# How does one use python as a submission script using the PBS scheduler?

**URL:** <https://community.openpbs.org/t/how-does-one-use-python-as-a-submission-script-using-the-pbs-scheduler/2271>\
**Category:** Developers\
**Created:** [September 14, 2020, 7:55pm UTC](https://community.openpbs.org/t/how-does-one-use-python-as-a-submission-script-using-the-pbs-scheduler/2271 "2020-09-14T19:55:02Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![brando90](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.openpbs.org/brando90/32/347_2.png) [@brando90](https://community.openpbs.org/u/brando90)\
**Post date:** [September 14, 2020, 7:55pm UTC](https://community.openpbs.org/t/how-does-one-use-python-as-a-submission-script-using-the-pbs-scheduler/2271/1 "2020-09-14T19:55:02Z")

</div>

I’ve used python as my submission script in the past rather than bash etc. In slurm conder I usually instructed the path of the compiler at the top. I tried it in qsub but it didn’t work. Any idea how to make it work?

Code:

```auto
#/homes/miranda9/.conda/envs/automl-meta-learning/lib/python3.7
#PBS -V
#PBS -M brando.wontputithere@gmail.com
#PBS -m abe

import sys

for p in sys.path:
    print(p)

```

error msg:

```auto
$ cat test_qsub.py.e381299 
/homes/miranda9/.profile: line 2: /opt/intel/compilers_and_libraries_2017/linux/mpi/intel64/bin/mpivars.sh: No such file or directory
/homes/miranda9/.profile: line 3: /opt/intel/compilers_and_libraries_2017/linux/bin/compilervars.sh: No such file or directory
import: unable to open X server `' @ error/import.c/ImportImageCommand/369.
/var/spool/pbs/mom_priv/jobs/381299.iam-pbs.SC: line 9: syntax error near unexpected token `print'
/var/spool/pbs/mom_priv/jobs/381299.iam-pbs.SC: line 9: ` print(p)'

```

* * *

after I added `!` and made ‘#!/homes/miranda9/.conda/envs/automl-meta-learning/lib/python3.7’ at the top I got a new error:

```auto
$ cat test_qsub.py.e381301 
/homes/miranda9/.profile: line 2: /opt/intel/compilers_and_libraries_2017/linux/mpi/intel64/bin/mpivars.sh: No such file or directory
/homes/miranda9/.profile: line 3: /opt/intel/compilers_and_libraries_2017/linux/bin/compilervars.sh: No such file or directory
-bash: /var/spool/pbs/mom_priv/jobs/381301.iam-pbs.SC: /homes/miranda9/.conda/envs/automl-meta-learning/lib/python3.7: bad interpreter: Permission denied

```

* * *

crossposted:

- [How does one use python as a submission script using the PBS scheduler?](https://community.openpbs.org/t/how-does-one-use-python-as-a-submission-script-using-the-pbs-scheduler/2271)
- [https://stackoverflow.com/questions/63891078/how-does-one-use-python-as-a-submission-script-using-the-pbs-scheduler](https://stackoverflow.com/questions/63891078/how-does-one-use-python-as-a-submission-script-using-the-pbs-scheduler)
- [https://www.reddit.com/r/HPC/comments/issqbu/how\_does\_one\_use\_python\_as\_a\_submission\_script/](https://www.reddit.com/r/HPC/comments/issqbu/how_does_one_use_python_as_a_submission_script/)

* * *

not sure why the reply I pasted is not appearing but here is my soln:

First don’t forget the `!` at the top.

The trick is to figure out where the binary for python is (with your conda environment for example) and tell PBS at the top for your submission script. I tried using `sys.path` but that lead to a path to a folder that PBS couldn’t use. I had to find out the `sys.executable` to find it. Then I just put it at the top.

Demo session to find it:

```auto
$ python
Python 3.7.7 (default, Mar 26 2020, 15:48:22) 
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys
>>> sys.executable
'/homes/miranda9/.conda/envs/myenv/bin/python'

```

then place it properly with the exclamation mark:

```auto
#!/homes/miranda9/.conda/envs/YOURENV/bin/python
#PBS -V
#PBS -M youremail@gmail.com
#PBS -m abe
#PBS -lselect=1:ncpus=112

import sys
import os

for p in sys.path:
    print(p)

print(os.environ)

```

works now!

---

<div class="post-metadata">

**Author:** ![brando90](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.openpbs.org/brando90/32/347_2.png) [@brando90](https://community.openpbs.org/u/brando90)\
**Post date:** [September 14, 2020, 8:57pm UTC](https://community.openpbs.org/t/how-does-one-use-python-as-a-submission-script-using-the-pbs-scheduler/2271/2 "2020-09-14T20:57:06Z")

</div>

First don’t forget the `!` at the top.

The trick is to figure out where the binary for python is (with your conda environment for example) and tell PBS at the top for your submission script. I tried using `sys.path` but that lead to a path to a folder that PBS couldn’t use. I had to find out the `sys.executable` to find it. Then I just put it at the top.

Demo session to find it:

```auto
$ python
Python 3.7.7 (default, Mar 26 2020, 15:48:22) 
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys
>>> sys.executable
'/homes/miranda9/.conda/envs/myenv/bin/python'

```

then place it properly with the exclamation mark:

```auto
#!/homes/miranda9/.conda/envs/YOURENV/bin/python
#PBS -V
#PBS -M youremail@gmail.com
#PBS -m abe
#PBS -lselect=1:ncpus=112

import sys
import os

for p in sys.path:
    print(p)

print(os.environ)

```

works now!