...

• How can I find out what hosts are available for given requirements (LongJobs, memory, staging)
  • condor_status -compact -constraint "HasChtcStaging==true" -constraint 'DetectedMemory>500000' -constraint "CanRunLongJobs isnt Undefined"
• It looks to me like most hosts at CHTC are setup to run LongJobs.  The following shows a small list of about 20 hosts.  Is the correct?
  
  • condor_status -compact -constraint "CanRunLongJobs is Undefined"
• How can I know if my job swapped?
  
  • ANSWER: CHTC nodes have no or minimal swap space.
• 
  

  
  

• Are there bugs in the condor.log output of a DAG node?  For example, I have a condor.log file that clearly shows the job taking about three hours to run yet at the bottom lists user time of 13 hours and system time of 1 hour.  https://open-confluence.nrao.edu/download/attachments/40541486/step07.py.condor.log?api=v2

  • And as for the cpu usage report, there could very well be a bug, but first, is your job multi-threaded or multi-process?  If so, the cpu usage will be the aggregate across all cpu cores.

  • Yes they are all parallel jobs to some extent so I accept your answer for that job.  But I have another job that took 21 hours of wallclock time and yet the condor.log shows 55 minutes of user and 5:34 hours of system time
  Is there a ganglia server or some other monitor service at CHTC we can view?

  We have a bunch of ganglia and grafana graphs for the system, but I think they are restricted to campus folks and tend to show system-wide utliization and problem -- are there particular nationalizations you'd like to see?

  Are there bugs in the condor.log output of a DAG node?  For example, I have a condor.log file that clearly shows the job taking about three hours to run yet at the bottom lists user time of 13 hours and system time of 1 hour
  • .  https://open-confluence.nrao.edu/download/attachments/40541486/
  step07
  • step05.py.condor.log?api=v2

  • And as for the cpu usage report, there could very well be a bug, but first, is your job multi-threaded or multi-process?  If so, the cpu usage will be the aggregate across all cpu cores.

  • Yes they are all parallel jobs to some extent so I accept your answer for that job.  But I have another job that took 21 hours of wallclock time and yet the condor.log shows 55 minutes of user and 5:34 hours of system time.  https://open-confluence.nrao.edu/download/attachments/40541486/step05.py.condor.log?api=v2
  Condor Annex processing in AWS.  Is there support for spot marketANSWER: Condor Annex does indeed support the spot market.  It is a bit more work to set up because you don't say "give my X of Y", but "I'll pay d1 dollars for machines like X1 and d2 for machines like X2, etc.".What network mask should we use to allow ssh from CHTC into NRAO?  Is it a class B or several class Cs?
  ANSWER: The ip (v4 !) ranges for CHTC execute nodes are

  128.104.100.0/22

  128.104.55.0/24

  128.104.58.0/23

  128.105.244.0/23

Answered Questions:

• JOB ID question from Daniel

  • When I submit a job, I get a job ID back. My plan is to hold onto that job ID permanently for tracking. We have had issues in the past with Torque/Maui because the job IDs got recycled later and our internal bookkeeping got mixed up. So my questions are:

     - Are job IDs guaranteed to be unique in HTCondor?
     - How unique are they—are they _globally_ unique or just unique within a particular namespace (such as our cluster or the submit node)?

  • A Job ID (ClusterID.ProcID)
  • DNS name of the schedd and ctime of the job_queued.log file.
  • It is unique to a schedd.
  • We should talk with Daniel about this.  They should craft their own ID.  It could be seeded with a JobID but should not depend on just it.
• UpgradingHTCondor without killing jobs?
  • schedd can be upgraded and restarted without loosing state assuming the restart is less than the timeout.
  • currently restarting execute services will kill jobs.  CHTC is working on improving this.
  • negotiator and collector can be restarted without killing jobs.
  • CHTC works hard to ensure 8.8.x is compatible with 8.8.y or 8.9.x is compatible with 8.9.y.
• Leaving data on execution host between jobs (data reuse)
  • Todd is working on this now.
• Ask about installation of CASA locally and ancillary data (cfcache)
  • CHTC has a Ceph filesystem that is available to many of their execution hosts (notibly the larger ones)
  • There is another software filesystem where CASA could live that is more used for admin usage but might be available to us.
  • We could download the tarball each time over HTTP.  CHTC uses a proxy server so it would often be cached.
• Environment:  Is there a way to have condor "login" when a job starts thus sourcing /etc/proflie and the user's rc files? Currently, not even $HOME is set.
  • A good analogy is Torque does a su - _username_ while HTCondor just does a su _username_
  • WORKAROUND: setting getenv = True which is like the -V option to qsub, may help. It doesn't source rc files but does inherit your current environment. This may be a problem if your current environment is not what you want on the cluster node. Perhaps the cluster node is a different OS or architecture.
  • ANSWER: condor doesn't execute things with a shell.  You could set your executable as /bin/bash and then have the arguments be the executable you used to have.  I just changed our stuff to staticly set $HOME and I think that is good enough.

Answered Questions:

• JOB ID question from Daniel

  • When I submit a job, I get a job ID back. My plan is to hold onto that job ID permanently for tracking. We have had issues in the past with Torque/Maui because the job IDs got recycled later and our internal bookkeeping got mixed up. So my questions are:

     - Are job IDs guaranteed to be unique in HTCondor?
     - How unique are they—are they _globally_ unique or just unique within a particular namespace (such as our cluster or the submit node)?

  • A Job ID (ClusterID.ProcID)
  • DNS name of the schedd and ctime of the job_queued.log file.
  • It is unique to a schedd.
  • We should talk with Daniel about this.  They should craft their own ID.  It could be seeded with a JobID but should not depend on just it.
• UpgradingHTCondor without killing jobs?
  • schedd can be upgraded and restarted without loosing state assuming the restart is less than the timeout.
  • currently restarting execute services will kill jobs.  CHTC is working on improving this.
  • negotiator and collector can be restarted without killing jobs.
  • CHTC works hard to ensure 8.8.x is compatible with 8.8.y or 8.9.x is compatible with 8.9.y.
• Leaving data on execution host between jobs (data reuse)
  • Todd is working on this now.
• Ask about installation of CASA locally and ancillary data (cfcache)
  • CHTC has a Ceph filesystem that is available to many of their execution hosts (notibly the larger ones)
  • There is another software filesystem where CASA could live that is more used for admin usage but might be available to us.
  • We could download the tarball each time over HTTP.  CHTC uses a proxy server so it would often be cached.
• Environment:  Is there a way to have condor "login" when a job starts thus sourcing /etc/proflie and the user's rc files? Currently, not even $HOME is set.
  • A good analogy is Torque does a su - _username_ while HTCondor just does a su _username_
  • WORKAROUND: setting getenv = True which is like the -V option to qsub, may help. It doesn't source rc files but does inherit your current environment. This may be a problem if your current environment is not what you want on the cluster node. Perhaps the cluster node is a different OS or architecture.
  • ANSWER: condor doesn't execute things with a shell.  You could set your executable as /bin/bash and then have the arguments be the executable you used to have.  I just changed our stuff to staticly set $HOME and I think that is good enough.

• Flocking: Suppose I have two hosts in the same pool.  testpost-master is a submit-host and testpost-serv-1 is both a submit-host and the central-manager.  testpost-serv-1 is configured to flock to CHTC but testpost-master is not. Is it possible to submit a job on testpost-master that will flock to Flocking: Suppose I have two hosts in the same pool.  testpost-master is a submit-host and testpost-serv-1 is both a submit-host and the central-manager.  testpost-serv-1 is configured to flock to CHTC but testpost-master is not. Is it possible to submit a job on testpost-master that will flock to CHTC by somehow leveraging testpost-serv-1?  In other words, do I have to setup flocking and an external IP on every submit host?
  • ANSWER: there isn't a good way to do this.  So eventually we will need to make testpost-master flock to CHTC and possibly remove the ability of testpost-serv-1 to flock.

...

• It seems the transfer mechanism won't transfer symlinks to directories (e.g. data/vlass.ms → /lustre/aoc/...) Is there a way around this?around this?
  • ANSWER: there is no flag to chase symlinks at the moment.  The top level dir (e.g. data) could be a symlink if transfer_input_files=data/ but it will then transfer the contents of data instead of data itself.
  • If symlink → data and transfer_input_files=symlink I get the error Transfer of symlinks to directories is not supported.
  • if symlink → ../data and
  • ANSWER: there is no flag to chase symlinks at the moment.  The top level dir (e.g. data) could be a symlink if transfer_input_files=datasymlink/ but it will then transfer the contents of data instead of data itself.transfers the contents not the directory.  In other words I don't have a data directory in scratch I have a VLASS... directory.
  • If data/VLASS → /some/path/VLASS and transfer_input_files=data/VLASS/
  • If data/VLASS → /some/path/VLASS If symlink → data and transfer_input_files=symlink data/ I get the error Transfer of symlinks to directories is not supported.
  • if symlink → ../data and transfer_input_files=symlink/ it transfers the contents not the directory.  In other words I don't have a data directory in scratch I have a VLASS... directory.
  • If data/VLASS → /some/path/VLASS and transfer_input_files=data/VLASS/
  If data/VLASS → /some/path/VLASS and transfer_input_files=data/ I get the error Transfer of symlinks to directories is not supported.
  
  • 
    
    
• DAG log time stamps,  is there a way to differentiate data import/export time and process run time.
  • Look in the job log file not the dag log file
  • 040 (150.000.000) 2020-06-15 13:05:45 Started transferring input files
            Transferring to host: <10.64.10.172:9618?addrs=10.64.10.172-9618&alias=nmpost072.aoc.nrao.edu&noUDP&sock=slot1_1_72656_7984_60>
    ...
    
  DAG log time stamps,  is there a way to differentiate data import/export time and process run time.
  • Look in the job log file not the dag log file
  • 040 (150.000.000) 2020-06-15 13:0506:45 Started 04 Finished transferring input files        Transferring to host: <10.64.10.172:9618?addrs=10.64.10.172-9618&alias=nmpost072.aoc.nrao.edu&noUDP&sock=slot1_1_72656_7984_60>
    ...
    040 (150.000.000) 2020-06-15 13:06:04 Finished transferring input files

• Rank and Premption: Can we use Rank to set "preferences" without requiring job preemption?
  • ANSWER: There are 2 kinds of rank (job rank, machine rank).  job rank (RANK=... in a submit file) is purely a preference.  That does not preempt.  Machine rank (in startd.config) will preempt.  Negotiator pre-job rank is a third type of rank that works at a pool level and is often used to pack jobs efficiently.

...

• Rank and Premption: Can we use Rank to set "preferences" without requiring job preemption?
  • ANSWER: There are 2 kinds of rank (job rank, machine rank).  job rank (RANK=... in a submit file) is purely a preference.  That does not preempt.  Machine rank (in startd.config) will preempt.  Negotiator pre-job rank is a third type of rank that works at a pool level and is often used to pack jobs efficiently.

• Update on software store for CASA either on shared Ceph storage or admin software storage
  • Staging area for datasets 100MB - TBs.  This is where we could try keeping the cfcache assuming doing so doesn't overwhelm the filesystem.
    • /staging/nu_jrobnett

    • Requirements = (Target.HasCHTCStaging == true)

    • Quota: 100GB, 100K files
  • Squid area for 100MB - 1GB input or shared software.  This is where we could keep casa.tgz and then have the execution host retrieve it via HTTP.
    • /squid/nu_jrobnett
    • only accessable via this path on the submit hosts.  Execution hosts will need to access it via HTTP.

    • transfer_input_files = http://proxy.chtc.wisc.edu/SQUID/nu_jrobnett/casa.tgz

  • Software area We can use this in run-time applications.  Think of it like /usr/local.

    • /software/nu_jrobnett/casa/casa-pipeline-release-5.6.1-8.el7

    • export PATH=/opt/local/bin:/software/nu_jrobnett/casa/casa-pipeline-release-5.6.1-8.el7/bin:${PATH}
    • Quota: 5GB, 100K files
      
      

• Public_input_files: How is this different than transfer_input files and when would one want to use it instead of files or URLs with transfer_input_files?
  • https://htcondor.readthedocs.io/en/latest/users-manual/file-transfer.html#public-input-files
  • This is still a work in progress.  It may allow for caching on a squid server, fetchable by others someday.

• Flocking: When we flock to CHTC what is the data path for transfer_input_files?  Is it our submit host and CHTC's execution host, is CHTCs submit host involved ?
  • Dataflow is from our schedd (submit host) to their execute host but CCB will reverse the connection.  Their execution hosts are publicly addressable but that may not be necessary.
    
    
• How can we choose the data path for transfer_input_files to our clients given multiple networks.  Currently we assume it will use the 1Gb link but we have IB links.    Is there a way for condor to use the IB link just for transferring files, is that hostname based ? Other ideas?
  • CHTC doesn't have a good solution for this.
  • We could upgrade from 1Gb to 10Gb
  • We could use the IB names for everything (problematic for submit hosts that don't have IB)
  • We could not use transfer mechanism and instead use something else like scp
  • We could use a custom transfer plugin
    
    
• Are there known issues with distributed scratch via NFS or Lustre w.r.t tmpdir or other,  e.g. OpenMPI complains about tmpdir being on network FS?
  • Some problems with log files on the submit host but rare.
• Any general best practices to support MPI in terms of class ads or other.
  • Use the shared memory transport for security
    
    
•  Is there a way DAGMan can be told to ignore errors, in some cases we want a DAG to mindlessly continue vs retry.
  • The job is considered successful based on the return of the post script.  If there isn't a post script, the success is based on the return of the job.
    
    
• Transfer mechanism: Documentation implies that only files with an mtime newer than when the transfer_input_files finished will be transferred back to the submit host.  While running a dag, the files in my working directory (which is in both transfer_input_files and transfer_output_files) seem to always have an mtime around the most recent step in the DAG suggesting that the entire working directory is copied from the execution host to the submit host at the end of each DAG step.  Perhaps this means the transfer mechanism only looks at the mtime of the files/dirs specified in transfer_output_files and doesn't descend into the directories.
  • Subdirectories are treated differently
  • SOLUTION: I think casa just touches every file and therefore condor is forced to copy everything in the working directory.  I have been unable to reproduce the problem outside of casa.
  • SOLUTION: If you specify a directory, HTCondor will transfer the entire directory not just files with new mtime.

• Does the trasnfer mechanism accept any sort of regular expression?  E.g. transfer_input_files=*.txt
  • No
    
    
• Can the transfer mechanism accept manifest files?  E.g. a file that is a list of files?
  • Use include : <some file> in the submit script where <some file> contains the full transfer_input_files line
  • use queue FILES from manifest Which defines the submit variable $(FILES) which could be used in a transfer_input_files like: transfer_input_files = $(FILES)
  • Perhaps a plugin
    
    
• What other options are there than holding a job?  I find myself not noticing, sometimes for hours, that a job is on hold.  Is there a way to make jobs fail instead of getting held?  I assume others will make this mistake like me.
  • I see I can set periodic_remove = (JobStatus == 5) but HTCondor doesn't seem to think that is an error so if I have notification = Error I don't get any email.
  • Greg will look into adding a Hold option to notification
  • The HTCondor idea of held jobs is that you submitted a large DAG of jobs, one step is missing a file and you would like to put that file in place and continue the job instead of the whole DAG failing and having to be resubmitted.  This makes sense but it would be nice to be notified when a job gets held.

  • Greg wrote "notification = error in the submit file is supposed to send email when the job is held by the system, but there's a bug now where it doesn't.  I'll fix this."

• What limits are there to transfer_input_files?  I would sometimes get Failed to transfer files when the number of files was around 10,000
  • ANSWER: There is a memory limit because of ClassAds but in general there isn't a defined limit.
• Is there a way to generate the dag.dot file without having to submit the job?
  • The -no_submit option doesn't create the .dot file
  • Is adding NOOP to all the JOB commands the right thing to do?  The DAG still gets submitted but then quickly ends.
  • ANSWER: You need to submit the DAG.  NOOP is the current solution
• Is there a way to start a dag at a given point?  E.g. if there are 5 steps in the dag, can you start the job at step 3?
  • Is the answer again to add NOOP to the JOB commands you don't want to run?
  • ANSWER: Splices may work here but NOOP is certainly a tool to use.
• I see at CHTC jobs now require a request_disk setting.  How does one launch interactive jobs?
  • ANSWER: This is a bug.
• For our initial tests, we want to flock jobs to CHTC that transfer about 60GB input and output.  Eventually we will reduce this significantly but for now what can we do?
  • Globus or rsync to move data?  If Globus, how to do so in an automated way (E.g. no password)?
  • ANSWER: Using the Transfer Mechanism from our submit server to CHTC's execution host is ok with CHTC because it doesn't interfere with their submit host.  Outbound from their execute hosts is also allowed (scp, rsync, etc).
• Use +Longjobs = true attribute for 24+ hour jobs.  This is a CHTC-specific knob.

• How can I know if my job swapped?
  • ANSWER: CHTC nodes have no or minimal swap space.

• Condor Annex processing in AWS.  Is there support for spot market
  • ANSWER: Condor Annex does indeed support the spot market.  It is a bit more work to set up because you don't say "give my X of Y", but "I'll pay d1 dollars for machines like X1 and d2 for machines like X2, etc.".

• What network mask should we use to allow ssh from CHTC into NRAO?  Is it a class B or several class Cs?
  • ANSWER: The ip (v4 !) ranges for CHTC execute nodes are

    128.104.100.0/22

    128.104.55.0/24

    128.104.58.0/23

    128.105.244.0/23

• Is there a ganglia server or some other monitor service at CHTC we can view?

  • ANSWER: We have a bunch of ganglia and grafana graphs for the system, but I think they are restricted to campus folks and tend to show system-wide utliization and problem

...

• /staging/nu_jrobnett

• Requirements = (Target.HasCHTCStaging == true)

• Quota: 100GB, 100K files

...

• /squid/nu_jrobnett
• only accessable via this path on the submit hosts.  Execution hosts will need to access it via HTTP.

• transfer_input_files = http://proxy.chtc.wisc.edu/SQUID/nu_jrobnett/casa.tgz

Software area We can use this in run-time applications.  Think of it like /usr/local.

...

/software/nu_jrobnett/casa/casa-pipeline-release-5.6.1-8.el7

...

• Public_input_files: How is this different than transfer_input files and when would one want to use it instead of files or URLs with transfer_input_files?
  • https://htcondor.readthedocs.io/en/latest/users-manual/file-transfer.html#public-input-files
  • This is still a work in progress.  It may allow for caching on a squid server, fetchable by others someday.

Flocking: When we flock to CHTC what is the data path for transfer_input_files?  Is it our submit host and CHTC's execution host, is CHTCs submit host involved ?Dataflow is from our schedd (submit host) to their execute host but CCB will reverse the connection.  Their execution hosts are publicly addressable but that may not be necessary.
How can we choose the data path for transfer_input_files to our clients given multiple networks.  Currently we assume it will use the 1Gb link but we have IB links.    Is there a way for condor to use the IB link just for transferring files, is that hostname based ? Other ideas?
• CHTC doesn't have a good solution for this.
• We could upgrade from 1Gb to 10Gb
• We could use the IB names for everything (problematic for submit hosts that don't have IB)
• We could not use transfer mechanism and instead use something else like scp
We could use a custom transfer plugin

• Are there known issues with distributed scratch via NFS or Lustre w.r.t tmpdir or other,  e.g. OpenMPI complains about tmpdir being on network FS?
  • Some problems with log files on the submit host but rare.
Any general best practices to support MPI in terms of class ads or other.Use the shared memory transport for security
 Is there a way DAGMan can be told to ignore errors, in some cases we want a DAG to mindlessly continue vs retry.The job is considered successful based on the return of the post script.  If there isn't a post script, the success is based on the return of the job.

• Transfer mechanism: Documentation implies that only files with an mtime newer than when the transfer_input_files finished will be transferred back to the submit host.  While running a dag, the files in my working directory (which is in both transfer_input_files and transfer_output_files) seem to always have an mtime around the most recent step in the DAG suggesting that the entire working directory is copied from the execution host to the submit host at the end of each DAG step.  Perhaps this means the transfer mechanism only looks at the mtime of the files/dirs specified in transfer_output_files and doesn't descend into the directories.
  • Subdirectories are treated differently
  • SOLUTION: I think casa just touches every file and therefore condor is forced to copy everything in the working directory.  I have been unable to reproduce the problem outside of casa.
  • SOLUTION: If you specify a directory, HTCondor will transfer the entire directory not just files with new mtime.
Does the trasnfer mechanism accept any sort of regular expression?  E.g. transfer_input_files=*.txtNo
Can the transfer mechanism accept manifest files?  E.g. a file that is a list of files?
• Use include : <some file> in the submit script where <some file> contains the full transfer_input_files line
• use queue FILES from manifest Which defines the submit variable $(FILES) which could be used in a transfer_input_files like: transfer_input_files = $(FILES)
Perhaps a plugin

• What other options are there than holding a job?  I find myself not noticing, sometimes for hours, that a job is on hold.  Is there a way to make jobs fail instead of getting held?  I assume others will make this mistake like me.
  • I see I can set periodic_remove = (JobStatus == 5) but HTCondor doesn't seem to think that is an error so if I have notification = Error I don't get any email.
  • Greg will look into adding a Hold option to notification
  • The HTCondor idea of held jobs is that you submitted a large DAG of jobs, one step is missing a file and you would like to put that file in place and continue the job instead of the whole DAG failing and having to be resubmitted.  This makes sense but it would be nice to be notified when a job gets held.

  • Greg wrote "notification = error in the submit file is supposed to send email when the job is held by the system, but there's a bug now where it doesn't.  I'll fix this."

• What limits are there to transfer_input_files?  I would sometimes get Failed to transfer files when the number of files was around 10,000
  • ANSWER: There is a memory limit because of ClassAds but in general there isn't a defined limit.
• Is there a way to generate the dag.dot file without having to submit the job?
  • The -no_submit option doesn't create the .dot file
  • Is adding NOOP to all the JOB commands the right thing to do?  The DAG still gets submitted but then quickly ends.
  • ANSWER: You need to submit the DAG.  NOOP is the current solution
• Is there a way to start a dag at a given point?  E.g. if there are 5 steps in the dag, can you start the job at step 3?
  • Is the answer again to add NOOP to the JOB commands you don't want to run?
  • ANSWER: Splices may work here but NOOP is certainly a tool to use.
• I see at CHTC jobs now require a request_disk setting.  How does one launch interactive jobs?
  • ANSWER: This is a bug.
• For our initial tests, we want to flock jobs to CHTC that transfer about 60GB input and output.  Eventually we will reduce this significantly but for now what can we do?
  • Globus or rsync to move data?  If Globus, how to do so in an automated way (E.g. no password)?
  • ANSWER: Using the Transfer Mechanism from our submit server to CHTC's execution host is ok with CHTC because it doesn't interfere with their submit host.  Outbound from their execute hosts is also allowed (scp, rsync, etc).
• Use +Longjobs = true attribute for 24+ hour jobs.  This is a CHTC-specific knob.