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Python script runs on terminal but fails on SGE cluster [on hold]
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I'm trying to run a python script on a SGE cluster that will submit and cancel jobs on its own. I can run the program directly from the terminal, but am not sure how to format a job script that I can qsub to.
I've tried things such as
#!/usr/bin/env python2.7
...
python2.7 /home/andli/KMC/3d/optimization_wrapper.py
and submitted the sh file using
qsub script.mpi.sh
but have gotten the errors such as
sh: g++: command not found
Unable to run job: denied: host "compute-1-0.local" is not a submit host
Exiting.
I'm new to all of this and am looking for a sample format which I could follow, or some guide that I can read to figure out this submission process.
shell-script python
asked yesterday
Andrew LiAndrew Li
1
New contributor
Andrew Li is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
put on hold as off-topic by Kusalananda♦ yesterday
- This question does not appear to be about Unix or Linux within the scope defined in the help center.
If this question can be reworded to fit the rules in the help center, please edit the question.
add a comment |
I'm trying to run a python script on a SGE cluster that will submit and cancel jobs on its own. I can run the program directly from the terminal, but am not sure how to format a job script that I can qsub to.
I've tried things such as
#!/usr/bin/env python2.7
...
python2.7 /home/andli/KMC/3d/optimization_wrapper.py
and submitted the sh file using
qsub script.mpi.sh
but have gotten the errors such as
sh: g++: command not found
Unable to run job: denied: host "compute-1-0.local" is not a submit host
Exiting.
I'm new to all of this and am looking for a sample format which I could follow, or some guide that I can read to figure out this submission process.
shell-script python
asked yesterday
Andrew LiAndrew Li
1
New contributor
Andrew Li is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
put on hold as off-topic by Kusalananda♦ yesterday
- This question does not appear to be about Unix or Linux within the scope defined in the help center.
If this question can be reworded to fit the rules in the help center, please edit the question.
2
Something in one of your scripts is callingg++(a C++ compiler) for whatever reason. The compute nodes do not haveg++installed. It is likely that no compute node has development tools installed, or at least not available by default. You should talk to you team of system administrators about this to see whether it's a simple fix that has to be made when submitting the job, or whether they need to installg++on the nodes, or if there is something else that could be done.
– Kusalananda♦
yesterday
Likewise, the "is not a submit host" is something you would have to talk to local admins about. It sounds as if your cluster software only allows jobs submitted from particular nodes, and since your job submits its own jobs it has to run on a node that you are allowed to submit new jobs from. We can't tell you what nodes to use for this. This is a local issue.
– Kusalananda♦
yesterday
I'm voting to close this question as off-topic because it is an issue that can only be resolved in dialogue with local system administrators.
– Kusalananda♦
yesterday
Hi Kusalananda. Thanks for the reply! My script calls on g++ because it is running another C++ code. I'll try to see if any of the local admins can help me with other answers.
– Andrew Li
yesterday
add a comment |
I'm trying to run a python script on a SGE cluster that will submit and cancel jobs on its own. I can run the program directly from the terminal, but am not sure how to format a job script that I can qsub to.
I've tried things such as
#!/usr/bin/env python2.7
...
python2.7 /home/andli/KMC/3d/optimization_wrapper.py
and submitted the sh file using
qsub script.mpi.sh
but have gotten the errors such as
sh: g++: command not found
Unable to run job: denied: host "compute-1-0.local" is not a submit host
Exiting.
I'm new to all of this and am looking for a sample format which I could follow, or some guide that I can read to figure out this submission process.
shell-script python
asked yesterday
Andrew LiAndrew Li
1
New contributor
Andrew Li is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
I'm trying to run a python script on a SGE cluster that will submit and cancel jobs on its own. I can run the program directly from the terminal, but am not sure how to format a job script that I can qsub to.
I've tried things such as
#!/usr/bin/env python2.7
...
python2.7 /home/andli/KMC/3d/optimization_wrapper.py
and submitted the sh file using
qsub script.mpi.sh
but have gotten the errors such as
sh: g++: command not found
Unable to run job: denied: host "compute-1-0.local" is not a submit host
Exiting.
I'm new to all of this and am looking for a sample format which I could follow, or some guide that I can read to figure out this submission process.
shell-script python
shell-script python
asked yesterday
Andrew LiAndrew Li
1
New contributor
Andrew Li is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
asked yesterday
Andrew LiAndrew Li
1
New contributor
Andrew Li is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
asked yesterday
Andrew LiAndrew Li
1
New contributor
Andrew Li is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
asked yesterday
Andrew LiAndrew Li
1
asked yesterday
Andrew LiAndrew Li
1
1
New contributor
Andrew Li is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
New contributor
Andrew Li is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
put on hold as off-topic by Kusalananda♦ yesterday
- This question does not appear to be about Unix or Linux within the scope defined in the help center.
If this question can be reworded to fit the rules in the help center, please edit the question.
put on hold as off-topic by Kusalananda♦ yesterday
- This question does not appear to be about Unix or Linux within the scope defined in the help center.
If this question can be reworded to fit the rules in the help center, please edit the question.
put on hold as off-topic by Kusalananda♦ yesterday
- This question does not appear to be about Unix or Linux within the scope defined in the help center.
If this question can be reworded to fit the rules in the help center, please edit the question.
2
Something in one of your scripts is callingg++(a C++ compiler) for whatever reason. The compute nodes do not haveg++installed. It is likely that no compute node has development tools installed, or at least not available by default. You should talk to you team of system administrators about this to see whether it's a simple fix that has to be made when submitting the job, or whether they need to installg++on the nodes, or if there is something else that could be done.
– Kusalananda♦
yesterday
Likewise, the "is not a submit host" is something you would have to talk to local admins about. It sounds as if your cluster software only allows jobs submitted from particular nodes, and since your job submits its own jobs it has to run on a node that you are allowed to submit new jobs from. We can't tell you what nodes to use for this. This is a local issue.
– Kusalananda♦
yesterday
I'm voting to close this question as off-topic because it is an issue that can only be resolved in dialogue with local system administrators.
– Kusalananda♦
yesterday
Hi Kusalananda. Thanks for the reply! My script calls on g++ because it is running another C++ code. I'll try to see if any of the local admins can help me with other answers.
– Andrew Li
yesterday
add a comment |
2
Something in one of your scripts is callingg++(a C++ compiler) for whatever reason. The compute nodes do not haveg++installed. It is likely that no compute node has development tools installed, or at least not available by default. You should talk to you team of system administrators about this to see whether it's a simple fix that has to be made when submitting the job, or whether they need to installg++on the nodes, or if there is something else that could be done.
– Kusalananda♦
yesterday
Likewise, the "is not a submit host" is something you would have to talk to local admins about. It sounds as if your cluster software only allows jobs submitted from particular nodes, and since your job submits its own jobs it has to run on a node that you are allowed to submit new jobs from. We can't tell you what nodes to use for this. This is a local issue.
– Kusalananda♦
yesterday
I'm voting to close this question as off-topic because it is an issue that can only be resolved in dialogue with local system administrators.
– Kusalananda♦
yesterday
Hi Kusalananda. Thanks for the reply! My script calls on g++ because it is running another C++ code. I'll try to see if any of the local admins can help me with other answers.
– Andrew Li
yesterday
2
2
Something in one of your scripts is calling
g++ (a C++ compiler) for whatever reason. The compute nodes do not have g++ installed. It is likely that no compute node has development tools installed, or at least not available by default. You should talk to you team of system administrators about this to see whether it's a simple fix that has to be made when submitting the job, or whether they need to install g++ on the nodes, or if there is something else that could be done.– Kusalananda♦
yesterday
Something in one of your scripts is calling
g++ (a C++ compiler) for whatever reason. The compute nodes do not have g++ installed. It is likely that no compute node has development tools installed, or at least not available by default. You should talk to you team of system administrators about this to see whether it's a simple fix that has to be made when submitting the job, or whether they need to install g++ on the nodes, or if there is something else that could be done.– Kusalananda♦
yesterday
Likewise, the "is not a submit host" is something you would have to talk to local admins about. It sounds as if your cluster software only allows jobs submitted from particular nodes, and since your job submits its own jobs it has to run on a node that you are allowed to submit new jobs from. We can't tell you what nodes to use for this. This is a local issue.
– Kusalananda♦
yesterday
Likewise, the "is not a submit host" is something you would have to talk to local admins about. It sounds as if your cluster software only allows jobs submitted from particular nodes, and since your job submits its own jobs it has to run on a node that you are allowed to submit new jobs from. We can't tell you what nodes to use for this. This is a local issue.
– Kusalananda♦
yesterday
I'm voting to close this question as off-topic because it is an issue that can only be resolved in dialogue with local system administrators.
– Kusalananda♦
yesterday
I'm voting to close this question as off-topic because it is an issue that can only be resolved in dialogue with local system administrators.
– Kusalananda♦
yesterday
Hi Kusalananda. Thanks for the reply! My script calls on g++ because it is running another C++ code. I'll try to see if any of the local admins can help me with other answers.
– Andrew Li
yesterday
Hi Kusalananda. Thanks for the reply! My script calls on g++ because it is running another C++ code. I'll try to see if any of the local admins can help me with other answers.
– Andrew Li
yesterday
add a comment |
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2
Something in one of your scripts is calling
g++(a C++ compiler) for whatever reason. The compute nodes do not haveg++installed. It is likely that no compute node has development tools installed, or at least not available by default. You should talk to you team of system administrators about this to see whether it's a simple fix that has to be made when submitting the job, or whether they need to installg++on the nodes, or if there is something else that could be done.– Kusalananda♦
yesterday
Likewise, the "is not a submit host" is something you would have to talk to local admins about. It sounds as if your cluster software only allows jobs submitted from particular nodes, and since your job submits its own jobs it has to run on a node that you are allowed to submit new jobs from. We can't tell you what nodes to use for this. This is a local issue.
– Kusalananda♦
yesterday
I'm voting to close this question as off-topic because it is an issue that can only be resolved in dialogue with local system administrators.
– Kusalananda♦
yesterday
Hi Kusalananda. Thanks for the reply! My script calls on g++ because it is running another C++ code. I'll try to see if any of the local admins can help me with other answers.
– Andrew Li
yesterday