C-I-TASSER - Segmentation fault (core dumped)

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ATVincent
Posts: 3
Joined: Sat Jan 15, 2022 10:37 pm

C-I-TASSER - Segmentation fault (core dumped)

Post by ATVincent »

Hello,

I'm trying to use C-I-TASSER locally on my server. I am at the stage of generating the indexes for DeepMSA with esl-sfetch. However, I get "Segmentation fault (core dumped)" when I run the command "../../contact/DeepMSA/bin/esl-sfetch --index uniref90.fasta". In fact, several binaries of the package give "Segmentation fault (core dumped)" when I try to run them.

Does anyone have an idea of the cause of the problem?

Thank you,

Antony
jlspzw
Posts: 97
Joined: Tue May 04, 2021 5:04 pm

Re: C-I-TASSER - Segmentation fault (core dumped)

Post by jlspzw »

Dear user,

How large your computer memory is? I suspect it may due to the memory is not enough for creating index files.

You may try using some other larger memory computer to create the index files?

Best
Wei
ATVincent
Posts: 3
Joined: Sat Jan 15, 2022 10:37 pm

Re: C-I-TASSER - Segmentation fault (core dumped)

Post by ATVincent »

Dear Wei,

Thank you for the answer. I have 64 GB of RAM. I doubt RAM is the issue. I get the same problem with other binaries included in C-I-TASSER. For example, "./C-I-TASSER-1.0/contact/DeepMSA/bin/clustalo" also gives me the "segmentation fault" problem.

I tried manually downloading the DeepMSA package. It works ! I can do indexing. However, the other binaries in the package remain problematic.

Could there be a problem with the compilation? The whole thing works with another computer, which has an AMD processor (the problematic one has an Intel processor).

Sincerely,

Antony
jlspzw
Posts: 97
Joined: Tue May 04, 2021 5:04 pm

Re: C-I-TASSER - Segmentation fault (core dumped)

Post by jlspzw »

This seems interesting, I think we have tested in the intel CPUs, but what program you still has issue? Let me know the program name, I will see if the code is open-source codes.
ATVincent
Posts: 3
Joined: Sat Jan 15, 2022 10:37 pm

Re: C-I-TASSER - Segmentation fault (core dumped)

Post by ATVincent »

Terminal.txt.zip
(17.06 KiB) Downloaded 89 times
On my Intel, almost all the executables included in C-I-Tasser have the same problem (Segmentation fault).

On my AMD, the executables work. However, there seems to be another problem. Terminal output is attached to the message. Do you have any idea what could be causing the problem on the AMD?

Thank you !

Antony
Terminal.txt.zip
(17.06 KiB) Downloaded 89 times
rishab
Posts: 1
Joined: Fri Jan 21, 2022 2:18 pm

Re: C-I-TASSER - Segmentation fault (core dumped)

Post by rishab »

Thanks for sharing.
jlspzw
Posts: 97
Joined: Tue May 04, 2021 5:04 pm

Re: C-I-TASSER - Segmentation fault (core dumped)

Post by jlspzw »

Hi

from the message I believe it may be caused by the pytorch version problem, we develop the contact programs by pytorch 0.4, perhaps you run in higher version, you may try download those programs with pytorch updated (1.7) and replace the old programs in contacts folder of C-I-TASSER package.

https://zhanggroup.org/C-I-TASSER/stand ... orch17.zip

Best
IT team
ATVincentUL
Posts: 4
Joined: Fri Jan 28, 2022 12:14 am

Re: C-I-TASSER - Segmentation fault (core dumped)

Post by ATVincentUL »

Hello,

I changed the contacts folder and installed pytorch 1.7 in my conda environment. Unfortunately, I still have a problem (please see attachment).

Sincerely,

Antony
C-I-TASSER.txt.zip
(9.1 KiB) Downloaded 89 times
ATVincentUL
Posts: 4
Joined: Fri Jan 28, 2022 12:14 am

Re: C-I-TASSER - Segmentation fault (core dumped)

Post by ATVincentUL »

Hello,

I still have the problem. Does anyone have a solution?

Sincerely,

Antony
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