cigale issueshttps://gitlab.lam.fr/groups/cigale/-/issues2023-10-04T12:44:13Zhttps://gitlab.lam.fr/cigale/cigale/-/issues/24Too many open files2023-10-04T12:44:13ZLAMBERT Jean-charlesToo many open files### CIGALE version: 2022.0 — Python version: 3.10.3 — Platform: linux-x86_64
When running **pcigale** with many **blocks** and **cpu**, the program stop after several blocks (depend of pcigale.ini parameters) with the unix message "Too ...### CIGALE version: 2022.0 — Python version: 3.10.3 — Platform: linux-x86_64
When running **pcigale** with many **blocks** and **cpu**, the program stop after several blocks (depend of pcigale.ini parameters) with the unix message "Too many open files".
If I increase the limit (ex: ulimit -n 131000) in the terminal before running pcigale, it completes with no issue.
After investigating during a running pcigale run, I can see that **/proc/$PID/fd** folder is constantly increasing slightly. It looks like that some shared memory segments **/dev/shm/pym-xxxxxx** might not be deleted.
($PID is the process id of the running pcigale process)https://gitlab.lam.fr/cigale/cigale/-/issues/23Make nebular module ajustable to different SSP / IMF2023-03-20T14:46:22ZYannick Roehllyyannick.roehlly@lam.frMake nebular module ajustable to different SSP / IMFCurrently the nebular module uses a single “nebular model” that was build using a specific SSP (now BC03) and a given IMF (now Chabrier). The problem is that we may use this module with another IMF and / or another SSP. For instance, to ...Currently the nebular module uses a single “nebular model” that was build using a specific SSP (now BC03) and a given IMF (now Chabrier). The problem is that we may use this module with another IMF and / or another SSP. For instance, to use BPASS we need to replace the nebular models and rebuild the database.
The nebular module should be able to handle different models for different SSP and IMF and use the right one during the run by inspecting what was used by the stellar emission module.https://gitlab.lam.fr/cigale/cigale/-/issues/21Error when "emission = False" (nebular module) and data do not contain emissi...2019-02-09T16:33:28ZGuanggyang206265@gmail.comError when "emission = False" (nebular module) and data do not contain emission linesIf "emission" is set to False in the nebular module and the input data do not have emission lines, an error will occur.If "emission" is set to False in the nebular module and the input data do not have emission lines, an error will occur.https://gitlab.lam.fr/cigale/cigale/-/issues/18[WIP] Correct input data management2017-05-18T11:24:59ZYannick Roehllyyannick.roehlly@lam.fr[WIP] Correct input data managementCommit d0759666bb084f6e3eaf1100bac3b680be57de70 change the way input data is handled. Upper limits are now indicated with negative fluxes. The other parts of the code must be corrected before closing this bug.Commit d0759666bb084f6e3eaf1100bac3b680be57de70 change the way input data is handled. Upper limits are now indicated with negative fluxes. The other parts of the code must be corrected before closing this bug.https://gitlab.lam.fr/cigale/cigale/-/issues/17Add mass weighted and luminosity weighted ages2017-07-11T21:17:19ZMédéric BoquienAdd mass weighted and luminosity weighted agesThe definition of the age in cigale is uncommon and it causes a lot of confusion. We should add explicitly the mass-weighted and/or luminosity-weighted ages.The definition of the age in cigale is uncommon and it causes a lot of confusion. We should add explicitly the mass-weighted and/or luminosity-weighted ages.Médéric BoquienMédéric Boquienhttps://gitlab.lam.fr/cigale/cigale/-/issues/16Too few estimates of the IR → issue computing the synchrotron emission2017-07-11T21:17:19ZMédéric BoquienToo few estimates of the IR → issue computing the synchrotron emissionDifferent papers make different assumptions as to what is the infrared exactly. Some assume it is all the dust emission (as we do), some think of it as 8-1000 micron. Some just consider the FIR. We could compute it using different defini...Different papers make different assumptions as to what is the infrared exactly. Some assume it is all the dust emission (as we do), some think of it as 8-1000 micron. Some just consider the FIR. We could compute it using different definitions. This would also allow us to better estimate the synchrotron emission as we rely on the FIR-radio correlation, with the FIR being 42.5-122.5 micron. So in effect we overestimate the synchrotron emission.https://gitlab.lam.fr/cigale/cigale/-/issues/15Filters with decreasing wavelengths lead to wrong results2017-07-11T21:17:19ZYannick Roehllyyannick.roehlly@lam.frFilters with decreasing wavelengths lead to wrong resultsSometime filter response curves are provided with decreasing wavelengths. Such
filters can be imported into CIGALE database without error but when they are
used the produce negative fluxes.
The problem comes from the filter normali...Sometime filter response curves are provided with decreasing wavelengths. Such
filters can be imported into CIGALE database without error but when they are
used the produce negative fluxes.
The problem comes from the filter normalisation and from the integration with
trapz which produces negative values because of the order of the wavelengths.https://gitlab.lam.fr/cigale/cigale/-/issues/14Problem when error is set to 02017-07-11T21:17:19ZYannick Roehllyyannick.roehlly@lam.frProblem when error is set to 0Contrary to what is claimed, CIGALE does not replace errors lower than a tolerance (1e-12) with a 10% default error. This leads to problems in the fitting procedure because of division per 0 when the error column contains 0. Note that a...Contrary to what is claimed, CIGALE does not replace errors lower than a tolerance (1e-12) with a 10% default error. This leads to problems in the fitting procedure because of division per 0 when the error column contains 0. Note that a solution to this problem contradicts bug #12.https://gitlab.lam.fr/cigale/cigale/-/issues/13numpy minimal version is 1.9.02017-07-11T21:17:19ZYannick Roehllyyannick.roehlly@lam.frnumpy minimal version is 1.9.0The validation of the ini file makes use of the return_counts parameter of numpy.unique that was introduced in numpy version 1.9.0.
Either set numpy minimal version to 1.9.0 or modify the code to get rid of the parameter.The validation of the ini file makes use of the return_counts parameter of numpy.unique that was introduced in numpy version 1.9.0.
Either set numpy minimal version to 1.9.0 or modify the code to get rid of the parameter.https://gitlab.lam.fr/cigale/cigale/-/issues/12Minimal errors should not be systematically set2017-07-11T21:17:19ZMédéric BoquienMinimal errors should not be systematically setCurrently cigale systematically set a minimal error if the uncertainty is lower this this minimal value. This should be optionally disabled as it can add hide problems in the fitting procedure.
Request by Samir Salim.Currently cigale systematically set a minimal error if the uncertainty is lower this this minimal value. This should be optionally disabled as it can add hide problems in the fitting procedure.
Request by Samir Salim.https://gitlab.lam.fr/cigale/cigale/-/issues/11Systematic uncertainties should be tunable2017-07-11T21:17:19ZMédéric BoquienSystematic uncertainties should be tunableFor now cigale adds a systematic 10% uncertainty to the errors to take into account the uncertainties on the models. This is not always appropriate. We should be able to set the level in pcigale.ini.
Request by Samir Salim.For now cigale adds a systematic 10% uncertainty to the errors to take into account the uncertainties on the models. This is not always appropriate. We should be able to set the level in pcigale.ini.
Request by Samir Salim.https://gitlab.lam.fr/cigale/cigale/-/issues/10Negative fluxes should be treated at normal fluxes2017-07-11T21:17:19ZMédéric BoquienNegative fluxes should be treated at normal fluxesIn principle we should be able to treat negative fluxes as any other flux. Sawicki+12 points this out in footnote 2. A good option would be to treat such fluxes normally if the user does not request them to be treated as upper limits. Th...In principle we should be able to treat negative fluxes as any other flux. Sawicki+12 points this out in footnote 2. A good option would be to treat such fluxes normally if the user does not request them to be treated as upper limits. This should not incur any change in the pcigale.ini file format.
Request by Samir Salim.https://gitlab.lam.fr/cigale/cigale/-/issues/9Can't use a configuration file other than pcigale.ini2017-07-11T21:17:19ZYannick Roehllyyannick.roehlly@lam.frCan't use a configuration file other than pcigale.iniThe pcigale script has an option to indicate which configuration file to use instead of the pcigale.ini file in the work directory: -c. Nevertheless, using this option is not possible because CIGALE expects a pcigale.ini file to be copie...The pcigale script has an option to indicate which configuration file to use instead of the pcigale.ini file in the work directory: -c. Nevertheless, using this option is not possible because CIGALE expects a pcigale.ini file to be copies in the out directory:
```python
FileNotFoundError: [Errno 2] No such file or directory: 'pcigale.ini'
```
https://gitlab.lam.fr/cigale/cigale/-/issues/8Can't plot best SED without all error columns in the input file2017-07-11T21:17:19ZYannick Roehllyyannick.roehlly@lam.frCan't plot best SED without all error columns in the input fileWhen a flux column in the input table is not associated to an error column, CIGALE can proceed with the analysis using a default 10% error. Nevertheless, pcigale-plot does not work in that case an complain about a missing FOO_err column.When a flux column in the input table is not associated to an error column, CIGALE can proceed with the analysis using a default 10% error. Nevertheless, pcigale-plot does not work in that case an complain about a missing FOO_err column.