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

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

Hi,

as Gctf error indicates you need to check "CUDA Toolkit and Compatible
Driver Versions" from here
<https://docs.nvidia.com/cuda/cuda-toolkit-release-notes/index.html>, and
make sure that your cuda toolkit version is compatible with your
cuda-driver version


   - check *cuda driver version*
   ~$ nvidia-smi or ~$ cat /proc/driver/nvidia/version
   - check *local cuda version*
   ~$ nvcc --version or ~$ cat /usr/local/cuda/version.txt

For ctffind4, could you try to run it locally (not on cluster), no threads,
no MPI on a single micrograph and paste the run.stdout file here. Does the
scipion test for ctffind4 work?

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 3:20 PM Ana Andreea ARTENI <
ana...@i2...> wrote:

>
> Hi again,
> I do have CUDA 10.1.
> Jose Miguel also wrote me: I have Gctf_v1.18 wich is a VPP version. We'll
> install gctf-1.06.
> What about the second thing: cistem is still in "launched" mode, without
> actually running - how can I sort out this one?
> My best regards,
>                    ana.
> ------------------------------
>
>> 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.
>>
>
>
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