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Test conda environments on HPC batch scheduler
Raw
README.md

test-conda-env-hpc

Question

Does the conda environment that you have activated on the login node also get used in the compute nodes when submitting a job?

Methods

  • Used conda version 4.6.14
  1. Activate a conda env with snakemake installed.
    1. Submit the job & note the job id.
    2. The log file should have snakemake output.
  2. Activate a conda env without snakemake.
    1. Submit the job & note the job id.
    2. The log file should have an error message that the snakemake command was not found.

SLURM

  • HPC: beta-login.stage.arc-ts.umich.edu
  • Script: submit-slurm.sh
  • Conda environments:
    • With snakemake: slurm-with-smk.yaml
    • Without snakemake: slurm-no-smk.yaml

PBS-Torque

  • HPC: flux-login.arc-ts.umich.edu
  • Script: submit-pbs.sh
  • Conda environments:
    • With snakemake: pbs-with-smk.yaml
    • Without snakemake: pbs-no-smk.yaml

Results

SLURM job with snakemake: 33069

Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
	count	jobs
		1	touch
		1

[Mon Jun  3 14:06:20 2019]
rule touch:
	output: file.txt
	jobid: 0

[Mon Jun  3 14:06:20 2019]
Finished job 0.
1 of 1 steps (100%) done
Complete log: /home/sovacool/test-conda-env/.snakemake/log/2019-06-03T140620.029171.snakemake.log

SLURM job without snakemake: 33070

Conda environment: slurm-no-smk.yaml

/var/spool/slurmd.spool/job33070/slurm_script: line 49: snakemake: command not found

PBS job with snakemake: 33732423

nyx5568
/home/sovacool/test-conda-env-hpc
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
	count	jobs
	1	touch
	1

[Wed Jun  5 11:01:27 2019]
rule touch:
    output: file.txt
    jobid: 0

[Wed Jun  5 11:01:27 2019]
Finished job 0.
1 of 1 steps (100%) done
Complete log: /home/sovacool/test-conda-env-hpc/.snakemake/log/2019-06-05T110127.477703.snakemake.log

PBS job without snakemake: 33732416

nyx5089
/home/sovacool/test-conda-env-hpc
/var/spool/torque/mom_priv/jobs/33732416.nyx.arc-ts.umich.edu.SC: line 21: snakemake: command not found

Conclusion

Yes!

Raw
pbs-no-smk.yaml
name: base
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- _ipyw_jlab_nb_ext_conf=0.1.0=py37_0
- alabaster=0.7.11=py37_0
- anaconda=custom=py37_0
- anaconda-client=1.7.2=py37_0
- anaconda-navigator=1.9.2=py37_0
- anaconda-project=0.8.2=py37_0
- appdirs=1.4.3=py37h28b3542_0
- asn1crypto=0.24.0=py37_0
- astroid=2.0.4=py37_0
- astropy=3.0.4=py37h14c3975_0
- atomicwrites=1.2.1=py37_0
- attrs=18.2.0=py37h28b3542_0
- automat=0.7.0=py37_0
- babel=2.6.0=py37_0
- backcall=0.1.0=py37_0
- backports=1.0=py37_1
- backports.shutil_get_terminal_size=1.0.0=py37_2
- beautifulsoup4=4.6.3=py37_0
- bitarray=0.8.3=py37h14c3975_0
- bkcharts=0.2=py37_0
- blas=1.0=mkl
- blaze=0.11.3=py37_0
- bleach=2.1.4=py37_0
- blosc=1.14.4=hdbcaa40_0
- bokeh=0.13.0=py37_0
- boto=2.49.0=py37_0
- bottleneck=1.2.1=py37h035aef0_1
- bzip2=1.0.6=h14c3975_5
- ca-certificates=2019.5.15=0
- cairo=1.14.12=h8948797_3
- certifi=2019.3.9=py37_0
- cffi=1.11.5=py37he75722e_1
- chardet=3.0.4=py37_1
- click=6.7=py37_0
- cloudpickle=0.5.5=py37_0
- clyent=1.2.2=py37_1
- colorama=0.3.9=py37_0
- conda=4.6.14=py37_0
- conda-build=3.15.1=py37_0
- conda-env=2.6.0=1
- constantly=15.1.0=py37h28b3542_0
- contextlib2=0.5.5=py37_0
- cryptography=2.6.1=py37h1ba5d50_0
- curl=7.64.1=hbc83047_0
- cycler=0.10.0=py37_0
- cython=0.28.5=py37hf484d3e_0
- cytoolz=0.9.0.1=py37h14c3975_1
- dask=0.19.1=py37_0
- dask-core=0.19.1=py37_0
- datashape=0.5.4=py37_1
- dbus=1.13.2=h714fa37_1
- decorator=4.3.0=py37_0
- defusedxml=0.5.0=py37_1
- distributed=1.23.1=py37_0
- docutils=0.14=py37_0
- entrypoints=0.2.3=py37_2
- et_xmlfile=1.0.1=py37_0
- expat=2.2.6=he6710b0_0
- fastcache=1.0.2=py37h14c3975_2
- filelock=3.0.8=py37_0
- flask=1.0.2=py37_1
- flask-cors=3.0.6=py37_0
- fontconfig=2.13.0=h9420a91_0
- freetype=2.9.1=h8a8886c_1
- fribidi=1.0.5=h7b6447c_0
- get_terminal_size=1.0.0=haa9412d_0
- gevent=1.3.6=py37h7b6447c_0
- glib=2.56.2=hd408876_0
- glob2=0.6=py37_0
- gmp=6.1.2=h6c8ec71_1
- gmpy2=2.0.8=py37h10f8cd9_2
- graphite2=1.3.12=h23475e2_2
- greenlet=0.4.15=py37h7b6447c_0
- gst-plugins-base=1.14.0=hbbd80ab_1
- gstreamer=1.14.0=hb453b48_1
- h5py=2.8.0=py37h989c5e5_3
- harfbuzz=1.8.8=hffaf4a1_0
- hdf5=1.10.2=hba1933b_1
- heapdict=1.0.0=py37_2
- html5lib=1.0.1=py37_0
- hyperlink=18.0.0=py37_0
- icu=58.2=h9c2bf20_1
- idna=2.7=py37_0
- imageio=2.4.1=py37_0
- imagesize=1.1.0=py37_0
- incremental=17.5.0=py37_0
- intel-openmp=2019.0=118
- ipykernel=4.9.0=py37_1
- ipython=6.5.0=py37_0
- ipython_genutils=0.2.0=py37_0
- ipywidgets=7.4.1=py37_0
- isort=4.3.4=py37_0
- itsdangerous=0.24=py37_1
- jbig=2.1=hdba287a_0
- jdcal=1.4=py37_0
- jedi=0.12.1=py37_0
- jeepney=0.3.1=py37_0
- jinja2=2.10=py37_0
- jpeg=9b=h024ee3a_2
- jsonschema=2.6.0=py37_0
- jupyter=1.0.0=py37_7
- jupyter_client=5.2.3=py37_0
- jupyter_console=5.2.0=py37_1
- jupyter_core=4.4.0=py37_0
- jupyterlab=0.34.9=py37_0
- jupyterlab_launcher=0.13.1=py37_0
- keyring=13.2.1=py37_0
- kiwisolver=1.0.1=py37hf484d3e_0
- krb5=1.16.1=h173b8e3_7
- lazy-object-proxy=1.3.1=py37h14c3975_2
- libcurl=7.64.1=h20c2e04_0
- libedit=3.1.20170329=h6b74fdf_2
- libffi=3.2.1=hd88cf55_4
- libgcc-ng=8.2.0=hdf63c60_1
- libgfortran-ng=7.3.0=hdf63c60_0
- libpng=1.6.37=hbc83047_0
- libsodium=1.0.16=h1bed415_0
- libssh2=1.8.2=h1ba5d50_0
- libstdcxx-ng=8.2.0=hdf63c60_1
- libtiff=4.0.9=he85c1e1_2
- libtool=2.4.6=h544aabb_3
- libuuid=1.0.3=h1bed415_2
- libxcb=1.13=h1bed415_1
- libxml2=2.9.8=h26e45fe_1
- libxslt=1.1.32=h1312cb7_0
- llvmlite=0.24.0=py37hdbcaa40_0
- locket=0.2.0=py37_1
- lxml=4.2.5=py37hefd8a0e_0
- lzo=2.10=h49e0be7_2
- markupsafe=1.0=py37h14c3975_1
- matplotlib=2.2.3=py37hb69df0a_0
- mccabe=0.6.1=py37_1
- mistune=0.8.3=py37h14c3975_1
- mkl=2019.0=118
- mkl-service=1.1.2=py37h90e4bf4_5
- mkl_fft=1.0.4=py37h4414c95_1
- mkl_random=1.0.1=py37h4414c95_1
- more-itertools=4.3.0=py37_0
- mpc=1.1.0=h10f8cd9_1
- mpfr=4.0.1=hdf1c602_3
- mpmath=1.0.0=py37_2
- msgpack-python=0.5.6=py37h6bb024c_1
- multipledispatch=0.6.0=py37_0
- navigator-updater=0.2.1=py37_0
- nbconvert=5.4.0=py37_1
- nbformat=4.4.0=py37_0
- ncurses=6.1=hf484d3e_0
- networkx=2.1=py37_0
- nltk=3.3.0=py37_0
- nose=1.3.7=py37_2
- notebook=5.6.0=py37_0
- numba=0.39.0=py37h04863e7_0
- numexpr=2.6.8=py37hd89afb7_0
- numpy=1.15.1=py37h1d66e8a_0
- numpy-base=1.15.1=py37h81de0dd_0
- numpydoc=0.8.0=py37_0
- odo=0.5.1=py37_0
- olefile=0.46=py37_0
- openpyxl=2.5.6=py37_0
- openssl=1.1.1c=h7b6447c_1
- packaging=17.1=py37_0
- pandas=0.23.4=py37h04863e7_0
- pandoc=1.19.2.1=hea2e7c5_1
- pandocfilters=1.4.2=py37_1
- pango=1.42.4=h049681c_0
- parso=0.3.1=py37_0
- partd=0.3.8=py37_0
- patchelf=0.9=hf484d3e_2
- path.py=11.1.0=py37_0
- pathlib2=2.3.2=py37_0
- patsy=0.5.0=py37_0
- pcre=8.42=h439df22_0
- pep8=1.7.1=py37_0
- pexpect=4.6.0=py37_0
- pickleshare=0.7.4=py37_0
- pillow=5.2.0=py37heded4f4_0
- pip=10.0.1=py37_0
- pixman=0.34.0=hceecf20_3
- pkginfo=1.4.2=py37_1
- pluggy=0.7.1=py37h28b3542_0
- ply=3.11=py37_0
- prometheus_client=0.3.1=py37h28b3542_0
- prompt_toolkit=1.0.15=py37_0
- psutil=5.4.7=py37h14c3975_0
- ptyprocess=0.6.0=py37_0
- py=1.6.0=py37_0
- pyasn1=0.4.4=py37h28b3542_0
- pyasn1-modules=0.2.2=py37_0
- pycodestyle=2.4.0=py37_0
- pycosat=0.6.3=py37h14c3975_0
- pycparser=2.18=py37_1
- pycrypto=2.6.1=py37h14c3975_9
- pycurl=7.43.0.2=py37h1ba5d50_0
- pyflakes=2.0.0=py37_0
- pygments=2.2.0=py37_0
- pylint=2.1.1=py37_0
- pyodbc=4.0.24=py37he6710b0_0
- pyopenssl=18.0.0=py37_0
- pyparsing=2.2.0=py37_1
- pyqt=5.9.2=py37h05f1152_2
- pysocks=1.6.8=py37_0
- pytables=3.4.4=py37ha205bf6_0
- pytest=3.8.0=py37_0
- pytest-arraydiff=0.2=py37h39e3cac_0
- pytest-astropy=0.4.0=py37_0
- pytest-doctestplus=0.1.3=py37_0
- pytest-openfiles=0.3.0=py37_0
- pytest-remotedata=0.3.0=py37_0
- python=3.7.2=h0371630_0
- python-dateutil=2.7.3=py37_0
- pytz=2018.5=py37_0
- pywavelets=1.0.0=py37hdd07704_0
- pyyaml=3.13=py37h14c3975_0
- pyzmq=17.1.2=py37h14c3975_0
- qt=5.9.7=h5867ecd_1
- qtawesome=0.4.4=py37_0
- qtconsole=4.4.1=py37_0
- qtpy=1.5.0=py37_0
- readline=7.0=h7b6447c_5
- requests=2.19.1=py37_0
- rope=0.11.0=py37_0
- ruamel_yaml=0.15.46=py37h14c3975_0
- scikit-image=0.14.0=py37hf484d3e_1
- scikit-learn=0.19.2=py37h4989274_0
- scipy=1.1.0=py37hfa4b5c9_1
- seaborn=0.9.0=py37_0
- secretstorage=3.1.0=py37_0
- send2trash=1.5.0=py37_0
- service_identity=17.0.0=py37h28b3542_0
- setuptools=40.2.0=py37_0
- simplegeneric=0.8.1=py37_2
- singledispatch=3.4.0.3=py37_0
- sip=4.19.8=py37hf484d3e_0
- six=1.11.0=py37_1
- snappy=1.1.7=hbae5bb6_3
- snowballstemmer=1.2.1=py37_0
- sortedcollections=1.0.1=py37_0
- sortedcontainers=2.0.5=py37_0
- sphinx=1.7.9=py37_0
- sphinxcontrib=1.0=py37_1
- sphinxcontrib-websupport=1.1.0=py37_1
- spyder=3.3.1=py37_1
- spyder-kernels=0.2.6=py37_0
- sqlalchemy=1.2.11=py37h7b6447c_0
- sqlite=3.26.0=h7b6447c_0
- statsmodels=0.9.0=py37h035aef0_0
- sympy=1.2=py37_0
- tblib=1.3.2=py37_0
- terminado=0.8.1=py37_1
- testpath=0.3.1=py37_0
- tk=8.6.8=hbc83047_0
- toolz=0.9.0=py37_0
- tornado=5.1=py37h14c3975_0
- tqdm=4.26.0=py37h28b3542_0
- traitlets=4.3.2=py37_0
- twisted=18.7.0=py37h14c3975_1
- unicodecsv=0.14.1=py37_0
- unixodbc=2.3.7=h14c3975_0
- urllib3=1.23=py37_0
- wcwidth=0.1.7=py37_0
- webencodings=0.5.1=py37_1
- werkzeug=0.14.1=py37_0
- wheel=0.31.1=py37_0
- widgetsnbextension=3.4.1=py37_0
- wrapt=1.10.11=py37h14c3975_2
- xlrd=1.1.0=py37_1
- xlsxwriter=1.1.0=py37_0
- xlwt=1.3.0=py37_0
- xz=5.2.4=h14c3975_4
- yaml=0.1.7=had09818_2
- zeromq=4.2.5=hf484d3e_1
- zict=0.1.3=py37_0
- zlib=1.2.11=ha838bed_2
- zope=1.0=py37_1
- zope.interface=4.5.0=py37h14c3975_0
- pip:
- arrow==0.12.1
- binaryornot==0.4.4
- cookiecutter==1.6.0
- future==0.17.1
- jinja2-time==0.2.0
- poyo==0.4.2
- whichcraft==0.5.2
prefix: /home/sovacool/bin/anaconda3
Raw
pbs-with-smk.yaml
name: optiFit
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- _r-mutex=1.0.0=anacondar_1
- aioeasywebdav=2.2.0=py36_0
- aiohttp=3.5.4=py36h14c3975_0
- appdirs=1.4.3=py_1
- asn1crypto=0.24.0=py36_1003
- async-timeout=3.0.1=py_1000
- attrs=19.1.0=py_0
- bcrypt=3.1.4=py36h470a237_0
- binutils_impl_linux-64=2.31.1=h6176602_1
- binutils_linux-64=2.31.1=h6176602_3
- boost=1.68.0=py36h8619c78_1001
- boost-cpp=1.68.0=h11c811c_1000
- boto3=1.7.84=py_0
- botocore=1.10.84=py_0
- bwidget=1.9.11=1
- bzip2=1.0.6=h14c3975_1002
- ca-certificates=2019.3.9=hecc5488_0
- cachetools=2.1.0=py_0
- cairo=1.16.0=ha4e643d_1000
- certifi=2019.3.9=py36_0
- cffi=1.12.3=py36h8022711_0
- chardet=3.0.4=py36_1003
- configargparse=0.13.0=py_1
- cryptography=2.6.1=py36h72c5cf5_0
- curl=7.64.1=hf8cf82a_0
- datrie=0.7.1=py36h14c3975_0
- decorator=4.4.0=py_0
- docutils=0.14=py36_1001
- dropbox=7.3.1=py36_0
- expat=2.2.5=hf484d3e_1002
- filechunkio=1.6=py36_0
- fontconfig=2.13.1=he4413a7_1000
- freetype=2.10.0=he983fc9_0
- ftputil=3.2=py36_0
- gcc_impl_linux-64=7.3.0=habb00fd_1
- gcc_linux-64=7.3.0=h553295d_3
- gettext=0.19.8.1=hc5be6a0_1002
- gfortran_impl_linux-64=7.3.0=hdf63c60_1
- gfortran_linux-64=7.3.0=h553295d_3
- gitdb2=2.0.5=py_0
- gitpython=2.1.11=py_0
- glib=2.58.3=hf63aee3_1001
- google-api-core=1.10.0=py36_0
- google-auth=1.2.1=py_0
- google-cloud-core=0.29.1=py_0
- google-cloud-storage=1.15.0=py_0
- google-resumable-media=0.3.2=py_0
- googleapis-common-protos=1.5.9=py36_2
- graphite2=1.3.13=hf484d3e_1000
- graphviz=2.40.1=h0dab3d1_0
- gsl=2.4=h294904e_1006
- gxx_impl_linux-64=7.3.0=hdf63c60_1
- gxx_linux-64=7.3.0=h553295d_3
- harfbuzz=2.4.0=h37c48d4_0
- hdf5=1.10.4=nompi_h3c11f04_1106
- icu=58.2=hf484d3e_1000
- idna=2.8=py36_1000
- idna_ssl=1.1.0=py36_1000
- jinja2=2.10.1=py_0
- jmespath=0.9.4=py_0
- jpeg=9c=h14c3975_1001
- jsonschema=3.0.1=py36_0
- krb5=1.16.3=h05b26f9_1001
- libblas=3.8.0=8_openblas
- libcblas=3.8.0=8_openblas
- libcurl=7.64.1=hda55be3_0
- libedit=3.1.20170329=hf8c457e_1001
- libffi=3.2.1=he1b5a44_1006
- libgcc-ng=8.2.0=hdf63c60_1
- libgfortran-ng=7.3.0=hdf63c60_0
- libiconv=1.15=h516909a_1005
- liblapack=3.8.0=8_openblas
- libpng=1.6.37=hed695b0_0
- libprotobuf=3.7.1=h8b12597_0
- libssh2=1.8.2=h22169c7_2
- libstdcxx-ng=8.2.0=hdf63c60_1
- libtiff=4.0.10=h648cc4a_1001
- libtool=2.4.6=h14c3975_1002
- libuuid=2.32.1=h14c3975_1000
- libxcb=1.13=h14c3975_1002
- libxml2=2.9.9=h13577e0_0
- make=4.2.1=h14c3975_2004
- markupsafe=1.1.1=py36h14c3975_0
- multidict=4.5.2=py36h14c3975_1000
- ncurses=6.1=hf484d3e_1002
- networkx=2.3=py_0
- numpy=1.16.3=py36he5ce36f_0
- openblas=0.3.6=h6e990d7_1
- openssl=1.1.1b=h14c3975_1
- pandas=0.24.2=py36hf484d3e_0
- pandoc=2.7.2=0
- pango=1.40.14=h4ea9474_1004
- paramiko=2.4.2=py36_1000
- pcre=8.41=hf484d3e_1003
- pip=19.1=py36_0
- pixman=0.34.0=h14c3975_1003
- prettytable=0.7.2=py_2
- protobuf=3.7.1=py36he1b5a44_0
- psutil=5.6.2=py36h516909a_0
- pthread-stubs=0.4=h14c3975_1001
- pyasn1=0.4.4=py_1
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prefix: /home/sovacool/bin/anaconda3/envs/optiFit
Raw
slurm-no-smk.yaml
name: base
channels:
- conda-forge
- bioconda
- defaults
dependencies:
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- xz=5.2.4=h14c3975_4
- yaml=0.1.7=had09818_2
- zeromq=4.3.1=he6710b0_3
- zict=0.1.4=py37_0
- zipp=0.3.3=py37_1
- zlib=1.2.11=h7b6447c_3
- zstd=1.3.7=h0b5b093_0
prefix: /home/sovacool/bin/anaconda3
Raw
slurm-with-smk.yaml
name: test
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- aioeasywebdav=2.2.0=py36_0
- aiohttp=3.5.4=py36h14c3975_0
- appdirs=1.4.3=py_1
- asn1crypto=0.24.0=py36_1003
- async-timeout=3.0.1=py_1000
- attrs=19.1.0=py_0
- bcrypt=3.1.4=py36h470a237_0
- boto3=1.9.159=py_0
- botocore=1.12.159=py_0
- ca-certificates=2019.3.9=hecc5488_0
- cachetools=2.1.0=py_0
- cairo=1.16.0=ha4e643d_1000
- certifi=2019.3.9=py36_0
- cffi=1.12.3=py36h8022711_0
- chardet=3.0.4=py36_1003
- configargparse=0.13.0=py_1
- cryptography=2.6.1=py36h72c5cf5_0
- datrie=0.7.1=py36h14c3975_0
- decorator=4.4.0=py_0
- docutils=0.14=py36_1001
- dropbox=9.3.0=py_0
- expat=2.2.5=hf484d3e_1002
- filechunkio=1.8=py_2
- fontconfig=2.13.1=he4413a7_1000
- freetype=2.10.0=he983fc9_0
- ftputil=3.4=py_0
- gettext=0.19.8.1=hc5be6a0_1002
- gitdb2=2.0.5=py_0
- gitpython=2.1.11=py_0
- glib=2.58.3=hf63aee3_1001
- google-api-core=1.11.0=py36_0
- google-auth=1.6.3=py_0
- google-cloud-core=1.0.1=py_0
- google-cloud-storage=1.16.0=py_0
- google-resumable-media=0.3.2=py_0
- googleapis-common-protos=1.6.0=py36_0
- graphite2=1.3.13=hf484d3e_1000
- graphviz=2.38.0=hf68f40c_1011
- harfbuzz=2.4.0=h37c48d4_0
- icu=58.2=hf484d3e_1000
- idna=2.8=py36_1000
- idna_ssl=1.1.0=py36_1000
- jinja2=2.10.1=py_0
- jmespath=0.9.4=py_0
- jpeg=9c=h14c3975_1001
- jsonschema=3.0.1=py36_0
- libblas=3.8.0=10_openblas
- libcblas=3.8.0=10_openblas
- libffi=3.2.1=he1b5a44_1006
- libgcc-ng=8.2.0=hdf63c60_1
- libgfortran-ng=7.3.0=hdf63c60_0
- libiconv=1.15=h516909a_1005
- liblapack=3.8.0=10_openblas
- libpng=1.6.37=hed695b0_0
- libprotobuf=3.7.1=h8b12597_0
- libstdcxx-ng=8.2.0=hdf63c60_1
- libtiff=4.0.10=h57b8799_1003
- libtool=2.4.6=h14c3975_1002
- libuuid=2.32.1=h14c3975_1000
- libxcb=1.13=h14c3975_1002
- libxml2=2.9.9=h13577e0_0
- lz4-c=1.8.3=he1b5a44_1001
- markupsafe=1.1.1=py36h14c3975_0
- multidict=4.5.2=py36h14c3975_1000
- ncurses=6.1=hf484d3e_1002
- networkx=2.3=py_0
- numpy=1.16.4=py36h95a1406_0
- openblas=0.3.6=h6e990d7_2
- openssl=1.1.1b=h14c3975_1
- pandas=0.24.2=py36hb3f55d8_0
- pango=1.40.14=h4ea9474_1004
- paramiko=2.4.2=py36_1000
- pcre=8.41=hf484d3e_1003
- pip=19.1=py36_0
- pixman=0.34.0=h14c3975_1003
- prettytable=0.7.2=py_2
- protobuf=3.7.1=py36he1b5a44_0
- psutil=5.6.2=py36h516909a_0
- pthread-stubs=0.4=h14c3975_1001
- pyasn1=0.4.5=py_0
- pyasn1-modules=0.2.5=py_0
- pycparser=2.19=py36_1
- pygraphviz=1.5=py36h14c3975_1000
- pynacl=1.3.0=py36h14c3975_1000
- pyopenssl=19.0.0=py36_0
- pyrsistent=0.15.2=py36h516909a_0
- pysftp=0.2.9=py_1
- pysocks=1.7.0=py36_0
- python=3.6.7=h381d211_1004
- python-dateutil=2.8.0=py_0
- python-irodsclient=0.7.0=py_0
- pytz=2019.1=py_0
- pyyaml=5.1=py36h14c3975_0
- ratelimiter=1.2.0=py36_1000
- readline=7.0=hf8c457e_1001
- requests=2.22.0=py36_0
- rsa=3.4.2=py_1
- s3transfer=0.2.0=py36_0
- setuptools=41.0.1=py36_0
- six=1.12.0=py36_1000
- smmap2=2.0.5=py_0
- snakemake=5.5.0=0
- snakemake-minimal=5.5.0=py_0
- sqlite=3.28.0=h8b20d00_0
- tk=8.6.9=h84994c4_1001
- typing_extensions=3.7.2=py36_1000
- urllib3=1.24.3=py36_0
- wheel=0.33.4=py36_0
- wrapt=1.11.1=py36h516909a_0
- xmlrunner=1.7.7=py_0
- xorg-kbproto=1.0.7=h14c3975_1002
- xorg-libice=1.0.9=h516909a_1004
- xorg-libsm=1.2.3=h84519dc_1000
- xorg-libx11=1.6.7=h14c3975_1000
- xorg-libxau=1.0.9=h14c3975_0
- xorg-libxdmcp=1.1.3=h516909a_0
- xorg-libxext=1.3.4=h516909a_0
- xorg-libxpm=3.5.12=h14c3975_1002
- xorg-libxrender=0.9.10=h516909a_1002
- xorg-libxt=1.1.5=h14c3975_1002
- xorg-renderproto=0.11.1=h14c3975_1002
- xorg-xextproto=7.3.0=h14c3975_1002
- xorg-xproto=7.0.31=h14c3975_1007
- xz=5.2.4=h14c3975_1001
- yaml=0.1.7=h14c3975_1001
- yarl=1.3.0=py36h14c3975_1000
- zlib=1.2.11=h14c3975_1004
- zstd=1.4.0=h3b9ef0a_0
prefix: /home/sovacool/bin/anaconda3/envs/test
Raw
Snakefile
rule touch:
output:
"file.txt"
shell:
"touch {output}"
Raw
submit-pbs.sh
#PBS -N smk ## Name of the job for the scheduler
#PBS -A pschloss_fluxod ## name of the allocation (who is paying for the compute time)
#PBS -q fluxod ## name of the queue to submit the job to. Will match the suffix on allocation name
#PBS -l nodes=1:ppn=1,pmem=100MB,walltime=1:00 ## resource reservation max walltime = 672 hours
#PBS -l qos=flux ## quality of service DO NOT CHANGE THIS
#PBS -M ## send email notifications to umich email listed
#PBS -m a ## when to send email a=abort b=job begin e=job end
#PBS -j oe ## join output & error files to same file, and send to the email listed above
#PBS -V ## IMPORTANT always use this. send environment setup to node job will be run on
#
# Include the next three lines always
if [ "x${PBS_NODEFILE}" != "x" ] ; then
cat $PBS_NODEFILE # contains a list of the CPUs you were using if run with PBS
fi
# Always add this line to change to the working directory of the program. Otherwise
# the script will be run from the users /home directory
cd $PBS_O_WORKDIR
echo $PBS_O_WORKDIR
snakemake
Raw
submit-slurm.sh
#!/bin/bash
##################
#### Slurm preamble
#### #### #### These are the most frequently changing options
#### Job name
#SBATCH --job-name=smk
#### Request resources here
#### These are typically, number of processors, amount of memory,
#### an the amount of time a job requires. May include processor
#### type, too.
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=200m
#SBATCH --time=1:00
#### Slurm account and partition specification here
#### These will change if you work on multiple projects, or need
#### special hardware, like large memory nodes or GPUs.
#SBATCH --account=test
#SBATCH --partition=standard
#### #### #### These are the least frequently changing options
#### Your e-mail address and when you want e-mail
#SBATCH --mail-user=
#SBATCH --mail-type=BEGIN,END
# Add a note here to say what software modules should be loaded.
# for this job to run successfully.
# It will be convenient if you give the actual load command(s), e.g.,
#
# module load R
#### End Slurm preamble
##################
#### Commands your job should run follow this line
snakemake
## If you copied any files to /tmp, make sure you delete them here!
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