libcublas.so.11 error

[jychoi0616]

Dear tomotwin team,

Thanks for developing this software.
I just installed to our workstation (centos) and following your tutorial.
In this step:
tomotwin_tools.py extractref --tomo TS_14.mrc --coords coords/reference.coords --out reference/ --filename protein_a

I got an error message of this:

ImportError: /data/miniconda3/envs/tomotwin/lib/python3.10/site-packages/cuml/internals/../../../.././libcublas.so.11: symbol cublasLtHSHMatmulAlgoInit, version libcublasLt.so.11 not defined in file libcublasLt.so.11 with link time reference

When I went actual place of /data/miniconda3/envs/tomotwin/lib/, I couldn't list anything using "ls"command with the error message as this:

ls: relocation error: /lib64/libacl.so.1: symbol getxattr, version ATTR_1.0 not defined in file libattr.so.1 with link time reference

Could you please help me in this please?

Thanks a lot!
Joy

[thorstenwagner]

Sorry, I hadnt the time to look into it. What was the problem? How did you fix it?

[jychoi0616]

Hi Thorsten, It was some link issue between libcublas and libcublasLt (at least it seemed). For my case, removing libcublas* under the torch/lib directory helped solving the issue by following one of the suggestions in hpcaitech/ColossalAI#2901 Cheers, Joy On 18 Aug 2023, at 12:39, Thorsten Wagner ***@***.***> wrote: Sorry, I hadnt the time to look into it. What was the problem? How did you fix it? — Reply to this email directly, view it on GitHub<#42 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ASHIWUWFQMZD22KFJ57B4ETXV5IA7ANCNFSM6AAAAAA3SNW3YE>. You are receiving this because you modified the open/close state.Message ID: ***@***.***>

[thorstenwagner]

Is it possible that your PATH contains a path to cudotoolkit libs? Those might interfer with the one that comes with tomotwin. 18.08.2023 13:45:40 jychoi0616 ***@***.***>:

…

Hi Thorsten, It was some link issue between libcublas and libcublasLt (at least it seemed). For my case, removing libcublas* under the torch/lib directory helped solving the issue by following one of the suggestions in hpcaitech/ColossalAI#2901 Cheers, Joy On 18 Aug 2023, at 12:39, Thorsten Wagner ***@***.***> wrote: Sorry, I hadnt the time to look into it. What was the problem? How did you fix it? — Reply to this email directly, view it on GitHub<#42 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ASHIWUWFQMZD22KFJ57B4ETXV5IA7ANCNFSM6AAAAAA3SNW3YE>. You are receiving this because you modified the open/close state.Message ID: ***@***.***> — Reply to this email directly, view it on GitHub[#42 (comment)], or unsubscribe[https://github.com/notifications/unsubscribe-auth/AAIP66LBU7A5HV2AL3DN6NDXV5IWFANCNFSM6AAAAAA3SNW3YE]. You are receiving this because you commented.[Verfolgungsbild][https://github.com/notifications/beacon/AAIP66LDCVAPT44WMGDAAP3XV5IWFA5CNFSM6AAAAAA3SNW3YGWGG33NNVSW45C7OR4XAZNMJFZXG5LFINXW23LFNZ2KUY3PNVWWK3TUL5UWJTTELS5FY.gif]