def pre_loop(self):
"""
function : transfers input files and intermediate executables
pre_grlsd_loop :-
Purpose : Transfers files, Split the input file into smaller files to be used by each of the
gromacs instances in the first iteration.
Arguments : --inputfile = file to be split
--numCUs = number of simulation instances/ number of smaller files
"""
k = Kernel(name="md.pre_grlsd_loop")
k.upload_input_data = [
Kconfig.md_input_file,
Kconfig.lsdm_config_file,
Kconfig.top_file,
Kconfig.mdp_file,
"{0}/spliter.py".format(Kconfig.misc_loc),
"{0}/gro.py".format(Kconfig.misc_loc),
"{0}/run.py".format(Kconfig.misc_loc),
"{0}/pre_analyze.py".format(Kconfig.misc_loc),
"{0}/post_analyze.py".format(Kconfig.misc_loc),
"{0}/select.py".format(Kconfig.misc_loc),
"{0}/reweighting.py".format(Kconfig.misc_loc),
]
k.download_input_data = [
"http://sourceforge.net/p/lsdmap/git/ci/extasy-0.1-rc2/tree/lsdmap/lsdm.py?format=raw > lsdm.py"
]
k.arguments = [
"--inputfile={0}".format(os.path.basename(Kconfig.md_input_file)),
"--numCUs={0}".format(Kconfig.num_CUs),
]
return k
def step_1(self, instance):
k = Kernel(name="misc.chksum")
k.arguments = ["--inputfile=UTF-8-demo.txt", "--outputfile=checksum{0}.sha1".format(instance)]
k.download_input_data = "htpttpt://malformed.url"
k.download_output_data = "checksum{0}.sha1".format(instance)
return k
def pre_loop(self):
k = Kernel(name="misc.chksum")
k.arguments = ["--inputfile=UTF-8-demo.txt", "--outputfile=checksum.sha1"]
k.download_input_data = "htpttpt://malformed.url"
k.download_output_data = "checksum.sha1"
return k
def step_1(self, instance):
k = Kernel(name="misc.chksum")
k.arguments = [
"--inputfile=UTF-8-demo.txt",
"--outputfile=checksum{0}.sha1".format(instance)
]
k.download_input_data = "http://testing.saga-project.org/cybertools/UTF-8-demo.txt"
k.download_output_data = "checksum{0}.sha1".format(instance)
def step_1(self, instance):
k = Kernel(name="misc.chksum")
k.arguments = [
"--inputfile=UTF-8-demo.txt",
"--outputfile=checksum{0}.sha1".format(instance)
]
k.download_input_data = "htpttpt://malformed.url"
k.download_output_data = "checksum{0}.sha1".format(instance)
return k
def step_1(self, instance):
"""This step downloads a sample UTF-8 file from a remote websever and
calculates the SHA1 checksum of that file. The checksum is written
to an output file and tranferred back to the host running this
script.
"""
k = Kernel(name="misc.chksum")
k.arguments = ["--inputfile=UTF-8-demo.txt", "--outputfile=checksum{0}.sha1".format(instance)]
k.download_input_data = "http://gist.githubusercontent.com/oleweidner/6084b9d56b04389717b9/raw/611dd0c184be5f35d75f876b13604c86c470872f/gistfile1.txt > UTF-8-demo.txt"
k.download_output_data = "checksum{0}.sha1".format(instance)
return k
def step_1(self, instance):
"""This step downloads a sample UTF-8 file from a remote websever and
calculates the SHA1 checksum of that file. The checksum is written
to an output file and tranferred back to the host running this
script.
"""
k = Kernel(name="misc.chksum")
k.arguments = [
"--inputfile=UTF-8-demo.txt",
"--outputfile=checksum{0}.sha1".format(instance)
]
k.download_input_data = "http://gist.githubusercontent.com/oleweidner/6084b9d56b04389717b9/raw/611dd0c184be5f35d75f876b13604c86c470872f/gistfile1.txt > UTF-8-demo.txt"
k.download_output_data = "checksum{0}.sha1".format(instance)
return k
def step_01(self, instance):
"""This steps does the trajectory simulation. First, the input files
are downloaded from a remote HTTP server. Next, NAMD reads the 'inp'
("input") file and simulates the trajectory. Finally, the output is
transferred back to the machine on which this script is executed.
"""
namd = Kernel(name="md.namd")
namd.core = 4
namd.arguments = ["eq{0}.inp".format(instance)]
namd.download_input_data = ["http://testing.saga-project.org/cybertools/sampledata/BAC-SIMCHAIN/simchain-sample-data/complex.pdb > complex.pdb",
"http://testing.saga-project.org/cybertools/sampledata/BAC-SIMCHAIN/simchain-sample-data/complex.top > complex.top",
"http://testing.saga-project.org/cybertools/sampledata/BAC-SIMCHAIN/simchain-sample-data/cons.pdb > cons.pdb",
"http://testing.saga-project.org/cybertools/sampledata/BAC-SIMCHAIN/simchain-sample-data/eq0.inp > eq{0}.inp".format(instance)]
namd.download_output_data = "STDOUT > eq{0}.out".format(instance)
return namd
def step_01(self, instance):
"""This steps does the trajectory analysis, a.k.a free energy
calculation. First, the input files are downloaded from a remote
HTTP server. Next, MMPBSA reads the 'traj' ("trajectory") file and
carries out the analysis. Finally, the output is transferred back to
the machine on which this script is executed.
"""
mmpbsa = Kernel(name="md.mmpbsa")
mmpbsa.core = 4
mmpbsa.arguments = ["-i nmode.5h.py", "-cp com.top.2", "-rp rec.top.2", "-lp lig.top", "-y rep{0}.traj".format(instance)]
mmpbsa.download_input_data = ["http://testing.saga-project.org/cybertools/sampledata/BAC-MMBPSA/com.top.2 > com.top.2",
"http://testing.saga-project.org/cybertools/sampledata/BAC-MMBPSA/rec.top.2 > rec.top.2",
"http://testing.saga-project.org/cybertools/sampledata/BAC-MMBPSA/lig.top > lig.top",
"http://testing.saga-project.org/cybertools/sampledata/BAC-MMBPSA/nmode.5h.py > nmode.5h.py",
"http://testing.saga-project.org/cybertools/sampledata/BAC-MMBPSA/trajectories/rep1.traj > rep{0}.traj".format(instance)]
mmpbsa.download_output_data = "STDOUT > eq{0}.out".format(instance)
return mmpbsa
def step_01(self, instance):
"""This steps does the trajectory simulation. First, the input files
are downloaded from a remote HTTP server. Next, NAMD reads the 'inp'
("input") file and simulates the trajectory. Finally, the output is
transferred back to the machine on which this script is executed.
"""
namd = Kernel(name="md.namd")
namd.core = 4
namd.arguments = ["eq{0}.inp".format(instance)]
namd.download_input_data = [
"http://testing.saga-project.org/cybertools/sampledata/BAC-SIMCHAIN/simchain-sample-data/complex.pdb > complex.pdb",
"http://testing.saga-project.org/cybertools/sampledata/BAC-SIMCHAIN/simchain-sample-data/complex.top > complex.top",
"http://testing.saga-project.org/cybertools/sampledata/BAC-SIMCHAIN/simchain-sample-data/cons.pdb > cons.pdb",
"http://testing.saga-project.org/cybertools/sampledata/BAC-SIMCHAIN/simchain-sample-data/eq0.inp > eq{0}.inp"
.format(instance)
]
namd.download_output_data = "STDOUT > eq{0}.out".format(instance)
return namd
def set1element_initialization(self,element):
"""The initialization step creates the necessary files that will be
needed for the comparison over the elements of the set.
"""
print "Element creation {0}".format(element)
k = Kernel(name="my.qpc")
k.arguments = ["--inputfile=traj_flat%d.npz.npy"%(element),
"--filename=traj_flat%d.npz.npy"%(element)]
# When the input data are in a web server use download input data as the example below.
k.download_input_data = ["http://eceweb1.rutgers.edu/~ip176/traj_flat{0}.npz.npy > traj_flat{0}.npz.npy".format(element)]
# If the input data are in a local folder use the following
# k.upload_input_data = ["/<PATH>/<TO>/<FOLDER>/<WITH>/traj_flat{x}.npz.npy > traj_flat{x}.npz.npy"]
# If the input data are in a folder to the target machine use the following
# k.link_input_data = ["/<PATH>/<TO>/<FOLDER>/<WITH>/traj_flat{x}.npz.npy > traj_flat{x}.npz.npy"]
print "Created {0}".format(element)
return k
def step_01(self, instance):
"""This steps does the trajectory analysis, a.k.a free energy
calculation. First, the input files are downloaded from a remote
HTTP server. Next, MMPBSA reads the 'traj' ("trajectory") file and
carries out the analysis. Finally, the output is transferred back to
the machine on which this script is executed.
"""
mmpbsa = Kernel(name="md.mmpbsa")
mmpbsa.core = 4
mmpbsa.arguments = [
"-i nmode.5h.py", "-cp com.top.2", "-rp rec.top.2", "-lp lig.top",
"-y rep{0}.traj".format(instance)
]
mmpbsa.download_input_data = [
"http://testing.saga-project.org/cybertools/sampledata/BAC-MMBPSA/com.top.2 > com.top.2",
"http://testing.saga-project.org/cybertools/sampledata/BAC-MMBPSA/rec.top.2 > rec.top.2",
"http://testing.saga-project.org/cybertools/sampledata/BAC-MMBPSA/lig.top > lig.top",
"http://testing.saga-project.org/cybertools/sampledata/BAC-MMBPSA/nmode.5h.py > nmode.5h.py",
"http://testing.saga-project.org/cybertools/sampledata/BAC-MMBPSA/trajectories/rep1.traj > rep{0}.traj"
.format(instance)
]
mmpbsa.download_output_data = "STDOUT > eq{0}.out".format(instance)
return mmpbsa
def set1element_initialization(self, element):
"""The initialization step creates the necessary files that will be
needed for the comparison over the elements of the set.
"""
print "Element creation {0}".format(element)
k = Kernel(name="my.qpc")
k.arguments = [
"--inputfile=traj_flat%d.npz.npy" % (element),
"--filename=traj_flat%d.npz.npy" % (element)
]
# When the input data are in a web server use download input data as the example below.
k.download_input_data = [
"http://eceweb1.rutgers.edu/~ip176/traj_flat{0}.npz.npy > traj_flat{0}.npz.npy"
.format(element)
]
# If the input data are in a local folder use the following
# k.upload_input_data = ["/<PATH>/<TO>/<FOLDER>/<WITH>/traj_flat{x}.npz.npy > traj_flat{x}.npz.npy"]
# If the input data are in a folder to the target machine use the following
# k.link_input_data = ["/<PATH>/<TO>/<FOLDER>/<WITH>/traj_flat{x}.npz.npy > traj_flat{x}.npz.npy"]
print "Created {0}".format(element)
return k