Replace `run_cmd` and `run_cmd_qa` with `run_shell_cmd`

[branfosj]

The todo list for replacing run_cmd and run_cmd_qa with run_shell_cmd for EB5.

Please make sure this issue is updated with links to the PRs for the changes. PRs can contain multiple easyblock updates, but please consider the required testing so that there is not too many tests to be done for any one PR. Also, remember that some easyblocks are also used via easyblock = 'EB_name' or inherited.

run_cmd only

• adf.py: #3091
• amber.py: #3094
• anaconda.py: #3090
• ansys.py: #3099
• ant.py: #3098
• arb.py: #3096 ~~#3095~~
• atlas.py: #3103 ~~#3097~~
• bazel.py: #3102
• binutils.py: #3105
• blacs.py: #3104
• boost.py: #3100
• bzip2.py: #3101
• cfdemcoupling.py: #3151
• charmm.py: #3108
• chimera.py: #3109
• clang.py: #3139
• comsol.py: #3110
• cp2k.py: #3113
• cppcheck.py: #3111
• cryptography.py: #3107
• cudacompat.py: #3112
• dl_poly_classic.py: #3152
• dm_reverb.py: #3153
• dolfin.py: #3154
• doxygen.py: #3114
• dualsphysics.py: #3293
• esmf.py: #3115
• espresso.py: #3117 ~~#3116~~
• faststructure.py: #3155
• fdtd_solutions.py: #3156
• flexiblas.py: #3136
• fluent.py: #3135
• freefem.py: #3157
• fsl.py: #3134
• gamess_us.py: #3342 (having first done #3047 to eliminate use of run_cmd_qa)
• gate.py: #3133
• gcc.py: #3137
• go.py: #3132
• gromacs.py: #3131
• gurobi.py: #3130
• hadoop.py: #3129
• hpl.py: #3128
• hpcg.py: #3158
• icc.py: #3159
• imkl.py: #3122
• imod.py: #3126
• impi.py: #3124
• intel_compilers.py: #3127
• ironpython.py: #3125
• itac.py: #3123
• java.py: #3120
• lammps.py: #3244
• lapack.py: #3219
• libint.py: #3218
• libqglviewer.py: #3217
• libsmm.py: #3216
• matlab.py: #3215
• mcr.py: #3213
• metis.py: #3212
• mono.py: #3211
• mrbayes.py: #3210
• mrtrix.py: #3209
• msm.py: #3208
• mummer.py: #3207
• mxnet.py: #3206
• mymedialite.py: #3205
• namd.py: #3204
• ncl.py: #3203
• nemo.py: #3202
• neuron.py: #3201
• nim.py: #3200
• numpy.py: #3199
• nvhpc.py: #3198
• nwchem.py: #3197
• ocaml.py: #3243 ~~#3196~~
• openifs.py: #3194
• openblas.py: #3195
• openssl_wrapper.py: #3193
• openssl.py: #3193
• palm.py: #3166
• parmetis.py: #3167
• perl.py: #3162
• petsc.py: #3168
• pgi.py: #3181
• pplacer.py: #3185 ~~#3183~~
• psi.py: needed for #3214
• pybind11.py: #3171
• python.py: #3169
• python_meep.py: #3182
• qscintilla.py: #3150
• root.py: #3149
• rosetta.py: #3147 ~~#3148~~
• rust.py: #3146
• scalapack.py: #3106
• scipion.py: #3140
• scotch.py: #3141
• sepp.py: #3142
• slepc.py: #3143
• siesta.py: #3192
• star_ccm.py: #3144
• tbb.py: #3145
• tensorflow_compression.py: #3164
• tensorflow.py: #3165
• tensorrt.py: #3179
• tinker.py: #3180
• totalview.py: #3191
• trinity.py: #3190
• ucx_plugins.py: #3189
• vep.py: #3188
• vmd.py: #3187
• vsc_tools.py: #3138
• wxpython.py: #3093
• xmipp.py: #3092

run_cmd_qa

• [ ] abaqus.py: run_cmd_qa
• acml.py: #3172
• aladin.py: #3173
• bisearch.py: #3174
• cplex.py: #3295
• cuda.py: #3274
• doris.py: #3175
• geant4.py: #3296 and #3302
• healpix.py: #3285
• maple.py: #3286
• mathematica.py: #3298
• modeller.py: #3292
• molpro.py: #3294
• openfoam.py: #3299
• qt.py: #3291
• repeatmasker.py: #3290
• repeatmodeler.py: #3289
• samcef.py: #3176
• sas.py: #3177
• snphylo.py: run_cmd, #3178
• stata.py: #3288
• [ ] wien2k.py: run_cmd, run_cmd_qa
• wps.py: #3297
• wrf.py: #3270
• wrf_fire.py: #3271

Nothing to do

• a nothing to do: aocc.py, aomp.py, allinea.py, advisor.py, armadillo.py
• b nothing to do: bwa.py, bwise.py, bowtie2.py, bioconductor.py, berkeleygw.py, blat.py, blender.py, bowtie.py, bamtools.py
• c nothing to do: cblas.py, cgal.py, clang_aomp.py, code_server.py, cudnn.py, chapel.py, cufflinks.py, crispr_dav.py, cmake.py
• d nothing to do: db.py
• e nothing to do: extrae.py, eigen.py, epd.py, elsi.py, easybuildmeta.py, egglib.py, elpa.py
• f nothing to do: flex.py, ferret.py, fftw.py, freesurfer.py, foldx.py, fftwmpi.py, freetype.py
• g nothing to do: g2lib.py, gctf.py, ghc.py, g2clib.py
• h nothing to do: hypre.py, hdf5.py, hpcc.py
• i nothing to do: imkl_fftw.py, ifort.py, inspector.py, ipp.py, iccifort.py
• j nothing to do: jaxlib.py
• k no easyblocks
• l nothing to do: lua.py, libxml2.py, llvm.py, libdrm.py
• m nothing to do: mvapich2.py, mothur.py, motioncor2.py, metagenome_atlas.py, mutil.py, mamba.py, mesa.py, metavelvet.py, mpich.py, mumps.py, mtl4.py
• n nothing to do: numexpr.py, nose.py, nccl.py, netcdf_fortran.py, netcdf.py, netcdf4_python.py, ncurses.py
• o nothing to do: opencv.py, orca.py, octave.py, openbabel.py, openmpi.py
• p nothing to do: psmpi.py, pytorch.py, pyzmq.py, primer3.py, pasha.py, paraver.py, pbdmpi.py, pdt.py, pyquante.py, picard.py, pbdslap.py
• q nothing to do: quantumespresso.py
• r nothing to do: reticulate.py, r.py, ruby.py, rserve.py, rmpi.py
• s nothing to do: superlu.py, suitesparse.py, sympy.py, scalasca1.py, shrimp.py, swig.py, scipy.py, score_p.py, samtools.py, soapdenovo.py
• t nothing to do: torchvision.py, tkinter.py, tornado.py, tau.py, trilinos.py
• u nothing to do: ufc.py
• v nothing to do: velvet.py, vtune.py
• x nothing to do: xcrysden.py, xml.py, xalt.py
• y no easyblocks
• z no easyblocks