Entering edit mode
22 months ago
charlieclark1ee
▴
20
When I try and run alphafold from ubuntu command line with amber enabled, it's throwing these errors.
I0125 17:33:14.174568 47215575258112 amber_minimize.py:407] Minimizing protein, attempt 1 of 100.
I0125 17:33:14.555528 47215575258112 amber_minimize.py:68] Restraining 685 / 1336 particles.
I0125 17:33:14.747518 47215575258112 amber_minimize.py:417] There is no registered Platform called "CUDA"
I0125 17:33:14.748770 47215575258112 amber_minimize.py:407] Minimizing protein, attempt 2 of 100.
I0125 17:33:15.763125 47215575258112 amber_minimize.py:68] Restraining 685 / 1336 particles.
I0125 17:33:15.763381 47215575258112 amber_minimize.py:417] There is no registered Platform called "CUDA"
…
I0125 17:33:47.589029 47215575258112 amber_minimize.py:407] Minimizing protein, attempt 100 of 100.
I0125 17:33:48.487623 47215575258112 amber_minimize.py:68] Restraining 685 / 1336 particles.
I0125 17:33:48.487895 47215575258112 amber_minimize.py:417] There is no registered Platform called "CUDA"
I'm definitely calling the job to be run with NVIDIA GPU nodes on a cluster - does anyone know why amber might be failing to recognise CUDA?
These are all the modules I have loaded when the script is running (CUDA is loaded which is what's puzzling me):
Currently Loaded Modulefiles:
1) GCCcore/10.3.0
2) zlib/1.2.11-GCCcore-10.3.0
3) binutils/2.36.1-GCCcore-10.3.0
4) GCC/10.3.0
5) numactl/2.0.14-GCCcore-10.3.0
6) XZ/5.2.5-GCCcore-10.3.0
7) libxml2/2.9.10-GCCcore-10.3.0
8) libpciaccess/0.16-GCCcore-10.3.0
9) hwloc/2.4.1-GCCcore-10.3.0
10) OpenSSL/1.1
11) libevent/2.1.12-GCCcore-10.3.0
12) UCX/1.10.0-GCCcore-10.3.0
13) libfabric/1.12.1-GCCcore-10.3.0
14) PMIx/3.2.3-GCCcore-10.3.0
15) OpenMPI/4.1.1-GCC-10.3.0
16) OpenBLAS/0.3.15-GCC-10.3.0
17) FlexiBLAS/3.0.4-GCC-10.3.0
18) gompi/2021a
19) FFTW/3.3.9-gompi-2021a
20) ScaLAPACK/2.1.0-gompi-2021a-fb
21) foss/2021a
22) bzip2/1.0.8-GCCcore-10.3.0
23) ncurses/6.2-GCCcore-10.3.0
24) libreadline/8.1-GCCcore-10.3.0
25) Tcl/8.6.11-GCCcore-10.3.0
26) SQLite/3.35.4-GCCcore-10.3.0
27) GMP/6.2.1-GCCcore-10.3.0
28) libffi/3.3-GCCcore-10.3.0
29) Python/3.9.5-GCCcore-10.3.0
30) CUDA/11.3.1
31) pybind11/2.6.2-GCCcore-10.3.0
32) SciPy-bundle/2021.05-foss-2021a
33) libyaml/0.2.5-GCCcore-10.3.0
34) PyYAML/5.4.1-GCCcore-10.3.0
35) CUDAcore/11.3.1
36) cuDNN/8.2.1.32-CUDA-11.3.1
37) GDRCopy/2.2-GCCcore-10.3.0
38) UCX-CUDA/1.10.0-GCCcore-10.3.0-CUDA-11.3.1
39) NCCL/2.10.3-GCCcore-10.3.0-CUDA-11.3.1
40) Szip/2.1.1-GCCcore-10.3.0
41) HDF5/1.10.7-gompi-2021a
42) h5py/3.2.1-foss-2021a
43) cURL/7.76.0-GCCcore-10.3.0
44) double-conversion/3.1.5-GCCcore-10.3.0
45) flatbuffers/2.0.0-GCCcore-10.3.0
46) giflib/5.2.1-GCCcore-10.3.0
47) ICU/69.1-GCCcore-10.3.0
48) JsonCpp/1.9.4-GCCcore-10.3.0
49) NASM/2.15.05-GCCcore-10.3.0
50) libjpeg-turbo/2.0.6-GCCcore-10.3.0
51) LMDB/0.9.28-GCCcore-10.3.0
52) nsync/1.24.0-GCCcore-10.3.0
53) protobuf/3.17.3-GCCcore-10.3.0
54) protobuf-python/3.17.3-GCCcore-10.3.0
55) flatbuffers-python/2.0-GCCcore-10.3.0
56) typing-extensions/3.10.0.0-GCCcore-10.3.0
57) libpng/1.6.37-GCCcore-10.3.0
58) snappy/1.1.8-GCCcore-10.3.0
59) TensorFlow/2.6.0-foss-2021a-CUDA-11.3.1
60) Biopython/1.79-foss-2021a
61) expat/2.2.9-GCCcore-10.3.0
62) DB/18.1.40-GCCcore-10.3.0
63) Perl/5.32.1-GCCcore-10.3.0
64) HH-suite/3.3.0-gompi-2021a
65) HMMER/3.3.2-gompi-2021a
66) Kalign/3.3.1-GCCcore-10.3.0
67) jax/0.3.9-foss-2021a-CUDA-11.3.1
68) PCRE/8.44-GCCcore-10.3.0
69) SWIG/4.0.2-GCCcore-10.3.0
70) OpenMM/7.5.1-foss-2021a-DeepMind-patch
71) AlphaFold/2.2.2-foss-2021a-CUDA-11.3.1
