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Diffstat (limited to 'lib/sunhpc/commands/soft/gromacs/__init__.py')
| -rw-r--r-- | lib/sunhpc/commands/soft/gromacs/__init__.py | 209 |
1 files changed, 209 insertions, 0 deletions
diff --git a/lib/sunhpc/commands/soft/gromacs/__init__.py b/lib/sunhpc/commands/soft/gromacs/__init__.py new file mode 100644 index 0000000..0a02525 --- /dev/null +++ b/lib/sunhpc/commands/soft/gromacs/__init__.py @@ -0,0 +1,209 @@ +# +#coding:utf-8 +# +#Author : QCSun +#Email : qcsun@sunhpc.com +#Times : 2023-04-14 05:21:02 +#WebSite : https://www.sunhpc.com + +import os +import sys +import sunhpc +import shutil + +class command(sunhpc.commands.soft.command): + pass + +class Command(command): + """ + Build the Gromacs software. + + <arg type="string" name="version"> + Specifies the software version. e.g,, version=2022.6 + </arg> + + <param type="path" name="prefix"> + Specifies the software install path. + Default: /share/apps/soft/gromacs + </param> + + <param type="path" name="envs"> + Specifies the software env path. + Default: /share/apps/envs + </param> + + <param type="path" name="source"> + Specifies the software source path. e.g,, /mnt/usb + Default: /mnt/usb + </param> + + <param type="Bool" name="mpi"> + Enable mpi. Default: No + </param> + + <param type="Bool" name="cuda"> + Enable cuda. Default: No + </param> + + <example cmd='soft gromacs prefix=/share/apps/soft/gromacs version=2022.6'> + install the gromacs software. + </example> + """ + def run(self, params, args): + + (prefix, version, source, envs, mpistatus, cudastatus) = self.fillParams([ + ('prefix', '/share/apps/soft/gromacs'), + ('version', None), + ('source', '/mnt/usb'), + ('envs', '/share/apps/envs'), + ('mpi', None), + ('cuda', None), + ]) + + if len(args): + version = args[0] + + if not version: + self.msg('must supply an "Gromacs version" e.g,, version=2022.6, 2023, 2023.2', 'a') + + try: + os.makedirs(prefix) + self.msg("The %s directory does not exist,and it will be created." % prefix, 'w') + except FileExistsError: + pass + + if not os.path.exists(envs): + os.makedirs(envs) + + basename = 'gromacs-%s' % version + filename = '%s.tar.gz' % basename + + softname = os.path.join(source, 'hpcsoft/Gromacs', filename) + if not os.path.exists(softname): + self.msg('The "%s" not found.' % softname, 'a') + + destname = os.path.join(prefix, version) + self.msg('Start decompress the %s software to the /tmp directory...' % basename) + + tmpdir = os.path.join(os.sep, 'tmp', basename) + #if os.path.exists(tmpdir): + # os.system('rm -rf /tmp/%s' % basename) + #os.system('tar -xf %s -C /tmp' % softname) + + # chdir to /tmp/gromacs-version + os.chdir(tmpdir) + cwd = os.getcwd() + + cmake = shutil.which('cmake') + try: + os.makedirs('build/src/external/build-fftw/fftwBuild-prefix/src') + except FileExistsError: + pass + + # copy fftw to src dirs + srcfile = os.path.join(source, 'hpcsoft', 'fftw', 'fftw-3.3.8.tar.gz') + dstfile = 'build/src/external/build-fftw/fftwBuild-prefix/src/fftw-3.3.8.tar.gz' + shutil.copyfile(srcfile, dstfile) + + + regname = 'regressiontests-%s' % version + regfile = os.path.join(source, 'hpcsoft', 'Gromacs', '%s.tar.gz' % regname) + regpath = os.path.join(tmpdir, 'build', regname) + if os.path.exists(regpath): + shutil.rmtree(regpath) + + os.system('tar -xf %s -C build/' % regfile) + os.chdir('build') + + self.build_serial(destname, regname) + if mpistatus: + mpirun = shutil.which('mpirun') + if not mpirun: + self.msg('mpirun command not found.please install an mpirun software.', 'a') + self.build_mpirun(destname, regname) + + if cudastatus: + if not cudapath: + self.msg('must supply an CUDA Path. e.g,, cuda=/usr/local/cuda', 'a') + self.build_nvidia(destname, regname, cudapath) + + + gsenv = os.path.join(envs, '%s-env.sh' % basename) + with open(gsenv, 'w') as f: + f.write('#!/bin/sh\n') + f.write('#\n# %s env config\n#\n\n' % basename) + f.write('source %s/bin/GMXRC\n' % destname) + + # create shared user and group. + self.msg('') + self.msg('--------------------------------------------------------') + self.msg('Create a shared group to run the %s software.' % basename) + self.msg(' 1, groupadd -g 888 public ') + self.msg(' 2, usermod -G public dell ') + self.msg(' 3, chown -R root:public %s' % destname)) + self.msg('--------------------------------------------------------') + self.msg('') + self.msg(' source %s' % gsenv) + self.msg('--------------------------------------------------------') + + os.system('source %s' % gsenv) + os.system('gmx -version') + + def build_serial(self, destname, regname): + query = 'cmake .. -DCMAKE_INSTALL_PREFIX=%s ' % destname + query += '-DGMX_BUILD_OWN_FFTW=ON ' + query += '-DREGRESSIONTEST_PATH=%s' % regname + os.system(query) + os.system('make && make check && make install') + + def build_mpirun(self, destname, regname): + query = 'cmake .. -DCMAKE_INSTALL_PREFIX=%s ' % destname + query += '-DGMX_BUILD_OWN_FFTW=ON ' + query += '-DGMX_MPI=ON ' + query += '-DREGRESSIONTEST_PATH=%s' % regname + os.system(query) + os.system('make && make check && make install') + + def build_nvidia(self, destname, regname, cudapath): + query = 'cmake .. -DCMAKE_INSTALL_PREFIX=%s ' % destname + query += '-DGMX_BUILD_OWN_FFTW=ON ' + query += '-DGMX_GPU=CUDA ' # NVIDIA CUDA support enabled + query += '-DCUDA_TOOLKIT_ROOT_DIR=%s' % cudapath + #query += '-DGMX_GPU=OpenCL ' # OpenCL support enabled + #query += '-DGMX_GPU=SYCL ' # using Intel oneAPI DPC++ by default. + #query += '-DGMX_SYCL_HIPSYCL=ON ' + #query += '-DGMX_DOUBLE=on ' + #query += '-DGMX_SIMD=xxx ' # specify the level of SIMD support + #query += '-DBUILD_SHARED_LIBS=off ' + query += '-DREGRESSIONTEST_PATH=%s' % regname + os.system(query) + os.system('make && make check && make install') + + + + + + + + + + + + + + + + + + + + + + + + + + + + + |