[3dem] Relion 3.1 GPU issues

[Vidya Darbari]

Hello,

I am having trouble using GPUs for computation on my Ubuntu 18.04 
desktop with 2 GTX1070 cards. Previous versions of relion have worked.

I upgraded my ubuntu using the software updater from 16.04 to 18.04. I 
recently installed the relion3.1 stable release and initially had issues 
with cuda compatibility with gcc. So updated the CUDA toolkit to 11.0 
from developer site.

In order to get an install work I had to cmake 
-DCMAKE_INSTALL_PREFIX=/usr/local/relion3.1/ DFORCE_OWN_FFTW=ON 
-DFORCE_OWN_FLTK=ON ..

Without DFORCE_OWN_FFTW=ON -DFORCE_OWN_FLTK=ON .. nvcc issues meant it 
could not build.

Unable to use the GPUs (Error pasted below with nvcc version and 
nvidia-smi, if it helps). I have tried using --gpu 0, not working.

Any help would be much appreciated.

Best Regards

Vidya


The error I get now is:

If this occured at the start of a run, you might have GPUs which
are incompatible with either the data or your installation of relion.
If you

     -> INSTALLED RELION YOURSELF: if you e.g. specified -DCUDA_ARCH=50
        and are trying ot run on a compute 3.5 GPU (-DCUDA_ARCH=3.5),
        this may happen.

     -> HAVE MULTIPLE GPUS OF DIFFERNT VERSIONS: relion needs GPUS with
        at least compute 3.5. You may be trying to use a GPU older than
        this. If you have multiple generations, try specifying --gpu <X>
        with X=0. Then try X=1 in a new run, and so on. The numbering of
        GPUs may not be obvious from the driver or intuition. For a list
        of GPU compute generations, see

en.wikipedia.org/wiki/CUDA#Version_features_and_specifications

     -> ARE USING DOUBLE-PRECISION GPU CODE: relion was been written so
        as to not require this, and may thus have unforeseen requirements
        when run in this mode. If you think it is nonetheless necessary,
        please consult the developers with this error.

If this occurred at the middle or end of a run, it might be that

     -> YOUR DATA OR PARAMETERS WERE UNEXPECTED: execution on GPUs is
        subject to many restrictions, and relion is written to work within
        common restraints. If you have exotic data or settings, unexpected
        configurations may occur. See also above point regarding
        double precision.
If none of the above applies, please report the error to the relion
developers at    github.com/3dem/relion/issues

nvcc --version
Copyright (c) 2005-2020 NVIDIA Corporation
Built on Thu_Jun_11_22:26:38_PDT_2020
Cuda compilation tools, release 11.0, V11.0.194
Build cuda_11.0_bu.TC445_37.28540450_0

+-----------------------------------------------------------------------------+
| NVIDIA-SMI 440.100      Driver Version: 440.100      CUDA Version: 
10.2     |
|-------------------------------+----------------------+----------------------+
| GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile 
Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util 
Compute M. |
|===============================+======================+======================|
|   0  GeForce GTX 1070    Off  | 00000000:02:00.0 Off 
|                  N/A |
| 27%   32C    P8     6W / 151W |      2MiB /  8119MiB | 0%      Default |
+-------------------------------+----------------------+----------------------+
|   1  GeForce GTX 1070    Off  | 00000000:03:00.0  On 
|                  N/A |
| 28%   43C    P8     8W / 151W |    166MiB /  8111MiB | 0%      Default |
+-------------------------------+----------------------+----------------------+

+-----------------------------------------------------------------------------+
| Processes: GPU Memory |
|  GPU       PID   Type   Process name Usage      |
|=============================================================================|
|    1      1574      G /usr/lib/xorg/Xorg                           
104MiB |
|    1      4627      G   ...AAAAAAAAAAAACAAAAAAAAAA= --shared-files    
58MiB |
+-----------------------------------------------------------------------------+