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tlambert03 / LLSpy

Lattice light-sheet post-processing utility.
http://llspy.readthedocs.io
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segmentation fault in cudaDeconv #28

Closed VolkerH closed 8 months ago

VolkerH commented 4 years ago

Getting segmentation errors in cudaDeconv when starting processing in batch. There are also some other warnings about libtiff and createPixmap but am not sure whether they are related.

I will try and narrow it down a bit more, but here is a traceback. 


Restoring settings: /home/vhil0002/.config/llspy/llspyDefaults.conf
output nz=75
X_k allocated.                37MB   10179MB free Pinning Host RAM.  Copy raw.data to X_k HostToDevice.  Done.  
deskewedRaw allocated.        37MB   10125MB free Deskewing. Copy deskewedRaw back to X_k. Done.
rawGPUbuf allocated.          52MB   10109MB free
X_kminus1 allocated.          52MB   10055MB free
Y_k allocated.                52MB   10001MB free
CC allocated.                 52MB    9947MB free
G_kminus1 allocated.          52MB    9893MB free
G_kminus2 allocated.          52MB    9839MB free
fftGPUbuf allocated.          53MB    9785MB free
Iteration 0. 
Iteration 1. 
Iteration 2. Lambda = 0.56. 
Iteration 3. Lambda = 0.56. 
Iteration 4. Lambda = 0.66. 
Iteration 5. Lambda = 0.73. 
Iteration 6. Lambda = 0.76. 
Iteration 7. Lambda = 0.79. 
Iteration 8. Lambda = 0.81. 
Iteration 9. Lambda = 0.83. 
output nz=75
X_k allocated.                37MB   10108MB free Pinning Host RAM.  Copy raw.data to X_k HostToDevice.  Done.  
deskewedRaw allocated.        37MB   10054MB free Deskewing. Copy deskewedRaw back to X_k. Done.
rawGPUbuf allocated.          52MB   10038MB free
X_kminus1 allocated.          52MB    9984MB free
Y_k allocated.                52MB    9930MB free
CC allocated.                 52MB    9876MB free
G_kminus1 allocated.          52MB    9822MB free
G_kminus2 allocated.          52MB    9768MB free
fftGPUbuf allocated.          53MB    9714MB free
Iteration 0. 
Iteration 1. 
Iteration 2. Lambda = 0.55. 
Iteration 3. Lambda = 0.56. 
Iteration 4. Lambda = 0.66. 
Iteration 5. Lambda = 0.73. 
Iteration 6. Lambda = 0.76. 
Iteration 7. Lambda = 0.79. 
Iteration 8. Lambda = 0.81. 
Iteration 9. Lambda = 0.83. 
output nz=75
X_k allocated.                37MB   10036MB free Pinning Host RAM.  Copy raw.data to X_k HostToDevice.  Done.  
deskewedRaw allocated.        37MB    9982MB free Deskewing. Copy deskewedRaw back to X_k. Done.
rawGPUbuf allocated.          52MB    9966MB free
X_kminus1 allocated.          52MB    9912MB free
Y_k allocated.                52MB    9858MB free
CC allocated.                 52MB    9804MB free
G_kminus1 allocated.          52MB    9750MB free
G_kminus2 allocated.          52MB    9696MB free
fftGPUbuf allocated.          53MB    9642MB free
Iteration 0. 
Iteration 1. 
Iteration 2. Lambda = 0.55. 
Iteration 3. Lambda = 0.56. 
Iteration 4. Lambda = 0.66. 
Iteration 5. Lambda = 0.73. 
Iteration 6. Lambda = 0.76. 
Iteration 7. Lambda = 0.79. 
Iteration 8. Lambda = 0.81. 
Iteration 9. Lambda = 0.83. 
Iteration 10. Lambda = 0.85. 
Iteration 11. Lambda = 0.87. 
Iteration 12. Lambda = 0.88. 
Iteration 13. Lambda = 0.89. 
Iteration 14. Lambda = 0.89. 
Iteration 15. Lambda = 0.90. 
Iteration 16. Lambda = 0.91. 
output nz=75
X_k allocated.                37MB   10036MB free Pinning Host RAM.  Copy raw.data to X_k HostToDevice.  Done.  
deskewedRaw allocated.        37MB    9982MB free Deskewing. Copy deskewedRaw back to X_k. Done.
rawGPUbuf allocated.          52MB    9966MB free
X_kminus1 allocated.          52MB    9912MB free
Y_k allocated.                52MB    9858MB free
CC allocated.                 52MB    9804MB free
G_kminus1 allocated.          52MB    9750MB free
G_kminus2 allocated.          52MB    9696MB free
fftGPUbuf allocated.          53MB    9642MB free
Iteration 0. 
Iteration 1. 
Iteration 2. Lambda = 0.55. 
Iteration 3. Lambda = 0.56. 
Iteration 4. Lambda = 0.66. 
Iteration 5. Lambda = 0.73. 
Iteration 6. Lambda = 0.76. 
Iteration 7. Lambda = 0.79. 
Iteration 8. Lambda = 0.81. 
Iteration 9. Lambda = 0.83. 
Iteration 10. Lambda = 0.85. 
Iteration 11. Lambda = 0.87. 
Iteration 12. Lambda = 0.88. 
Iteration 13. Lambda = 0.89. 
Iteration 14. Lambda = 0.89. 
Iteration 15. Lambda = 0.90. 
Iteration 16. Lambda = 0.91. 
Iteration 17. Lambda = 0.91. 
Iteration 18. Lambda = 0.89. 
Iteration 19. Lambda = 0.89. 
output nz=75
X_k allocated.                37MB   10036MB free Pinning Host RAM.  Copy raw.data to X_k HostToDevice.  Done.  
deskewedRaw allocated.        37MB    9982MB free Deskewing. Copy deskewedRaw back to X_k. Done.
rawGPUbuf allocated.          52MB    9966MB free
X_kminus1 allocated.          52MB    9912MB free
Y_k allocated.                52MB    9858MB free
CC allocated.                 52MB    9804MB free
G_kminus1 allocated.          52MB    9750MB free
G_kminus2 allocated.          52MB    9696MB free
fftGPUbuf allocated.          53MB    9642MB free
Iteration 0. 
Iteration 1. 
Iteration 2. Lambda = 0.55. 
Iteration 3. Lambda = 0.56. 
Iteration 4. Lambda = 0.66. 
Iteration 5. Lambda = 0.73. 
Iteration 6. Lambda = 0.76. 
Iteration 7. Lambda = 0.79. 
Iteration 8. Lambda = 0.81. 
Iteration 9. Lambda = 0.83. 
output nz=75
X_k allocated.                37MB   10036MB free Pinning Host RAM.  Copy raw.data to X_k HostToDevice.  Done.  
deskewedRaw allocated.        37MB    9982MB free Deskewing. Copy deskewedRaw back to X_k. Done.
rawGPUbuf allocated.          52MB    9966MB free
X_kminus1 allocated.          52MB    9912MB free
Y_k allocated.                52MB    9858MB free
CC allocated.                 52MB    9804MB free
G_kminus1 allocated.          52MB    9750MB free
G_kminus2 allocated.          52MB    9696MB free
fftGPUbuf allocated.          53MB    9642MB free
Iteration 0. 
Iteration 1. 
Iteration 2. Lambda = 0.55. 
Iteration 3. Lambda = 0.56. 
Iteration 4. Lambda = 0.66. 
Iteration 5. Lambda = 0.73. 
Iteration 6. Lambda = 0.76. 
Iteration 7. Lambda = 0.79. 
Iteration 8. Lambda = 0.81. 
Iteration 9. Lambda = 0.83. 
WARNING: QXcbConnection: XCB error: 2 (BadValue), sequence: 7222, resource id: 32, major code: 53 (CreatePixmap), minor code: 0
WARNING: QXcbConnection: XCB error: 9 (BadDrawable), sequence: 7223, resource id: 37757652, major code: 55 (CreateGC), minor code: 0
WARNING: QXcbConnection: XCB error: 9 (BadDrawable), sequence: 7224, resource id: 37757652, major code: 55 (CreateGC), minor code: 0
WARNING: QXcbConnection: XCB error: 2 (BadValue), sequence: 7260, resource id: 32, major code: 53 (CreatePixmap), minor code: 0
WARNING: QXcbConnection: XCB error: 9 (BadDrawable), sequence: 7261, resource id: 37757660, major code: 55 (CreateGC), minor code: 0
WARNING: QXcbConnection: XCB error: 9 (BadDrawable), sequence: 7262, resource id: 37757660, major code: 55 (CreateGC), minor code: 0
Error in subprocess: CudaDeconv
/opt/anaconda/envs/llspy/bin/cudaDeconv: /opt/anaconda/envs/llspy/bin/../lib/libtiff.so.5: no version information available (required by /opt/anaconda/envs/llspy/bin/cudaDeconv)
/usr/local/bin/lls: line 3:  6967 Segmentation fault      (core dumped) lls $@
`
tlambert03 commented 4 years ago

hmmm, if you are unable to find any explanations, feel free to send me the dataset, and the output of conda list