diff --git a/Golden_Repo/a/AMBER/AMBER-22-gpsmkl-2022a.eb b/Golden_Repo/a/AMBER/AMBER-22-gpsmkl-2022a.eb new file mode 100644 index 0000000000000000000000000000000000000000..a286e14a83f55df35363d25b44f2991005e97a94 --- /dev/null +++ b/Golden_Repo/a/AMBER/AMBER-22-gpsmkl-2022a.eb @@ -0,0 +1,112 @@ +easyblock = 'CMakeMake' + +name = 'AMBER' +version = '22' +versionsuffix = '-AmberTools-23-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, H.M. Aktulga, K. Belfon, I.Y. Ben-Shalom, J.T. Berryman, +S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, G.A. Cisneros, +V.W.D. Cruzeiro, T.A. Darden, N. Forouzesh, G. Giambaşu, T. Giese, +M.K. Gilson, H. Gohlke, A.W. Goetz, J. Harris, S. Izadi, S.A. Izmailov, +K. Kasavajhala, M.C. Kaymak, E. King, A. Kovalenko, T. Kurtzman, +T.S. Lee, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, M. Machado, +V. Man, M. Manathunga, K.M. Merz, Y. Miao, O. Mikhailovskii, G. Monard, +H. Nguyen, K.A. O’Hearn, A. Onufriev, F. Pan, S. Pantano, R. Qi, +A. Rahnamoun, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, +A. Shajan, J. Shen, C.L. Simmerling, N.R. Skrynnikov, J. Smith, +J. Swails, R.C. Walker, J. Wang, J. Wang, H. Wei, X. Wu, Y. Wu, +Y. Xiong, Y. Xue, D.M. York, S. Zhao, Q. Zhu, and P.A. Kollman +(2023), Amber 2023, 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 = [ + 'AmberTools23.tar.bz2', + 'Amber22.tar.bz2', +] +patches = [ + 'AmberTools-21_CMake-FlexiBLAS.patch', + 'pmemd_xray_non_bulk_no_implicit_type.patch', +] + +checksums = [ + 'debb52e6ef2e1b4eaa917a8b4d4934bd2388659c660501a81ea044903bf9ee9d', + '3c887ccbad690fc76ff0b120a3448eae023c08e76582aac07900d4a9708ebd16', + '9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36', + '1dc2c70c597b19736b86d9f0e00743282da68eeeb1b57650db44dc3a5f4da898', +] + +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/amber22_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;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'