replace run_cmd with run_shell_cmd in custom easyblock for Amber (amber.py)

[branfosj]

(created using eb --new-pr)

• EB_Amber used in AmberTools
• No use of EB_Amber in blocks

[branfosj]

Test report by @branfosj

Overview of tested easyconfigs (in order)

• SUCCESS Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb
• SUCCESS Amber-22.4-foss-2022a-AmberTools-22.5-CUDA-11.7.0.eb

Build succeeded for 2 out of 2 (2 easyconfigs in total)
bear-pg0103u01a.bear.cluster - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Gold 6330 CPU @ 2.00GHz (icelake), 1 x NVIDIA NVIDIA A100-PCIE-40GB, 520.61.05, Python 3.6.8
See https://gist.github.com/branfosj/2c6059014b58a489cdb86dfb2384ecb9 for a full test report.

[boegel]

lgtm

[branfosj]

Test report by @branfosj

Overview of tested easyconfigs (in order)

• SUCCESS Amber-22.0-foss-2021b-AmberTools-22.3.eb
• SUCCESS AmberTools-21-intel-2021b.eb
• SUCCESS netCDF-Fortran-4.5.3-gompi-2020b.eb
• SUCCESS PnetCDF-1.12.2-gompi-2020b.eb
• SUCCESS Amber-20.11-foss-2020b-AmberTools-21.3.eb

Build succeeded for 5 out of 5 (3 easyconfigs in total)
bear-pg0105u03a - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Platinum 8360Y CPU @ 2.40GHz (icelake), Python 3.6.8
See https://gist.github.com/branfosj/0962ad06e74e4f63a89b0157da3f72f8 for a full test report.