add autodock,cmake,gaussian,gromacs

lib/sunhpc/commands/soft/autodock/__init__.py

@@ -16,39 +16,45 @@ class command(sunhpc.commands.soft.command):
 
 class Command(command):
     """
-    Build the Gaussian software.
+    Build the AutoDock software.
 
     <arg type="string" name="version">
-    Specifies the software version. e.g,, version=03/09/16
+    Specifies the software version. e.g,, version=4.2.6
     </arg>
 
     <param type="path" name="prefix">
     Specifies the software install path.
+    Default: /share/apps/soft/autodock
     </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>
 
-    <example cmd='soft gaussian prefix=/share/apps/soft version=16'>
+    <example cmd='soft autodock prefix=/share/apps/soft version=4.2.6'>
-    install the gaussian software.
+    install the autodock software.
     </example>
     """
     def run(self, params, args):
 
         (prefix, version, source, envs) = self.fillParams([
-            ('prefix', '/share/apps/soft'),
+            ('prefix', '/share/apps/soft/autodock'),
             ('version', None),
             ('source', '/mnt/usb'),
             ('envs', '/share/apps/envs'),
             ])
 
+        if len(args):
+            version = args[0]
+
         if not version:
-            self.msg('must supply an "Gaussian version" e.g,, version=03/09/16', 'a')
+            self.msg('must supply an "AutoDock version" e.g,, version=4.2.6', 'a')
 
         try:
             os.makedirs(prefix)
@@ -59,37 +65,43 @@ class Command(command):
         if not os.path.exists(envs):
             os.makedirs(envs)
 
-        softname = 'Gaussian%s' % version
+        if version == '4.2.6':
-
+            basename = 'autodock-4.2.6'
-        softdirs = os.path.join(source, 'hpcsoft')
-        softlist = os.listdir(softdirs)
-
-        if 'Gaussian' not in softlist:
-            self.msg('The "%s" software was not found in the %s directory.' % (softname, softdirs), 'a')
-
-        gspathname = os.path.join(softdirs, 'Gaussian', softname, 'Gaussian16-a03.tbz')
-
-
-        gaussian = os.path.join(prefix, 'g%s' % version)
-        if os.path.exists(gaussian):
-            self.msg('The %s already exists,to reinstall it, remove it first.' % gaussian)
         else:
-            self.msg('Start installing the %s software to the %s directory...' % (softname, prefix))
+            self.msg('Version error, Try use version number "4.2.6"', 'a')
-            os.system('tar -xf %s -C %s' % (gspathname, prefix))
 
-        gsenv = os.path.join(envs, 'g16-env.sh')
+        filename = '%s.tar.bz2' % basename
+
+        softname = os.path.join(source, 'hpcsoft/AutoDock', filename)
+        if not os.path.exists(softname):
+            self.msg('The "%s" not found.' % softname, 'a')
+
+        destname = os.path.join(prefix, basename)
+        softlist = os.listdir(prefix)
+
+        if basename in softlist:
+            self.msg('The %s already exists,to reinstall it, remove it first.' % basename, 'w')
+        else:
+            self.msg('Start installing the %s software to the %s directory...' % (basename, prefix))
+            os.system('tar -xf %s -C %s' % (softname, prefix))
+
+        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' % gaussian)
+            f.write('#\n# %s env config\n#\n\n' % basename)
-            f.write('export g%sroot=%s\n' % (version, prefix))
+            f.write('export PATH=%s/%s:$PATH\n' % (prefix, basename))
-            f.write('source $g%sroot/g%s/bsd/g%s.profile\n\n' % (version, version, version))
-            f.write('export GAUSS_SCDIR=~/gstmp\n')
 
         # create shared user and group.
-        self.msg('Create a shared group to run the %s software.' % softname) 
+        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/g%s' % (prefix, version))
+        self.msg('  3, chown    -R root:public %s/%s' % (prefix, basename))
+        self.msg('--------------------------------------------------------')
+        self.msg('')
+        self.msg('  source %s' % gsenv)
+        self.msg('--------------------------------------------------------')
 
 
 

lib/sunhpc/commands/soft/cmake/__init__.py

@@ -0,0 +1,137 @@
+#
+#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 Cmake software.
+
+    <arg type="string" name="version">
+    Specifies the software version. e.g,, version=3.26.4
+    </arg>
+
+    <param type="path" name="prefix">
+    Specifies the software install path.
+    Default: /share/apps/soft/cmake
+    </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>
+
+    <example cmd='soft cmake prefix=/share/apps/soft version=3.26.4'>
+    install the cmake software.
+    </example>
+    """
+    def run(self, params, args):
+
+        (prefix, version, source, envs) = self.fillParams([
+            ('prefix', '/share/apps/soft/cmake'),
+            ('version', '3.26.4'),
+            ('source', '/mnt/usb'),
+            ('envs', '/share/apps/envs'),
+            ])
+
+        if len(args):
+            version = args[0]
+
+        if not version:
+            self.msg('must supply an "Cmake version" e.g,, version=3.26.4', '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)
+
+        if version == '3.26.4':
+            basename = 'cmake-%s-linux-x86_64' % version
+        else:
+            self.msg('Version error, Try use version number "3.26.4"', 'a')
+
+        filename = '%s.sh' % basename
+
+        softname = os.path.join(source, 'hpcsoft/Cmake', filename)
+        if not os.path.exists(softname):
+            self.msg('The "%s" not found.' % softname, 'a')
+
+        destname = os.path.join(prefix, version)
+        if not os.path.exists(destname):
+            os.makedirs(destname)
+
+        makename = os.path.join(prefix, version, 'bin', 'cmake')
+        if os.path.exists(makename):
+            self.msg('The "cmake" already exists,to reinstall it, remove it first.', 'w')
+        else:
+            self.msg('Start installing the cmake software to the %s directory...' % (destname))
+            # ./cmake-3.26.4-linux-x86_64.sh --prefix=/share/apps/soft/cmake --skip-license
+            cmd = 'sh %s --prefix=%s --skip-license' % (softname, destname)
+            print ('cmd---->', cmd)
+            os.system('sh %s --prefix=%s --skip-license' % (softname, destname))
+
+        gsenv = os.path.join(envs, 'cmake-%s-env.sh' % version)
+        with open(gsenv, 'w') as f:
+            f.write('#!/bin/sh\n')
+            f.write('#\n# %s env config\n#\n\n' % basename)
+            f.write('export PATH=%s/bin:$PATH\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' % prefix)
+        self.msg('--------------------------------------------------------')
+        self.msg('')
+        self.msg('  source %s' % gsenv)
+        self.msg('--------------------------------------------------------')
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lib/sunhpc/commands/soft/gaussian/__init__.py

@@ -99,8 +99,6 @@ class Command(command):
 
 
         softlist = os.listdir(prefix)
-        print ('------softlist-----', softlist)
-        print ('------basename-----', basename)
         if basename in softlist:
             self.msg('The %s already exists,to reinstall it, remove it first.' % gaussian)
         else:
@@ -111,17 +109,21 @@ class Command(command):
         with open(gsenv, 'w') as f:
             f.write('#!/bin/sh\n')
             f.write('#\n# %s env config\n#\n\n' % gaussian)
-            f.write('export g%sroot=%s\n' % (version, prefix))
+            f.write('export g%sroot=%s/%s\n' % (version, prefix, basename))
             f.write('source $g%sroot/g%s/bsd/g%s.profile\n\n' % (version, version, version))
             f.write('export GAUSS_SCDIR=~/gstmp\n')
 
         # create shared user and group.
-        self.msg('Create a shared group to run the %s software.' % softname) 
+        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/%s' % (prefix, basename))
+        self.msg('--------------------------------------------------------')
         self.msg('')
         self.msg('  source %s' % gsenv)
+        self.msg('--------------------------------------------------------')
 
 
 

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')
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