Re: [scipion-users] error with protocols in Scipion3 CTF correction step

[Grigory S. <sha...@gm...>]

Hi Ana,

the gctf error is : Error CUDA driver version is insufficient for CUDA
runtime version at line 3059 in file src/ctf.cu
The binary you are using (default) requires CUDA 10.1

for ctffind4 it looks like you did not actually run the job, as there's no
output logs. I'll fix the methods message.

Best regards,
Grigory

--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.

MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267228 <+44%201223%20267228>
e-mail: gs...@mr...


On Wed, Nov 25, 2020 at 9:04 AM Ana Andreea ARTENI <
ana...@i2...> wrote:

>
> Concerning the gctf I found the following in the run.stdout
> STARTED: estimateCtfStep, step 3, time 2020-11-20 14:42:22.007666
> 00019:   Estimating CTF of micrograph: 2
> 00020:   Error CUDA driver version is insufficient for CUDA runtime
> version at line 3059 in file src/ctf.cu
> 00021:
> ***************************************************************************************************
> 00022:   Version:
> /data/sics/scipion/software/em/gctf-1.18/bin/Gctf_v1.18_sm30-75_cu10.1
> v1.18, updated on 2017-05-10
> 00023:   Author:        Kai Zhang@MRC Laboratory of Molecular Biology
> 00024:   Contact:       kz...@mr...
> 00025:   Description:   This is a simplified version of GCTF for CTF
> determination.
> 00026:
> ***************************************************************************************************
> 00027:
> 00028:   Opening
> Runs/000850_ProtGctf/tmp/mic_0001/Falcon_2012_06_12-14_33_35_0_movie_aligned_mic.mrc
> for initial test and preparation .......
> 00029:   ERROR: Gctf has failed on Runs/000850_ProtGctf/tmp/mic_0001/*.mrc
> 00030:
> /data/sics/scipion/software/em/gctf-1.18/bin/Gctf_v1.18_sm30-75_cu10.1
> --apix 3.540000 --kV 300.000000 --cs 2.000000 --ac 0.100000 --dstep
> 13.999992 --defL 5000.000000 --defH 90000.000000 --defS 500.000000 --astm
> 1000.000000 --resL 50.000000 --resH 8.230000 --do_EPA 0 --boxsize 512
> --plot_res_ring 1 --gid 2 --bfac 150 --B_resH 7.080000 --overlap 0.500000
> --convsize 85 --do_Hres_ref 0 --smooth_resL 1000 --EPA_oversmp 4 --ctfstar
> NONE --do_validation 0  Runs/000850_ProtGctf/tmp/mic_0002/*.mrc
> 00031:   Error CUDA driver version is insufficient for CUDA runtime
> version at line 3059 in file src/ctf.cu
>
> Hope this helps better...
>                       ana.
> ------------------------------
> *From: *"Ana Andreea ARTENI" <ana...@i2...>
> *To: *"sharov grigory" <sha...@gm...>
> *Cc: *"Anne-Pascale JAUDIER" <ann...@i2...>,
> "scipion-users" <sci...@li...>
> *Sent: *Wednesday, 25 November, 2020 09:51:06
> *Subject: *error with protocols in Scipion3 CTF correction step
>
>
> Dear Grigory,
>
> After installing Relion3, and start doing the mix and patch tutorial we
> have the following errors:
>
> At the CTF step:
>
>  via gctf:
>
> The test: scipion3 tests gctf.tests.test_protocols_gctf  gives no errors,
> but the output looks as in the image attached (that shows no psd and no
> correct values for the parameters).
> Any idea what is wrong and how can we fix this?
> --------------------------------------------
>
> via ctffind4
> METHODS:
> > cistem - ctffind4
> ERROR generating methods info: 'CistemProtCTFFind' object has no attribute
> 'outputCTF'
>
> File 'Runs/000979_CistemProtCTFFind/logs/run.stdout' doesn't existFile
> 'Runs/000979_CistemProtCTFFind/logs/run.stdout' doesn't existFile
> 'Runs/000979_CistemProtCTFFind/logs/run.stdout' doesn't existFile
> 'Runs/000979_CistemProtCTFFind/logs/run.stdout' doesn't existFile
> 'Runs/000979_CistemProtCTFFind/logs/run.stdout' doesn't existFile
> 'Runs/000979_CistemProtCTFFind/logs/run.stdout' doesn't existFile
> 'Runs/000979_CistemProtCTFFind/logs/run.stdout' doesn't existFile
> 'Runs/000979_CistemProtCTFFind/logs/run.stdout' doesn't existFile
> 'Runs/000979_CistemProtCTFFind/logs/run.stdout' doesn't existFile
> 'Runs/000979_CistemProtCTFFind/logs/run.stdout' doesn't exist
>
> Need also help here...
> My kind regards,
>                   ana.
>
>