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vmd_job.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
import configparser
import sys,os,time
import code
import argparse
import re, datetime
import inspect
# sys.path.append(os.path.realpath('/TiledViz/TVConnections/'))
# from connect import sock
import json
if (os.path.exists("config.tar")):
os.system("tar xf config.tar")
SITE_config='./site_config.ini'
CASE_config="./case_config.ini"
actions_file=open("/home/myuser/actions.json",'r')
tiles_actions=json.load(actions_file)
#launch_actions()
config = configparser.ConfigParser()
config.optionxform = str
config.read(SITE_config)
TILEDOCKERS_path=config['SITE']['TILEDOCKER_DIR']
DOCKERSPACE_DIR=config['SITE']['DOCKERSPACE_DIR']
#NOVNC_URL=config['SITE']['NOVNC_URL']
GPU_FILE=config['SITE']['GPU_FILE']
SSH_FRONTEND=config['SITE']['SSH_FRONTEND']
SSH_LOGIN=config['SITE']['SSH_LOGIN']
SSH_IP=config['SITE']['SSH_IP']
init_IP=config['SITE']['init_IP']
config.read(CASE_config)
CASE=config['CASE']['CASE_NAME']
App="OpenGL Display"
NUM_DOCKERS=int(config['CASE']['NUM_DOCKERS'])
CASE_DOCKER_PATH=config['CASE']['CASE_DOCKER_PATH']
network=config['CASE']['network']
nethost=config['CASE']['nethost']
domain=config['CASE']['domain']
OPTIONssh=config['CASE']['OPTIONssh']
SOCKETdomain=config['CASE']['SOCKETdomain']
DOCKER_NAME=config['CASE']['DOCKER_NAME']
DATA_PATH=config['CASE']['DATA_PATH']
DATA_MOUNT_DOCKER=config['CASE']['DATA_MOUNT_DOCKER']
DATA_PATH_DOCKER=config['CASE']['DATA_PATH_DOCKER']
BIN_PATH=config['CASE']['BIN_PATH']
PYTHON_PATH=config['CASE']['PYTHON_PATH']
OPTIONS=config['CASE']['OPTIONS'].replace("$","").replace('"','')
print("\nOPTIONS from CASE_CONFIG : "+OPTIONS)
OPTIONS=OPTIONS.replace("JOBPath",JOBPath)
OPTIONS=OPTIONS.replace('{','|{').replace('}','}|').split('|')
OPTIONS="".join(list(map( replaceconf,OPTIONS)))
print("OPTIONS after replacement : "+OPTIONS)
CreateTS='create TS='+TileSet+' Nb='+str(NUM_DOCKERS)
client.send_server(CreateTS)
COMMANDStop="echo 'JobID is not defined.'"
# Global commands
# Execute on each/a set of tiles
ExecuteTS='execute TS='+TileSet+" "
# Launch a command on the frontend
LaunchTS='launch TS='+TileSet+" "+JOBPath+' '
# Build VMD dir
# client.send_server(LaunchTS+" mkdir "+CASE)
# print("Out of mkdir %s : %s" % (CASE, str(client.get_OK())))
# get TiledAstrochem package from Github
COMMAND_GIT="git clone -q https://github.com/mmancip/TiledAstrochem.git"
print("command_git : "+COMMAND_GIT)
os.system(COMMAND_GIT)
# Send CASE and SITE files
try:
client.send_server(LaunchTS+' chmod og-rxw '+JOBPath)
print("Out of chmod JOBPath : "+ str(client.get_OK()))
send_file_server(client,TileSet,".", CASE_config, JOBPath)
CASE_config=os.path.join(JOBPath,CASE_config)
send_file_server(client,TileSet,".", SITE_config, JOBPath)
SITE_config=os.path.join(JOBPath,os.path.basename(SITE_config))
send_file_server(client,TileSet,".", "tagliste", JOBPath)
send_file_server(client,TileSet,".", GPU_FILE, JOBPath)
except:
print("Error sending files !")
traceback.print_exc(file=sys.stdout)
try:
code.interact(banner="Try sending files by yourself :",local=dict(globals(), **locals()))
except SystemExit:
pass
COMMAND_TiledAstrochem=LaunchTS+COMMAND_GIT
client.send_server(COMMAND_TiledAstrochem)
print("Out of git clone TiledAstrochem : "+ str(client.get_OK()))
COMMAND_copy=LaunchTS+"cp -rp TiledAstrochem/vmd_client "+\
"TiledAstrochem/kill_vmd "+\
"TiledAstrochem/build_nodes_file "+\
"TiledAstrochem/script_vmd_Spezia.py "+\
"TiledAstrochem/script_vmd_Spezia.vmd "+\
"./"
client.send_server(COMMAND_copy)
print("Out of copy scripts from TiledAstrochem : "+ str(client.get_OK()))
# Launch containers HERE
REF_CAS=str(NUM_DOCKERS)+" "+DATE+" "+DOCKERSPACE_DIR+" "+DOCKER_NAME
#TiledSet=list(range(NUM_DOCKERS))
print("\nREF_CAS : "+REF_CAS)
COMMANDStop=os.path.join(TILEDOCKERS_path,"stop_dockers")+" "+REF_CAS+" "+os.path.join(JOBPath,GPU_FILE)
print("\n"+COMMANDStop)
sys.stdout.flush()
try:
stateVM=Run_dockers()
sys.stdout.flush()
except:
stateVM=False
traceback.print_exc(file=sys.stdout)
kill_all_containers()
try:
taglist = open("tagliste", "r")
except:
stateVM=False
traceback.print_exc(file=sys.stdout)
kill_all_containers()
# TODO : give a liste of lines !
# tab=taglist.readlines()
# line=tab[123]
# file_name=(line[1].split('='))[1].replace('"','')
# Get password file with right number of lines (NUM_DOCKERS)
out_get=0
try:
out_get=get_file_client(client,TileSet,JOBPath,"list_dockers_pass",".")
logging.warning("out get list_dockers_pass : "+str(out_get))
except:
pass
try:
count=0
while( int(out_get) <= 0):
time.sleep(10)
os.system('mv list_dockers_pass list_dockers_pass_')
out_get=get_file_client(client,TileSet,JOBPath,"list_dockers_pass",".")
logging.warning("out get list_dockers_pass : "+str(out_get))
count=count+1
if (count > 10):
logging.error("Error create list_dockers_pass. Job stopped.")
kill_all_containers()
sys.exit(0)
except:
pass
size=0
try:
with open('list_dockers_pass') as f:
size=len([0 for _ in f])
except:
pass
while(size != NUM_DOCKERS):
time.sleep(10)
os.system('mv list_dockers_pass list_dockers_pass_')
try:
out_get=get_file_client(client,TileSet,JOBPath,"list_dockers_pass",".")
except:
pass
try:
with open('list_dockers_pass') as f:
size=len([0 for _ in f])
except:
pass
logging.warning("list_dockers_pass OK %d %d" % (size,NUM_DOCKERS))
try:
if (stateVM):
build_nodes_file()
while(os.path.getsize("nodes.json_init") < 50):
time.sleep(5)
logging.warning("nodes.json_init to small. Try another build.")
build_nodes_file()
if (os.path.getsize("nodes.json_init") < 50):
logging.error("Something has gone wrong with build_nodes_file 2.")
kill_all_containers()
else:
break
sys.stdout.flush()
except:
stateVM=False
traceback.print_exc(file=sys.stdout)
kill_all_containers()
logging.warning("after build_nodes_json %r" % (stateVM))
try:
if (stateVM):
nodes_json_init()
sys.stdout.flush()
except:
stateVM=False
traceback.print_exc(file=sys.stdout)
kill_all_containers()
logging.warning("after nodes_json_init %r" % (stateVM))
try:
if (stateVM):
stateVM=share_ssh_key()
sys.stdout.flush()
except:
stateVM=False
traceback.print_exc(file=sys.stdout)
kill_all_containers()
logging.warning("after share ssh keys %r" % (stateVM))
time.sleep(2)
logging.warning("Before launch_tunnel.")
try:
if (stateVM):
stateVM=launch_tunnel()
sys.stdout.flush()
except:
stateVM=False
traceback.print_exc(file=sys.stdout)
kill_all_containers()
print("after launch tunnel servers %r" % (stateVM))
try:
nodesf=open("nodes.json",'r')
nodes=json.load(nodesf)
nodesf.close()
except:
print("nodes.json doesn't exists !")
print("ls -la")
stateVM=False
traceback.print_exc(file=sys.stdout)
kill_all_containers()
print("after read nodes.json %r" % (stateVM))
try:
if (stateVM):
stateVM=launch_vnc()
except:
print("Problem when launch vnc !")
stateVM=False
traceback.print_exc(file=sys.stdout)
kill_all_containers()
print("after launch vnc servers %r" % (stateVM))
time.sleep(2)
# Launch docker tools
if (stateVM):
all_resize("1440x800")
time.sleep(2)
def launch_one_client(script='vmd_client',tileNum=-1,tileId='001'):
line=taglist.readline().split(' ')
file_name=(line[1].split('='))[1].replace('"','')
COMMAND=' '+os.path.join(CASE_DOCKER_PATH,script)+' '+DATA_PATH_DOCKER+' '+file_name
if ( tileNum > -1 ):
TilesStr=' Tiles=('+containerId(tileNum+1)+') '
else:
TilesStr=' Tiles=('+tileId+') '
print("%s VMD command : %s" % (TilesStr,COMMAND))
CommandTS=ExecuteTS+TilesStr+COMMAND
client.send_server(CommandTS)
client.get_OK()
# TODO : give a list of lines !
def Run_clients():
for i in range(NUM_DOCKERS):
launch_one_client(tileNum=i)
Last_Elt=NUM_DOCKERS-1
try:
if (stateVM):
Run_clients()
sys.stdout.flush()
except:
stateVM=False
traceback.print_exc(file=sys.stdout)
def next_element(script='vmd_client',tileNum=-1,tileId='001'):
line2=taglist.readline()
line=line2.split(' ')
file_name=(line[1].split('='))[1].replace('"','')
COMMAND=' '+os.path.join(CASE_DOCKER_PATH,script)+' '+DATA_PATH_DOCKER+' '+file_name
COMMANDKill=' '+CASE_DOCKER_PATH+"kill_vmd"
if ( tileNum > -1 ):
tileId=containerId(tileNum+1)
else:
tileNum=int(tileId)-1
TilesStr=' Tiles=('+tileId+') '
print("%s VMD command : %s" % (TilesStr,COMMAND))
CommandTSK=ExecuteTS+TilesStr+COMMANDKill
client.send_server(CommandTSK)
client.get_OK()
CommandTS=ExecuteTS+TilesStr+COMMAND
client.send_server(CommandTS)
client.get_OK()
nodes["nodes"][tileNum]["title"]=tileId+" "+os.path.basename(file_name)
if ("variable" in nodes["nodes"][tileNum]):
nodes["nodes"][tileNum]["variable"]="ID-"+tileId+"_"+os.path.basename(file_name)
nodes["nodes"][tileNum]["comment"]=line2
if ("usersNotes" in nodes["nodes"][tileNum]):
nodes["nodes"][tileNum]["usersNotes"]=re.sub(r'file .*',"file "+file_name,
nodes["nodes"][tileNum]["usersNotes"])
nodes["nodes"][tileNum]["tags"]=[]
nodes["nodes"][tileNum]["tags"].append(TileSet)
nodes["nodes"][tileNum]["tags"].append(line[2].replace('"','').replace('Reactants=','1_'))
nodes["nodes"][tileNum]["tags"].append(line[3].replace('"','').replace('Products=','2_'))
nodes["nodes"][tileNum]["tags"].append(line[5].replace('"','').replace('Type=','3_'))
nodes["nodes"][tileNum]["tags"].append(line[7].replace('"','').replace('Method=','4_'))
nodes["nodes"][tileNum]["tags"].append(line[8].replace('"','').replace('Impact_factor={','{5_'))
nodes["nodes"][tileNum]["tags"].append(line[4].replace('"','').replace('Energy={','{6_'))
nodes["nodes"][tileNum]["tags"].append(line[9].replace('"','').replace('Temperature={','{7_'))
nodes["nodes"][tileNum]["tags"].append(line[6].replace('"','').replace('Final_time={','{8_'))
nodesf=open("nodes.json",'w')
nodesf.write(json.dumps(nodes))
nodesf.close()
def init_wmctrl():
client.send_server(ExecuteTS+' wmctrl -l -G')
print("Out of wmctrl : "+ str(client.get_OK()))
if (stateVM):
init_wmctrl()
# def clear_vnc(tileNum=-1,tileId='001'):
# if ( tileNum > -1 ):
# TilesStr=' Tiles=('+containerId(tileNum+1)+') '
# else:
# TilesStr=' Tiles=('+tileId+') '
# client.send_server(ExecuteTS+TilesStr+' x11vnc -R clear-all')
# print("Out of clear-vnc : "+ str(client.get_OK()))
try:
if (stateVM):
clear_vnc_all()
except:
traceback.print_exc(file=sys.stdout)
def start_traj(tileNum=-1,tileId='001'):
Xstart=466
Ystart=198
if ( tileNum > -1 ):
click_point(tileNum=tileNum,X=Xstart,Y=Ystart)
else:
click_point(tileId=tileId,X=Xstart,Y=Ystart)
def stop_traj(tileNum=-1,tileId='001'):
Xstart=446
Ystart=198
if ( tileNum > -1 ):
click_point(tileNum=tileNum,X=Xstart,Y=Ystart)
else:
click_point(tileId=tileId,X=Xstart,Y=Ystart)
def toggle_fullscr():
for i in range(NUM_DOCKERS):
client.send_server(ExecuteTS+' Tiles=('+containerId(i+1)+') '+
'/opt/movewindows OpenGL -b toggle,fullscreen')
client.get_OK()
def launch_changesize(RESOL="1920x1080",tileNum=-1,tileId='001'):
if ( tileNum > -1 ):
TilesStr=' Tiles=('+containerId(tileNum+1)+') '
else:
TilesStr=' Tiles=('+tileId+') '
COMMAND=ExecuteTS+TilesStr+' xrandr --fb '+RESOL
print("call server with : "+COMMAND)
client.send_server(COMMAND)
print("server answer is "+str(client.get_OK()))
def launch_smallsize(tileNum=-1,tileId='001'):
print("Launch launch_changesize smallsize for tile "+str(tileNum))
launch_changesize(tileNum=tileNum,RESOL="950x420")
def launch_bigsize(tileNum=-1,tileId='001'):
print("Launch launch_changesize bigsize for tile "+str(tileNum))
launch_changesize(tileNum=tileNum,RESOL="1920x1200")
def fullscreenApp(windowname="VMD 1.9.2 OpenGL Display",tileNum=-1):
movewindows(windowname=windowname,wmctrl_option='toggle,fullscreen',tileNum=tileNum)
def showGUI(windowname="VMD Main",tileNum=-1):
COMMAND='/opt/movewindows '+windowname+' -b '
movewindows(windowname=windowname,wmctrl_option='toggle,fullscreen',tileNum=tileNum)
launch_actions_and_interact()
try:
print("isActions: "+str(isActions))
except:
print("isActions not defined.")
kill_all_containers()
sys.exit(0)