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SKIRT / SKIRT9

SKIRT version 9 -- advanced radiative transfer in dusty systems
http://www.skirt.ugent.be
GNU Affero General Public License v3.0
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Error of a ski file #183

Closed huanian closed 1 year ago

huanian commented 1 year ago

Description I run the SIGME code by Dr. Karen Olsen. The code generated a set of ski file for skirt running. The error is the following:

---------------> mpirun -np 4 skirt simba_25Mpc_G207_w_hii.ski 06/06/2023 09:17:02.164 Welcome to SKIRT v9.0 (git cbcac09 built on 05/06/2023 at 11:19:21) 06/06/2023 09:17:02.164 Running on HuaniandeiMac.local for huanianzhang 06/06/2023 09:17:02.164 Constructing a simulation from ski file 'simba_25Mpc_G207_w_hii.ski'... 06/06/2023 09:17:02.165 Welcome to SKIRT v9.0 (git cbcac09 built on 05/06/2023 at 11:19:21) 06/06/2023 09:17:02.165 Running on HuaniandeiMac.local for huanianzhang 06/06/2023 09:17:02.165 Constructing a simulation from ski file 'simba_25Mpc_G207_w_hii.ski'... 06/06/2023 09:17:02.166 * * Error: Error in XML stream 'simba_25Mpc_G207_w_hii.ski' at line 29 06/06/2023 09:17:02.166 Error: Item of type 'MediumSystem' has no property named 'numDensitySamples' 06/06/2023 09:17:02.166 * * Error: On line 185 in file /Users/huanianzhang/ISM_MIRemission/SIGAME_v3-master/SKIRT/git/SMILE/fundamentals/XmlReader.cpp 06/06/2023 09:17:02.166 Error: In function throwError 06/06/2023 09:17:02.166 * * Error: Call stack: 06/06/2023 09:17:02.166 Error: 1 skirt 0x00000001081f8016 _ZN10FatalErrorC2ENSt3112basic_stringIcNS0_11char_traitsIcEENS09allocatorIcEEEEPKciS8 + 1158 06/06/2023 09:17:02.166 * *** Error: 2 skirt 0x00000001082034aa _ZN9XmlReader10throwErrorENSt3112basic_stringIcNS0_11char_traitsIcEENS0_9allocatorIcEEEE + 346 06/06/2023 09:17:02.166 * * Error: 3 skirt 0x00000001081c9da5 _ZN12_GLOBAL__N_115setupPropertiesEP4ItemPK9SchemaDefP11NameManagerR9XmlReader + 805 06/06/2023 09:17:02.166 Error: 4 skirt 0x00000001081cd058 _ZN12_GLOBAL__N_120ReaderPropertySetter20visitPropertyHandlerEP19ItemPropertyHandler + 2088

When I comment out the line including "numDensitySamples", it has other issues as the following:

---------------> mpirun -np 4 skirt simba_25Mpc_G207_w_hii.ski 07/06/2023 11:16:26.379 Welcome to SKIRT v9.0 (git cbcac09 built on 05/06/2023 at 11:19:21) 07/06/2023 11:16:26.379 Running on on-campus-10-138-74-100.vpn.arizona.edu for huanianzhang 07/06/2023 11:16:26.379 Constructing a simulation from ski file 'simba_25Mpc_G207_w_hii.ski'... 07/06/2023 11:16:26.379 Welcome to SKIRT v9.0 (git cbcac09 built on 05/06/2023 at 11:19:21) 07/06/2023 11:16:26.379 Running on on-campus-10-138-74-100.vpn.arizona.edu for huanianzhang 07/06/2023 11:16:26.379 Constructing a simulation from ski file 'simba_25Mpc_G207_w_hii.ski'... 07/06/2023 11:16:26.380 * * Error: Type 'photonPacketOptions' is not defined in the schema 07/06/2023 11:16:26.380 Error: On line 870 in file /Users/huanianzhang/ISM_MIRemission/SIGAME_v3-master/SKIRT/git/SMILE/schema/SchemaDef.cpp 07/06/2023 11:16:26.380 * * Error: In function typeDef 07/06/2023 11:16:26.380 Error: Call stack: 07/06/2023 11:16:26.380 * * Error: 1 skirt 0x0000000103299016 _ZN10FatalErrorC2ENSt3__112basic_stringIcNS0_11char_traitsIcEENS09allocatorIcEEEEPKciS8 + 1158 07/06/2023 11:16:26.380 Error: 2 skirt 0x000000010328d059 _ZNK9SchemaDef7typeDefENSt3112basic_stringIcNS0_11char_traitsIcEENS0_9allocatorIcEEEE + 169 07/06/2023 11:16:26.380 * * Error: 3 skirt 0x000000010328d3e5 _ZNK9SchemaDef8inheritsENSt3__112basic_stringIcNS0_11char_traitsIcEENS09allocatorIcEEEES6 + 277 07/06/2023 11:16:26.380 Error: 4 skirt 0x000000010326dc32 _ZN12_GLOBALN_120ReaderPropertySetter20visitPropertyHandlerEP19ItemPropertyHandler + 1026 07/06/2023 11:16:26.380 * * Error: 5 skirt 0x000000010326b22e _ZN12_GLOBAL__N_115setupPropertiesEP4ItemPK9SchemaDefP11NameManagerR9XmlReader + 1966 07/06/2023 11:16:26.380 Error: 6 skirt 0x000000010326a02b _ZN12_GLOBALN_14readEPK9SchemaDefR9XmlReader + 2683 07/06/2023 11:16:26.380 * *** Error: 7 skirt 0x00000001032694bc _ZN19XmlHierarchyCreator8readFileEPK9SchemaDefNSt3112basic_stringIcNS3_11char_traitsIcEENS3_9allocatorIcEEEE + 108 07/06/2023 11:16:26.380 * * Error: 8 skirt 0x0000000103261c8c _ZN23SkirtCommandLineHandler12doSimulationEm + 636 07/06/2023 11:16:26.380 Error: 9 skirt 0x000000010325f3b1 _ZN23SkirtCommandLineHandler7doBatchEv + 513 07/06/2023 11:16:26.380 * * Error: 10 skirt 0x000000010325e6c0 _ZN23SkirtCommandLineHandler7performEv + 80 07/06/2023 11:16:26.380 Error: 11 skirt 0x0000000103265d50 main + 224 07/06/2023 11:16:26.380 * *** Error: 12 dyld 0x00007ff80d8f641f start + 1903

Data

I could not upload the .ski file. But below is the content.

<?xml version="1.0" encoding="UTF-8"?>

mbaes commented 1 year ago

Dear Huanian,

It seems that the ski files generated by SIGAME are not up to date to the latest version of SKIRT. You can attempt to upgrade them by running the skiupgrade comment in PTS (https://skirt.ugent.be/pts9/namespacepts_1_1skiupgrade.html).

Kind regards, Maarten

On 7 Jun 2023, at 05:39, Huanian Zhang @.**@.>> wrote:

Description I run the SIGME code by Dr. Karen Olsen. The code generated a set of ski file for skirt running. The error is the following:

---------------> mpirun -np 4 skirt simba_25Mpc_G207_w_hii.ski 06/06/2023 09:17:02.164 Welcome to SKIRT v9.0 (git cbcac09https://github.com/SKIRT/SKIRT9/commit/cbcac09ec4c73dfa9af26349a430a1f6e39ca4d8 built on 05/06/2023 at 11:19:21) 06/06/2023 09:17:02.164 Running on HuaniandeiMac.local for huanianzhang 06/06/2023 09:17:02.164 Constructing a simulation from ski file 'simba_25Mpc_G207_w_hii.ski'... 06/06/2023 09:17:02.165 Welcome to SKIRT v9.0 (git cbcac09https://github.com/SKIRT/SKIRT9/commit/cbcac09ec4c73dfa9af26349a430a1f6e39ca4d8 built on 05/06/2023 at 11:19:21) 06/06/2023 09:17:02.165 Running on HuaniandeiMac.local for huanianzhang 06/06/2023 09:17:02.165 Constructing a simulation from ski file 'simba_25Mpc_G207_w_hii.ski'... 06/06/2023 09:17:02.166 * * Error: Error in XML stream 'simba_25Mpc_G207_w_hii.ski' at line 29 06/06/2023 09:17:02.166 Error: Item of type 'MediumSystem' has no property named 'numDensitySamples' 06/06/2023 09:17:02.166 * * Error: On line 185 in file /Users/huanianzhang/ISM_MIRemission/SIGAME_v3-master/SKIRT/git/SMILE/fundamentals/XmlReader.cpp 06/06/2023 09:17:02.166 Error: In function throwError 06/06/2023 09:17:02.166 * * Error: Call stack: 06/06/2023 09:17:02.166 Error: 1 skirt 0x00000001081f8016 ZN10FatalErrorC2ENSt3112basic_stringIcNS0_11char_traitsIcEENS0_9allocatorIcEEEEPKciS8 + 1158 06/06/2023 09:17:02.166 * * Error: 2 skirt 0x00000001082034aa _ZN9XmlReader10throwErrorENSt3__112basic_stringIcNS0_11char_traitsIcEENS0_9allocatorIcEEEE + 346 06/06/2023 09:17:02.166 Error: 3 skirt 0x00000001081c9da5 _ZN12_GLOBAL__N_115setupPropertiesEP4ItemPK9SchemaDefP11NameManagerR9XmlReader + 805 06/06/2023 09:17:02.166 * *** Error: 4 skirt 0x00000001081cd058 _ZN12_GLOBALN_120ReaderPropertySetter20visitPropertyHandlerEP19ItemPropertyHandler + 2088

When I comment out the line including "numDensitySamples", it has other issues as the following:

---------------> mpirun -np 4 skirt simba_25Mpc_G207_w_hii.ski 07/06/2023 11:16:26.379 Welcome to SKIRT v9.0 (git cbcac09https://github.com/SKIRT/SKIRT9/commit/cbcac09ec4c73dfa9af26349a430a1f6e39ca4d8 built on 05/06/2023 at 11:19:21) 07/06/2023 11:16:26.379 Running on on-campus-10-138-74-100.vpn.arizona.eduhttp://on-campus-10-138-74-100.vpn.arizona.edu/ for huanianzhang 07/06/2023 11:16:26.379 Constructing a simulation from ski file 'simba_25Mpc_G207_w_hii.ski'... 07/06/2023 11:16:26.379 Welcome to SKIRT v9.0 (git cbcac09https://github.com/SKIRT/SKIRT9/commit/cbcac09ec4c73dfa9af26349a430a1f6e39ca4d8 built on 05/06/2023 at 11:19:21) 07/06/2023 11:16:26.379 Running on on-campus-10-138-74-100.vpn.arizona.eduhttp://on-campus-10-138-74-100.vpn.arizona.edu/ for huanianzhang 07/06/2023 11:16:26.379 Constructing a simulation from ski file 'simba_25Mpc_G207_w_hii.ski'... 07/06/2023 11:16:26.380 * * Error: Type 'photonPacketOptions' is not defined in the schema 07/06/2023 11:16:26.380 Error: On line 870 in file /Users/huanianzhang/ISM_MIRemission/SIGAME_v3-master/SKIRT/git/SMILE/schema/SchemaDef.cpp 07/06/2023 11:16:26.380 * * Error: In function typeDef 07/06/2023 11:16:26.380 Error: Call stack: 07/06/2023 11:16:26.380 * * Error: 1 skirt 0x0000000103299016 ZN10FatalErrorC2ENSt3__112basic_stringIcNS0_11char_traitsIcEENS0_9allocatorIcEEEEPKciS8 + 1158 07/06/2023 11:16:26.380 Error: 2 skirt 0x000000010328d059 _ZNK9SchemaDef7typeDefENSt3112basic_stringIcNS0_11char_traitsIcEENS0_9allocatorIcEEEE + 169 07/06/2023 11:16:26.380 * *** Error: 3 skirt 0x000000010328d3e5 ZNK9SchemaDef8inheritsENSt3112basic_stringIcNS0_11char_traitsIcEENS0_9allocatorIcEEEES6 + 277 07/06/2023 11:16:26.380 * * Error: 4 skirt 0x000000010326dc32 _ZN12_GLOBAL__N_120ReaderPropertySetter20visitPropertyHandlerEP19ItemPropertyHandler + 1026 07/06/2023 11:16:26.380 Error: 5 skirt 0x000000010326b22e _ZN12_GLOBAL__N_115setupPropertiesEP4ItemPK9SchemaDefP11NameManagerR9XmlReader + 1966 07/06/2023 11:16:26.380 * * Error: 6 skirt 0x000000010326a02b _ZN12_GLOBAL__N_14readEPK9SchemaDefR9XmlReader + 2683 07/06/2023 11:16:26.380 Error: 7 skirt 0x00000001032694bc _ZN19XmlHierarchyCreator8readFileEPK9SchemaDefNSt3__112basic_stringIcNS3_11char_traitsIcEENS3_9allocatorIcEEEE + 108 07/06/2023 11:16:26.380 * * Error: 8 skirt 0x0000000103261c8c _ZN23SkirtCommandLineHandler12doSimulationEm + 636 07/06/2023 11:16:26.380 Error: 9 skirt 0x000000010325f3b1 _ZN23SkirtCommandLineHandler7doBatchEv + 513 07/06/2023 11:16:26.380 * * Error: 10 skirt 0x000000010325e6c0 _ZN23SkirtCommandLineHandler7performEv + 80 07/06/2023 11:16:26.380 Error: 11 skirt 0x0000000103265d50 main + 224 07/06/2023 11:16:26.380 * *** Error: 12 dyld 0x00007ff80d8f641f start + 1903

Data

I could not upload the .ski file. But below is the content.

— Reply to this email directly, view it on GitHubhttps://github.com/SKIRT/SKIRT9/issues/183, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AB5O6DEKF2TRGEUG2JCTMHDXJ7ZWRANCNFSM6AAAAAAY5IAMLM. You are receiving this because you are subscribed to this thread.Message ID: @.***>

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huanian commented 1 year ago

Dear Maarten, Thanks for the quick response. I read the website you provided, but I still could not make it work. Could you provide me more details? My ski files are located at such directory: /home/skifiles/*.ski I am not sure how I should do for this "pts.skiupgrade.do.test_upgrade_ski_files Namespace Reference". Thanks, Huanian

mbaes commented 1 year ago

Dear Huanian,

You have to install PTS on your system – see https://skirt.ugent.be/root/_install_p_t_s.html.

When PTS is installed, go to the directory where you have your ski files and enter the command

pts skiupgrade/upgrade_ski_files .

Good luck ! Maarten

On 12 Jun 2023, at 05:29, Huanian Zhang @.**@.>> wrote:

Dear Maarten, Thanks for the quick response. I read the website you provided, but I still could not make it work. Could you provide me more details? My ski files are located at such directory: /home/skifiles/*.ski I am not sure how I should do for this "pts.skiupgrade.do.test_upgrade_ski_files Namespace Reference". Thanks, Huanian

— Reply to this email directly, view it on GitHubhttps://github.com/SKIRT/SKIRT9/issues/183#issuecomment-1586521321, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AB5O6DCZBHYEGFEOTP6DS73XK2EKJANCNFSM6AAAAAAY5IAMLM. You are receiving this because you commented.Message ID: @.***>

Maarten Baes Sterrenkundig Observatorium Department of Physics and Astronomy Universiteit Gent Krijgslaan 281 S9, B-9000 Gent, Belgium phone +32-9-264-4793 @.**@.> http://users.ugent.be/~mbaes

mbaes commented 1 year ago

Dear Huanian,

I have been told by Peter Camps that there actually is a user guide section that deals with this issue: https://skirt.ugent.be/root/_user_upgrade_ski.html You can find more complete information there.

Kind regards, Maarten

On 12 Jun 2023, at 09:39, Maarten Baes @.**@.>> wrote:

Dear Huanian,

You have to install PTS on your system – see https://skirt.ugent.be/root/_install_p_t_s.html.

When PTS is installed, go to the directory where you have your ski files and enter the command

pts skiupgrade/upgrade_ski_files .

Good luck ! Maarten

On 12 Jun 2023, at 05:29, Huanian Zhang @.**@.>> wrote:

Dear Maarten, Thanks for the quick response. I read the website you provided, but I still could not make it work. Could you provide me more details? My ski files are located at such directory: /home/skifiles/*.ski I am not sure how I should do for this "pts.skiupgrade.do.test_upgrade_ski_files Namespace Reference". Thanks, Huanian

— Reply to this email directly, view it on GitHubhttps://github.com/SKIRT/SKIRT9/issues/183#issuecomment-1586521321, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AB5O6DCZBHYEGFEOTP6DS73XK2EKJANCNFSM6AAAAAAY5IAMLM. You are receiving this because you commented.Message ID: @.***>

Maarten Baes Sterrenkundig Observatorium Department of Physics and Astronomy Universiteit Gent Krijgslaan 281 S9, B-9000 Gent, Belgium phone +32-9-264-4793 @.**@.> http://users.ugent.be/~mbaes

Maarten Baes Sterrenkundig Observatorium Department of Physics and Astronomy Universiteit Gent Krijgslaan 281 S9, B-9000 Gent, Belgium phone +32-9-264-4793 @.**@.> http://users.ugent.be/~mbaes

huanian commented 1 year ago

Dear Maarten, Thank you so much for the detailed explanation. I have updated the ski files and those errors are all clear. But there is a new one as the following:

---------------> skirt -t 8 -r .ski 12/06/2023 16:00:48.257 Welcome to SKIRT v9.0 (git cbcac09 built on 05/06/2023 at 11:19:21) 12/06/2023 16:00:48.257 Running on HuaniandeiMac.local for huanianzhang 12/06/2023 16:00:50.665 Starting a set of 240 simulations... 12/06/2023 16:00:50.665 ! Performing simulation #1 of 240 12/06/2023 16:00:50.665 Constructing a simulation from ski file 'simba_25Mpc_G0_w_hii.ski'... 12/06/2023 16:00:50.673 * Error: Error in XML stream 'simba_25Mpc_G0_w_hii.ski' at line 99 12/06/2023 16:00:50.673 Error: Value '' for property 'writeWavelengthGrid' can't be converted to bool 12/06/2023 16:00:50.673 * * Error: On line 185 in file /Users/huanianzhang/ISM_MIRemission/SIGAME_v3-master/SKIRT/git/SMILE/fundamentals/XmlReader.cpp 12/06/2023 16:00:50.673 Error: In function throwError

I am quite new to this package, then I do not have a clue how to resolve it. Could you shed a light on me? Thanks, Huanian

mbaes commented 1 year ago

Dear Huanian,

In general, if you are quite new to SKIRT, it is worth taking some time to go through the user guide (https://skirt.ugent.be/root/_user_guide.html) and try the different tutorials. That will help you a lot in understanding the setup and methodology of SKIRT.

Concerning the specific error that you encountered: there are several classes that have a “writeWavelengthGrid” property: you can check that by looking at the page on the SKIRT website that lists all the properties for each class (https://skirt.ugent.be/root/_ski_file_help_properties.html). This property always has a boolean value, and it seems that your ski file does not give it a boolean value.

Kind regards, Maarten

On 15 Jun 2023, at 13:59, Huanian Zhang @.**@.>> wrote:

Dear Maarten, Thank you so much for the detailed explanation. I have updated the ski files and those errors are all clear. But there is a new one as the following:

---------------> skirt -t 8 -r .ski 12/06/2023 16:00:48.257 Welcome to SKIRT v9.0 (git cbcac09https://github.com/SKIRT/SKIRT9/commit/cbcac09ec4c73dfa9af26349a430a1f6e39ca4d8 built on 05/06/2023 at 11:19:21) 12/06/2023 16:00:48.257 Running on HuaniandeiMac.local for huanianzhang 12/06/2023 16:00:50.665 Starting a set of 240 simulations... 12/06/2023 16:00:50.665 ! Performing simulation #1https://github.com/SKIRT/SKIRT9/issues/1 of 240 12/06/2023 16:00:50.665 Constructing a simulation from ski file 'simba_25Mpc_G0_w_hii.ski'... 12/06/2023 16:00:50.673 * Error: Error in XML stream 'simba_25Mpc_G0_w_hii.ski' at line 99 12/06/2023 16:00:50.673 Error: Value '' for property 'writeWavelengthGrid' can't be converted to bool 12/06/2023 16:00:50.673 * * Error: On line 185 in file /Users/huanianzhang/ISM_MIRemission/SIGAME_v3-master/SKIRT/git/SMILE/fundamentals/XmlReader.cpp 12/06/2023 16:00:50.673 Error: In function throwError

I am quite new to this package, then I do not have a clue how to resolve it. Could you shed a light on me? Thanks, Huanian

— Reply to this email directly, view it on GitHubhttps://github.com/SKIRT/SKIRT9/issues/183#issuecomment-1592906385, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AB5O6DF6JLTFVJCH7UONGI3XLL2IXANCNFSM6AAAAAAY5IAMLM. You are receiving this because you commented.Message ID: @.***>

Maarten Baes Sterrenkundig Observatorium Department of Physics and Astronomy Universiteit Gent Krijgslaan 281 S9, B-9000 Gent, Belgium phone +32-9-264-4793 @.**@.> http://users.ugent.be/~mbaes

huanian commented 1 year ago

Dear Maarten, Thank you so much for the kind help. It helps a lot, will read it and try to fix those issues. Best, Huanian