0-h1ad7b7a_1003
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-7.3.0-hdf63c60_0
  libtiff            conda-forge/linux-64::libtiff-4.0.10-h9022e91_1002
  libuuid            conda-forge/linux-64::libuuid-2.32.1-h14c3975_1000
  libxcb             conda-forge/linux-64::libxcb-1.13-h14c3975_1002
  libxml2            conda-forge/linux-64::libxml2-2.9.8-h143f9aa_1005
  make               conda-forge/linux-64::make-4.2.1-h14c3975_2004
  matplotlib         conda-forge/linux-64::matplotlib-3.0.3-py36_0
  matplotlib-base    conda-forge/linux-64::matplotlib-base-3.0.3-py36h167e16e_0
  ncurses            conda-forge/linux-64::ncurses-6.1-hf484d3e_1002
  numpy              conda-forge/linux-64::numpy-1.16.2-py36_blas_openblash1522bff_0
  olefile            conda-forge/noarch::olefile-0.46-py_0
  openblas           conda-forge/linux-64::openblas-0.3.3-h9ac9557_1001
  openssl            conda-forge/linux-64::openssl-1.0.2r-h14c3975_0
  pandas             conda-forge/linux-64::pandas-0.24.1-py36hf484d3e_0
  pango              conda-forge/linux-64::pango-1.40.14-hf0c64fd_1003
  pcre               conda-forge/linux-64::pcre-8.41-hf484d3e_1003
  pillow             conda-forge/linux-64::pillow-5.4.1-py36h00a061d_1000
  pip                conda-forge/linux-64::pip-19.0.3-py36_0
  pixman             conda-forge/linux-64::pixman-0.34.0-h14c3975_1003
  pthread-stubs      conda-forge/linux-64::pthread-stubs-0.4-h14c3975_1001
  pyfaidx            bioconda/noarch::pyfaidx-0.5.5.2-py_0
  pyparsing          conda-forge/noarch::pyparsing-2.3.1-py_0
  pyqt               conda-forge/linux-64::pyqt-5.6.0-py36h13b7fb3_1008
  pysam              bioconda/linux-64::pysam-0.15.2-py36h1671916_1
  python             conda-forge/linux-64::python-3.6.7-hd21baee_1002
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.0-py_0
  pytz               conda-forge/noarch::pytz-2018.9-py_0
  qt                 conda-forge/linux-64::qt-5.6.2-hbe13537_1012
  r-base             conda-forge/linux-64::r-base-3.5.1-h391c2eb_5
  r-cghflasso        conda-forge/linux-64::r-cghflasso-0.2_1-r351h9ac9557_1001
  readline           conda-forge/linux-64::readline-7.0-hf8c457e_1001
  reportlab          conda-forge/linux-64::reportlab-3.5.13-py36hbd3ef63_1000
  samtools           bioconda/linux-64::samtools-1.9-h57cc563_7
  scipy              conda-forge/linux-64::scipy-1.2.1-py36_blas_openblash1522bff_0
  setuptools         conda-forge/linux-64::setuptools-40.8.0-py36_0
  sip                conda-forge/linux-64::sip-4.18.1-py36hf484d3e_1000
  six                conda-forge/linux-64::six-1.12.0-py36_1000
  sqlite             conda-forge/linux-64::sqlite-3.26.0-h67949de_1000
  tk                 conda-forge/linux-64::tk-8.6.9-h84994c4_1000
  tktable            pkgs/main/linux-64::tktable-2.10-h14c3975_0
  tornado            conda-forge/linux-64::tornado-6.0.1-py36h14c3975_0
  wheel              conda-forge/linux-64::wheel-0.33.1-py36_0
  xorg-kbproto       conda-forge/linux-64::xorg-kbproto-1.0.7-h14c3975_1002
  xorg-libice        conda-forge/linux-64::xorg-libice-1.0.9-h14c3975_1004
  xorg-libsm         conda-forge/linux-64::xorg-libsm-1.2.3-h4937e3b_1000
  xorg-libx11        conda-forge/linux-64::xorg-libx11-1.6.7-h14c3975_1000
  xorg-libxau        conda-forge/linux-64::xorg-libxau-1.0.9-h14c3975_0
  xorg-libxdmcp      conda-forge/linux-64::xorg-libxdmcp-1.1.2-h14c3975_1007
  xorg-libxext       conda-forge/linux-64::xorg-libxext-1.3.3-h14c3975_1004
  xorg-libxrender    conda-forge/linux-64::xorg-libxrender-0.9.10-h14c3975_1002
  xorg-libxt         conda-forge/linux-64::xorg-libxt-1.1.5-h14c3975_1002
  xorg-renderproto   conda-forge/linux-64::xorg-renderproto-0.11.1-h14c3975_1002
  xorg-xextproto     conda-forge/linux-64::xorg-xextproto-7.3.0-h14c3975_1002
  xorg-xproto        conda-forge/linux-64::xorg-xproto-7.0.31-h14c3975_1007
  xz                 conda-forge/linux-64::xz-5.2.4-h14c3975_1001
  zlib               conda-forge/linux-64::zlib-1.2.11-h14c3975_1004
  zstd               conda-forge/linux-64::zstd-1.3.3-1


Proceed ([y]/n)? y

.
.
.

done
#
# To activate this environment, use:
# > source activate cnvkit
#
# To deactivate an active environment, use:
# > source deactivate
#


real	3m4.988s
user	1m35.123s
sys	0m15.064s
@ctb

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ctb commented Mar 12, 2019

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