Many SCC software packages have been updated to a newer version or an updated name in
System software version changes
Much of the software on the SCC is delivered via the module system. However some software packages are installed in the Linux system directories. Launching any of these packages does not require loading a module. Many of these packages have been updated in CentOS 7 and the version changes to popular software packages are listed in the following table:
| Command Name | Version in CentOS 6 | Version in CentOS 7 |
|---|---|---|
| cmake/ccmake | 2.6-patch-4 | 2.8.12.2 |
| emacs | 23.1.1 | 24.3.1 |
| firefox | 45.0.2 | 60.2.2 |
| gcc/g++/gfortran | 4.4.7 | 4.8.5 |
| geany | 0.21 | 1.31 |
| gedit | 2.28.4 | 3.22.0 |
| git | 1.7.1 | 1.8.3.1 |
| gnuplot | 4.2 patch 6 | 4.6 patch 2 |
| make | 3.81 | 3.82 |
| octave | 3.4.3 | 3.8.2 |
| perl | 5.10.1 | 5.16.3 |
| python | 2.6.6 | 2.7.5 |
| tex | 3.5.6 | 6.1.1 |
| zlib | 1.2.3 | 1.2.7 |
Module default version changes
Some software packages will load a newer version under module load command is run without specifying a version. Below is a table showing some popular software packages and their default module versions under both CentOS 6 and CentOS 7:
| Module Name | Default Version in CentOS 6 | Default Version in CentOS 7 |
|---|---|---|
| matlab | 2018b | 2019a |
| python | 2.7.13 | none (use python2 or python3) |
| python2 | 2.7.13 | 2.7.16 |
| python3 | 3.6.4 | 3.6.5 |
| R | 3.2.3 | 3.6.0 |
Module name changes
Some module names have changed in CentOS 7. The table below lists the changes made in module names and versions:
| Module Name and Version in CentOS 6 | Module Name and Version in CentOS 7 |
|---|---|
| 2brad_denovo/2019-01-22_eec5016 | 2brad_denovo/2019-01-22_giteec5016 |
| 2brad_gatk/2019-01-22_1fcc9e8 | 2brad_gatk/2019-01-22_git1fcc9e8 |
| afni/2017.01.29.1818_openmp | afni/17.0.18-omp |
| afni/AFNI_2011_12_21_1014 | afni/2011-12-21.1014 |
| afni/AFNI_2011_12_21_1014-xorg7 | afni/2011-12-21.1014-xorg |
| anaconda | anaconda2 |
| ANTs/1.9.2 | ants/1.9.2 |
| ashs/20170223 ASHS/rev97 |
ashs/2017-02-23 |
| bgw/2.0.0_intel-2016 | bgw/2.0.0_intel-2018 |
| EIGENSOFT/EIGENSOFT-4.2_gnu447 EIGENSOFT/EIGENSOFT-5.0.1_gnu447 |
eigensoft/7.2.1 |
| elpa/2018.11.001_intel-2016 | elpa/2018.11.001_intel-2018 |
| emmax/20120210 | emmax/2012-02-10 |
| fiji/2015.12.22 | fiji/2015-12-22 |
| LDOPE/1.6 | ldope/1.7 |
| ledaps/20120925 ledaps/20120925-LC8 |
ledaps/2012-09-25 |
| macs/2.1.1.20160309 | macs2/2.1.2.1 |
| MDAnalysis/0.19.0 MDAnalysis/0.8 |
mdanalysis/0.18.0 |
| meshclust/1.0.0 meshclust/2018-08-29_git8ea11e1 |
meshclust2/2.1.0 |
| miniconda2/4.4.10 | miniconda/4.5.12 |
| minimac2/20140915 | minimac2/2014-09-15 |
| mmap/2018.04.07 | mmap/2018-04-07 |
| mricrogl/2017_07_14 | mricrogl/2017-07-14 |
| mricron/6_2013 | mricron/2013-6 |
| namd/2.12_multicore_cuda | namd/2.13_mc-cuda |
| netcdf/4.4.0_intel2016 | netcdf/4.6.1_intel-2018 |
| netcdf-fortran/4.4.2_intel2016 | netcdf-fortran/4.4.4_intel-2018 |
| ngsld/2019-01-22_5708758 | ngsld/2019-01-22_git5708758 |
| ngspopgen/2019-01-22_9ee3a6d | ngspopgen/2019-01-22_git9ee3a6d |
| OpenBUGS/3.2.3 | openbugs/3.2.3 |
| openmpi/3.1.2_gcc-7.2.0 | openmpi/3.1.1 |
| OpenSceneGraph/3.2.1 | openscenegraph/3.2.1 |
| ossim/mar_6_2017 | ossim/2018-12-11 |
| parallel/20171122 | parallel/2019-02-22 |
| QuantumEspresso/6.3_intel-2018 | quantumespresso/6.3_intel-2018 |
| QuantumEspresso/6.4.1 | quantumespresso/6.4.1 |
| rvtests/20171010 rvtests/v2.1.0 |
rvtests/2.1.0 |
| SDP_ToolKit/5.2.13 SDP_ToolKit/5.2.18v1.00 |
sdp_toolkit/5.2.20 |
| szip/2.1 | szip/2.1.1 |
| tabix/1.1 | htslib/1.9, tabix no longer exists as a separate module but is included in the ‘htslib’ module |
| texlive/20150411 | texlive/2018 |
| trim_galore/0.4.2 | trimgalore/0.5.0 |
| ucscutils/20171205 | ucscutils/2018-11-27 |
| velvet/1.2.10_149-mp-ls-ba | velvet/1.2.10 |
| xnat2proj/v0.1 | xnat2proj/0.1 |