Here you will find basic information about the software modules system users will find in 'Dalma'
The default software environment is NYUAD/3.0. The number comes from past iterations we have worked on during the last couple of years and that have helped us to define what we consider is a robust easy to use modules system. Yet this is an ongoing project and you might expect slight changes in the future.
The main features of the current modules environment could be summarised as:
Two name spaces default and all
1.- default contains the commonly used software (no need to load it. It will be available by default)
[hpc@~]$ module avail
-------------------------------------------- /share/apps/NYUAD/modules/SOFTWARE ---------------------------------------------------------------
Desmond-Maestro/2014.02 cfitsio/3.380 gaussian/09.D.01 lapack/3.6.0 ngsTools/1.0.0 sofia-ml/2015.01
R/3.1.2 charm/6.7.0 gaussview/5.0.9 libffi/3.2.1 openmpi/1.10.2 spades/3.7.1
admirable/2015.01 clapack/3.2.1 gcc/4.9.3 libgd/2.1.1 openssl/1.0.1q sparsehash/2.0.2
allinea/5.0 cmake/3.4.2 genblasta/1.0.4 libtool/2.4.6 parallel/20160222 sqlite/3.11.0
allpathslg/52488 comsol/4.4 glib/2.44.0 libxml2/2.9.2 perl/5.22.1 srilm/1.6.0
amber/14 cp2k/2.6.0 gmp/6.0.0 m4/1.4.17 pgplot/5.2 stata/14
anaconda/2.4.1 cpmd/3.17.1 gnuplot/5.0.0 mathematica/10.3.0 platanus/1.2.4 svmtool/1.3.1
atlas/3.10.2 crystal14/v1.0.1 gromacs/5.0.4 matlab/R2016a presto/2015.02 szip/2.1
autoconf/2.69 cufflinks/2.2.1 gsl/2.1 mosesdecoder/3.0 psrchive/6.0 tangram/0.3.1
autodock/4.2.6 discovar/52488 hdf5/1.8.16 mpiblacs/3 python/2.7.11 tcltk/8.5.17
automake/1.15 discovardenovo/52488 help2man/1.47.3 musket/1.1 readline/6.3 tedna/1.2.2
bedtools/2.25.0 eigen/3.2.8 hmmer/3.1b2 mvapich2/2.2b root/5.34.36 tempo/2015.02
blas/3.6.0 expat/2.1.0 intel/16.1 namd/2.10 root/6.06.02 trimmomatic/0.32
blast/2.3.0 fftw2/2.1.5 jags/3.4.0 nbo/6 ruby/2.3.0 vcftools/0.1.14
boost/1.57.0 fftw3/3.3.4 jdk/1.8.0_31 nco/4.5.2 scalapack/2.0.2 velvet/1.2.10
bzip2/1.0.6 fftw3_mpi/3.3.4 jellyfish/2.2.5 ncurses/6.0 screen/4.3.1 velvet-k127/1.2.10
cblas/3.6.0 fuse/2.9.3 jemalloc/4.1.0 netcdf/4.4.0 soapdenovo2/r240 wien2k/13
cegma/2.5 gapcloser/1.12r6 lammps/2014.12 netcdf-fortran/4.4.2 soapdenovo2-prepare/2.0 zlib/1.2.8
--------------------------------------------- /share/apps/NYUAD/modules/SECTIONS ---------------------------------------------------------------
all devel retired
----------------------------------------------- /share/apps/NYUAD/modules/BASE -----------------------------------------------------------------
NYUAD/2.0 NYUAD/3.0(default) NYUAD-Test
2.- **all** Contains all available combinations that have been built in the system beyond that what are provided by default
[hpc@~]$ module load all
Loading module 'all'
[hpc@~]$ module avail
------------------------------------- /share/apps/NYUAD/modules/ALL ----------------------------------------------------------------------------
Desmond-Maestro/2014.02 fftw3/gcc_4.9.3/mvapich2_2.2b/sse4.2/3.3.4 netcdf/gcc_4.9.3/openmpi_1.10.2/4.4.0
R/avx2/3.1.2 fftw3/gcc_4.9.3/openmpi_1.10.2/avx/3.3.4 netcdf/intel_16.1/mvapich2_2.2b/4.4.0
admirable/avx2/2015.01 fftw3/gcc_4.9.3/openmpi_1.10.2/avx2/3.3.4 netcdf/intel_16.1/openmpi_1.10.2/4.4.0
allinea/5.0 fftw3/gcc_4.9.3/openmpi_1.10.2/sse4.2/3.3.4 netcdf-fortran/gcc_4.9.3/4.4.2
allpathslg/52488 fftw3/intel_16.1/mvapich2_2.2b/avx/3.3.4 netcdf-fortran/gcc_4.9.3/mvapich2_2.2b/4.4.2
amber/openmpi_1.10.2/sse4.2/14 fftw3/intel_16.1/mvapich2_2.2b/avx2/3.3.4 netcdf-fortran/gcc_4.9.3/openmpi_1.10.2/4.4.2
amber/sse4.2/14 fftw3/intel_16.1/mvapich2_2.2b/sse4.2/3.3.4 netcdf-fortran/intel_16.1/4.4.2
anaconda/2.4.1 fftw3/intel_16.1/openmpi_1.10.2/avx/3.3.4 netcdf-fortran/intel_16.1/mvapich2_2.2b/4.4.2
atlas/avx2/3.10.2 fftw3/intel_16.1/openmpi_1.10.2/avx2/3.3.4 netcdf-fortran/intel_16.1/openmpi_1.10.2/4.4.2
autoconf/2.69 fftw3/intel_16.1/openmpi_1.10.2/sse4.2/3.3.4 ngsTools/1.0.0
autodock/4.2.6 fftw3/sse4.2/3.3.4 openmpi/gcc_4.9.3/1.10.2
automake/1.15 fuse/2.9.3 openmpi/intel_16.1/1.10.2
bedtools/2.25.0 gapcloser/1.12r6 openssl/1.0.1q
blas/avx/3.6.0 gaussian/09.D.01 parallel/20160222
blas/avx2/3.6.0 gaussview/5.0.9 perl/5.22.1
blas/sse4.2/3.6.0 gcc/4.9.3 pgplot/avx2/5.2
blast/2.3.0 genblasta/1.0.4 platanus/1.2.4
boost/gcc_4.9.3/openmpi_1.10.2/avx2/1.57.0 glib/2.44.0 pnetcdf/gcc_4.9.3/mvapich2_2.2b/1.0.2
bzip2/1.0.6 gmp/6.0.0 pnetcdf/gcc_4.9.3/mvapich2_2.2b/1.7.0
cblas/avx/3.6.0 gnuplot/5.0.0 pnetcdf/gcc_4.9.3/openmpi_1.10.2/1.0.2
cblas/avx2/3.6.0 gromacs/openmpi_1.10.2/avx2/5.0.4 pnetcdf/gcc_4.9.3/openmpi_1.10.2/1.7.0
cblas/sse4.2/3.6.0 gsl/avx/2.1 pnetcdf/intel_16.1/mvapich2_2.2b/1.0.2
cegma/2.5 gsl/avx2/2.1 pnetcdf/intel_16.1/mvapich2_2.2b/1.7.0
cfitsio/avx2/3.380 gsl/sse4.2/2.1 pnetcdf/intel_16.1/openmpi_1.10.2/1.0.2
cfitsio/sse4.2/3.380 hdf5/gcc_4.9.3/1.8.16 pnetcdf/intel_16.1/openmpi_1.10.2/1.7.0
charm/openmpi_1.10.2/sse4.2/6.7.0 hdf5/gcc_4.9.3/mvapich2_2.2b/1.8.16 presto/openmpi_1.10.2/avx2/2015.02
clapack/avx/3.2.1 hdf5/gcc_4.9.3/openmpi_1.10.2/1.8.16 psrchive/6.0
clapack/avx2/3.2.1 hdf5/intel_16.1/1.8.16 python/2.7.11
clapack/sse4.2/3.2.1 help2man/1.47.3 python/3.5.1
cmake/3.4.2 hmmer/3.1b2 readline/6.3
comsol/4.4 intel/16.1 root/sse4.2/5.34.36
cp2k/avx2/2.6.0 jags/3.4.0 root/sse4.2/6.06.02
cp2k/openmpi_1.10.2/avx2/2.6.0 jdk/1.8.0_31 ruby/2.3.0
cpmd/openmpi_1.10.2/avx2/3.17.1 jellyfish/2.2.5 scalapack/gcc_4.9.3/openmpi_1.10.2/avx/2.0.2
crystal14/v1.0.1 jemalloc/4.1.0 scalapack/gcc_4.9.3/openmpi_1.10.2/avx2/2.0.2
cufflinks/2.2.1 lammps/omp/avx2/2014.12 scalapack/gcc_4.9.3/openmpi_1.10.2/sse4.2/2.0.2
discovar/52488 lammps/openmpi_1.10.2/omp/avx2/2014.12 screen/4.3.1
discovardenovo/52488 lapack/avx/3.6.0 soapdenovo2/r240
eigen/3.2.8 lapack/avx2/3.6.0 soapdenovo2-prepare/2.0
expat/2.1.0 lapack/sse4.2/3.6.0 sofia-ml/2015.01
fftw2/avx/2.1.5 libffi/3.2.1 spades/3.7.1
fftw2/avx2/2.1.5 libgd/2.1.1 sparsehash/2.0.2
fftw2/gcc_4.9.3/mvapich2_2.2b/avx/2.1.5 libtool/2.4.6 sqlite/3.11.0
fftw2/gcc_4.9.3/mvapich2_2.2b/avx2/2.1.5 libxml2/2.9.2 srilm/1.6.0
fftw2/gcc_4.9.3/mvapich2_2.2b/sse4.2/2.1.5 m4/1.4.17 stata/14
fftw2/gcc_4.9.3/openmpi_1.10.2/avx/2.1.5 mathematica/10.3.0 svmtool/1.3.1
fftw2/gcc_4.9.3/openmpi_1.10.2/avx2/2.1.5 matlab/R2015b szip/2.1
fftw2/gcc_4.9.3/openmpi_1.10.2/sse4.2/2.1.5 matlab/R2016a tangram/0.3.1
fftw2/intel_16.1/mvapich2_2.2b/avx/2.1.5 mosesdecoder/3.0 tcltk/8.5.17
fftw2/intel_16.1/mvapich2_2.2b/avx2/2.1.5 mpiblacs/gcc_4.9.3/openmpi_1.10.2/avx2/3 tedna/1.2.2
fftw2/intel_16.1/mvapich2_2.2b/sse4.2/2.1.5 musket/1.1 tempo/avx2/2015.02
fftw2/intel_16.1/openmpi_1.10.2/avx/2.1.5 mvapich2/gcc_4.9.3/2.2b trimmomatic/0.32
fftw2/intel_16.1/openmpi_1.10.2/avx2/2.1.5 mvapich2/intel_16.1/2.2b vcftools/0.1.14
fftw2/intel_16.1/openmpi_1.10.2/sse4.2/2.1.5 namd/openmpi_1.10.2/avx2/2.10 velvet/1.2.10
fftw2/sse4.2/2.1.5 nbo/6 velvet-k127/1.2.10
fftw3/avx/3.3.4 nco/4.5.2 wien2k/openmpi_1.10.2/avx2/13
fftw3/avx2/3.3.4 ncurses/6.0 zlib/1.2.8
fftw3/gcc_4.9.3/mvapich2_2.2b/avx/3.3.4 netcdf/4.4.0
fftw3/gcc_4.9.3/mvapich2_2.2b/avx2/3.3.4 netcdf/gcc_4.9.3/mvapich2_2.2b/4.4.0
------------------------------------ /share/apps/NYUAD/modules/SECTIONS --------------------------------------------------------------------------
all devel retired
-------------------------------------- /share/apps/NYUAD/modules/BASE ----------------------------------------------------------------------------
NYUAD/2.0 NYUAD/3.0(default) NYUAD-Test
1.- Selecting the dafault FFTW3
[hpc@~]$ module avail fftw
------------------------------------------ /share/apps/NYUAD/modules/SOFTWARE ----------------------------------------------------------------------------
fftw2/2.1.5 fftw3/3.3.4
[hpc@~]$ module load fftw3
Loading module 'fftw3/3.3.4'
Here FFTW3 is loaded, let's confirm it...
[hpc@~]$ module list
Currently Loaded Modulefiles:
1) NYUAD/3.0 2) fftw3/3.3.4
[hpc@~]$ echo $LD_LIBRARY_PATH
/share/apps/NYUAD/fftw3/avx2/3.3.4/lib
That shows the default version of FFTW3 is the serial build for avx2.
2.- Selecting the same FFTW3 as before but from inside 'all'
[hpc@~]$ module load all
Unloading module 'fftw3/3.3.4'
Loading module 'all'
[hpc@~]$ module avail fftw3
------------------------------------- /share/apps/NYUAD/modules/ALL ------------------------------------------------------------------------------
fftw3/avx/3.3.4 fftw3/gcc_4.9.3/mvapich2_2.2b/sse4.2/3.3.4 fftw3/intel_16.1/mvapich2_2.2b/avx/3.3.4 fftw3/intel_16.1/openmpi_1.10.2/avx2/3.3.4
fftw3/avx2/3.3.4 fftw3/gcc_4.9.3/openmpi_1.10.2/avx/3.3.4 fftw3/intel_16.1/mvapich2_2.2b/avx2/3.3.4 fftw3/intel_16.1/openmpi_1.10.2/sse4.2/3.3.4
fftw3/gcc_4.9.3/mvapich2_2.2b/avx/3.3.4 fftw3/gcc_4.9.3/openmpi_1.10.2/avx2/3.3.4 fftw3/intel_16.1/mvapich2_2.2b/sse4.2/3.3.4 fftw3/sse4.2/3.3.4
fftw3/gcc_4.9.3/mvapich2_2.2b/avx2/3.3.4 fftw3/gcc_4.9.3/openmpi_1.10.2/sse4.2/3.3.4 fftw3/intel_16.1/openmpi_1.10.2/avx/3.3.4
[hpc@~]$ module load fftw3/avx2/3.3.4
Loading module 'fftw3/avx2/3.3.4'
Here FFTW3 is loaded, let's confirm it...
[hpc@~]$ module list
Currently Loaded Modulefiles:
1) NYUAD/3.0 2) all 3) fftw3/avx2/3.3.4
[hpc@~]$ echo $LD_LIBRARY_PATH
/share/apps/NYUAD/fftw3/avx2/3.3.4/lib
NYUAD HPC Apps Team:
--------------------
- Benoit Marchand
- Guowei He
- Jorge Naranjo
Please refer to the online documentation available here