Weed out software pages we don't need.

[owainkenwayucl]

[heatherkellyucl]

Bahleeted:

• Running_DL_Poly_Classic_1.2_on_Legion.md
• Running_DL_Poly_Classic_1.9_on_Legion.md
• Running_DTI-TK_on_Legion.md (no longer installed)
• Running_GaussView_5_on_Legion.md
• Running_Gaussian_03_on_Legion.md
• Running_R_3.0.1_on_Legion.md
• Running_SPM_on_Legion.md
• Running_StarCCM%2B_on_Legion.md
• Running_StarCD_on_Legion.md
• Running_Stata__MP_on_Legion.md
• Running_TopHat_on_Legion.md

Needs a small entry about jobscript changes:

• [x] ABAQUS
• [x] BEAST
• [x] Bowtie
• [x] CASTEP
• [x] Cctools
• [x] CP2K
• [x] CRYSTAL (in general, not just 14)
• [x] FreeSurfer
• [x] GAMESS
• [x] GATK
• [ ] not sure if want to mention the GaussView X-forwarding issues?
• [x] Hammock
• [x] HOPSPACK
• [x] IDL
• [x] JAGS
• [ ] LAMMPS (split into here and the page on building your own)
• [x] MEME Suite (just a lot of modules)
• [x] miRDeep2 (lot of modules)
• [x] MISO/misopy (python, but can submit jobs)
• [x] MOLPRO
• [x] MRtrix
• [x] MuTect
• [x] NONMEM
• [x] NWChem
• [x] Picard (picard-tools)
• [x] Quantum Espresso ($ESPRESSO_PSEUDO)
• [x] Repast HPC (so many modules)
• [x] ROOT (batch mode)
• [x] SAS (maybe not necessary at all?)
• [x] StarCCM+
• [x] StarCD
• [x] Stata/MP
• [x] Torch
• [x] Turbomole
• [x] VarScan
• [x] VASP (short here and section on building page)
• [x] XMDS (unless we decide to expand what it says here into a whole page?)

Needs a whole page:

• [ ] ADF
• [ ] ANSYS (CFX and Fluent)
• [ ] CESM
• [ ] DL_POLY 4
• [ ] FSL (probably - can choose jobs that submit other jobs or prevent)
• [ ] GROMACS (probably - exec names, noninteractive options, the first half of checkpointing)
• [ ] Gaussian and Linda
• [ ] Mathematica
• [x] MATLAB
• [ ] TractoR
• [ ] VisIt

Separate types of page:

• [ ] How to build own versions of software that users often want their own copies of (eg LAMMPS, VASP, OpenFOAM, GROMACS±PLUMED)
• [ ] Proper Singularity documentation

[heatherkellyucl]

• [x] Make small entry for COMSOL as running it in parallel has a fairly complex set of options.

module load comsol/53a
# $NHOSTS gets the number of nodes the job is running on and
# $TMPDIR/machines is the machinefile that tells it which nodes.
# These are automatically set up in a "-pe mpi" job environment.
comsol -nn $NHOSTS -clustersimple batch -f $TMPDIR/machines -inputfile micromixer_batch.mph -outputfile micromixer_batch_output_${JOB_ID}.mph

# On Myriad, needs to be this?
comsol batch -f $TMPDIR/machines -np $NSLOTS -mpifabrics shm:tcp -inputfile batchmodel -outputfile simpletest_batch_output_${JOB_ID}.mph

52 and 52a also need to load xulrunner/3.6.28/gnu-4.9.2

[heatherkellyucl]

• [x] CFD-ACE needs a small entry

module load cfd-ace/2018.0

# This is in case your input model is in another directory
modelIn=~/Scratch/test_cfd-ace/3Dstepchannel_060414.DTF
model=$(basename $modelIn)
echo "Model to run is $model"
# Makes an output directory just for this job and copies the input file there
jobDir=${JOB_NAME}_${JOB_ID}
mkdir $jobDir
cp $modelIn $jobDir
cd $jobDir

CFD-SOLVER -model $model -num $NSLOTS -wd `pwd` -hosts $TMPDIR/machines -rsh=ssh -decomp -metis -sim 1 -platformmpi -job

[heatherkellyucl]

In software/unedited/mediawiki_only I also deleted the above, plus

• BamTools_on_Legion.mediawiki
• Bioconductor_on_Legion.mediawiki (all it did was link to the other R pages)
• BLAST_on_Legion.mediawiki
• BWA_on_Legion.mediawiki
• Cake_on_Legion.mediawiki (no longer installed)
• Cmgui_on_Legion.mediawiki (no longer installed)
• Cutadapt_on_Legion.mediawiki (python)
• EIGENSOFT_on_RC_Systems.mediawiki
• Ghostscript_on_Legion.mediawiki
• Gnuplot_on_Legion.mediawiki
• Grace_on_Legion.mediawiki (the most confusingly-named page!)
• GULP_on_Legion.mediawiki (incredibly out of date)
• GULP_on_RC_Systems.mediawiki (very out of date)
• MACS_on_Legion.mediawiki (python)
• Molden_on_Legion.mediawiki
• NAMD_on_Legion.mediawiki
• ORCA_on_Legion.mediawiki (no longer installed)
• PGPLOT_on_Legion.mediawiki
• Plink_on_Legion.mediawiki
• ProbABEL_on_Legion.mediawiki
• Rmpi_on_RC_Systems.mediawiki (is a link to the R page)
• SAMTools_on_Legion.mediawiki
• Valgrind_on_Legion.mediawiki (no content)
• Vienna_RNA_on_Legion.mediawiki

[heatherkellyucl]

Gone through all the unedited software pages as well and put them in categories above.

[heatherkellyucl]

Done all the small pages. I don't know if there is a license check to put in the jobscript for CFD-ACE, and I don't have the ones for COMSOL. (William was adding one for the ChemEng version).

[heatherkellyucl]

The big MATLAB page is there, along with config files.

• [x] Need example on how to use GPUs with MATLAB

[heatherkellyucl]

I'm not currently putting -ac exclusive in the MATLAB example jobscripts. I think this ought to be ok now because of cpusets containing all the MATLAB threads. (Particularly in the GPU case it seems a bad idea to reserve an entire GPU node if only using one GPU). We should make sure this is the case.

It may be worth suggesting that MATLAB works well if you request an entire node's-worth of cores, however.