jisraeli / deepbind Goto Github PK

Dear Deepbind team,

I'm interested in using the methods discussed in Deepbind to train a new model with a slight twist; I want to slightly edit the model architecture. Can you provide me with the code that you used to train deepbind models?

Thanks!

-Eugene

In conda environment, I am trying to install DeepBind, and got the following error message.
Please help me, I need to get something done with DeepBind before Monday.
Thank you!

(base) kong@kong-HP-Laptop-17-ca0xxx:~/Documents/Personal_Add/Apple/Swiss/Hall_Heim/Articles$ kipoi env create DeepBind
INFO [kipoi.cli.env] Writing environment file: /tmp/kipoi/envfiles/5070a3c5
INFO [kipoi.cli.env] Loading model: DeepBind description
INFO [kipoi.sources] Update /home/kong/.kipoi/models/
Already up to date.
INFO [kipoi.cli.env] Found 927 models under the model name: DeepBind. Merging dependencies for all
INFO [kipoi.cli.env] Environment name: kipoi-DeepBind
INFO [kipoi.cli.env] Output env file: /tmp/kipoi/envfiles/5070a3c5/kipoi-DeepBind.yaml
INFO [kipoi.cli.env] Done writing the environment file!
Traceback (most recent call last):
File "/home/kong/Software/anaconda3/bin/kipoi", line 8, in
sys.exit(main())
File "/home/kong/Software/anaconda3/lib/python3.7/site-packages/kipoi/main.py", line 105, in main
command_fn(args.command, sys.argv[2:])
File "/home/kong/Software/anaconda3/lib/python3.7/site-packages/kipoi/cli/env.py", line 696, in cli_main
command_fn(args.command, raw_args[1:])
File "/home/kong/Software/anaconda3/lib/python3.7/site-packages/kipoi/cli/env.py", line 457, in cli_create
envdb.save()
File "/home/kong/Software/anaconda3/lib/python3.7/site-packages/kipoi/env_db.py", line 128, in save
self.db.purge()
File "/home/kong/Software/anaconda3/lib/python3.7/site-packages/tinydb/database.py", line 250, in getattr
return getattr(self.table(self.default_table_name), name)
AttributeError: 'Table' object has no attribute 'purge'

When I try to make in kangaroo_smat, the first execution of nvcc raise an error:
nvcc -c -o ../build/release/obj/KANGAROO_SMAT/autotune.o -I. -I/usr/local/cuda/include -I../../smat/src -DKANGAROO_SMAT_EXPORTS -use_fast_math -gencode arch=compute_50,code=sm_50 -include nvcc_preinclude.h -maxrregcount 64 -Xcompiler -m64,-fPIC,-fvisibility=hidden,--param,max-inline-recursive-depth=24,--param,max-inline-recursive-depth-auto=24,-O3, autotune.cu
/usr/local/cuda/include/cuda.h(60): error: "uint64_t" is ambiguous

1 error detected in the compilation of "/tmp/tmpxft_000020b5_00000000-7_autotune.cpp1.ii".
makefile:159: recipe for target '../build/release/obj/KANGAROO_SMAT/autotune.o' failed
make: *** [../build/release/obj/KANGAROO_SMAT/autotune.o] Error 2

What about it? I don't know where is the problem.
Thanks!
Mauro

When I run make on libs/smat/src I get the following error -

./smat_cuda/launch_util.h(67): error: function "atomicAdd(double *, double)" has already been defined

1 error detected in the compilation of "/tmp/tmpxft_00000e6b_00000000-4_reduce.cpp4.ii".
makefile:230: recipe for target '../build/release/obj/SMAT_CUDA/reduce.o' failed
make: *** [../build/release/obj/SMAT_CUDA/reduce.o] Error 2

I think it is happening because I am using CUDA 9.2 and the code doesn't support it. The CUDA samples from NVIDIA were running perfectly. Please look into it.

Thanks

This python fails with the aforementioned CUDA error. The error looks like:

Predicting... ['TF_34']

AssertionError: CUDA error in Memcpy2DAsync: initialization error.
copy_from(...) raised an exception
AssertionError: CUDA error in Memcpy2DAsync: initialization error.
in smat_cuda/copy.cu:190
Traceback (most recent call last):
File "libs/kangaroo/kangaroo/predict.py", line 405, in call
model = load_model(modelinfo)
File "libs/kangaroo/kangaroo/predict.py", line 107, in load_model
model = cp.load(f)
File "libs/smat/py/smat/smat.py", line 230, in setstate
dll.api_copy_from(self._ptr,data.ctypes.data_as(c_void_p),data.strides[0],data.strides[1]) # Copy from data
File "libs/smat/py/smat/smat_dll.py", line 183, in call
raise SmatException(msg)
SmatException: copy_from(...) raised an exception
AssertionError: CUDA error in Memcpy2DAsync: initialization error.
in smat_cuda/copy.cu:190

Error in Worker...
copy_from(...) raised an exception
AssertionError: CUDA error in Memcpy2DAsync: initialization error.
in smat_cuda/copy.cu:190
Traceback (most recent call last):
File "libs/kangaroo/kangaroo/predict.py", line 405, in call
model = load_model(modelinfo)
File "libs/kangaroo/kangaroo/predict.py", line 107, in load_model
model = cp.load(f)
File "libs/smat/py/smat/smat.py", line 230, in setstate
dll.api_copy_from(self._ptr,data.ctypes.data_as(c_void_p),data.strides[0],data.strides[1]) # Copy from data
File "libs/smat/py/smat/smat_dll.py", line 183, in call
raise SmatException(msg)
SmatException: copy_from(...) raised an exception
AssertionError: CUDA error in Memcpy2DAsync: initialization error.
in smat_cuda/copy.cu:190

Hello I am new to to deep learning modules and I am using DeepBind for comparison with other tools, I am getting a following error when I run
python deepbind_train_encode.py top calib,train,test,report

-------------- calib: ARID3A_K562_ARID3A_(sc-8821)Stanford --------------
load_traindata: ARID3A_K562_ARID3A(sc-8821)_Stanford
calibrating...
Failed to load extension deepity_smat:
attempt: build/release/bin/
reason: build/release/bin/libdeepity_smat.so: cannot open shared object file: No such file or directory
attempt: ../smat/build/release/bin/
reason: ../smat/build/release/bin/libdeepity_smat.so: cannot open shared object file: No such file or directory
attempt: libs/smat/build/release/bin/
reason: libs/smat/build/release/bin/libdeepity_smat.so: cannot open shared object file: No such file or directory
attempt: libs/deepity/build/release/bin/
reason: libs/deepity/build/release/bin/libdeepity_smat.so: cannot open shared object file: No such file or directory
attempt: libs/kangaroo/build/release/bin/
reason: libs/kangaroo/build/release/bin/libdeepity_smat.so: cannot open shared object file: No such file or directory
attempt: /usr/local/cuda-10.2/bin/
reason: /usr/local/cuda-10.2/bin/libdeepity_smat.so: cannot open shared object file: No such file or directory
attempt: /usr/local/sbin/
reason: /usr/local/sbin/libdeepity_smat.so: cannot open shared object file: No such file or directory
attempt: /usr/local/bin/
reason: /usr/local/bin/libdeepity_smat.so: cannot open shared object file: No such file or directory
attempt: /usr/sbin/
reason: /usr/sbin/libdeepity_smat.so: cannot open shared object file: No such file or directory
attempt: /usr/bin/
reason: /usr/bin/libdeepity_smat.so: cannot open shared object file: No such file or directory
attempt: /sbin/
reason: /sbin/libdeepity_smat.so: cannot open shared object file: No such file or directory
attempt: /bin/
reason: /bin/libdeepity_smat.so: cannot open shared object file: No such file or directory
attempt: /usr/games/
reason: /usr/games/libdeepity_smat.so: cannot open shared object file: No such file or directory
attempt: /usr/local/games/
reason: /usr/local/games/libdeepity_smat.so: cannot open shared object file: No such file or directory
attempt: /snap/bin$/
reason: /snap/bin$/libdeepity_smat.so: cannot open shared object file: No such file or directory
attempt: /home/aishwarya/deepbind/DeepBind/code/libs/smat/build/release/bin/
reason: /home/aishwarya/deepbind/DeepBind/code/libs/smat/build/release/bin/libdeepity_smat.so: cannot open shared object file: No such file or directory
attempt: ../deepity/build/release/bin/
reason: ../deepity/build/release/bin/libdeepity_smat.so: cannot open shared object file: No such file or directory

AssertionError: CUDA error: no kernel image is available for execution on the device.
terminate called after throwing an instance of 'std::runtime_error'
what(): AssertionError: CUDA error: no kernel image is available for execution on the device.
in smat_cuda/cuda_context.cpp:107

demo_convnet.py run with error for the reason of libsmat_cudnn.so
code/libs/smat/py/demo_convnet.py
$ demo_convnet.py --device 1
code/libs/smat/build/release/bin/libsmat_cudnn.so: cannot open shared object file: No such file or directory
and then I found that libsmat_cudnn.so is not being compiled in folder code/libs/smat/build/release/bin
check the makefile , found smat_cudnn is not compiled by default.
so I try to re-compile, and failed with

collect2: error: ld returned 1 exit status
make: *** [../build/release/bin/libsmat_cudnn.so] Error 1


sadly failed， please help！