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Zuricho
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ParallelFold
Modified version of Alphafold to divide CPU part (MSA and template searching) and GPU part. This can accelerate Alphafold when predicting multiple structures
https://parafold.sjtu.edu.cn
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jaxlib.xla_extension.XlaRuntimeError
#50
Xiaojun928
opened
6 days ago
0
Wrong mgnify db name
#49
WishIWasBornInTheCreteaceousEra
opened
2 months ago
1
How to perform parallel search when generating MSA in the CPU section？
#48
Kangfengyuuuu
opened
4 months ago
0
simtk.openmm.OpenMMException: Particle coordinate is nan
#47
Kangfengyuuuu
opened
5 months ago
0
ValueError: Minimization failed after 100 attempts.
#46
Kangfengyuuuu
closed
6 months ago
3
How to run ParaFold in the CPU mode on a machine with GPU.
#45
Tiramisu023
opened
7 months ago
0
kalign glitch
#44
erdaqorri
opened
9 months ago
0
Why not recommend install by docker?
#43
Autumn-Roy
opened
10 months ago
1
hhalignment.cpp:3539: MergeMasterSlave
#42
Licko0909
opened
1 year ago
1
known good nvidia driver?
#41
rocketman8080
opened
1 year ago
0
The GPU step is requiring large amounts of CPU VMEM
#40
johnire80
opened
1 year ago
0
Run on GPU Error
#39
erdaqorri
opened
1 year ago
3
Multimer prediction error: "ValueError: Unable to retrieve parameter 'scale' for module......."
#38
tclin422
opened
1 year ago
5
add cpu multiprocessing
#37
GingaVictory
opened
1 year ago
1
openmm not found
#36
NielsBDS
closed
1 year ago
1
Distributed database usage
#35
juankaamez
opened
1 year ago
0
Has CPU acceleration (the parallelization of the 3 library lookup) been implemented in this repo yet?
#34
cmkstien
opened
1 year ago
1
pdb_seqres_database_path must not be set when running with "--model_preset=monomer_casp14".
#33
mbassalbioinformatics
opened
1 year ago
0
About the test datasets
#32
xihongshilamu
opened
1 year ago
2
`run_alphafold.sh` on fresh Linux install has "bad interpreter" error
#31
cerebis
closed
1 year ago
2
could you share JAX compile optimization codes/files?
#30
rocke2020
closed
1 year ago
0
Where is the `run_figure.py` file?
#29
beaulian
opened
1 year ago
1
uniclust30 database version is inconsistent in download_uniref30.sh and run_alphafold.sh
#28
beaulian
closed
1 year ago
2
Parafold run failing since pulling latest changes
#27
gauravdiwan89
opened
1 year ago
8
Is CPU acceleration failed?
#26
yanchenmochen
opened
2 years ago
3
Where Can I find The Protein sequence？
#25
yanchenmochen
closed
2 years ago
4
Could not find HHsearch database
#24
YiningWang2
opened
2 years ago
1
failed to alloc 2147483648 bytes on host: CUDA_ERROR_OPERATING_SYSTEM: OS call failed or operation not supported on this OS
#23
yanchenmochen
opened
2 years ago
3
Too many command-line arguments
#22
AnaValero
opened
2 years ago
1
Alphafold2 v/s Parafold timings
#21
adi1bioinfo
opened
2 years ago
1
An error in feature generation
#20
YiningWang2
opened
2 years ago
1
GPU computing is slow
#19
chenshixinnb
opened
2 years ago
3
Why not using docker?
#18
xbiome-it
closed
2 years ago
1
is CPU acceleration available in this repo?
#17
wttat
opened
2 years ago
3
Bulk inference
#16
YumengYan
closed
2 years ago
1
IndexError: too many indices for array: array is 0-dimensional, but 1 were indexed
#15
chenshixinnb
closed
2 years ago
16
2022-01-11 09:19:03.536275: F external/org_tensorflow/tensorflow/compiler/xla/service/gpu/nvptx_compiler.cc:479] ptxas returned an error during compilation of ptx to sass: 'Internal: ptxas exited with non-zero error code 32512, output: ' If the error message indicates that a file could not be written, please verify that sufficient filesystem space is provided. Fatal Python error: Aborted
#14
chenshixinnb
closed
2 years ago
3
ValueError: jaxlib is version 0.1.69, but this version of jax requires version 0.1.74.
#13
chenshixinnb
closed
2 years ago
3
Limit RAM usage
#12
hrzolix
closed
2 years ago
1
Running ParallelFold on reduced database?
#11
xinyu-g
closed
2 years ago
0
How to run GPU part?
#10
hrzolix
closed
2 years ago
4
where's run_feature.sh ?
#9
yyshell
closed
2 years ago
2
这个是将1，2，3个序列，并行到0，1，2显卡完成吗？
#8
ChrisLou-bioinfo
closed
2 years ago
1
why is `run_figure.py` down now?
#7
RodenLuo
opened
3 years ago
2
GPU利用率问题
#6
zhoujingyu13687306871
closed
2 years ago
1
GPU number set up
#5
yuntaoyang
closed
2 years ago
1
Error after GPU part
#4
ebettler
closed
2 years ago
1
运行脚本后，还是有问题。
#3
zhoujingyu13687306871
closed
2 years ago
16
somthing wrong occured when I run the job
#2
zhoujingyu13687306871
closed
2 years ago
2
How to accelerate the HHBLITS step with GPU
#1
Licko0909
closed
2 years ago
4
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