Commit 27220ee2 authored by Gao, Shang's avatar Gao, Shang
Browse files

added qsub script for moldyn example

parent 1204b5ab

crossbow/crossbowGlobus.py

+9 −1
Original line number Diff line number Diff line
@@ -206,6 +206,7 @@ class crossbowGlobus(crossbowBase): 
        self._activate_endpoint(self.cadesdtn)



        #execute transfer

        print "uploading %s" % filename

        tdata = globus_sdk.TransferData(self.transfer, source_endpoint, self.cadesdtn,

                                    label="Crossbow Transfer", sync_level="checksum")

        tdata.add_item(resource_path,'/data/cades-crossbow/'+package+'/'+filename)
@@ -254,6 +255,7 @@ class crossbowGlobus(crossbowBase): 
        self._activate_endpoint(self.cadesdtn)



        #execute transfer

        print "downloading %s" % resource

        tdata = globus_sdk.TransferData(self.transfer, self.cadesdtn, dest_endpoint,

                                    label="Crossbow Transfer", sync_level="checksum")

        tdata.add_item(resource_path,dest_path+filename)
@@ -336,10 +338,16 @@ class crossbowGlobus(crossbowBase): 
        output: boolean

            whether or not the resource already exists on the endpoint

        '''

        #make sure endpoints are activated

        self._activate_endpoint(endpoint)

        

        #make sure file exists

        filename = os.path.basename(resource_path)

        directory,_ = os.path.split(resource_path)

        try:

            r = self.transfer.operation_ls(endpoint,path=directory,filter='name:'+filename)

        except:

            return False

        found = 0

        for item in r:

            found += 1

crossbow/crossbowMount.py

+2 −0
Original line number Diff line number Diff line
@@ -134,6 +134,7 @@ class crossbowMount(crossbowBase): 
            os.makedirs(self.NFS_path + package)



        #copy file to crossbow NFS

        print "uploading %s" % filename

        prog = ProgressBar(widgets=[Percentage(), Bar()], maxval=100).start()

        self._copy_with_progress(

                resource_path, nfs_path,
@@ -181,6 +182,7 @@ class crossbowMount(crossbowBase): 
        dest_path = destination + os.path.basename(resource_path)

        

        #copy file to local drive

        print "downloading %s" % resource

        prog = ProgressBar(widgets=[Percentage(), Bar()], maxval=100).start()

        self._copy_with_progress(

                resource_path, dest_path,

moldyn_example/conv_vae.pbs

0 → 100644
+35 −0
Original line number Diff line number Diff line 
#!/bin/bash

#PBS -A CSC237

#PBS -N MOLDYN_TEST

#PBS -l walltime=12:00:00

#PBS -l nodes=1

#PBS -lpartition=gpu



module load cudatoolkit

module load cuda



#clone repo/get latest

cd ${HOME}/

if [ ! -d crossbow ]; then

    git clone https://code.ornl.gov/v33/crossbow.git

else

    cd ${HOME}/crossbow/

    git pull

fi



# set python paths

export PATH=/ccs/home/iamshang/anaconda2/bin:/ccs/home/iamshang/anaconda2/lib/python2.7/site-packages:$PATH

export PYTHONPATH=/ccs/home/iamshang/crossbow/crossbow:$PYTHONPATH



# run scripts

cd ${HOME}/crossbow/moldyn_example/scripts/



if [ ! -f 1FME-0_contact_matrix.npy ]; then

    python dcd2array.py ${HOME}/1fme-0

fi



python conv_vae.py 1FME-0_contact_matrix.npy



#cleanup

cd ${HOME}/

rm conv_vae.pbs

moldyn_example/run_experiment.py

0 → 100644
+48 −0
Original line number Diff line number Diff line 
from crossbowGlobus import crossbowGlobus

from crossbowOlcf import crossbowOlcf

import time

import sys



#get pbs to submit

args = (sys.argv)

if len(args) != 2:

    raise Exception("Usage: python run_experiment.py <.pbs file>")

pbs_script = args[1]



#connect to CKAN, make sure 1fme-0 dataset exists

cbow = crossbowGlobus(api_key="eaabd7d9-3cb4-4014-85fe-73736e658472",

                      token_file='../crossbow/refresh-tokens.json')

packages = cbow.list_packages()

if '1fme-0' not in packages:

    raise Exception("1fme-0 package is missing from CKAN")



#connect to OLCF before download starts

olcf = crossbowOlcf('rhea')



#download 1fme-0 dataset if it doesn't exist

print 'downloading resources'

olcf_endpoint = 'ef1a9560-7ca1-11e5-992c-22000b96db58'

path = '/~/1fme-0/'

idx = packages.index("1fme-0")

resources = cbow.list_resources(packages[idx])

dl = []

for resource in resources:

    print 'checking %s' % resource

    if not cbow.check_resource_exists_endpoint('/~/1fme-0/%s' % resource):

        dl_id = cbow.download_resource('1fme-0',resource,dest_endpoint=olcf_endpoint,

                                       dest_path=path,wait_for_download=False)

        dl.append(resource)

                               

#wait for downloads to complete

print "waiting for downloads to complete"

timeout = 600

start = time.time()

for resource in dl:

    while not cbow.check_resource_exists_endpoint('/~/1fme-0/%s' % resource):

        time.sleep(10)

        if time.time() - start > timeout:

            raise Exception('transfer timeout reached')



#submit pbs

print 'submitting pbs script to start experiment'

olcf.qsub(pbs_script)