gdat issueshttps://gitlab.epfl.ch/spc/gdat/-/issues2019-08-15T10:01:21Zhttps://gitlab.epfl.ch/spc/gdat/-/issues/9Set up tag-based deployment for gdat2019-08-15T10:01:21ZFederico FeliciSet up tag-based deployment for gdatgdat migration to gitlabFederico FeliciFederico Felicihttps://gitlab.epfl.ch/spc/gdat/-/issues/4Set gdat SVN to read-only2019-08-19T09:00:09ZFederico FeliciSet gdat SVN to read-onlygdat migration to gitlabAntoine MerleAntoine Merlehttps://gitlab.epfl.ch/spc/gdat/-/issues/3Setup automated testing2019-07-19T07:29:09ZFederico FeliciSetup automated testinggdat migration to gitlabFederico FeliciFederico Felicihttps://gitlab.epfl.ch/spc/gdat/-/issues/2Push git repo to gitlab2019-07-19T07:29:23ZFederico FeliciPush git repo to gitlab```
cd existing_repo
git remote rename origin old-origin
git remote add origin git@gitlab.epfl.ch:spc/tcv/tbx/gdat.git
git push -u origin --all
git push -u origin --tags
``````
cd existing_repo
git remote rename origin old-origin
git remote add origin git@gitlab.epfl.ch:spc/tcv/tbx/gdat.git
git push -u origin --all
git push -u origin --tags
```gdat migration to gitlabJoan DeckerJoan Deckerhttps://gitlab.epfl.ch/spc/gdat/-/issues/1Check git repo creation with or without tags2019-07-19T07:43:48ZFederico FeliciCheck git repo creation with or without tagsDiscussion on how to move SPC TCV toolboxes to GIT.
Commands used: (also documented on [SPC wiki](https://spcwiki.epfl.ch/wiki/GIT)) when final commands are defined..
Inspired from this [git manual](https://git-scm.com/book/en/v2/Git-a...Discussion on how to move SPC TCV toolboxes to GIT.
Commands used: (also documented on [SPC wiki](https://spcwiki.epfl.ch/wiki/GIT)) when final commands are defined..
Inspired from this [git manual](https://git-scm.com/book/en/v2/Git-and-Other-Systems-Migrating-to-Git)
and from [here](https://gist.github.com/epicserve/1219858/9f30d5ffca7d6b6e4130c4b9b300b8167c868a5f) and [here](http://john.albin.net/git/convert-subversion-to-git)
```
# Generate empty Authors table
svn log -q https://spcsvn.epfl.ch/repos/TCV/gdat | \
awk -F '|' '/^r/ {sub("^ ", "", $2); sub(" $", "", $2); \
print $2" = "$2" <"$2">"}' | sort -u > authors.txt
# Then fill in the authors table e.g. username = FirstName LastName <name.lastname@bla.com>
# Clone from SVN with separate branches and tags, ignoring matlast
git svn clone --trunk /gdat/trunk --branches /gdat/branches/* --tags=/gdat/tags/* --ignore-refs=.*matlast \
https://spcsvn.epfl.ch/repos/TCV --authors-file=authors.txt gdat
# inspect all the branches (incl remote)
git branch -av
# turn tag branches into real git tags and remove branches (may need to play with cut -f argument)
git for-each-ref --format='%(refname)' refs/remotes/origin/tags/ | cut -d / -f 5 |
while read ref; do
git tag "$ref" "refs/remotes/origin/tags/$ref" && git branch -D -r "origin/tags/$ref";
done
# inspect the result
git tag
# Create local branches from remote branches and delete remote branches
# (may need to play with cut -f argument).
# This is necessary since git-svn stores remote branches in a non-default way
# to keep backwards compatibility with the svn repository (which we don't want).
git for-each-ref --format='%(refname)' refs/remotes/origin/ | cut -d / -f 4 |
while read ref;
do
git branch "$ref" "refs/remotes/origin/$ref" && git branch -D -r "origin/$ref";
done;
# inspect the result
git branch -av
# remove trunk branch (identical to master)
git branch -d trunk
# test pushing to a local git repo
git init --bare ~/test-bare.git
git remote add bare ~/test-bare
git push --all bare
git push --tags bare
#then clone a new repo from bare and inspect the result
cd ..
git clone ~/test-bare test
# Go back to the original repo and inspect its size.
du -d1 -h
# If it is unreasonably large (more than a few 10MB typically means it's too large)
# then clean it using tools like [BFG](https://rtyley.github.io/bfg-repo-cleaner/)
# finally (in original extraction repo)
git remote add origin <remote (gitlab) repository url>
git push --all origin
git push --tags origingdat migration to gitlabJoan DeckerJoan Deckerhttps://gitlab.epfl.ch/spc/gdat/-/issues/64Job Failed #8328542024-02-19T13:51:28ZOlivier SauterJob Failed #832854Job [#832854](https://gitlab.epfl.ch/spc/gdat/-/jobs/832854) failed for 467e9cbfff6cfe59f1d0c38a2b802a18f9ef6712:
@amerle something changed for the deployment?Job [#832854](https://gitlab.epfl.ch/spc/gdat/-/jobs/832854) failed for 467e9cbfff6cfe59f1d0c38a2b802a18f9ef6712:
@amerle something changed for the deployment?Antoine MerleAntoine Merlehttps://gitlab.epfl.ch/spc/gdat/-/issues/57Job Failed #4092412022-06-29T09:33:28ZOlivier SauterJob Failed #409241Job [#409241](https://gitlab.epfl.ch/spc/gdat/-/jobs/409241) failed for 853e79e6920bb2345ed0014513b1fbf2beb86468:
@amerle gdat tests fail from time to time only with matlab960 when constructing eqdsk, it seems it does not save properly ...Job [#409241](https://gitlab.epfl.ch/spc/gdat/-/jobs/409241) failed for 853e79e6920bb2345ed0014513b1fbf2beb86468:
@amerle gdat tests fail from time to time only with matlab960 when constructing eqdsk, it seems it does not save properly the files during the call ala:
[fnames_readresults]=read_results_for_chease(65565,1,1,3,[],[],[],0,0,1,[129,129]);
and so does not find the file /tmp/$USER/eqdsksigns.65565t1.0000 which is then read by read_eqdsk
Any idea/suggestions? I could never reproduce the error on lacshttps://gitlab.epfl.ch/spc/gdat/-/issues/56Problems loading the core_profiles ids2022-04-08T08:26:10ZMichele MarinProblems loading the core_profiles idsI found a problem loading the core_profiles ids. The commands are
```
[ids_from_tcv]=tcv2ids(64958,'ids_names',{'core_profiles'});
[ids_from_tcv]=tcv2ids(73461,'ids_names',{'core_profiles'});
```
The first works on spcimas but does not...I found a problem loading the core_profiles ids. The commands are
```
[ids_from_tcv]=tcv2ids(64958,'ids_names',{'core_profiles'});
[ids_from_tcv]=tcv2ids(73461,'ids_names',{'core_profiles'});
```
The first works on spcimas but does not work on lac9, the second works on lac9 but does not work on spcimas. The error message is
```
cd /home/matlab/crpptbx-9.6.0/gdat/TCV_IMAS; git describe --tags --first-parent --abbrev=11 --long --dirty --always: Signal 1
Warning: !!!!!!!!!!!!!!!!!!!!!!!!!\results::thomson:times is empty? Check
> In gdat_tcv>get_thomson_raw_data (line 3571)
In gdat_tcv (line 2089)
In gdat (line 190)
In tcv_get_ids_core_profiles (line 39)
In gdat_tcv (line 1487)
In gdat (line 190)
In tcv2ids (line 117)
!!!!!!!!!!!!!!!!!!!!!!!!! cannot continue with ne_rho
Warning: problems with: psi = psitbxtcv(gdat_data.shot,t_eq,'*0',psitbx_str);
> In gdat_tcv>psi_scatvol_zshift (line 3769)
In gdat_tcv (line 2103)
In gdat (line 190)
In tcv_get_ids_core_profiles (line 39)
In gdat_tcv (line 1487)
In gdat (line 190)
In tcv2ids (line 117)
gdat_data.shot = 73461
Name Size Bytes Class Attributes
t_eq 0x0 0 double
Warning: problems calling gdat_tcv
> In gdat (line 196)
In tcv_get_ids_core_profiles (line 39)
In gdat_tcv (line 1487)
In gdat (line 190)
In tcv2ids (line 117)
there is a problem with: tcv_get_ids_core_profiles , may be check if it exists in your path or test it by itself
Warning: problems calling gdat_tcv
> In gdat (line 196)
In tcv2ids (line 117)
Index exceeds matrix dimensions.
Error in gdat_tcv>psi_scatvol_zshift (line 3772)
disp(['t_eq(1) = ' num2str(t_eq(1))])
Error in gdat_tcv (line 2103)
[psiscatvol,psi_max] = psi_scatvol_zshift(gdat_data, zshift, psitbx_str, gdat_params);
Error in gdat (line 190)
[gdat_data,gdat_params,error_status,varargout] = feval(['gdat_' lower(machine_eff)],args{:});
Error in tcv_get_ids_core_profiles (line 39)
temp_1d.ne_rho = gdat(params_cores_profiles.shot,params_eff);
Error in gdat_tcv (line 1487)
[ids_top,ids_top_description] = feval(['tcv_get_ids_' ids_top_name],shot,ids_empty,gdat_data.gdat_params);
Error in gdat (line 190)
[gdat_data,gdat_params,error_status,varargout] = feval(['gdat_' lower(machine_eff)],args{:});
Error in tcv2ids (line 117)
tmp = gdat(shot,gdat_params);
```
It seems that gdat cannot find the thomson data, but I do not know why... The error is the same in both servers (but on different shots).https://gitlab.epfl.ch/spc/gdat/-/issues/53Move standard tests to spc-ci2022-03-03T16:16:33ZAntoine MerleMove standard tests to spc-ciAntoine MerleAntoine Merlehttps://gitlab.epfl.ch/spc/gdat/-/issues/52Clarify how to handle invalid profile data2022-02-03T10:11:40ZFederico FeliciClarify how to handle invalid profile dataFollowing discussion in RAPTOR: https://gitlab.epfl.ch/spc/raptor/-/commit/33811c45281388434dab1f33da4794d47b6efe76#note_111832
To be clarified how to handle invalid points being passed by `gdat` in such a way that users don't need to ...Following discussion in RAPTOR: https://gitlab.epfl.ch/spc/raptor/-/commit/33811c45281388434dab1f33da4794d47b6efe76#note_111832
To be clarified how to handle invalid points being passed by `gdat` in such a way that users don't need to second-guess.https://gitlab.epfl.ch/spc/gdat/-/issues/46Discrepancy in equilibrium ids from liuqe and from eqdsk2021-11-01T14:06:42ZMatteo Vallarmatteo.vallar@epfl.chDiscrepancy in equilibrium ids from liuqe and from eqdsk@osauter @amerle @mmarin
I was generated the equilibrium ids from liuqe data (`tcv2ids` function, standard call, only asking for `equilibrium` and `core_profiles` ids).
In such case, reading the ids yelds a negative q profile. ~~This fe...@osauter @amerle @mmarin
I was generated the equilibrium ids from liuqe data (`tcv2ids` function, standard call, only asking for `equilibrium` and `core_profiles` ids).
In such case, reading the ids yelds a negative q profile. ~~This feels weird... should IMAS convention be COCOS=11 (thus q>0)?~~ In the matlab structure out of `tcv2ids` q is positive. In the database, it is negative.
If I try to generate the equilibrium using an `eqdsk` in the ids I get a positive q profile.
I am confident about the cocos of the `eqdsk`: I generate it with `cocos_out=2`, and `find_cocos` tells me it is either `1` or `2`. I anyway tried converting from the `eqdsk` telling it was `cocos=1` but I get the same result (looking only at q).
Have you ever encountered similar issues?https://gitlab.epfl.ch/spc/gdat/-/issues/43Error in extracting nbi data2021-10-21T15:54:28ZMichele MarinError in extracting nbi dataThe following warnings are issued when using 'tcv2ids2database(64862,0001,'ids_names','nbi')' on spcimas.
```
Warning: problems loading data for tdi('\results::nbh:energy'); for data_request= \results::nbh:energy
Warning: problems loadi...The following warnings are issued when using 'tcv2ids2database(64862,0001,'ids_names','nbi')' on spcimas.
```
Warning: problems loading data for tdi('\results::nbh:energy'); for data_request= \results::nbh:energy
Warning: problems loading data for tdi('\results::nbh:fraction'); for data_request= \results::nbh:fraction
```
Similarly, the following are issued when using 'aa=gdat(64862,'ids','source','nbi')' (full error message)
```
Warning: problems loading data for tdi('\results::nbh:powr_tcv'); for data_request= \results::nbh:powr_tcv
> In gdat_tcv (line 529)
In tcv_get_ids_nbi (line 75)
In gdat_tcv (line 1487)
In gdat (line 190)
Warning: problems loading data for tdi('\results::nbh:energy'); for data_request= \results::nbh:energy
> In gdat_tcv (line 529)
In tcv_get_ids_nbi (line 81)
In gdat_tcv (line 1487)
In gdat (line 190)
Warning: problems loading data for tdi('\results::nbh:fraction'); for data_request= \results::nbh:fraction
> In gdat_tcv (line 529)
In gdat (line 190)
In tcv_get_ids_nbi (line 87)
In gdat_tcv (line 1487)
In gdat (line 190)
```
The code still goes through, but I guess that some of the IDSs are not filled properlyMatteo Vallarmatteo.vallar@epfl.chMatteo Vallarmatteo.vallar@epfl.chhttps://gitlab.epfl.ch/spc/gdat/-/issues/40Read NB22021-10-11T14:48:39ZMatteo Vallarmatteo.vallar@epfl.chRead NB2TCV NB2 is online, we should add it in the gdat call to powers
The signal I use is `\RESULTS::NB2:POWR_TCV`, but all the names are the same as `NBH`
An example shot is 71588TCV NB2 is online, we should add it in the gdat call to powers
The signal I use is `\RESULTS::NB2:POWR_TCV`, but all the names are the same as `NBH`
An example shot is 71588https://gitlab.epfl.ch/spc/gdat/-/issues/37core_profiles.profiles_1d[0].ion[0].label2021-02-04T11:39:32ZMatteo Vallarmatteo.vallar@epfl.chcore_profiles.profiles_1d[0].ion[0].label@amerle @osauter
Is the field `core_profiles.profiles_1d[0].ion[0].label` filled using `ids2database`?@amerle @osauter
Is the field `core_profiles.profiles_1d[0].ion[0].label` filled using `ids2database`?https://gitlab.epfl.ch/spc/gdat/-/issues/35Error using CXRS_get_profiles from ITER gateway2021-02-08T10:53:55ZMatteo Vallarmatteo.vallar@epfl.chError using CXRS_get_profiles from ITER gatewayI get the following error trying to connect from ITER HPC
```
>>> %here above stuff to connect are set
>>> shot=69087;
>>> [ids_from_tcv,idsok] = tcv2ids(shot,'ids_names',ids2get);
use structure in .mat file: /home/ITER/sautero/public/m...I get the following error trying to connect from ITER HPC
```
>>> %here above stuff to connect are set
>>> shot=69087;
>>> [ids_from_tcv,idsok] = tcv2ids(shot,'ids_names',ids2get);
use structure in .mat file: /home/ITER/sautero/public/matlab/gdat/matlab/TCV/../TCV_IMAS/ids_empty/ids_empty_core_profiles
Warning: problems calling gdat_tcv
> In gdat (line 196)
In tcv_get_ids_core_profiles (line 236)
In gdat_tcv (line 1419)
In gdat (line 190)
In tcv2ids (line 115)
there is a problem with: tcv_get_ids_core_profiles , may be check if it exists in your path or test it by itself
Warning: problems calling gdat_tcv
> In gdat (line 196)
In tcv2ids (line 115)
Undefined function or variable 'CXRS_get_profiles'.
Error in gdat_tcv (line 939)
aa=CXRS_get_profiles; cxrs_params = aa.param;
Error in gdat (line 190)
[gdat_data,gdat_params,error_status,varargout] = feval(['gdat_' lower(machine_eff)],args{:});
Error in tcv_get_ids_core_profiles (line 236)
temp_1d.cxrs_rho = gdat(params_cores_profiles.shot,params_eff_fit1);
Error in gdat_tcv (line 1419)
[ids_top,ids_top_description] = feval(['tcv_get_ids_' ids_top_name],shot,ids_empty,gdat_data.gdat_params);
Error in gdat (line 190)
[gdat_data,gdat_params,error_status,varargout] = feval(['gdat_' lower(machine_eff)],args{:});
Error in tcv2ids (line 115)
tmp = gdat(shot,gdat_params);
```https://gitlab.epfl.ch/spc/gdat/-/issues/32Load/Plot ASTRA results without CXRS data2020-09-17T07:57:27ZAlexander KarpushovLoad/Plot ASTRA results without CXRS dataThere is an error in ASTRA_TCV_summary.m for TCV shots without the CXRS data - need to updateThere is an error in ASTRA_TCV_summary.m for TCV shots without the CXRS data - need to updateMatteo Vallarmatteo.vallar@epfl.chMatteo Vallarmatteo.vallar@epfl.chhttps://gitlab.epfl.ch/spc/gdat/-/issues/31No deployment for 8302020-06-16T13:25:31ZFederico FeliciNo deployment for 830@amerle @osauter@amerle @osauterFederico FeliciFederico Felicihttps://gitlab.epfl.ch/spc/gdat/-/issues/30Job Failed #1181142020-06-16T10:41:41ZFederico FeliciJob Failed #118114@osauter this is not related to the deployment problems but the 'all' tests run overnight failed on the new `master`...
Job [#118114](https://gitlab.epfl.ch/spc/gdat/-/jobs/118114) failed for 88253476d1461618ace614a2875e33d0c9b9cf31:@osauter this is not related to the deployment problems but the 'all' tests run overnight failed on the new `master`...
Job [#118114](https://gitlab.epfl.ch/spc/gdat/-/jobs/118114) failed for 88253476d1461618ace614a2875e33d0c9b9cf31:Olivier SauterOlivier Sauterhttps://gitlab.epfl.ch/spc/gdat/-/issues/29deployment fails again https://gitlab.epfl.ch/spc/gdat/pipelines/429902020-05-27T07:42:24ZOlivier Sauterdeployment fails again https://gitlab.epfl.ch/spc/gdat/pipelines/42990How do you create an issue directly from there?
@ffelici I cannot resolve the new problemHow do you create an issue directly from there?
@ffelici I cannot resolve the new problemJoan DeckerJoan Deckerhttps://gitlab.epfl.ch/spc/gdat/-/issues/28Job Failed #1180502020-05-27T07:43:35ZFederico FeliciJob Failed #118050Job [#118050](https://gitlab.epfl.ch/spc/gdat/-/jobs/118050) failed for 88253476d1461618ace614a2875e33d0c9b9cf31:Job [#118050](https://gitlab.epfl.ch/spc/gdat/-/jobs/118050) failed for 88253476d1461618ace614a2875e33d0c9b9cf31:Olivier SauterOlivier Sauter