diff --git a/Golden_Repo/a/AMBER/AMBER-20-gpsmkl-2023.eb b/Golden_Repo/a/AMBER/AMBER-20-gpsmkl-2023.eb new file mode 100644 index 0000000000000000000000000000000000000000..69a30d503da9198842da9f6dc142c9e73f07ca69 --- /dev/null +++ b/Golden_Repo/a/AMBER/AMBER-20-gpsmkl-2023.eb @@ -0,0 +1,122 @@ +easyblock = 'CMakeMake' + +name = 'AMBER' +version = '20' +versionsuffix = '-AmberTools-21-plumed' + +homepage = 'http://ambermd.org' +description = """ +AMBER: 'Assisted Model Building with Energy Refinement' is a set of molecular +mechanics force fields and a package of molecular simulation programs. + +Citation: +D.A. Case, K. Belfon, I.Y. Ben-Shalom, S.R. Brozell, D.S. Cerutti, +T.E. Cheatham, III, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, G. Giambasu, +M.K. Gilson, H. Gohlke, A.W. Goetz, R. Harris, S. Izadi, S.A. Izmailov, +K. Kasavajhala, A. Kovalenko, R. Krasny, T. Kurtzman, T.S. Lee, S. LeGrand, +P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, V. Man, K.M. Merz, Y. Miao, +O. Mikhailovskii, G. Monard, H. Nguyen, A. Onufriev, F.Pan, S. Pantano, +R. Qi, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, J. Shen, +C. Simmerling, N.R.Skrynnikov, J. Smith, J. Swails, R.C. Walker, J. Wang, +L. Wilson, R.M. Wolf, X. Wu, Y. Xiong, Y. Xue, D.M. York +and P.A. Kollman (2020), +AMBER 2020, University of California, San Francisco. +""" + +toolchain = {'name': 'gpsmkl', 'version': '2022a'} +toolchainopts = {'pic': True} +toolchainopts = {'openmp': True, 'usempi': True} + +builddependencies = [ + ('CMake', '3.23.1'), + ('binutils', '2.38'), +] +dependencies = [ + # ('FFTW.MPI', '3.3.10'), + ('Boost', '1.79.0'), + ('flex', '2.6.4'), + ('NCCL', 'default', '-CUDA-11.7'), + ('netCDF', '4.9.0'), + ('netCDF-Fortran', '4.6.0'), + ('PnetCDF', '1.12.3'), + ('Python', '3.10.4'), + ('matplotlib', '3.5.2', '', ('gcccoremkl', '11.3.0-2022.1.0')), + # ('mpi4py', '3.1.4', '', ('gompi', '2022a')) + ('PLUMED', '2.8.1'), +] + +sources = [ + 'AmberTools21.tar.bz2', + 'Amber20.tar.bz2', +] +patches = [ + 'fix_nmrat_error.patch', + 'adapt_to_python_3_10_api_changes.patch', + 'AmberTools-21_CMake-FlexiBLAS.patch', + 'AmberTools-21_fix_more_blas_argument_problems.patch', + 'AmberTools-21_fix_rism_argument_mismatch.patch', + 'AmberTools-21_fix_xray_fftpack_arg_mismatch.patch', + 'Fix_FFTW_find_error_due_to_MPI_components.patch', + 'Fix_netcdf_find_error_due_to_missed_F77_F90_interfaces.patch', +] + +checksums = [ + 'f55fa930598d5a8e9749e8a22d1f25cab7fcf911d98570e35365dd7f262aaafd', + 'a4c53639441c8cc85adee397933d07856cc4a723c82c6bea585cd76c197ead75', + '00394f987105f047cbacf5f002170a11720f0decbd399a59db6b3b6c8e950677', + 'f5e7ff2fb5e782f5b64a70e750d1ccc6566fd600663dd339f1769ceca60f64d6', + '9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36', + 'c6279b57752239184b942d37f760749494ae0eff95236f3368c76ac0d2726a7c', + '14255e5739cec39303df570f06820c7532f7395e1b73b1e4104377984e2c9fc1', + '99c954e693659efc2a1d121f91510f56408006f0751d91595f45a34b03364e2f', + '468acfd764e8e3787f8f855e724a16ae11e92d36576994297eec26e6e0b41dd0', + '4f409c139ff49f61b1f617a34202b61223c2d8ae474ac9de62313aaad2284afd', +] + +separate_build_dir = True +local_build_mpi_parts = "TRUE" +local_build_cuda_parts = "TRUE" +local_build_cuda_nccl = "TRUE" + +preconfigopts = "CC=gcc && CXX=g++ && COMPILER=GNU " +preconfigopts += " && cd %(builddir)s/amber20_src && " +preconfigopts += " ./update_amber --update && cd ../easybuild_obj && " + +configopts = "-DCOMPILER=GNU -DCHECK_UPDATES=OFF -DAPPLY_UPDATES=OFF -DBUILD_GUI=FALSE " +configopts += " -DINSTALL_TESTS=TRUE -DOPENMP=TRUE -DMPI=%s " % local_build_mpi_parts +configopts += " -DDOWNLOAD_MINICONDA=FALSE -DTRUST_SYSTEM_LIBS=TRUE " +configopts += " -DCUDA=%s " % local_build_cuda_parts +configopts += " -DNCCL=%s " % local_build_cuda_nccl +configopts += " -DBLA_VENDOR=FlexiBLAS " +configopts += " -DFORCE_EXTERNAL_LIBS='boost;netcdf;netcdf-fortran;pnetcdf' " +configopts += " -DUSE_FFT=TRUE " +buildopts = 'NVCC_GENCODE="-gencode=arch=compute_70,code=sm_70 \ + -gencode=arch=compute_75,code=sm_75 \ + -gencode=arch=compute_80,code=sm_80"' + +modextravars = { + 'AMBERHOME': '%(installdir)s/', +} +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +modluafooter = ''' +add_property("arch","gpu") +''' + +group = "amber" + +modloadmsg = ''' + +Info: (1) Check the loaded modules to see if loading the AMBER module +succeeded. If it did, ignore the rest of this message. (2) If AMBER +didn't load, one possible reason is that "amber" is not currently +your primary group. You can temporarily change your primary group by +typing "newgrp amber". (3) If that didn't work, you are probably +not a member of the group "amber", you have to first add yourself +to that group. Visit "https://judoor.fz-juelich.de/", follow the +link "Request access to restricted software", enable "amber" for +your account, wait 15-20 minutes and then try "newgrp amber" again. + +''' + +moduleclass = 'bio'