drelu
commented
11 years ago It works on Stampede as well:
03/28/2013 02:42:48 PM - bigjob - INFO - Loading BigJob version: 0.4.128 on login1.stampede.tacc.utexas.edu 03/28/2013 02:42:53 PM - bigjob - INFO - Using SAGA Bliss. Start Pilot Job/BigJob at: fork://localhost 03/28/2013 02:42:53 PM - bigjob - DEBUG - Utilizing Redis Backend 03/28/2013 02:42:53 PM - bigjob - DEBUG - Parsing URL: redis://Oily9tourSorenavyvault@redis01.tacc.utexas.edu:6379 03/28/2013 02:42:55 PM - bigjob - DEBUG - redis:// redis01.tacc.utexas.edu 6379 03/28/2013 02:42:55 PM - bigjob - DEBUG - Connect to Redis: redis01.tacc.utexas.edu Port: 6379 03/28/2013 02:42:55 PM - bigjob - DEBUG - init BigJob w/: redis://Oily9tourSorenavyvault@redis01.tacc.utexas.edu:6379 03/28/2013 02:42:55 PM - bigjob - DEBUG - initialized BigJob: bigjob:bj-afbad9ba-97df-11e2-ab5e-d4ae52a0f02f 03/28/2013 02:42:55 PM - bigjob - DEBUG - create pilot job entry on backend server: bigjob:bj-afbad9ba-97df-11e2-ab5e-d4ae52a0f02f:localhost 03/28/2013 02:42:55 PM - bigjob - DEBUG - update state of pilot job to: Unknown stopped: False 03/28/2013 02:42:55 PM - bigjob - DEBUG - update description of pilot job to: None 03/28/2013 02:42:55 PM - bigjob - DEBUG - set pilot state to: Unknown 03/28/2013 02:42:55 PM - bigjob - DEBUG - setting walltime to: 10 03/28/2013 02:42:55 PM - bigjob - DEBUG - Use SSH backend 03/28/2013 02:42:56 PM - bigjob - DEBUG - ['/home1/01131/tg804093/src/BigJob/pilot/filemanagement/../../../webhdfs-py/', '/home1/01131/tg804093/src/BigJob/examples/../', '/home1/01131/tg804093/src/BigJob/examples', '/home1/01131/tg804093/.bigjob/python/lib/python2.7/site-packages/distribute-0.6.34-py2.7.egg', '/home1/01131/tg804093/.bigjob/python/lib/python2.7/site-packages/pip-1.2.1-py2.7.egg', '/home1/01131/tg804093/.bigjob/python/lib/python2.7/site-packages/pexpect-2.4-py2.7.egg', '/home1/01131/tg804093/.bigjob/python/lib/python2.7/site-packages/simplejson-2.0.9-py2.7-linux-x86_64.egg', '/home1/01131/tg804093/.bigjob/python/lib/python2.7/site-packages/boto-2.2.2-py2.7.egg', '/home1/01131/tg804093/.bigjob/python/lib/python2.7/site-packages/globusonline_transfer_api_client-0.10.13-py2.7.egg', '/home1/01131/tg804093/.bigjob/python/lib/python2.7/site-packages/google_api_python_client-1.0-py2.7.egg', '/home1/01131/tg804093/.bigjob/python/lib/python2.7/site-packages/bliss-0.2.7-py2.7.egg', '/home1/01131/tg804093/.bigjob/python/lib/python2.7/site-packages/redis-2.2.4-py2.7.egg', '/home1/01131/tg804093/.bigjob/python/lib/python2.7/site-packages/virtualenv-1.8.4-py2.7.egg', '/home1/01131/tg804093/.bigjob/python/lib/python2.7/site-packages/threadpool-1.2.7-py2.7.egg', '/home1/01131/tg804093/.bigjob/python/lib/python2.7/site-packages/uuid-1.30-py2.7.egg', '/home1/01131/tg804093/.bigjob/python/lib/python2.7/site-packages/python_gflags-2.0-py2.7.egg', '/home1/01131/tg804093/.bigjob/python/lib/python2.7/site-packages/httplib2-0.7.7-py2.7.egg', '/home1/01131/tg804093/.bigjob/python/lib/python2.7/site-packages/paramiko_on_pypi-1.7.6-py2.7.egg', '/home1/01131/tg804093/.bigjob/python/lib/python2.7/site-packages/pycrypto_on_pypi-2.3-py2.7-linux-x86_64.egg', '/home1/01131/tg804093/.bigjob/python/lib/python2.7/site-packages/python_hostlist-1.14-py2.7.egg', '/home1/01131/tg804093/.bigjob/python/lib/python2.7/site-packages/BigJob-0.4.128-py2.7.egg', '/opt/apps/python/epd/7.3.2/modules/lib/python', '/opt/apps/python/epd/7.3.2/lib', '/home1/01131/tg804093/.bigjob/python/lib/python27.zip', '/home1/01131/tg804093/.bigjob/python/lib/python2.7', '/home1/01131/tg804093/.bigjob/python/lib/python2.7/plat-linux2', '/home1/01131/tg804093/.bigjob/python/lib/python2.7/lib-tk', '/home1/01131/tg804093/.bigjob/python/lib/python2.7/lib-old', '/home1/01131/tg804093/.bigjob/python/lib/python2.7/lib-dynload', '/opt/apps/python/epd/7.3.2/lib/python2.7', '/opt/apps/python/epd/7.3.2/lib/python2.7/plat-linux2', '/opt/apps/python/epd/7.3.2/lib/python2.7/lib-tk', '/home1/01131/tg804093/.bigjob/python/lib/python2.7/site-packages', '/opt/apps/python/epd/7.3.2/lib/python2.7/site-packages', '/opt/apps/python/epd/7.3.2/lib/python2.7/site-packages/PIL', '/home1/01131/tg804093/src/BigJob/examples/../bigjob', '/home1/01131/tg804093/src/BigJob/examples/../pilot/impl/../..', '/home1/01131/tg804093/src/BigJob/examples/../pilot/filemanagement/../..'] 03/28/2013 02:42:56 PM - bigjob - WARNING - WebHDFS package not found. 03/28/2013 02:42:56 PM - bigjob - DEBUG - Security Context: None 03/28/2013 02:42:56 PM - bigjob - DEBUG - BigJob working directory: ssh://localhost//tmp/bj-afbad9ba-97df-11e2-ab5e-d4ae52a0f02f 03/28/2013 02:42:56 PM - bigjob - DEBUG - Create directory: //tmp/bj-afbad9ba-97df-11e2-ab5e-d4ae52a0f02f 03/28/2013 02:42:56 PM - bigjob - DEBUG - ssh -o UserKnownHostsFile=/dev/null -o StrictHostKeyChecking=no -o NumberOfPasswordPrompts=0 localhost mkdir //tmp/bj-afbad9ba-97df-11e2-ab5e-d4ae52a0f02f 03/28/2013 02:42:57 PM - bigjob - DEBUG - Run ssh -o UserKnownHostsFile=/dev/null -o StrictHostKeyChecking=no -o NumberOfPasswordPrompts=0 localhost mkdir //tmp/bj-afbad9ba-97df-11e2-ab5e-d4ae52a0f02f Output: ["Warning: Permanently added 'localhost' (RSA) to the list of known hosts.\r\r\n"] 03/28/2013 02:42:57 PM - bigjob - WARNING - No file staging adaptor found. 03/28/2013 02:42:57 PM - bigjob - DEBUG - BJ Working Directory: /tmp 03/28/2013 02:42:57 PM - bigjob - DEBUG - Adaptor specific modifications: fork 03/28/2013 02:42:57 PM - bigjob - DEBUG - Escape Bliss 03/28/2013 02:42:57 PM - bigjob - DEBUG - "import sys import os import urllib import sys import time start_time = time.time() home = os.environ.get(\"HOME\")
print \"Home: \" + home
if home==None: home = os.getcwd() BIGJOB_AGENT_DIR= os.path.join(home, \".bigjob\") if not os.path.exists(BIGJOB_AGENT_DIR): os.mkdir (BIGJOB_AGENT_DIR) BIGJOB_PYTHON_DIR=BIGJOB_AGENT_DIR+\"/python/\" if not os.path.exists(BIGJOB_PYTHON_DIR): os.mkdir(BIGJOB_PYTHON_DIR) BOOTSTRAP_URL=\"https://raw.github.com/saga-project/BigJob/master/bootstrap/bigjob-bootstrap.py\" BOOTSTRAP_FILE=BIGJOB_AGENT_DIR+\"/bigjob-bootstrap.py\"
ensure that BJ in .bigjob is upfront in sys.path
sys.path.insert(0, os.getcwd() + \"/../\") p = list() for i in sys.path: if i.find(\".bigjob/python\")>1: p.insert(0, i) for i in p: sys.path.insert(0, i) print \"Python path: \" + str(sys.path) print \"Python version: \" + str(sys.version_info) try: import saga except: print \"SAGA and SAGA Python Bindings not found.\"; try: import bigjob.bigjob_agent except: print \"BigJob not installed. Attempt to install it.\"; opener = urllib.FancyURLopener({}); opener.retrieve(BOOTSTRAP_URL, BOOTSTRAP_FILE); print \"Execute: \" + \"python \" + BOOTSTRAP_FILE + \" \" + BIGJOB_PYTHON_DIR os.system(\"/usr/bin/env\") try: os.system(\"python \" + BOOTSTRAP_FILE + \" \" + BIGJOB_PYTHON_DIR); activate_this = os.path.join(BIGJOB_PYTHON_DIR, \"bin/activate_this.py\"); execfile(activate_this, dict(file=activate_this)) except: print \"BJ installation failed. Trying system-level python (/usr/bin/python)\"; os.system(\"/usr/bin/python \" + BOOTSTRAP_FILE + \" \" + BIGJOB_PYTHON_DIR); activate_this = os.path.join(BIGJOB_PYTHON_DIR, \"bin/activate_this.py\"); execfile(activate_this, dict(file=activate_this))
try to import BJ once again
import bigjob.bigjob_agent
execute bj agent
args = list() args.append(\"bigjob_agent.py\") args.append(\"redis://Oily9tourSorenavyvault@redis01.tacc.utexas.edu:6379\") args.append(\"bigjob:bj-afbad9ba-97df-11e2-ab5e-d4ae52a0f02f:localhost\") args.append(\"\") print \"Bootstrap time: \" + str(time.time()-start_time) print \"Starting BigJob Agents with following args: \" + str(args) bigjob_agent = bigjob.bigjob_agent.bigjob_agent(args) " 03/28/2013 02:42:57 PM - bigjob - DEBUG - Working directory: /tmp Job Description: {'Executable' : '/usr/bin/env','WorkingDirectory' : '/tmp','SPMDVariation' : 'single','Queue' : 'normal','WallTimeLimit' : '10','Arguments' : '['python', '-c', '"import sys\nimport os\nimport urllib\nimport sys\nimport time\nstart_time = time.time()\nhome = os.environ.get(\"HOME\")\n#print \"Home: \" + home\nif home==None: home = os.getcwd()\nBIGJOB_AGENT_DIR= os.path.join(home, \".bigjob\")\nif not os.path.exists(BIGJOB_AGENT_DIR): os.mkdir (BIGJOB_AGENT_DIR)\nBIGJOB_PYTHON_DIR=BIGJOB_AGENT_DIR+\"/python/\"\nif not os.path.exists(BIGJOB_PYTHON_DIR): os.mkdir(BIGJOB_PYTHON_DIR)\nBOOTSTRAP_URL=\"https://raw.github.com/saga-project/BigJob/master/bootstrap/bigjob-bootstrap.py\\"\nBOOTSTRAP_FILE=BIGJOB_AGENT_DIR+\\"/bigjob-bootstrap.py\\"\n#ensure that BJ in .bigjob is upfront in sys.path\nsys.path.insert(0, os.getcwd() + \"/../\")\np = list()\nfor i in sys.path:\n if i.find(\".bigjob/python\")>1:\n p.insert(0, i)\nfor i in p: sys.path.insert(0, i)\nprint \"Python path: \" + str(sys.path)\nprint \"Python version: \" + str(sys.version_info)\ntry: import saga\nexcept: print \"SAGA and SAGA Python Bindings not found.\";\ntry: import bigjob.bigjob_agent\nexcept: \n print \"BigJob not installed. Attempt to install it.\"; \n opener = urllib.FancyURLopener({}); \n opener.retrieve(BOOTSTRAP_URL, BOOTSTRAP_FILE); \n print \"Execute: \" + \"python \" + BOOTSTRAP_FILE + \" \" + BIGJOB_PYTHON_DIR\n os.system(\"/usr/bin/env\")\n try:\n os.system(\"python \" + BOOTSTRAP_FILE + \" \" + BIGJOB_PYTHON_DIR); \n activate_this = os.path.join(BIGJOB_PYTHON_DIR, \"bin/activate_this.py\"); \n execfile(activate_this, dict(file=activate_this))\n except:\n print \"BJ installation failed. Trying system-level python (/usr/bin/python)\";\n os.system(\"/usr/bin/python \" + BOOTSTRAP_FILE + \" \" + BIGJOB_PYTHON_DIR); \n activate_this = os.path.join(BIGJOB_PYTHON_DIR, \"bin/activate_this.py\"); \n execfile(activate_this, dict(file=activate_this))\n#try to import BJ once again\nimport bigjob.bigjob_agent\n# execute bj agent\nargs = list()\nargs.append(\"bigjob_agent.py\")\nargs.append(\"redis://Oily9tourSorenavyvault@redis01.tacc.utexas.edu:6379\")\nargs.append(\"bigjob:bj-afbad9ba-97df-11e2-ab5e-d4ae52a0f02f:localhost\")\nargs.append(\"\")\nprint \"Bootstrap time: \" + str(time.time()-start_time)\nprint \"Starting BigJob Agents with following args: \" + str(args)\nbigjob_agent = bigjob.bigjob_agent.bigjob_agent(args)\n"']','TotalCPUCount' : '8',} 03/28/2013 02:42:57 PM - bigjob - DEBUG - Creating pilot job with description: {'Executable' : '/usr/bin/env','WorkingDirectory' : '/tmp','SPMDVariation' : 'single','Queue' : 'normal','WallTimeLimit' : '10','Arguments' : '['python', '-c', '"import sys\nimport os\nimport urllib\nimport sys\nimport time\nstart_time = time.time()\nhome = os.environ.get(\"HOME\")\n#print \"Home: \" + home\nif home==None: home = os.getcwd()\nBIGJOB_AGENT_DIR= os.path.join(home, \".bigjob\")\nif not os.path.exists(BIGJOB_AGENT_DIR): os.mkdir (BIGJOB_AGENT_DIR)\nBIGJOB_PYTHON_DIR=BIGJOB_AGENT_DIR+\"/python/\"\nif not os.path.exists(BIGJOB_PYTHON_DIR): os.mkdir(BIGJOB_PYTHON_DIR)\nBOOTSTRAP_URL=\"https://raw.github.com/saga-project/BigJob/master/bootstrap/bigjob-bootstrap.py\\"\nBOOTSTRAP_FILE=BIGJOB_AGENT_DIR+\\"/bigjob-bootstrap.py\\"\n#ensure that BJ in .bigjob is upfront in sys.path\nsys.path.insert(0, os.getcwd() + \"/../\")\np = list()\nfor i in sys.path:\n if i.find(\".bigjob/python\")>1:\n p.insert(0, i)\nfor i in p: sys.path.insert(0, i)\nprint \"Python path: \" + str(sys.path)\nprint \"Python version: \" + str(sys.version_info)\ntry: import saga\nexcept: print \"SAGA and SAGA Python Bindings not found.\";\ntry: import bigjob.bigjob_agent\nexcept: \n print \"BigJob not installed. Attempt to install it.\"; \n opener = urllib.FancyURLopener({}); \n opener.retrieve(BOOTSTRAP_URL, BOOTSTRAP_FILE); \n print \"Execute: \" + \"python \" + BOOTSTRAP_FILE + \" \" + BIGJOB_PYTHON_DIR\n os.system(\"/usr/bin/env\")\n try:\n os.system(\"python \" + BOOTSTRAP_FILE + \" \" + BIGJOB_PYTHON_DIR); \n activate_this = os.path.join(BIGJOB_PYTHON_DIR, \"bin/activate_this.py\"); \n execfile(activate_this, dict(file=activate_this))\n except:\n print \"BJ installation failed. Trying system-level python (/usr/bin/python)\";\n os.system(\"/usr/bin/python \" + BOOTSTRAP_FILE + \" \" + BIGJOB_PYTHON_DIR); \n activate_this = os.path.join(BIGJOB_PYTHON_DIR, \"bin/activate_this.py\"); \n execfile(activate_this, dict(file=activate_this))\n#try to import BJ once again\nimport bigjob.bigjob_agent\n# execute bj agent\nargs = list()\nargs.append(\"bigjob_agent.py\")\nargs.append(\"redis://Oily9tourSorenavyvault@redis01.tacc.utexas.edu:6379\")\nargs.append(\"bigjob:bj-afbad9ba-97df-11e2-ab5e-d4ae52a0f02f:localhost\")\nargs.append(\"\")\nprint \"Bootstrap time: \" + str(time.time()-start_time)\nprint \"Starting BigJob Agents with following args: \" + str(args)\nbigjob_agent = bigjob.bigjob_agent.bigjob_agent(args)\n"']','Error' : '/tmp/stderr-bj-afbad9ba-97df-11e2-ab5e-d4ae52a0f02f-agent.txt','Output' : '/tmp/stdout-bj-afbad9ba-97df-11e2-ab5e-d4ae52a0f02f-agent.txt','TotalCPUCount' : '8',} 03/28/2013 02:42:57 PM - bigjob - DEBUG - Submit pilot job to: fork://localhost Pilot Job/BigJob URL: bigjob:bj-afbad9ba-97df-11e2-ab5e-d4ae52a0f02f:localhost State: Unknown 03/28/2013 02:42:57 PM - bigjob - DEBUG - add subjob to queue of PJ: bigjob:bj-afbad9ba-97df-11e2-ab5e-d4ae52a0f02f:localhost 03/28/2013 02:42:57 PM - bigjob - DEBUG - create dictionary for job description. Job-URL: bigjob:bj-afbad9ba-97df-11e2-ab5e-d4ae52a0f02f:localhost:jobs:sj-b0e5aeaa-97df-11e2-ab5e-d4ae52a0f02f 03/28/2013 02:42:57 PM - bigjob - DEBUG - SJ Attributes: {'Executable' : '/bin/echo','Environment' : '['HELLOWORLD=hello_world']','Arguments' : '['$HELLOWORLD']','NumberOfProcesses' : '1','Error' : 'stderr.txt','Output' : 'stdout.txt',} 03/28/2013 02:42:57 PM - bigjob - DEBUG - job dict: {'Executable': '/bin/echo', 'NumberOfProcesses': 1, 'Environment': ['HELLOWORLD=hello_world'], 'state': 'Unknown', 'Arguments': ['$HELLOWORLD'], 'Error': 'stderr.txt', 'Output': 'stdout.txt', 'job-id': 'sj-b0e5aeaa-97df-11e2-ab5e-d4ae52a0f02f'} 03/28/2013 02:42:57 PM - bigjob - DEBUG - set job state to: Unknown 03/28/2013 02:42:57 PM - bigjob - DEBUG - Get subjob state: bigjob:bj-afbad9ba-97df-11e2-ab5e-d4ae52a0f02f:localhost:jobs:sj-b0e5aeaa-97df-11e2-ab5e-d4ae52a0f02f state: Unknown 03/28/2013 02:42:59 PM - bigjob - DEBUG - Get subjob state: bigjob:bj-afbad9ba-97df-11e2-ab5e-d4ae52a0f02f:localhost:jobs:sj-b0e5aeaa-97df-11e2-ab5e-d4ae52a0f02f state: Unknown 03/28/2013 02:43:01 PM - bigjob - DEBUG - Get subjob state: bigjob:bj-afbad9ba-97df-11e2-ab5e-d4ae52a0f02f:localhost:jobs:sj-b0e5aeaa-97df-11e2-ab5e-d4ae52a0f02f state: Running 03/28/2013 02:43:03 PM - bigjob - DEBUG - Get subjob state: bigjob:bj-afbad9ba-97df-11e2-ab5e-d4ae52a0f02f:localhost:jobs:sj-b0e5aeaa-97df-11e2-ab5e-d4ae52a0f02f state: Running 03/28/2013 02:43:05 PM - bigjob - DEBUG - Get subjob state: bigjob:bj-afbad9ba-97df-11e2-ab5e-d4ae52a0f02f:localhost:jobs:sj-b0e5aeaa-97df-11e2-ab5e-d4ae52a0f02f state: Running 03/28/2013 02:43:07 PM - bigjob - DEBUG - Get subjob state: bigjob:bj-afbad9ba-97df-11e2-ab5e-d4ae52a0f02f:localhost:jobs:sj-b0e5aeaa-97df-11e2-ab5e-d4ae52a0f02f state: Done 03/28/2013 02:43:07 PM - bigjob - DEBUG - Cancel Pilot Job 03/28/2013 02:43:07 PM - bigjob - DEBUG - stop pilot job: bigjob:bj-afbad9ba-97df-11e2-ab5e-d4ae52a0f02f:localhost 03/28/2013 02:43:07 PM - bigjob - DEBUG - update state of pilot job to: Done stopped: True 03/28/2013 02:43:07 PM - bigjob - DEBUG - delete pilot job: bigjob:bj-afbad9ba-97df-11e2-ab5e-d4ae52a0f02f:localhost 03/28/2013 02:43:07 PM - bigjob - DEBUG - Cancel Pilot Job finished
On Wed, Mar 27, 2013 at 2:17 PM, Melissa notifications@github.com wrote:
This is more of a reminder to myself...
BigJob is not working with the new redis server at TACC, but it is ping-able and works within SAGA. This COULD be an issue with the parsing happening in SAGA URL, but I have to diagnose what is really going on.
If anyone who works these tickets would like to help me diagnose, please ping me for the new password.
— Reply to this email directly or view it on GitHub.
oleweidner
ashleyz
This is more of a reminder to myself...
BigJob is not working with the new redis server at TACC, but the redis server is ping-able through the redis-cli.
If anyone who works these tickets would like to help me diagnose, please ping me for the new password.