Lancium-provided images

Contents

Generic Linux Images

Ubuntu

Path: lancium/ubuntu

Version: 18.04

Included Packages:

  • csh
  • flex
  • patch
  • gcc
  • gfortran
  • g++
  • make
  • build-essential
  • wget
  • python-dev
  • xorg-dev
  • xutils-dev
  • libbz2-dev
  • zlib1g-dev
  • libboost-dev
  • libboost-thread-dev
  • libboost-system-dev

Ubuntu with CUDA Libraries

Path: lancium/ubuntu_cuda

Version: Ubuntu 18.04, CUDA 9.2

Included Packages:

  • csh
  • flex
  • patch
  • gcc
  • gfortran
  • g++
  • make
  • build-essential
  • wget
  • python-dev
  • xorg-dev
  • xutils-dev
  • libbz2-dev
  • zlib1g-dev
  • libboost-dev
  • libboost-thread-dev
  • libboost-system-dev

Environment:

CUDA_HOME=/usr/local/cuda

Molecular Dynamics

GROMACS

Path: lancium/gromacs

Version: 2018.8

Author: KTH Royal Institute Access here

$ gmx --version
	GROMACS:      gmx, version 2018.8
	Executable:   /usr/local/gromacs/bin/gmx
	Data prefix:  /usr/local/gromacs
	Working dir:  /tmp
	Command line:
	  gmx --version
	
	GROMACS version:    2018.8
	Precision:          single
	Memory model:       64 bit
	MPI library:        thread_mpi
	OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
	GPU support:        CUDA
	SIMD instructions:  AVX_256
	FFT library:        fftw-3.3.8-sse2-avx-avx2-avx2_128-avx512
	RDTSCP usage:       enabled
	TNG support:        enabled
	Hwloc support:      disabled
	Tracing support:    disabled
	Built on:           2019-12-02 16:33:44
	Built by:           root@lmf03ab2300 [CMAKE]
	Build OS/arch:      Linux 4.15.0-62-generic x86_64
	Build CPU vendor:   Intel
	Build CPU brand:    Intel(R) Xeon(R) CPU E5-2680 0 @ 2.70GHz
	Build CPU family:   6   Model: 45   Stepping: 7
	Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
	C compiler:         /usr/bin/cc GNU 7.4.0
	C compiler flags:    -mavx     -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
	C++ compiler:       /usr/bin/c++ GNU 7.4.0
	C++ compiler flags:  -mavx    -std=c++11   -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
	CUDA compiler:      /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2019 NVIDIA Corporation;Built on Sun_Jul_28_19:07:16_PDT_2019;Cuda compilation tools, release 10.1, V10.1.243
	CUDA compiler flags:-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_75,code=compute_75;-use_fast_math;-D_FORCE_INLINES;; ;-mavx;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;
	CUDA driver:        10.20
	CUDA runtime:       10.10

Environment:

There is nothing specific to GROMACS setup in the environment apart from /usr/local/gromacs/bin/ being added to the search path.

QuantumEspresso

Path: lancium/quantum_espresso

Version: 6.4.1

Environment:

QE_BIN_PATH=/q-e-qe-6.4.1/bin/ the install directory of Quantum Espresso

Included binaries:

	$ ls $QE_BIN_PATH
	
	alpha2f.x     fermi_velocity.x		     ld1.x		   pp.x		   simple_bse.x
	average.x     fqha.x			     manycp.x		   ppacf.x	   simple_ip.x
	bands.x       fs.x			     manypw.x		   projwfc.x	   spectra_correction.x
	bse_main.x    generate_rVV10_kernel_table.x  matdyn.x		   pw.x		   sumpdos.x
	cell2ibrav.x  generate_vdW_kernel_table.x    molecularnexafs.x	   pw2bgw.x	   turbo_davidson.x
	cp.x	      gww.x			     molecularpdos.x	   pw2critic.x	   turbo_eels.x
	dist.x	      gww_fit.x			     neb.x		   pw2gw.x	   turbo_lanczos.x
	dos.x	      head.x			     open_grid.x	   pw2wannier90.x  turbo_spectrum.x
	dynmat.x      hp.x			     path_interpolation.x  pw4gww.x	   wannier_ham.x
	epa.x	      ibrav2cell.x		     ph.x		   pwcond.x	   wannier_plot.x
	epsilon.x     initial_state.x		     phcg.x		   pwi2xsf.x	   wfck2r.x
	ev.x	      iotk			     plan_avg.x		   q2qstar.x	   wfdd.x
	fd.x	      iotk.x			     plotband.x		   q2r.x	   xspectra.x
	fd_ef.x       iotk_print_kinds.x	     plotproj.x		   q2trans.x
	fd_ifc.x      kpoints.x			     plotrho.x		   q2trans_fd.x
	fermi_proj.x  lambda.x			     pmw.x		   simple.x

AMBER

Path: lancium/amber

Version: Amber 18

CUDA Version: 9.2

Environment:

AMBERHOME=/opt/amber, the install directory of AMBER.

Included Binaries:

	$ ls $AMBERHOME/bin
	
	AddToBox	    atomtype		  lmanal		 nef_to_RST	      resp
	CartHess2FC.py	    bondtype		  makeANG_RST		 new2oldparm	      respgen
	ChBox		    car_to_files.py	  makeCHIR_RST		 new_crd_to_dyn       rism1d
	CheckMD		    ceinutil.py		  makeDIST_RST		 new_to_old_crd       rism3d.orave
	FEW.pl		    cestats		  make_crd_hg		 nf-config	      rism3d.snglpnt
	IPMach.py	    charmmlipid2amber.py  mdgx			 nfe-umbrella-slice   rism3d.thermo
	MCPB.py		    cpeinutil.py	  mdnab			 nmode		      sander
	MMPBSA.py	    cphstats		  mdout2pymbar.pl	 packmol	      sander.LES
	OptC4.py	    cpinutil.py		  mdout_analyzer.py	 packmol-memgen       saxs_md
	PdbSearcher.py	    cpptraj		  memembed		 paramfit	      saxs_rism
	ProScrs.py	    cpptraj.cuda	  metatwist		 parmchk2	      senergy
	PropPDB		    dacdif		  minab			 parmed		      sgldinfo.sh
	UnitCell	    elsize		  mm_pbsa.pl		 pbsa		      sgldwt.sh
	addles		    espgen		  mm_pbsa_nabnmode	 pbsa.cuda	      softcore_setup.py
	am1bcc		    espgen.py		  mm_pbsa_statistics.pl  pdb4amber	      sqm
	amb2chm_par.py	    fantasian		  mmpbsa_py_energy	 pmemd		      sviol
	amb2chm_psf_crd.py  ffgbsa		  mmpbsa_py_nabnmode	 pmemd.cuda	      sviol2
	amber.conda	    fftw-wisdom		  mol2rtf.py		 pmemd.cuda_DPFP      teLeap
	amber.ipython	    fftw-wisdom-to-conf   molsurf		 pmemd.cuda_SPFP      tinker_to_amber
	amber.jupyter	    finddgref.py	  nab			 prepgen	      tleap
	amber.pip	    fitpkaeo.py		  nab2c			 process_mdout.perl   to_be_dispatched
	amber.python	    fix_new_inpcrd_vel	  nc-config		 process_minout.perl  ucpp
	ambmask		    fixremdcouts.py	  nccopy		 pymdpbsa	      volslice
	ambpdb		    gbnsr6		  ncdump		 pytleap	      xaLeap
	ante-MMPBSA.py	    genremdinputs.py	  ncgen			 reduce		      xleap
	antechamber	    hcp_getpdb		  ncgen3		 residuegen	      xparmed

Machine Learning

PyCaffe

Path:

  • lancium/caffe-py2 (python 2.7)
  • lancium/caffe-py3 (python 3.7)

Version: 1.0.0

Environment:

$PATH includes the directory containing the binaries for caffe.

/opt/conda/envs/caffe2/bin in Python2 Container

/opt/conda/envs/caffe/bin in Python3 Container

Tensorflow

Path:

  • lancium/tensorflow-py2 (python 2.7)
  • lancium/tensorflow-py3 (python 3.7)

Version:

  • 1.14.0 in Python 2 Container
  • 1.13.1 in Python 3 Container

Environment:

Tensorflow binary path included in search path.

/opt/conda/envs/tensorflow-gpu2/bin in Python 2 Container

/opt/conda/envs/tensorflow-gpu/bin in Python 3 Container

Theano

Path: lancium/theano-py2

Version: 1.0.4

Environment:

Theano binary path included in search path.

/opt/conda/envs/theano2/bin in Python 2 Container

PyTorch

Path:

  • lancium/pytorch-py2 (python 2.7)
  • lancium/pytorch-py3 (python 3.7)

Version:

  • 1.1.0 in Python 2 Container
  • 1.0.0 in Python 3 Container

Environment:

PyTorch binary path included in search path.

/opt/conda/envs/pytorch2/bin in Python 2 Container

/opt/conda/envs/pytorch/bin in Python 3 Container

Bioinformatics

BLAST+

Path: lancium/blast

Version: 2.9.0

Environment:

$PATH includes the directory containing the all binaries included in the NCBI Blast package.

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