error in run cubep3m

[wuseyu]

After solving the missing file problem( ../cubep3m.threads.070515/input/checkpoints_high), I encountered some new problems. At first, I met this problem. By ltrace I found It may be a problem with missing files table_M_Delta.dat, so I added it after that.The log file output after that shows that the file was found, but the problem is still not solved(FFT direction error). Finally,I tried to revise File Run10Codes.pbs because log file show it has mpirun program,maybe it can't find working directory.(I'm not sure if the direction is correct,it's just a try) Now I got the final log file.c.log May I ask what caused the problem? Looking forward to your reply.

[jharno]

You need to include a '/' at the end of your paths:

/scratch/wuseyu/

and not

/scratch/wuseyu

[wuseyu]

Thanks for reply. Now I tried to rum cubep3m, but its not going well. This is my parameters file. (Should I pin "ic_path" to the ic file?) Is there anything else I need to do before running the software, maybe I'm missing something?

[jharno]

The IC path should be the absolute path the xv0.ic file

---

From: wuseyu @.> Sent: 13 November 2022 08:25 To: jharno/cubep3m @.> Cc: Joachim Harnois-Deraps @.>; Comment @.> Subject: Re: [jharno/cubep3m] error in run cubep3m (Issue #15)

⚠ External sender. Take care when opening links or attachments. Do not provide your login details.

Thanks for reply. Now I tried to rum cubep3m, but its not going well. This is my parameters file. [image]https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fuser-images.githubusercontent.com%2F96163054%2F201512671-d0bbd3e9-6907-447c-a8b8-05650eddb905.png&data=05%7C01%7CJoachim.Harnois-Deraps%40newcastle.ac.uk%7Ce664023d0eb94a95b9c608dac550a33f%7C9c5012c9b61644c2a91766814fbe3e87%7C1%7C0%7C638039247364988347%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=CfRxK5xC%2FeT421yYBS9dNairew03x2uZLiYhzv4H7b8%3D&reserved=0 (Should I pin "ic_path" to the ic file?) Is there anything else I need to do before running the software, maybe I'm missing something? [image]https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fuser-images.githubusercontent.com%2F96163054%2F201512705-6bcbaa01-331e-4fca-b8f8-f24ebdf057b9.png&data=05%7C01%7CJoachim.Harnois-Deraps%40newcastle.ac.uk%7Ce664023d0eb94a95b9c608dac550a33f%7C9c5012c9b61644c2a91766814fbe3e87%7C1%7C0%7C638039247364988347%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=wQPrZLiqyBRbxbwL5l0ANI%2F2T9rLWTjs3bMyO5rm8Vg%3D&reserved=0

— Reply to this email directly, view it on GitHubhttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fjharno%2Fcubep3m%2Fissues%2F15%23issuecomment-1312669574&data=05%7C01%7CJoachim.Harnois-Deraps%40newcastle.ac.uk%7Ce664023d0eb94a95b9c608dac550a33f%7C9c5012c9b61644c2a91766814fbe3e87%7C1%7C0%7C638039247364988347%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=5jx%2FYA%2FuSh9A1Hyg5NPvmVbl3LFrQURmmy26gnpIU20%3D&reserved=0, or unsubscribehttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAAISJHI73I5WNFGRKK2Z7LDWICQX5ANCNFSM6AAAAAARZ45NOE&data=05%7C01%7CJoachim.Harnois-Deraps%40newcastle.ac.uk%7Ce664023d0eb94a95b9c608dac550a33f%7C9c5012c9b61644c2a91766814fbe3e87%7C1%7C0%7C638039247364988347%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=VmK8nVRbBlh6Ly6v%2Bhd8Ab0GXGjcbSwHGUgWZOs7WcU%3D&reserved=0. You are receiving this because you commented.Message ID: @.***>

[wuseyu]

Sorry, I just saw the email, I tried setting it as an absolute path yesterday, it doesn't seem to work.

[jharno]

Can you make sure that when you run ciubep3m, the code looks for the IC in /scratch/wuseyu/xv0.ic, and not /scratch/$USER/ ?

You need to recompile cubep3m for this to take effect.

[wuseyu]

Hello, I tried reimplementing everything I did, now I make sure all files are new, then I recompiled "cubep3m", but still get "FFT direction error" error and file "xv0.ic" not found file error.

This is my parameters file.

This is log

If I modify ic_path to "/scratch/$USER/xv0.ic", the log file will show like this

[jharno]

Right, so you want ic_path = /scratch/wuseyu/

Can you check the size of the xv0.ic? Maybe the file is found but can't be read properly. In particular, you should make sure you do not have the -DBINARY flag in your makefile.

[wuseyu]

It looks like there has been some breakthrough!

Can this be considered a successful start of the service? The log will still report "FFT direction error", does this affect the program?

[wuseyu]

Now the dormitory is powered off, any new suggestions I will try after calling tomorrow. Thanks again for your detailed guidance.

[wuseyu]

Sorry for not updating the progress for such a long time. I was busy with my final exam some time ago, and it is almost over now, so I hope to continue with the next work. What is the cause of the current memory error problem? This error It is generated when the executable is run, maybe I should modify some code that generates the executable? Anyway, thank you for your continued support.

[jharno]

I am not sure. The problem you are trying to solve is very small, it caused issues in the past. Perhaps it would help if you scaled it up a little.

can you print your parameter file?

[wuseyu]

This is the result of my running the program yesterday, don't know if you need more information.

[wuseyu]

According to the printed log, it seems to have read the correct file. I searched for some similar errors on the Internet. It seems to be classified as a memory error, but there is no unified solution. After all, there are too many causes.

[jharno]

Can you print the parameter file please (not the log)

[wuseyu]

Do you mean the "parameters" file? And under the folder “/scratch/${USER}”, this is the current state。

[wuseyu]

This is the log file generated by the current run, I think this may help to solve the problem. a.log

[wuseyu]

May I ask if this line of error caused the operation to fail?

[jharno]

Sorry, I don't know what that memory line means in terms is problems in the code.

[wuseyu]

Signal 11, or officially know as "segmentation fault", means that the program accessed a memory location that was not assigned. That's usually a bug in the program. This is the relevant explanation I found on the Internet, and I don't know much about this type of error.

[wuseyu]

This may be caused by stack limits or error passing parameters or something else.

[jharno]

Could you increase the "tiles_node_dim" from 2 to 4 in the parameters file, then recompile both the initial conditions and main code, re-run the initial and main codes. I suspect that the problem could be caused by equivalences between arrays, which can sometimes be broken if the problem is too small.

[wuseyu]

This doesn’t seem to work. This run is much slower than the previous one. I checked the update time of the cubep3m executable file. It has indeed been updated. The data used for analysis is also different, but the program still reports the same mistake.

[jharno]

Can you run it through a debugger and see what line is causing the crash?

---

From: wuseyu @.> Sent: 08 December 2022 16:11 To: jharno/cubep3m @.> Cc: Joachim Harnois-Deraps @.>; Comment @.> Subject: Re: [jharno/cubep3m] error in run cubep3m (Issue #15)

⚠ External sender. Take care when opening links or attachments. Do not provide your login details.

[image]https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fuser-images.githubusercontent.com%2F96163054%2F206497873-ce53d29c-a043-47e6-92d8-daaf96d6aa3d.png&data=05%7C01%7CJoachim.Harnois-Deraps%40newcastle.ac.uk%7C4c984eee24ae4f0e69f108dad936e170%7C9c5012c9b61644c2a91766814fbe3e87%7C1%7C0%7C638061126971551599%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Tk45Y0DQFeCPRU5bUo1WmudgxMuyt4jsRedfaEn0v8I%3D&reserved=0 This doesn’t seem to work. This run is much slower than the previous one. I checked the update time of the cubep3m executable file. It has indeed been updated. The data used for analysis is also different, but the program still reports the same mistake.

— Reply to this email directly, view it on GitHubhttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fjharno%2Fcubep3m%2Fissues%2F15%23issuecomment-1342960699&data=05%7C01%7CJoachim.Harnois-Deraps%40newcastle.ac.uk%7C4c984eee24ae4f0e69f108dad936e170%7C9c5012c9b61644c2a91766814fbe3e87%7C1%7C0%7C638061126971551599%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=VobyeDM4LmIAgG86D7Uq4DWtgX2lkFXVaDSidXI0X2Q%3D&reserved=0, or unsubscribehttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAAISJHOPNKVJVC6SANVJ3ALWMICDNANCNFSM6AAAAAARZ45NOE&data=05%7C01%7CJoachim.Harnois-Deraps%40newcastle.ac.uk%7C4c984eee24ae4f0e69f108dad936e170%7C9c5012c9b61644c2a91766814fbe3e87%7C1%7C0%7C638061126971551599%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=dsuyuz2TavI%2BtY%2F6UDaNFbrYBT8uX0Y0KUx0BxOfDBg%3D&reserved=0. You are receiving this because you commented.Message ID: @.***>

[wuseyu]

Sorry, there are more things in school than I thought, but now all have been resolved, I tried to add -g, -Og, -fcheck=all and -fbacktrace in the fflags of the Make_PP_THREADS file that generates the executable file, and then run cubep3m , however this debug flag does not work.Should I make these changes to this file, or to some other file?