runOPAL issueshttps://gitlab.psi.ch/OPAL/runOPAL/-/issues2020-11-26T09:12:45+01:00https://gitlab.psi.ch/OPAL/runOPAL/-/issues/15MLLIB library should not be necessary2020-11-26T09:12:45+01:00albajacas_aarnau.albajacas@psi.chMLLIB library should not be necessaryCurrently when you clone, install, and run `runOPAL`, you get the following error:
```
File "/home/arnau/documents/ETHZ/Semester_Project_Master_Thesis/runOPAL/runOPAL/opalrunner.py", line 7, in <module>
from mllib.data.opal_stat_fi...Currently when you clone, install, and run `runOPAL`, you get the following error:
```
File "/home/arnau/documents/ETHZ/Semester_Project_Master_Thesis/runOPAL/runOPAL/opalrunner.py", line 7, in <module>
from mllib.data.opal_stat_file_to_dataframe import StatFile
ModuleNotFoundError: No module named 'mllib.data'
```
Together with @bellotti\_r we found that this is easily solved by cloning and installing [MLLIB](https://gitlab.psi.ch/adelmann/mllib), but this should not be the case. When installing `runOPAL` with `setup.py` MLLIB should be automatically installed. And in fact it is installed, but in some broken way that makes it unusable.albajacas_aarnau.albajacas@psi.chalbajacas_aarnau.albajacas@psi.chhttps://gitlab.psi.ch/OPAL/runOPAL/-/issues/10Documentation2020-05-11T13:28:04+02:00bellotti_rDocumentationAdd docstrings to the important functions. Right now, one has to go through the code to understand how to use it.Add docstrings to the important functions. Right now, one has to go through the code to understand how to use it.bellotti_rbellotti_rhttps://gitlab.psi.ch/OPAL/runOPAL/-/issues/11Improve default job resources for Merlin62020-05-11T13:27:50+02:00bellotti_rImprove default job resources for Merlin6Suggestion:
- run time `24:00:00` --> `23:59:59`
- partition `general` --> `daily`
This would increase the priority of the job.Suggestion:
- run time `24:00:00` --> `23:59:59`
- partition `general` --> `daily`
This would increase the priority of the job.bellotti_rbellotti_rhttps://gitlab.psi.ch/OPAL/runOPAL/-/issues/8runOPAL not running optimiser jobs2018-07-09T20:20:32+02:00snuverink_jjochem.snuverink@psi.chrunOPAL not running optimiser jobsNoticed by @ext-bershanska_a. Currently runOPAL doesn't run optimiser jobs correctly since it tries to build a new input file from the template file, something that it shouldn't actually do in this case.Noticed by @ext-bershanska_a. Currently runOPAL doesn't run optimiser jobs correctly since it tries to build a new input file from the template file, something that it shouldn't actually do in this case.ext-bershanska_aext-bershanska_ahttps://gitlab.psi.ch/OPAL/runOPAL/-/issues/9recursive directory creation with lndir2018-07-02T10:36:17+02:00snuverink_jjochem.snuverink@psi.chrecursive directory creation with lndirNoticed by @ext-bershanska_a : lndir can create a recursive directory structure if the path is inside the current directory.Noticed by @ext-bershanska_a : lndir can create a recursive directory structure if the path is inside the current directory.snuverink_jjochem.snuverink@psi.chsnuverink_jjochem.snuverink@psi.chhttps://gitlab.psi.ch/OPAL/runOPAL/-/issues/7Suggested improvements for Merlin52018-05-23T15:35:03+02:00Valeria RizzoglioSuggested improvements for Merlin5Here the suggestions from a discussion with Dmitry Ozerov:
1- prepare a single slurm script containing an **array of jobs**
`ex: sbatch -a 1-100 test.sh`
this will submit in one command 100 jobs to slurm. The trick to be nice with...Here the suggestions from a discussion with Dmitry Ozerov:
1- prepare a single slurm script containing an **array of jobs**
`ex: sbatch -a 1-100 test.sh`
this will submit in one command 100 jobs to slurm. The trick to be nice with the other users:
`sbatch -a 1-100%10 test.sh`
(or similar %25, %50)
2- **nodes and tasks**:
for ntasks < 16 than it would be more meaningful to ensure that the ntasks run on the same node. Now:
`#SBATCH --ntasks=4`
`#SBATCH --ntasks-per-node=4`
suggested:
`#SBATCH --ntasks=4`
`#SBATCH --nodes=1`
3- **Loading modules** in slurm script
`module load gcc.....`
so everything what is needed to load, setup to run the job (otherwise it's a dependence on what there is in .bashrc or environment (from which the job is submitted).snuverink_jjochem.snuverink@psi.chsnuverink_jjochem.snuverink@psi.chhttps://gitlab.psi.ch/OPAL/runOPAL/-/issues/4update runoptpilot for Merlin5 and OPAL integration2018-04-23T16:28:23+02:00snuverink_jjochem.snuverink@psi.chupdate runoptpilot for Merlin5 and OPAL integrationrunoptpilot.py needs to be updated. Both for the new Merlin5 and for the opt-pilot integration into OPAL.runoptpilot.py needs to be updated. Both for the new Merlin5 and for the opt-pilot integration into OPAL.snuverink_jjochem.snuverink@psi.chsnuverink_jjochem.snuverink@psi.chhttps://gitlab.psi.ch/OPAL/runOPAL/-/issues/6Python3 issues2018-04-19T09:17:54+02:00ext-roussel_rPython3 issuesHi, I was trying to run a scan on BEBOP @ ANL and got the following message:
```
[roussel@beboplogin1 DEEX]$ runOPAL.py --test PHASE=0.0:1.0:0.1
REMOVE existing directory DEEX_PHASE=0.0:1.0:0.1
{'PHASE': [0.0, 1.0, 0.1]}
Traceback (most...Hi, I was trying to run a scan on BEBOP @ ANL and got the following message:
```
[roussel@beboplogin1 DEEX]$ runOPAL.py --test PHASE=0.0:1.0:0.1
REMOVE existing directory DEEX_PHASE=0.0:1.0:0.1
{'PHASE': [0.0, 1.0, 0.1]}
Traceback (most recent call last):
File "/lcrc/project/AWA-beam-dynamics/software/runOPAL/runOPAL/runOPAL.py", line 232, in <module>
main(sys.argv[1:])
File "/lcrc/project/AWA-beam-dynamics/software/runOPAL/runOPAL/runOPAL.py", line 220, in main
traverseRanges(ranges.items(), opaldict, args)
File "/lcrc/project/AWA-beam-dynamics/software/runOPAL/runOPAL/runOPAL.py", line 74, in traverseRanges
head = list[0]
TypeError: 'dict_items' object does not support indexing
```
I think its a python3 conversion issue. I am currently working on it among other things so if you guys can get to it first that would be helpful.
Thanks,
Ryan Roussel - ANLsnuverink_jjochem.snuverink@psi.chsnuverink_jjochem.snuverink@psi.chhttps://gitlab.psi.ch/OPAL/runOPAL/-/issues/2Replace use of depecrated commands module by subprocess module2018-03-05T10:56:35+01:00snuverink_jjochem.snuverink@psi.chReplace use of depecrated commands module by subprocess moduleThe module `commands` is deprecated: https://docs.python.org/2/library/commands.html and instead the module `subprocess` is recommended. https://docs.python.org/2/library/subprocess.htmlThe module `commands` is deprecated: https://docs.python.org/2/library/commands.html and instead the module `subprocess` is recommended. https://docs.python.org/2/library/subprocess.htmlsnuverink_jjochem.snuverink@psi.chext-neveu_nsnuverink_jjochem.snuverink@psi.chhttps://gitlab.psi.ch/OPAL/runOPAL/-/issues/5option --block no longer working2017-12-01T12:26:44+01:00snuverink_jjochem.snuverink@psi.choption --block no longer workingThe option `--block` is no longer working (and was only for merlin4).
Is there a good use case for this option? I propose to drop it.The option `--block` is no longer working (and was only for merlin4).
Is there a good use case for this option? I propose to drop it.snuverink_jjochem.snuverink@psi.chsnuverink_jjochem.snuverink@psi.chhttps://gitlab.psi.ch/OPAL/runOPAL/-/issues/3update runOPAL for Merlin5 job submission2017-11-06T13:40:11+01:00snuverink_jjochem.snuverink@psi.chupdate runOPAL for Merlin5 job submissionIn order to use runOPAL on the new Merlin5 cluster, runOPAL needs to be updated. [Merlin5 uses the `Slurm Workload Manager`](https://intranet.psi.ch/PSI_HPC/Merlin5#Using_Batch_System_to_Submit_Jobs_to_Merlin5).In order to use runOPAL on the new Merlin5 cluster, runOPAL needs to be updated. [Merlin5 uses the `Slurm Workload Manager`](https://intranet.psi.ch/PSI_HPC/Merlin5#Using_Batch_System_to_Submit_Jobs_to_Merlin5).snuverink_jjochem.snuverink@psi.chadelmannsnuverink_jjochem.snuverink@psi.ch2017-10-31https://gitlab.psi.ch/OPAL/runOPAL/-/issues/1Request: replace string in .tmpl2017-10-11T05:53:47+02:00Valeria RizzoglioRequest: replace string in .tmplMerge problem has been found in the following configuration:
- in .data file
`BEAMDISTR /afs/psi.ch/project/SCGantry/nobackup//beam/Beam_185MeV.dat`
- in .tmpl file
`File1: DISTRIBUTION, DISTRIBUTION=FROMFILE, FNAME="_BEAMDISTR_"``,...Merge problem has been found in the following configuration:
- in .data file
`BEAMDISTR /afs/psi.ch/project/SCGantry/nobackup//beam/Beam_185MeV.dat`
- in .tmpl file
`File1: DISTRIBUTION, DISTRIBUTION=FROMFILE, FNAME="_BEAMDISTR_"``, INPUTMOUNITS=NONE, OFFSETX = 0.0, OFFSETY = 0.0, OFFSETZ =_MIDPLANE_/1000;`
The output (in .in file) from runOPAL.py is:
`File1: DISTRIBUTION, DISTRIBUTION=FROMFILE, FNAME="_BEAMDISTR_", INPUTMOUNITS=NONE, OFFSETX = 0.0, OFFSETY = 0.0, OFFSETZ =120.000000/1000;`
Two error messages appear in the terminal output
**sed: -e expression #1, char 14: unknown option to `s'**
**sed: -e expression #1, char 16: unknown option to `s'**
However, the .data file seems to be read properly:
Parameter set in SCGantry.in are:
:::: NPART= 10000
:::: MAPNAME= /afs/psi.ch/project/SCGantry/nobackup//3D_Maps/Optim_1//map-TILTA=13.1864624812-QSUCUR=0.806451353134-QCUR=1.01348311666.dat
:::: LATTICE= 1375.000000
:::: BEAMPOS= -1000.000000
:::: BEAMDISTR= /afs/psi.ch/project/SCGantry/nobackup//beam/Beam_185MeV.dat
:::: CORES= 1
:::: MIDPLANE= 120.000000
('On host ', 'opalrunner')
Done with setup of the OPAL simulation but not submitting the job (--test)
All the numbers specified in the .data file are correctly replaced. The problem appears only with string.adelmannadelmann