[3dem] Relion 3.1 GPU issues
Vidya Darbari
v.darbari at qmul.ac.uk
Wed Jul 8 05:14:49 PDT 2020
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 |
+-----------------------------------------------------------------------------+
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